1
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Lu Y, Huang X, Adpressa DA, Mou L, Taylor PR, Clark BR. Vitifolignans, 3,4-dibenzyltetrahydrofuran lignans from Anemone vitifolia Buch.-Ham. PHYTOCHEMISTRY 2024:114217. [PMID: 38972442 DOI: 10.1016/j.phytochem.2024.114217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/09/2024]
Abstract
Anemone vitifolia is a small herb found in Asia that is used to treat a range of diseases in Chinese traditional medicine. GNPS-based molecular networking of an Anemone vitifolia specimen revealed the presence of a network containing numerous ions indicating the presence of lignans, several of which suggested that there might be previously undescribed compounds in the extract. Fractionation of the organic extract yielded five undescribed lignans, the vitifolignans, together with one known. The structures were identified based on extensive spectroscopic data analysis (NMR, HR-ESI-MS, and UV), coupling constant calculation and comparison with reported data. Their absolute configurations were determined by comparison of experimental ECD spectra with calculated spectra. Compounds 4/5 showed weak inhibition of LPS-induced NO production in mouse mononuclear macrophages.
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Affiliation(s)
- Ya Lu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, Tianjin, P. R. China
| | - Xueyan Huang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, Tianjin, P. R. China
| | | | - Linyun Mou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, Tianjin, P. R. China
| | - Peter R Taylor
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, Tianjin, P. R. China
| | - Benjamin R Clark
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, Tianjin, P. R. China.
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2
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Rau T, Sedlmair M, Köhn A. chARpack: The Chemistry Augmented Reality Package. J Chem Inf Model 2024; 64:4700-4708. [PMID: 38814047 DOI: 10.1021/acs.jcim.4c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Off-loading visualization and interaction into virtual reality (VR) using head-mounted displays (HMDs) has gained considerable popularity in simulation sciences, particularly in chemical modeling. Because of its unique way of soft immersion, augmented reality (AR) HMD technology has even more potential to be integrated into the everyday workflow of computational chemists. In this work, we present our environment to explore the prospects of AR in chemistry and general molecular sciences: The chemistry in Augmented Reality package (chARpack). Besides providing an extensible framework, our software focuses on a seamless transition between a 3D stereoscopic view with true 3D interactions and the traditional desktop PC setup to provide users with the best setup for all tasks in their workflow. Using feedback from domain experts, we discuss our design requirements for this kind of hybrid working environment (AR + PC), regarding input, features, degree of immersion, and collaboration.
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Affiliation(s)
- Tobias Rau
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart 70569, Germany
- Institute for Visualization and Interactive Systems, University of Stuttgart, Stuttgart 70569, Germany
| | - Michael Sedlmair
- Institute for Visualization and Interactive Systems, University of Stuttgart, Stuttgart 70569, Germany
| | - Andreas Köhn
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart 70569, Germany
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3
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Hehn L, Deglmann P, Kühn M. Chelate Complexes of 3d Transition Metal Ions─A Challenge for Electronic-Structure Methods? J Chem Theory Comput 2024; 20:4545-4568. [PMID: 38805381 DOI: 10.1021/acs.jctc.3c01375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Different electronic-structure methods were assessed for their ability to predict two important properties of the industrially relevant chelating agent nitrilotriacetic acid (NTA): its selectivity with respect to six different first-row transition metal ions and the spin-state energetics of its complex with Fe(III). The investigated methods encompassed density functional theory (DFT), the random phase approximation (RPA), coupled cluster (CC) theory, and the auxiliary-field quantum Monte Carlo (AFQMC) method, as well as the complete active space self-consistent field (CASSCF) method and the respective on-top methods: second-order N-electron valence state perturbation theory (NEVPT2) and multiconfiguration pair-density functional theory (MC-PDFT). Different strategies for selecting active spaces were explored, and the density matrix renormalization group (DMRG) approach was used to solve the largest active spaces. Despite somewhat ambiguous multi-reference diagnostics, most methods gave relatively good agreement with experimental data for the chemical reactions connected to the selectivity, which only involved transition-metal complexes in their high-spin state. CC methods yielded the highest accuracy followed by range-separated DFT and AFQMC. We discussed in detail that even higher accuracies can be obtained with NEVPT2, under the prerequisite that consistent active spaces along the entire chemical reaction can be selected, which was not the case for reactions involving Fe(III). A bigger challenge for electronic-structure methods was the prediction of the spin-state energetics, which additionally involved lower spin states that exhibited larger multi-reference diagnostics. Conceptually different, typically accurate methods ranging from CC theory via DMRG-NEVPT2 in combination with large active spaces to AFQMC agreed well that the high-spin state is energetically significantly favored over the other spin states. This was in contrast to most DFT functionals and RPA which yielded a smaller stabilization and some common DFT functionals and MC-PDFT even predicting the low-spin state to be energetically most favorable.
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Affiliation(s)
- Lukas Hehn
- Next Generation Computing, BASF SE, Pfalzgrafenstr. 1, 67061 Ludwigshafen, Germany
| | - Peter Deglmann
- Quantum Chemistry, BASF SE, Carl-Bosch-Str. 38, 67063 Ludwigshafen, Germany
| | - Michael Kühn
- Next Generation Computing, BASF SE, Pfalzgrafenstr. 1, 67061 Ludwigshafen, Germany
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4
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Yang Y, Zwijnenburg MA, Gardner AM, Adamczyk S, Yang J, Sun Y, Jiang Q, Cowan AJ, Sprick RS, Liu LN, Cooper AI. Conjugated Polymer/Recombinant Escherichia coli Biohybrid Systems for Photobiocatalytic Hydrogen Production. ACS NANO 2024; 18:13484-13495. [PMID: 38739725 PMCID: PMC11140839 DOI: 10.1021/acsnano.3c10668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Biohybrid photocatalysts are composite materials that combine the efficient light-absorbing properties of synthetic materials with the highly evolved metabolic pathways and self-repair mechanisms of biological systems. Here, we show the potential of conjugated polymers as photosensitizers in biohybrid systems by combining a series of polymer nanoparticles with engineered Escherichia coli cells. Under simulated solar light irradiation, the biohybrid system consisting of fluorene/dibenzo [b,d]thiophene sulfone copolymer (LP41) and recombinant E. coli (i.e., a LP41/HydA BL21 biohybrid) shows a sacrificial hydrogen evolution rate of 3.442 mmol g-1 h-1 (normalized to polymer amount). It is over 30 times higher than the polymer photocatalyst alone (0.105 mmol g-1 h-1), while no detectable hydrogen was generated from the E. coli cells alone, demonstrating the strong synergy between the polymer nanoparticles and bacterial cells. The differences in the physical interactions between synthetic materials and microorganisms, as well as redox energy level alignment, elucidate the trends in photochemical activity. Our results suggest that organic semiconductors may offer advantages, such as solution processability, low toxicity, and more tunable surface interactions with the biological components over inorganic materials.
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Affiliation(s)
- Ying Yang
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, United
Kingdom
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | | | - Adrian M. Gardner
- Stephenson
Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Early
Career Laser Laboratory, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Sylwia Adamczyk
- Macromolecular
Chemistry Group and Institute for Polymer Technology, Bergische Universität Wuppertal, Gauss-Straße 20, D-42097 Wuppertal, Germany
| | - Jing Yang
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, United
Kingdom
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Yaqi Sun
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiuyao Jiang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Alexander J. Cowan
- Stephenson
Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Early
Career Laser Laboratory, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Reiner Sebastian Sprick
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Glasgow G1 1XL, United
Kingdom
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE Key Laboratory
of Evolution and Marine Biodiversity, Frontiers Science Center for
Deep Ocean Multispheres and Earth System & College of Marine Life
Sciences, Ocean University of China, Qingdao 266003, China
| | - Andrew I. Cooper
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, United
Kingdom
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5
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Werner L, Radius U. How to Decarbonize N-Heterocyclic Carbenes (NHCs): The simple Alane Adducts (NHC) ⋅ AlR 3 (R=H, Me, Et). Angew Chem Int Ed Engl 2024; 63:e202403639. [PMID: 38446008 DOI: 10.1002/anie.202403639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The reaction of the amine-stabilized alane (NMe3) ⋅ AlH3 1 with the backbone-saturated N-heterocyclic carbene (NHC) SIDipp (SIDipp=1,3-bis-{2,6-di-iso-propyl-phenyl}-imidazolidin-2-ylidene) at 0 °C yielded the NHC alane adduct (SIDipp) ⋅ AlH3 2. Reaction at elevated temperatures or prolonged reaction at room temperature gave the product of a ring expansion reaction (RER) of the NHC, (NMe3) ⋅ AlH(RER-SIDippH2) 3 ⋅ (NMe3). Subsequent reaction of the latter with sterically less hindered NHCs (IMeMe {=1,3,4,5-tetramethyl-imidazolin-2-ylidene}, IiPrMe {=1,3-di-iso-propyl-4,5-dimethyl-imidazolin-2-ylidene}, and IiPr {=1,3-di-iso-propyl-imidazolin-2-ylidene}) afforded the NHC-stabilized RER-products (NHC) ⋅ AlH(RER-SIDippH2) 3 ⋅ (NHC) (NHC=IMeMe, IiPrMe, IiPr), while no reaction was observed with the sterically more demanding NHCs IDipp (=1,3-bis-{2,6-di-iso-propyl-phenyl}-imidazolin-2-ylidene), SIDipp and ItBu (=1,3-di-tert-butyl-imidazolin-2-ylidene). The compounds 3 ⋅ (NHC) were also obtained starting from (SIDipp) ⋅ AlH3 2 and NHC at room temperature. Heating solutions of (SIDipp) ⋅ AlH3 2 without additional base to 95 °C resulted in decarbonization of the NHC and substitution of the carbene carbon atom with aluminum hydride under loss of ethene. Subsequent dimerization afforded cis-[AlH{μ-N(Dipp)CH2CH2N(Dipp)}]2 4_dimer. Heating solutions of the NHC-ligated aluminum alkyls (SIDipp) ⋅ AlR3 2R (R=Me, Et) to 145 °C instead led to complete scission of the NHC backbone with evolution of ethene and isolation of the dialkylaluminium(III) amidinates {DippNC(R)NDipp}AlR2 5R (R=Me, Et).
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Affiliation(s)
- Luis Werner
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Udo Radius
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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6
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Yu KX, Liu SN, Xing YY, Huang F, Wang WJ, Wang Q, Chen DZ, Wang J. Mechanistic Investigation on the Regioselectivity of Electrochemical Co(II)-Catalyzed [2 + 2 + 2] Cycloaddition of Terminal Acetylenes. J Org Chem 2024. [PMID: 38779840 DOI: 10.1021/acs.joc.4c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
In this paper, the regioselectivity of electrochemical Co(II)-catalyzed [2 + 2 + 2] cycloaddition of terminal alkynes was investigated using density functional theory. We explored in detail the energy profiles for both 1,2,4- and 1,3,5-regioselectivity pathways and revealed the origin of the regioselectivity. Two kinds of conformational isomers derived from the different coordination modes of alkynes with cobaltacyclopentadiene have been found, which were formed through electrochemically mediated redox processes. The regioselectivity of the reaction depends on the two coordination modes. When the Co(II) center attacks α-C of the third alkyne, while β2-C in cyclopentadiene bonds to β-C of the alkyne, the reaction favors the formation of 1,2,4-products. In contrast, when the Co(II) center connects to β-C of the alkyne, it forms only the 1,3,5-products via [4 + 2] cycloaddition because of the steric repulsion between the bulky ligand on Co(II) and the phenyl group in the alkyne.
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Affiliation(s)
- Kai-Xin Yu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Sheng-Nan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Yang-Yang Xing
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Fang Huang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wen-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Qiong Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - De-Zhan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Jin Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
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7
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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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8
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Elayan IA, Rib L, A Mendes R, Brown A. Beyond Explored Functionals: A Computational Journey of Two-Photon Absorption. J Chem Theory Comput 2024; 20:3879-3893. [PMID: 38648613 DOI: 10.1021/acs.jctc.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a thorough investigation into the efficacy of 19 density functional theory (DFT) functionals, relative to RI-CC2 results, for computing two-photon absorption (2PA) cross sections (σ2PA) and key dipole moments (|μ00|, |μ11|, |Δμ|, |μ01|) for a series of coumarin dyes in the gas-phase. The functionals include different categories, including local density approximation (LDA), generalized gradient approximation (GGA), hybrid-GGA (H-GGA), range-separated hybrid-GGA (RSH-GGA), meta-GGA (M-GGA), and hybrid M-GGA (HM-GGA), with 14 of them being subjected to analysis for the first time with respect to predicting σ2PA values. Analysis reveals that functionals integrating both short-range (SR) and long-range (LR) corrections, particularly those within the RSH-GGA and HM-GGA classes, outperform the others. Furthermore, the range-separation approach was found more impactful compared to the varying percentages of Hartree-Fock exchange (HF Ex) within different functionals. The functionals traditionally recommended for 2PA do not appear among the top 9 in our study, which is particularly interesting, as these top-performing functionals have not been previously investigated in this context. This list is dominated by M11, QTP variants, ωB97X, ωB97X-V, and M06-2X, surpassing the performance of other functionals, including the commonly used CAM-B3LYP.
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Affiliation(s)
- Ismael A Elayan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Laura Rib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Rodrigo A Mendes
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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9
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Mohan M, Jetti KD, Smith MD, Demerdash ON, Kidder MK, Smith JC. Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents. J Chem Theory Comput 2024; 20:3911-3926. [PMID: 38387055 DOI: 10.1021/acs.jctc.3c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their viscosities under both a range of environmental factors and formulations hinders their general application. While DESs may serve as designer solvents, with nearly unlimited combinations, this unfortunately makes it experimentally infeasible to comprehensively measure the viscosities of all DESs of potential industrial interest. To assist in the design of DESs, we have developed several new machine learning (ML) models that accurately and rapidly predict the viscosities of a diverse group of DESs at different temperatures and molar ratios using, to date, one of the most comprehensive data sets containing the properties of over 670 DESs over a wide range of temperatures (278.15-385.25 K). Three ML models, including support vector regression (SVR), feed forward neural networks (FFNNs), and categorical boosting (CatBoost), were developed to predict DES viscosity as a function of temperature and molar ratio and contrasted with multilinear and two-factor polynomial regression baselines. Quantum chemistry-based, COSMO-RS-derived sigma profile (σ-profile) features were used as inputs for the ML models. The CatBoost model is excellent at externally predicting DES viscosity, as indicated by high R2 (0.99) and low root-mean-square-error (RMSE) and average absolute relative deviations (AARD) (5.22%) values for the testing data sets, and 98% of the data points lie within the 15% of AARD deviations. Furthermore, SHapley additive explanation (SHAP) analysis was employed to interpret the ML results and rationalize the viscosity predictions. The result is an ML approach that accurately predicts viscosity and will aid in accelerating the design of appropriate DESs for industrial applications.
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Affiliation(s)
- Mood Mohan
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Karuna Devi Jetti
- Department of Biotechnology, GIS, GITAM,Vishakhapatnam, Andhra Pradesh 530045, India
| | - Micholas Dean Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Omar N Demerdash
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michelle K Kidder
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States
| | - Jeremy C Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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10
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Valverde D, Ser CT, Ricci G, Jorner K, Pollice R, Aspuru-Guzik A, Olivier Y. Computational Investigations of the Detailed Mechanism of Reverse Intersystem Crossing in Inverted Singlet-Triplet Gap Molecules. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38728616 DOI: 10.1021/acsami.4c04347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Inverted singlet-triplet gap (INVEST) materials have promising photophysical properties for optoelectronic applications due to an inversion of their lowest singlet (S1) and triplet (T1) excited states. This results in an exothermic reverse intersystem crossing (rISC) process that potentially enhances triplet harvesting, compared to thermally activated delayed fluorescence (TADF) emitters with endothermic rISCs. However, the processes and phenomena that facilitate conversion between excited states for INVEST materials are underexplored. We investigate the complex potential energy surfaces (PESs) of the excited states of three heavily studied azaphenalene INVEST compounds, namely, cyclazine, pentazine, and heptazine using two state-of-the-art computational methodologies, namely, RMS-CASPT2 and SCS-ADC(2) methods. Our findings suggest that ISC and rISC processes take place directly between the S1 and T1 electronic states in all three compounds through a minimum-energy crossing point (MECP) with an activation energy barrier between 0.11 to 0.58 eV above the S1 state for ISC and between 0.06 and 0.36 eV above the T1 state for rISC. We predict that higher-lying triplet states are not populated, since the crossing point structures to these states are not energetically accessible. Furthermore, the conical intersection (CI) between the ground and S1 states is high in energy for all compounds (between 0.4 to 2.0 eV) which makes nonradiative decay back to the ground state a relatively slow process. We demonstrate that the spin-orbit coupling (SOC) driving the S1-T1 conversion is enhanced by vibronic coupling with higher-lying singlet and triplet states possessing vibrational modes of proper symmetry. We also rationalize that the experimentally observed anti-Kasha emission of cyclazine is due to the energetically inaccessible CI between the bright S2 and the dark S1 states, hindering internal conversion. Finally, we show that SCS-ADC(2) is able to qualitatively reproduce excited state features, but consistently overpredict relative energies of excited state structural minima compared to RMS-CASPT2. The identification of these excited state features elaborates design rules for new INVEST emitters with improved emission quantum yields.
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Affiliation(s)
- Danillo Valverde
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, Université de Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Cher Tian Ser
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H4, Canada
- Department of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
| | - Gaetano Ricci
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, Université de Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Kjell Jorner
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H4, Canada
- Department of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Kemigård, Sweden
| | - Robert Pollice
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H4, Canada
- Department of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H4, Canada
- Department of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College St., Ontario M5S 3E5, Canada
- Department of Materials Science & Engineering, University of Toronto, 184 College St., Ontario M5S 3E4, Canada
- Vector Institute for Artificial Intelligence, 661 University Ave., Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration Consortium, 700 University Ave., Toronto, Ontario M5G 1X6, Canada
| | - Yoann Olivier
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, Université de Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
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11
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Riethmann M, Föhrenbacher SA, Keiling H, Ignat'ev NV, Finze M, Radius U. Fluoride Abstraction Induced by Tris(pentafluoroethyl)difluorophosphorane: A Convenient Way to Synthesize Cationic N-Heterocyclic Carbene- and Cyclic (Alkyl)(amino)carbene-Ligated Copper Alkyne and Arene Complexes. Inorg Chem 2024; 63:8351-8365. [PMID: 38639397 DOI: 10.1021/acs.inorgchem.4c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
We herein report the convenient synthesis of different N-heterocyclic carbene (NHC)- and cyclic (alkyl)(amino)carbene (cAAC)-ligated copper cations using the weakly coordinating tris(pentafluoroethyl)trifluorophosphate counterion (FAP anion, [(C2F5)3PF3]-). The reaction of the fluorido complexes [(carbene)CuF] (carbene = NHC, cAACMe) 2a-2f and the tris(pentafluoroethyl)difluorophosphorane (C2F5)3PF2 in the presence of alkynes or arenes led to fluoride transfer from Cu to the phosphorane with formation of the cationic transition metal complexes [(carbene)Cu(L)]+ and the weakly coordinating counteranion [(C2F5)3PF3]- (FAP). Using this method, the complexes [(IDipp)Cu(L)]+FAP- (IDipp = 1,3-bis(2,6-di-iso-propylphenyl)-imidazolin-2-ylidene; L = PhC≡CPh, 4d; PhC≡CMe, 5d), [(cAACMe)Cu(L)]+FAP- (cAACMe = 1-(2,6-di-iso-propylphenyl)-3,3,5,5-tetramethyl-pyrrolidin-2-ylidene; L = PhC≡CPh, 4f; PhC≡CMe, 5f), [(SIDipp)Cu(C6Me6)]+FAP- (6e), (SIDipp = 1,3-bis(2,6-di-iso-propylphenyl)-imidazolidine-2-ylidene), and [(cAACMe)Cu(C6Me6)]+FAP- (6f) have been synthesized and characterized. The complexes [(IDipp)Cu(C6Me6)]+FAP- (6d) and [(cAACMe)Cu(C6Me6)]+FAP- (6f) have been used as catalysts for the copper(I)-catalyzed cycloaddition of benzyl azide to terminal alkynes.
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Affiliation(s)
- Melanie Riethmann
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Steffen A Föhrenbacher
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Hannes Keiling
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Nikolai V Ignat'ev
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron (ICB), Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
- Consultant, Merck KGaA, Frankfurter Straße 250, Darmstadt 64293, Germany
| | - Maik Finze
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron (ICB), Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Udo Radius
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg 97074, Germany
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12
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Verteramo ML, Ignjatović MM, Kumar R, Wernersson S, Ekberg V, Wallerstein J, Carlström G, Chadimová V, Leffler H, Zetterberg F, Logan DT, Ryde U, Akke M, Nilsson UJ. Interplay of halogen bonding and solvation in protein-ligand binding. iScience 2024; 27:109636. [PMID: 38633000 PMCID: PMC11021960 DOI: 10.1016/j.isci.2024.109636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein-ligand complexes involving single halogen substitutions - F, Cl, Br, and I - and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.
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Affiliation(s)
| | | | - Rohit Kumar
- Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, Lund, Sweden
| | | | | | - Ulf Ryde
- Department of Chemistry, Lund University, Lund, Sweden
| | - Mikael Akke
- Department of Chemistry, Lund University, Lund, Sweden
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13
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Hicks CB, Martinez TJ. Massively scalable workflows for quantum chemistry: BigChem and ChemCloud. J Chem Phys 2024; 160:142501. [PMID: 38591672 DOI: 10.1063/5.0190834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Electronic structure theory, i.e., quantum chemistry, is the fundamental building block for many problems in computational chemistry. We present a new distributed computing framework (BigChem), which allows for an efficient solution of many quantum chemistry problems in parallel. BigChem is designed to be easily composable and leverages industry-standard middleware (e.g., Celery, RabbitMQ, and Redis) for distributed approaches to large scale problems. BigChem can harness any collection of worker nodes, including ones on cloud providers (such as AWS or Azure), local clusters, or supercomputer centers (and any mixture of these). BigChem builds upon MolSSI packages, such as QCEngine to standardize the operation of numerous computational chemistry programs, demonstrated here with Psi4, xtb, geomeTRIC, and TeraChem. BigChem delivers full utilization of compute resources at scale, offers a programable canvas for designing sophisticated quantum chemistry workflows, and is fault tolerant to node failures and network disruptions. We demonstrate linear scalability of BigChem running computational chemistry workloads on up to 125 GPUs. Finally, we present ChemCloud, a web API to BigChem and successor to TeraChem Cloud. ChemCloud delivers scalable and secure access to BigChem over the Internet.
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Affiliation(s)
- Colton B Hicks
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J Martinez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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14
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Draženović J, Laconsay CJ, Došlić N, I-Chia Wu J, Basarić N. Excited-state antiaromaticity relief drives facile photoprotonation of carbons in aminobiphenyls. Chem Sci 2024; 15:5225-5237. [PMID: 38577382 PMCID: PMC10988595 DOI: 10.1039/d4sc00642a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
A combined computational and experimental study reveals that ortho-, meta- and para-aminobiphenyl isomers undergo distinctly different photochemical reactions involving proton transfer. Deuterium exchange experiments show that the ortho-isomer undergoes a facile photoprotonation at a carbon atom via excited-state intramolecular proton transfer (ESIPT). The meta-isomer undergoes water-assisted excited-state proton transfer (ESPT) and a photoredox reaction via proton-coupled electron transfer (PCET). The para-isomer undergoes a water-assisted ESPT reaction. All three reactions take place in the singlet excited-state, except for the photoredox process of the meta-isomer, which involves a triplet excited-state. Computations illustrate the important role of excited-state antiaromaticity relief in these photoreactions.
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Affiliation(s)
- Josip Draženović
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička Cesta 54 10000 Zagreb Croatia
| | - Croix J Laconsay
- Department of Chemistry, University of Houston Houston TX 77204 USA
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute Bijenička Cesta 54 10000 Zagreb Croatia
| | - Judy I-Chia Wu
- Department of Chemistry, University of Houston Houston TX 77204 USA
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička Cesta 54 10000 Zagreb Croatia
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15
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Gasevic T, Kleine Büning JB, Grimme S, Bursch M. Benchmark Study on the Calculation of 207Pb NMR Chemical Shifts. Inorg Chem 2024; 63:5052-5064. [PMID: 38446045 PMCID: PMC10951955 DOI: 10.1021/acs.inorgchem.3c04539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
A benchmark set for the computation of 207Pb nuclear magnetic resonance (NMR) chemical shifts is presented. The PbS50 set includes conformer ensembles of 50 lead-containing molecular compounds and their experimentally measured 207Pb NMR chemical shifts. Various bonding motifs at the Pb center with up to seven bonding partners are included. Six different solvents were used in the measurements. The respective shifts lie in the range between +10745 and -5030 ppm. Several calculation settings are assessed by evaluating computed 207Pb NMR shifts for the use with different density functional approximations (DFAs), relativistic approaches, treatment of the conformational space, and levels for geometry optimization. Relativistic effects were included explicitly with the zeroth order regular approximation (ZORA), for which only the spin-orbit variant was able to yield reliable results. In total, seven GGAs and three hybrid DFAs were tested. Hybrid DFAs significantly outperform GGAs. The most accurate DFAs are mPW1PW with a mean absolute deviation (MAD) of 429 ppm and PBE0 with an MAD of 446 ppm. Conformational influences are small as most compounds are rigid, but more flexible structures still benefit from Boltzmann averaging. Including explicit relativistic treatments such as SO-ZORA in the geometry optimization does not show any significant improvement over the use of effective core potentials (ECPs).
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Affiliation(s)
- Thomas Gasevic
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Julius B. Kleine Büning
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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16
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Jafari S, Ryde U, Irani M. QM/MM study of the catalytic reaction of aphid myrosinase. Int J Biol Macromol 2024; 262:130089. [PMID: 38360236 DOI: 10.1016/j.ijbiomac.2024.130089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran.
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17
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Marsili E, Curchod BFE. A Theoretical Perspective on the Photochemistry of Boron-Nitrogen Lewis Adducts. J Phys Chem A 2024; 128:996-1008. [PMID: 38236050 PMCID: PMC10875676 DOI: 10.1021/acs.jpca.3c07016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
Boron-Nitrogen (B-N) Lewis adducts form a versatile family of compounds with numerous applications in functional molecules. Despite the growing interest in this family of compounds for optoelectronic applications, little is currently known about their photophysics and photochemistry. Even the electronic absorption spectrum of ammonia borane, the textbook example of a B-N Lewis adduct, is unavailable. Given the versatility of the light-induced processes exhibited by these molecules, we propose in this work a detailed theoretical study of the photochemistry and photophysics of simple B-N Lewis adducts. We used advanced techniques in computational photochemistry to identify and characterize the possible photochemical pathways followed by ammonia borane and extended this knowledge to the substituted B-N Lewis adducts pyridine-borane and pyridine-boric acid. The photochemistry observed for this series of molecules allows us to extract qualitative rules to rationalize the light-induced behavior of more complex B-N-containing molecules.
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Affiliation(s)
- Emanuele Marsili
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Basile F. E. Curchod
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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18
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Kleine Büning JB, Grimme S, Bursch M. Machine learning-based correction for spin-orbit coupling effects in NMR chemical shift calculations. Phys Chem Chem Phys 2024; 26:4870-4884. [PMID: 38230684 DOI: 10.1039/d3cp05556f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
As one of the most powerful analytical methods for molecular and solid-state structure elucidation, NMR spectroscopy is an integral part of chemical laboratories associated with a great research interest in its computational simulation. Particularly when heavy atoms are present, a relativistic treatment is essential in the calculations as these influence also the nearby light atoms. In this work, we present a Δ-machine learning method that approximates the contribution to 13C and 1H NMR chemical shifts that stems from spin-orbit (SO) coupling effects. It is built on computed reference data at the spin-orbit zeroth-order regular approximation (ZORA) DFT level for a set of 6388 structures with 38 740 13C and 64 436 1H NMR chemical shifts. The scope of the methods covers the 17 most important heavy p-block elements that exhibit heavy atom on the light atom (HALA) effects to covalently bound carbon or hydrogen atoms. Evaluated on the test data set, the approach is able to recover roughly 85% of the SO contribution for 13C and 70% for 1H from a scalar-relativistic PBE0/ZORA-def2-TZVP calculation at virtually no extra computational costs. Moreover, the method is transferable to other baseline DFT methods even without retraining the model and performs well for realistic organotin and -lead compounds. Finally, we show that using a combination of the new approach with our previous Δ-ML method for correlation contributions to NMR chemical shifts, the mean absolute NMR shift deviations from non-relativistic DFT calculations to experimental values can be halved.
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Affiliation(s)
- Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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19
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Joshi P, Voora VK. Generalized perturbative singles corrections to the random phase approximation method: Impact on noncovalent interaction energies of closed- and open-shell dimers. J Chem Phys 2024; 160:044104. [PMID: 38258929 DOI: 10.1063/5.0180526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The post-Kohn-Sham (KS) random phase approximation (RPA) method may provide a poor description of interaction energies of weakly bonded molecules due to inherent density errors in approximate KS functionals. To overcome these errors, we develop a generalized formalism to incorporate perturbative singles (pS) corrections to the RPA method using orbital rotations as a perturbation parameter. The pS schemes differ in the choice of orbital-rotation gradient and Hessian. We propose a pS scheme termed RPA singles (RPAS)[Hartree-Fock (HF)] that uses the RPA orbital-rotation gradient and time-dependent HF Hessian. This correction reduces the errors in noncovalent interaction energies of closed- and open-shell dimers. For the open-shell dimers, the RPAS(HF) method leads to a consistent error reduction by 50% or more compared to the RPA method for the cases of hydrogen-bonding, metal-solvent, carbene-solvent, and dispersion interactions. We also find that the pS corrections are more important in error reduction compared to higher-order exchange corrections to the RPA method. Overall, for open shells, the RPAS(HF)-corrected RPA method provides chemical accuracy for noncovalent interactions and is more reliable than other perturbative schemes and dispersion-corrected density functional approximations, highlighting its importance as a reliable beyond-RPA correction.
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Affiliation(s)
- Pulkit Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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20
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Song Z, Chen J, Cheng J, Chen G, Qi Z. Computer-Aided Molecular Design of Ionic Liquids as Advanced Process Media: A Review from Fundamentals to Applications. Chem Rev 2024; 124:248-317. [PMID: 38108629 DOI: 10.1021/acs.chemrev.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The unique physicochemical properties, flexible structural tunability, and giant chemical space of ionic liquids (ILs) provide them a great opportunity to match different target properties to work as advanced process media. The crux of the matter is how to efficiently and reliably tailor suitable ILs toward a specific application. In this regard, the computer-aided molecular design (CAMD) approach has been widely adapted to cover this family of high-profile chemicals, that is, to perform computer-aided IL design (CAILD). This review discusses the past developments that have contributed to the state-of-the-art of CAILD and provides a perspective about how future works could pursue the acceleration of the practical application of ILs. In a broad context of CAILD, key aspects related to the forward structure-property modeling and reverse molecular design of ILs are overviewed. For the former forward task, diverse IL molecular representations, modeling algorithms, as well as representative models on physical properties, thermodynamic properties, among others of ILs are introduced. For the latter reverse task, representative works formulating different molecular design scenarios are summarized. Beyond the substantial progress made, some future perspectives to move CAILD a step forward are finally provided.
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Affiliation(s)
- Zhen Song
- State Key laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiahui Chen
- State Key laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jie Cheng
- State Key laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guzhong Chen
- State Key laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhiwen Qi
- State Key laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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21
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Haaf S, Engels E, Kaifer E, Himmel HJ. Hexaguanidino-Triptycenes and Triphenylenes: Electronic Coupling in Molecules Containing Three Redox-Active o-Diguanidinobenzene Units Connected either Directly or Interacting Through Homoconjugation. Chemistry 2024; 30:e202301903. [PMID: 37815019 DOI: 10.1002/chem.202301903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/22/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Novel redox-active hexaguanidine molecules with multiple redox states were synthesized by connecting three o-diguanidinobenzene units. In 2,3,6,7,14,15-hexaguanidino-triptycenes, the three redox-active o-diguanidinobenzene units are connected through C-C bonds to the sp3 -hybridized bridgehead C atoms, and in 2,3,6,7,10,11-hexaguanidino-triphenylenes they are directly connected. The connectivity difference leads to different electronic coupling between the three redox-active o-diguanidinobenzene units, with homoconjugation being present in the triptycene, but not in the triphenylene compounds. Motivated by the appearance of an intense low-energy electronic transition, we especially analysed the effect of homoconjugation on the electronic structure and charge delocalization in the dicationic redox state of the triptycene derivatives. Then, several trinuclear high-spin cobalt (and copper) complexes were synthesized with the triphenylene and triptycene ligands, and the magnetic coupling and redox properties analysed. By choice of the coligands (hexafluoroacetylacetonate, trifluoroacetylacetonate and acetylacetonate), oxidation could be switched between metal- and ligand-centered redox events, leading to drastic changes in the magnetic or optical properties, especially as a consequence of homoconjugation in the triptycene derivatives.
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Affiliation(s)
- Sebastian Haaf
- Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Eliane Engels
- Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Elisabeth Kaifer
- Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Hans-Jörg Himmel
- Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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22
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Mackintosh MJ, Hoischen D, Martin HD, Schapiro I, Gärtner W. Merocyanines form bacteriorhodopsins with strongly bathochromic absorption maxima. Photochem Photobiol Sci 2024; 23:31-53. [PMID: 38070056 DOI: 10.1007/s43630-023-00496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 02/02/2024]
Abstract
There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR's [Formula: see text] of 568 nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the [Formula: see text] was 766, 755, and 736 nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φf) several orders of magnitude greater than native bR (Φf 0.02 to 0.18 versus 1.5 × 10-5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000 cm-1 versus 4030 cm-1 in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental [Formula: see text] and the calculated [Formula: see text] was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.
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Affiliation(s)
- Megan J Mackintosh
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dorothee Hoischen
- Institute for Organic Chemistry and Macromolecular Chemistry, University of Düsseldorf, 40225, Düsseldorf, Germany
- ISK Biosciences Europe N.V., 1831, Diegem, Belgium
| | - Hans-Dieter Martin
- Institute for Organic Chemistry and Macromolecular Chemistry, University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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23
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Taylor JT, Tozer DJ, Curchod BFE. On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2). J Chem Phys 2023; 159:214115. [PMID: 38059547 DOI: 10.1063/5.0176140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.
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Affiliation(s)
- Jack T Taylor
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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24
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Jiang H, Lundgren KJM, Ryde U. Protonation of Homocitrate and the E 1 State of Fe-Nitrogenase Studied by QM/MM Calculations. Inorg Chem 2023; 62:19433-19445. [PMID: 37987624 DOI: 10.1021/acs.inorgchem.3c02329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E0 state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E1 state, we find that protonation of the S2B μ2 belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E1 state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E1 state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Kristoffer J M Lundgren
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
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25
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Werner L, Hagn J, Radius U. NHC-Stabilized Dialanes(4) of Al 2 Mes 4. Chemistry 2023; 29:e202303111. [PMID: 37792718 DOI: 10.1002/chem.202303111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023]
Abstract
The synthesis and characterization of novel N-heterocyclic carbene (NHC) stabilized dialanes Al2 Mes4 as well as first investigations concerning the reactivity of these compounds are reported. The synthesis of these compounds proceeds via the mesityl-substituted alanes (NHC)⋅AlHMes2 (NHC=IMeMe {=1,3,4,5-tetramethyl-imidazolin-2-ylidene}, IiPrMe {=1,3-di-iso-propyl-4,5-dimethylimidazolin-2-ylidene}) and iodo-alanes (NHC)⋅AlIMes2 (NHC=IMeMe , IiPrMe ). Metallic reduction of (NHC)⋅AlIMes2 afforded the new NHC-stabilized dialanes (NHC)2 ⋅Al2 Mes4 (NHC=IMeMe , IiPrMe ). The NHC-ligated dialanes are thermally robust and storable synthons for the dialane Al2 Mes4 . First reactivity studies on (IMeMe )2 ⋅Al2 Mes4 towards small molecules confirm this, as this compound shows controlled and selective reactions with several substrates. Reaction with CuCl leads to oxidation of the dialane and formation of (IMeMe )⋅AlClMes2 , reactions with pyridine N-oxide and t Bu-N=C=S, respectively, gave the chalcogenide-bridged dimers {(IMeMe )⋅AlMes2 }2 -μ-E (E=O, S), and reaction with acetylene afforded the dimetallaacetylide {(IMeMe )⋅AlMes2 }2 -μ-(C≡C).
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Affiliation(s)
- Luis Werner
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Julika Hagn
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Udo Radius
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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26
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Pattanaik L, Menon A, Settels V, Spiekermann KA, Tan Z, Vermeire FH, Sandfort F, Eiden P, Green WH. ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents. J Phys Chem B 2023; 127:10151-10170. [PMID: 37966798 DOI: 10.1021/acs.jpcb.3c05904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Predicting Gibbs free energy of solution is key to understanding the solvent effects on thermodynamics and reaction rates for kinetic modeling. Accurately computing solution free energies requires the enumeration and evaluation of relevant solute conformers in solution. However, even after generation of relevant conformers, determining their free energy of solution requires an expensive workflow consisting of several ab initio computational chemistry calculations. To help address this challenge, we generate a large data set of solution free energies for nearly 44,000 solutes with almost 9 million conformers calculated in 41 different solvents using density functional theory and COSMO-RS and quantify the impact of solute conformers on the solution free energy. We then train a message passing neural network to predict the relative solution free energies of a set of solute conformers, enabling the identification of a small subset of thermodynamically relevant conformers. The model offers substantial computational time savings with predictions usually substantially within 1 kcal/mol of the free energy of the solution calculated by using computational chemical methods.
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Affiliation(s)
- Lagnajit Pattanaik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Angiras Menon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Volker Settels
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - Kevin A Spiekermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zipei Tan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Florence H Vermeire
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Frederik Sandfort
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - Philipp Eiden
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Zhang Z, Slak D, Krebs T, Leuschner M, Schmickler N, Kuchuk E, Schmidt J, Domenianni LI, Kleine Büning JB, Grimme S, Vöhringer P, Gansäuer A. A Chiral Titanocene Complex as Regiodivergent Photoredox Catalyst: Synthetic Scope and Mechanism of Catalyst Generation. J Am Chem Soc 2023. [PMID: 38016173 DOI: 10.1021/jacs.3c08029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
We describe a combined synthetic, spectroscopic, and computational study of a chiral titanocene complex as a regiodivergent photoredox catalyst (PRC). With Kagan's complex catCl2 either monoprotected 1,3-diols or 1,4-diols can be obtained in high selectivity from a common epoxide substrate in a regiodivergent epoxide opening depending on which enantiomer of the catalyst is employed. Due to the catalyst-controlled regioselectivity of ring opening and the broader substrate scope, the PRC with catCl2 is also a highly attractive branching point for diversity-oriented synthesis. The photochemical processes of cat(NCS)2, a suitable model for catCl2, were probed by time-correlated single-photon counting. The photoexcited complex displays a thermally activated delayed fluorescence as a result of a singlet-triplet equilibration, S1 ⇄ T1, via intersystem crossing and recrossing. Its triplet state is quenched by electron transfer to the T1 state. Computational and cyclic voltammetry studies highlight the importance of our sulfonamide additive. By bonding to sulfonamide additives, chloride abstraction from [catCl2]- is facilitated, and catalyst deactivation by coordination of the sulfonamide group is circumvented.
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Affiliation(s)
- Zhenhua Zhang
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Daniel Slak
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Tim Krebs
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Marcel Leuschner
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Niklas Schmickler
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Ekaterina Kuchuk
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jonas Schmidt
- Clausius Institute for Physical and Theoretical Chemistry, Universität Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Luis Ignacio Domenianni
- Clausius Institute for Physical and Theoretical Chemistry, Universität Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Peter Vöhringer
- Clausius Institute for Physical and Theoretical Chemistry, Universität Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Andreas Gansäuer
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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28
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Franzke Y, Holzer C, Andersen JH, Begušić T, Bruder F, Coriani S, Della Sala F, Fabiano E, Fedotov DA, Fürst S, Gillhuber S, Grotjahn R, Kaupp M, Kehry M, Krstić M, Mack F, Majumdar S, Nguyen BD, Parker SM, Pauly F, Pausch A, Perlt E, Phun GS, Rajabi A, Rappoport D, Samal B, Schrader T, Sharma M, Tapavicza E, Treß RS, Voora V, Wodyński A, Yu JM, Zerulla B, Furche F, Hättig C, Sierka M, Tew DP, Weigend F. TURBOMOLE: Today and Tomorrow. J Chem Theory Comput 2023; 19:6859-6890. [PMID: 37382508 PMCID: PMC10601488 DOI: 10.1021/acs.jctc.3c00347] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 06/30/2023]
Abstract
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Affiliation(s)
- Yannick
J. Franzke
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Christof Holzer
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Josefine H. Andersen
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Tomislav Begušić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Florian Bruder
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Sonia Coriani
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Daniil A. Fedotov
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Susanne Fürst
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Sebastian Gillhuber
- Institute
of Inorganic Chemistry, Karlsruhe Institute
of Technology (KIT), Engesserstr. 15, 76131 Karlsruhe, Germany
| | - Robin Grotjahn
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Max Kehry
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Marjan Krstić
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Fabian Mack
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sourav Majumdar
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Brian D. Nguyen
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Shane M. Parker
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 United States
| | - Fabian Pauly
- Institute
of Physics, University of Augsburg, Universitätsstr. 1, 86159 Augsburg, Germany
| | - Ansgar Pausch
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Eva Perlt
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Gabriel S. Phun
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Ahmadreza Rajabi
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dmitrij Rappoport
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Bibek Samal
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Tim Schrader
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Manas Sharma
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Enrico Tapavicza
- Department
of Chemistry and Biochemistry, California
State University, Long Beach, 1250 Bellflower Boulevard, Long
Beach, California 90840-9507, United States
| | - Robert S. Treß
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vamsee Voora
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Artur Wodyński
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Jason M. Yu
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Benedikt Zerulla
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz-Platz
1, 76344 Eggenstein-Leopoldshafen Germany
| | - Filipp Furche
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Christof Hättig
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Marek Sierka
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - David P. Tew
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | - Florian Weigend
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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29
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Braese J, Lehnfeld F, Annibale VT, Oswald T, Beckhaus R, Manners I, Scheer M. Titanium-Catalyzed Polymerization of a Lewis Base-Stabilized Phosphinoborane. Chemistry 2023; 29:e202301741. [PMID: 37498679 DOI: 10.1002/chem.202301741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
The reaction of the Lewis base-stabilized phosphinoborane monomer tBuHPBH2 NMe3 (2 a) with catalytic amounts of bis(η5 :η1 -adamantylidenepentafulvene)titanium (1) provides a convenient new route to the polyphosphinoborane [tBuPH-BH2 ]n (3 a). This method offers access to high molar mass materials under mild conditions and with short reaction times (20 °C, 1 h in toluene). It represents an unprecedented example of a transition metal-mediated polymerization of a Lewis base-stabilized Group 13/15 compound. Preliminary studies of the substrate scope and a potential mechanism are reported.
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Affiliation(s)
- Jens Braese
- Universität Regensburg, Institut für Anorganische Chemie, 94053, Regensburg, Germany
| | - Felix Lehnfeld
- Universität Regensburg, Institut für Anorganische Chemie, 94053, Regensburg, Germany
| | - Vincent T Annibale
- University of Victoria, Department of Chemistry, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Tim Oswald
- Carl von Ossietzky Universität Oldenburg, Institut für Chemie Carl-von-Ossietzky, Straße 9-11, 26129, Oldenburg, Germany
| | - Rüdiger Beckhaus
- Carl von Ossietzky Universität Oldenburg, Institut für Chemie Carl-von-Ossietzky, Straße 9-11, 26129, Oldenburg, Germany
| | - Ian Manners
- University of Victoria, Department of Chemistry, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Manfred Scheer
- Universität Regensburg, Institut für Anorganische Chemie, 94053, Regensburg, Germany
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30
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Salahshoori I, Baghban A, Yazdanbakhsh A. Novel hybrid QSPR-GPR approach for modeling of carbon dioxide capture using deep eutectic solvents. RSC Adv 2023; 13:30071-30085. [PMID: 37842683 PMCID: PMC10573873 DOI: 10.1039/d3ra05360a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023] Open
Abstract
In recent years, deep eutectic solvents (DESs) have garnered considerable attention for their potential in carbon capture and utilization processes. Predicting the carbon dioxide (CO2) solubility in DES is crucial for optimizing these solvent systems and advancing their application in sustainable technologies. In this study, we presented an evolving hybrid Quantitative Structure-Property Relationship and Gaussian Process Regression (QSPR-GPR) model that enables accurate predictions of CO2 solubility in various DESs. The QSPR-GPR model combined the strengths of both approaches, leveraging molecular descriptors and structural features of DES components to establish a robust and adaptable predictive framework. Through a systematic evolution process, we iteratively refined the model, enhancing its performance and generalization capacity. By incorporating experimental CO2 solubility data in varied DES compositions and temperatures, we trained the model to capture the intricate solubility behaviour precisely. The analytical capability of the evolving hybrid model was validated against an extensive dataset of experimental CO2 solubility values, demonstrating its superiority over individual QSPR and GPR models. The model achieves high accuracy, capturing the complex interactions between CO2 and DES components under varying thermodynamic conditions. The versatility of the evolving hybrid model was highlighted by its ability to accommodate new experimental data and adapt to different DES compositions and temperatures. The proposed QSPR-GPR model presented a powerful tool for predicting CO2 solubility in DES, providing valuable insights for designing and optimizing solvent systems in carbon capture technologies. The model's remarkable performance enhances our understanding of CO2 solubility mechanisms and contributes to sustainable solutions for mitigating greenhouse gas emissions. As research in DESs progresses, the evolving hybrid QSPR-GPR model offers a versatile and accurate means for predicting CO2 solubility, supporting advancements in carbon capture and utilization processes towards a greener and more sustainable future.
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Affiliation(s)
- Iman Salahshoori
- Discipline of Chemical Engineering, School of Engineering, University of KwaZulu-Natal, Howard College Campus King George V Avenue Durban 4041 South Africa
- Department of Polymer Processing, Iran Polymer and Petrochemical Institute P.O. Box 14965-115 Tehran Iran
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University Tehran Iran
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31
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Fortino M, Schifino G, Pietropaolo A. Simulation workflows to predict the circular dichroism and circularly polarized luminescence of chiral materials. Chirality 2023; 35:673-680. [PMID: 36896846 DOI: 10.1002/chir.23546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/11/2023]
Abstract
Chiral materials are attracting considerable interest in various fields in view of their unique properties and optical activity. Indeed, the peculiar features of chiral materials to absorb and emit circularly polarized light enable their use in an extensive range of applications. Motivated by the interest in boosting the development of chiral materials characterized by enhanced chiroptical properties such as circular dichroism (CD) and circular polarized luminescence (CPL), we herein illustrate in this tutorial how theoretical simulations can be used for the predictions and interpretations of chiroptical data and for the identification of chiral geometries. We are focusing on computational frameworks that can be used to investigate the theoretical aspects of chiral materials' photophysical and conformational characteristics. We will then illustrate ab initio methods based on density functional theory (DFT) and its time-dependent extension (TD-DFT) to simulate CD and CPL signals, and we will exemplify a variety of enhanced sampling techniques useful for an adequate sampling of the configurational space for chiral systems.
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Affiliation(s)
- Mariagrazia Fortino
- Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy
| | - Gioacchino Schifino
- Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy
| | - Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy
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32
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Daas KJ, Kooi DP, Peters NC, Fabiano E, Della Sala F, Gori-Giorgi P, Vuckovic S. Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost. J Phys Chem Lett 2023; 14:8448-8459. [PMID: 37721318 DOI: 10.1021/acs.jpclett.3c01832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.
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Affiliation(s)
- Kimberly J Daas
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Derk P Kooi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Nina C Peters
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Eduardo Fabiano
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Fabio Della Sala
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Paola Gori-Giorgi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Stefan Vuckovic
- Department of Chemistry, Faculty of Science and Medicine, Université de Fribourg/Universität Freiburg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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33
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Horrer G, Luff MS, Radius U. N-Heterocyclic carbene and cyclic (alkyl)(amino)carbene ligated half-sandwich complexes of chromium(II) and chromium(I). Dalton Trans 2023; 52:13244-13257. [PMID: 37667868 DOI: 10.1039/d3dt02123h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The synthesis and characterization of a series of Cr(II) N-Heterocyclic Carbene (NHC) complexes of the type [{Cr(NHC)Cl(μ-Cl)}2] and [(Cyp)Cr(NHC)X] (Cyp = η5-C5H5, cyclopentadienyl; η5-C5Me5, pentamethylcyclopentadienyl; X = Cl, η3-C3H5; NHC = IMeMe, IiPrMe, IMes, IDipp) as well as the cyclic (alkyl)(amino)carbene cAACMe ligated complexes [(η5-C5H5)Cr(cAACMe)X] (X = Cl, NPh2), [(η5-C9H7)Cr(cAACMe)Cl] (C9H7 = Ind, indenyl) and [(η5-C13H9)Cr(cAACMe)Cl] (C13H9 = Fl, fluorenyl) are reported. The reduction of [(η5-C5Me5)Cr(IMeMe)Cl] with KC8 in the presence of CO afforded the NHC ligated Cr(I) metallo-radical [(η5-C5Me5)Cr(IMeMe)(CO)2]. Quantum chemical calculations performed on [(η5-C5Me5)Cr(IMeMe)(CO)2] confirm for this complex a predominantly chromium centered radical.
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Affiliation(s)
- Günther Horrer
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Martin S Luff
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Udo Radius
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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34
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Gemen J, Church JR, Ruoko TP, Durandin N, Białek MJ, Weißenfels M, Feller M, Kazes M, Odaybat M, Borin VA, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. Disequilibrating azobenzenes by visible-light sensitization under confinement. Science 2023; 381:1357-1363. [PMID: 37733864 DOI: 10.1126/science.adh9059] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host-photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.
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Affiliation(s)
- Julius Gemen
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jonathan R Church
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tero-Petri Ruoko
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33101 Tampere, Finland
| | - Nikita Durandin
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33101 Tampere, Finland
| | - Michał J Białek
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie St., 50383 Wrocław, Poland
| | - Maren Weißenfels
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moran Feller
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Kazes
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Magdalena Odaybat
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London W12 7SL, UK
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Rishir Kalepu
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan Oron
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew J Fuchter
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London W12 7SL, UK
| | - Arri Priimagi
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33101 Tampere, Finland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Rafal Klajn
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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35
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Nusser BD, Accardo JV, Zhu L. Luminescence and Stability of 1,4,5-Triaryl-1,2,3-Triazoles. Chemphyschem 2023; 24:e202300209. [PMID: 37395382 DOI: 10.1002/cphc.202300209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/04/2023]
Abstract
The fluorescence, phosphorescence, and photochemical properties of di- and triaryl-substituted-1,2,3-triazoles are reported in this work. The ease of synthesis of regioisomers of substituted triazoles enables a systematic study on the correlation between regiochemistry and excited state properties, which include the solvent dependence of fluorescence, energy gap between singlet and triplet emitters, and propensity to photon-triggered transformations. The triazoles that carry electron (e)-donor and e-acceptor aryl substituents show high fluorescence quantum yields in weakly polar solvents and exhibit solvent-dependent fluorescence. The luminescence properties of these compounds in glass matrices at 77 K are characterized. The thermal and photo-stability, two parameters that are crucial to their potential utilities in optical devices, of these compounds are determined. The position of the e-donor substituent has a significant impact on the fluorescence emission energy and solvent sensitivity, singlet-triplet energy gap, and photochemical reactivity and stability. The experimental observations on the structural correlation with the photophysical and photochemical properties are explained by quantum chemical calculations. This study provides a rationale on the placement of substituent on a donor-acceptor type fluorophore to maneuver a range of photo-related properties.
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Affiliation(s)
- Brandon D Nusser
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
| | - Joseph V Accardo
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA
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36
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Prlj A, Hollas D, Curchod BFE. Deciphering the Influence of Ground-State Distributions on the Calculation of Photolysis Observables. J Phys Chem A 2023; 127:7400-7409. [PMID: 37556330 PMCID: PMC10493954 DOI: 10.1021/acs.jpca.3c02333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Nonadiabatic molecular dynamics offers a powerful tool for studying the photochemistry of molecular systems. Key to any nonadiabatic molecular dynamics simulation is the definition of its initial conditions (ICs), ideally representing the initial molecular quantum state of the system of interest. In this work, we provide a detailed analysis of how ICs may influence the calculation of experimental observables by focusing on the photochemistry of methylhydroperoxide (MHP), the simplest and most abundant organic peroxide in our atmosphere. We investigate the outcome of trajectory surface hopping simulations for distinct sets of ICs sampled from different approximate quantum distributions, namely harmonic Wigner functions and ab initio molecular dynamics using a quantum thermostat (QT). Calculating photoabsorption cross-sections, quantum yields, and translational kinetic energy maps from the results of these simulations reveals the significant effect of the ICs, in particular when low-frequency (∼ a few hundred cm-1) normal modes are connected to the photophysics of the molecule. Overall, our results indicate that sampling ICs from ab initio molecular dynamics using a QT is preferable for flexible molecules with photoactive low-frequency modes. From a photochemical perspective, our nonadiabatic dynamics simulations offer an explanation for a low-energy tail observed at high excitation energy in the translational kinetic energy map of MHP.
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Affiliation(s)
- Antonio Prlj
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- Division
of Physical Chemistry, Ruđer Bošković
Institute, Zagreb 10000, Croatia
| | - Daniel Hollas
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Basile F. E. Curchod
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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37
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Freixas VM, Malone W, Li X, Song H, Negrin-Yuvero H, Pérez-Castillo R, White A, Gibson TR, Makhov DV, Shalashilin DV, Zhang Y, Fedik N, Kulichenko M, Messerly R, Mohanam LN, Sharifzadeh S, Bastida A, Mukamel S, Fernandez-Alberti S, Tretiak S. NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:5356-5368. [PMID: 37506288 DOI: 10.1021/acs.jctc.3c00583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.
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Affiliation(s)
- Victor M Freixas
- Departments of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Walter Malone
- Department of Physics, Tuskegee University, Tuskegee, Alabama 36088, United States
| | - Xinyang Li
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Huajing Song
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Hassiel Negrin-Yuvero
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | - Royle Pérez-Castillo
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | - Alexander White
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tammie R Gibson
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Dmitry V Makhov
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | | | - Yu Zhang
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nikita Fedik
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Maksim Kulichenko
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Richard Messerly
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Luke Nambi Mohanam
- Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, Murcia 30100, Spain
| | - Shaul Mukamel
- Departments of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | | | - Sergei Tretiak
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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38
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Vysotskiy VP, Torbjörnsson M, Jiang H, Larsson ED, Cao L, Ryde U, Zhai H, Lee S, Chan GKL. Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods. J Chem Phys 2023; 159:044106. [PMID: 37486046 DOI: 10.1063/5.0152611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (∆E) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ∆E estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree-Fock included (0%-54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ∆E is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn-Sham orbitals gives results within 4-11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ∼5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.
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Affiliation(s)
- Victor P Vysotskiy
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Magne Torbjörnsson
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Ernst D Larsson
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Lili Cao
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Huanchen Zhai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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39
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Jafari S, Ryde U, Irani M. Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods. Sci Rep 2023; 13:10832. [PMID: 37402767 PMCID: PMC10319735 DOI: 10.1038/s41598-023-37755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
[4Fe-4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe-Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe-4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O.Box 124, 221 00, Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran.
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40
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Kleine Büning JB, Grimme S. Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT. J Chem Theory Comput 2023. [PMID: 37262324 DOI: 10.1021/acs.jctc.3c00165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 1H and 4230 13C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for 1H and 92% for 13C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (1H) and from 0.38 to 1.07 ppm (13C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.
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Affiliation(s)
- Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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41
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Koidan G, Hurieva AN, Rozhenko AB, Manthe U, Spengler T, Zahorulko S, Shvydenko T, Kostyuk A. Latent Carbene in Diaminomethylation of Benzenes: Mechanism and Practical Application. J Org Chem 2023. [PMID: 37196314 DOI: 10.1021/acs.joc.3c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Silylformamidine 1 exists in equilibrium with its carbenic form 1' due to an easy migration of the silyl group. The reaction of 1 with variously substituted fluorobenzenes proceeds as an insertion of the nucleophilic carbene 1' into the most acidic C-H bond upon mixing the reagents and does not require any catalyst. According to DFT calculations, the classical interpretation of the insertion reaction proceeding via a three-membered transition state structure requires high activation energy. Instead, low activation barriers are predicted for a transfer of the most acidic proton in the aromatic substrate to the carbene carbon. As the next step, a barrierless rearrangement of the formed ion pair toward the product completes the process. The reactivity of substituted benzenes in the reaction with silylformamidine can be roughly assessed by calculated pKa (DMSO) values for the C-H hydrogens. Benzene derivatives having pKa approx. less than 31 can undergo C-H insertion. The reaction provides aminals as the first products, which can easily be transformed into the corresponding aldehydes via acidic hydrolysis. As silylformamidine 1 is tolerant to many functional groups, the reaction can be applied to numerous benzene derivatives, making it a reliable strategy for application in organic synthesis.
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Affiliation(s)
- Georgyi Koidan
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
| | - Anastasiia N Hurieva
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
| | - Alexander B Rozhenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
- University of Bielefeld, Universitätstr. 25, 33615 Bielefeld, Germany
| | - Uwe Manthe
- University of Bielefeld, Universitätstr. 25, 33615 Bielefeld, Germany
| | - Tobias Spengler
- University of Bielefeld, Universitätstr. 25, 33615 Bielefeld, Germany
| | - Serhii Zahorulko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
| | - Tetiana Shvydenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
| | - Aleksandr Kostyuk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 5, 02660 Kyiv, Ukraine
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42
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Shirazi J, Jafari S, Ryde U, Irani M. Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study. J Phys Chem B 2023; 127:4480-4495. [PMID: 37191640 DOI: 10.1021/acs.jpcb.3c01495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular mechanics (QM/MM) calculations and energy refinement utilizing the big-QM and QM/MM thermodynamic cycle perturbation methods to propose a mechanism for the GlxII reaction that starts with a nucleophilic attack of the bridging OH- group on the substrate. The coordination of the substrate to the Zn ions places its electrophilic center close to the hydroxide group, enabling the reaction to proceed. Our estimated reaction energies are in excellent agreement with experimental data, thus demonstrating the reliability of our approach and the proposed mechanism. Additionally, we examined alternative protonation states of Asp-29, Asp-58, Asp-134, and the bridging hydroxide ion in the catalytic process. However, these give less favorable reactions, a poorer reproduction of the crystal structure geometry of the active site, and higher root-mean-squared deviations of the active site residues in molecular dynamics simulations.
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Affiliation(s)
- Javad Shirazi
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
| | - Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
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43
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Yan S, Ji X, Peng W, Wang B. Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. J Phys Chem B 2023; 127:4245-4253. [PMID: 37155960 DOI: 10.1021/acs.jpcb.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Xinwei Ji
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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Arsenault-Escobar S, Fuentes-Galvez JF, Orellana C, Bollo S, Sierra-Rosales P, Miranda-Rojas S. Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122400. [PMID: 36739665 DOI: 10.1016/j.saa.2023.122400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x104M-1 (UV-vis) and 5.75x104M-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.
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Affiliation(s)
- S Arsenault-Escobar
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - J F Fuentes-Galvez
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - C Orellana
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - S Bollo
- Centro de Investigación de Procesos Redox (CiPRex), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile; Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile
| | - P Sierra-Rosales
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile.
| | - S Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275, Santiago, Chile.
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Torbjörnsson M, Hagemann MM, Ryde U, Hedegård ED. Histidine oxidation in lytic polysaccharide monooxygenase. J Biol Inorg Chem 2023; 28:317-328. [PMID: 36828975 PMCID: PMC10036459 DOI: 10.1007/s00775-023-01993-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/26/2023]
Abstract
The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu-O]+ moiety is sufficiently potent to oxidise the nearest C-H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu-OH]2+ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu-O]+ intermediate.
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Affiliation(s)
- Magne Torbjörnsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Marlisa M Hagemann
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
| | - Erik Donovan Hedegård
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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46
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Franzke YJ. Reducing Exact Two-Component Theory for NMR Couplings to a One-Component Approach: Efficiency and Accuracy. J Chem Theory Comput 2023; 19:2010-2028. [PMID: 36939092 DOI: 10.1021/acs.jctc.2c01248] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The self-consistent and complex spin-orbit exact two-component (X2C) formalism for NMR spin-spin coupling constants [ J. Chem. Theory Comput. 17, 2021, 3874-3994] is reduced to a scalar one-component ansatz. This way, the first-order response term can be partitioned into the Fermi-contact (FC) and spin-dipole (SD) interactions as well as the paramagnetic spin-orbit (PSO) contribution. The FC+SD terms are real and symmetric, while the PSO term is purely imaginary and antisymmetric. The relativistic one-component approach is combined with a modern density functional treatment up to local hybrid functionals including the response of the current density. Computational demands are reduced by factors of 8-24 as shown for a large tin compound consisting of 137 atoms. Limitations of the current ansatz are critically assessed for Sn, Pb, Pd, and Pt compounds, i.e. the one-component treatment is not sufficient for tin compounds featuring a few heavy halogen atoms.
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Affiliation(s)
- Yannick J Franzke
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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47
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Schwan S, Achazi AJ, Ziese F, Schreiner PR, Volz K, Dehnen S, Sanna S, Mollenhauer D. Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions. J Comput Chem 2023; 44:843-856. [PMID: 36507710 DOI: 10.1002/jcc.27047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/28/2022] [Accepted: 11/01/2022] [Indexed: 12/15/2022]
Abstract
A class of adamantane-like molecular materials attracts attention because they exhibit an extreme non-linear optical response and emit a broad white-light spectrum after illumination with a continuous-wave infrared laser source. According to recent studies, not only the nature of the cluster molecules, but also the macroscopic structure of the materials determines their non-linear optical properties. Here we present a systematic study of cluster dimers of the compounds AdR4 and [(RT)4 S6 ] (T = Si, Ge, Sn) with R = methyl, phenyl or 1-naphthyl to gain fundamental knowledge about the interactions in the materials. For all compounds, a similar type of dimer structures with a staggered arrangement of substituents was determined as the energetically most favorable configuration. The binding energy between the dimers, determined by including London dispersion interactions, increases with the size of the core and the substituents. The cluster interactions can be classified as substituent-substituent-dominated (small cores, large substituents) or core-core-dominated (large cores, small substituents). Among various possible dimer conformers, those with small core-core distances are energetically preferred. Trimer and tetramer clusters display similar trends regarding the minimal core-core distances and binding energies. The much lower energy barrier determined for the rotation of substituents as compared to the rotation of the cluster dimers past each other indicates that the rotation of substituents more easily leads to different conformers in the material. Thus, understanding the interaction of the cluster dimers allows an initial assessment of the interactions in the materials.
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Affiliation(s)
- Sebastian Schwan
- Institute of Physical Chemistry, Justus Liebig University, Giessen, Germany.,Center for Materials Research, Justus Liebig University, Giessen, Germany
| | - Andreas J Achazi
- Institute of Physical Chemistry, Justus Liebig University, Giessen, Germany.,Center for Materials Research, Justus Liebig University, Giessen, Germany
| | - Ferdinand Ziese
- Center for Materials Research, Justus Liebig University, Giessen, Germany.,Institute of Theoretical Physics, Justus Liebig University, Giessen, Germany
| | - Peter R Schreiner
- Center for Materials Research, Justus Liebig University, Giessen, Germany.,Institute of Organic Chemistry, Justus Liebig University, Giessen, Germany
| | - Kerstin Volz
- Department of Physics and Materials Science Center (WZMW), Philipps-Universität Marburg, Marburg, Germany
| | - Stefanie Dehnen
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Simone Sanna
- Center for Materials Research, Justus Liebig University, Giessen, Germany.,Institute of Theoretical Physics, Justus Liebig University, Giessen, Germany
| | - Doreen Mollenhauer
- Institute of Physical Chemistry, Justus Liebig University, Giessen, Germany.,Center for Materials Research, Justus Liebig University, Giessen, Germany
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48
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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Duran S, Anwar J, Moin ST. Interaction of gentamicin and gentamicin-AOT with poly-(lactide-co-glycolate) in a drug delivery system - density functional theory calculations and molecular dynamics simulation. Biophys Chem 2023; 294:106958. [PMID: 36682087 DOI: 10.1016/j.bpc.2023.106958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Gentamicin is used to treat brucellosis, an infectious disease caused by the Brucella species but the drug faces several issues such as low efficacy, instability, low solubility, and toxicity. It also has a very short half-life, therefore, requiring frequent dosing. Consequently, several other antibiotics are also being used for the treatment of brucellosis as a single dose as well as in combination with other antibiotics but none of these therapies are satisfactory. Nanoparticles in particular polymer-based ones utilizing polymers that are biodegradable and biocompatible for instance PLGA are a method of choice to overcome such drug delivery issues and enable potential targeted delivery. The current study focuses on the evaluation of the structural and dynamical properties of a drug-polymer system consisting of gentamicin drug and PLGA polymer nanoparticles in the water representing a targeted drug delivery system for the treatment of brucellosis. For this purpose, all-atom molecular dynamics simulations were carried out on the drug-polymer systems in the absence and presence of the surfactant bis(2-Ethylhexyl) sulfosuccinate (AOT) to determine the structural and dynamical properties as well as the effect of the surfactant on these properties. We also investigated systems in which the polymer constituents were in the form of monomeric units toward decoupling the primary interactions of the monomer units and polymer effects. The simulation results explain the nature of the interactions between the drug and the polymer as well as transport properties in terms of drug diffusion coefficients, which characterize the molecular behavior of gentamicin-polymer nanoparticles for use in brucellosis.
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Affiliation(s)
- Shahid Duran
- Third World Center for Science and Technology, H.E.J. Research, Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom.
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research, Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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Petrikat RI, Steiger ST, Barani E, Boden PJ, Huber ME, Ringenberg MR, Niedner-Schatteburg G, Fink K, Becker S. Cooperativity-Driven Reactivity of a Dinuclear Copper Dimethylglyoxime Complex. Chemistry 2023; 29:e202203438. [PMID: 36807660 DOI: 10.1002/chem.202203438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/22/2023]
Abstract
In this report, we present the dinuclear copper(II) dimethylglyoxime (H2 dmg) complex [Cu2 (H2 dmg)(Hdmg)(dmg)]+ (1), which, in contrast to its mononuclear analogue [Cu(Hdmg)2 ] (2), is subject to a cooperativity-driven hydrolysis. The combined Lewis acidity of both copper centers increases the electrophilicity of the carbon atom in the bridging μ2 -O-N=C-group of H2 dmg and thus, facilitates the nucleophilic attack of H2 O. This hydrolysis yields butane-2,3-dione monoxime (3) and NH2 OH that, depending on the solvent, is then either oxidized or reduced. In ethanol, NH2 OH is reduced to NH4 + , yielding acetaldehyde as the oxidation product. In contrast, in CH3 CN, NH2 OH is oxidized by CuII to form N2 O and [Cu(CH3 CN)4 ]+ . Herein are presented the combined synthetic, theoretical, spectroscopic and spectrometric methods that indicate and establish the reaction pathway of this solvent-dependent reaction.
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Affiliation(s)
- Raphael I Petrikat
- RPTU Kaiserslautern-Landau, Institut für Anorganische Chemie, Erwin-Schroedinger-Str. 54, 67663, Kaiserslautern, Germany
| | - Sophie T Steiger
- RPTU Kaiserslautern-Landau, Institut für Physikalische Chemie, Erwin-Schroedinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Elham Barani
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pit J Boden
- RPTU Kaiserslautern-Landau, Institut für Physikalische Chemie, Erwin-Schroedinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Maximilian E Huber
- RPTU Kaiserslautern-Landau, Institut für Physikalische Chemie, Erwin-Schroedinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Mark R Ringenberg
- Société Suisse des Explosifs, Fabrikstrasse 48, CH-3900, Brig, Switzerland
| | - Gereon Niedner-Schatteburg
- RPTU Kaiserslautern-Landau, Institut für Physikalische Chemie, Erwin-Schroedinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Karin Fink
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sabine Becker
- RPTU Kaiserslautern-Landau, Institut für Anorganische Chemie, Erwin-Schroedinger-Str. 54, 67663, Kaiserslautern, Germany
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