1
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Cao Y, Balduf T, Beachy MD, Bennett MC, Bochevarov AD, Chien A, Dub PA, Dyall KG, Furness JW, Halls MD, Hughes TF, Jacobson LD, Kwak HS, Levine DS, Mainz DT, Moore KB, Svensson M, Videla PE, Watson MA, Friesner RA. Quantum chemical package Jaguar: A survey of recent developments and unique features. J Chem Phys 2024; 161:052502. [PMID: 39092934 DOI: 10.1063/5.0213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.
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Affiliation(s)
- Yixiang Cao
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Ty Balduf
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Michael D Beachy
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - M Chandler Bennett
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Alan Chien
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pavel A Dub
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Kenneth G Dyall
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - James W Furness
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mathew D Halls
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Thomas F Hughes
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - H Shaun Kwak
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Daniel T Mainz
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Kevin B Moore
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mats Svensson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pablo E Videla
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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2
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Wang Y, Teng C, Begin E, Bussiere M, Bao JL. PW-SMD: A Plane-Wave Implicit Solvation Model Based on Electron Density for Surface Chemistry and Crystalline Systems in Aqueous Solution. J Chem Theory Comput 2024. [PMID: 39024317 DOI: 10.1021/acs.jctc.4c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Electron density-based implicit solvation models are a class of techniques for quantifying solvation effects and calculating free energies of solvation without an explicit representation of solvent molecules. Integral to the accuracy of solvation modeling is the proper definition of the solvation shell separating the solute molecule from the solvent environment, allowing for a physical partitioning of the free energies of solvation. Unlike state-of-the-art implicit solvation models for molecular quantum chemistry calculations, e.g., the solvation model based on solute electron density (SMD), solvation models for systems under periodic boundary conditions with plane-wave (PW) basis sets have been limited in their accuracy. Furthermore, a unified implicit solvation model with both homogeneous solution-phase and heterogeneous interfacial structures treated on equal footing is needed. In order to address this challenge, we developed a high-accuracy solvation model for periodic PW calculations that is applicable to molecular, ionic, interfacial, and bulk-phase chemistry. Our model, PW-SMD, is an extension of the SMD molecular solvation model to periodic systems in water. The free energy of solvation is partitioned into the electrostatic and cavity-dispersion-solvent structure (CDS) contributions. The electrostatic contributions of the solvation shell surrounding solute structures are parametrized based on their geometric and physical properties. In addition, the nonelectrostatic contribution to the solvation energy is accounted for by extending the CDS formalism of SMD to incorporate periodic boundary conditions. We validate the accuracy and robustness of our solvation model by comparing predicted solvation free energies against experimental data for molecular and ionic systems, carved-cluster composite energetic models of solvated reaction energies and barriers on surface systems, and deep-learning-accelerated ab initio molecular dynamics (AIMD). Our developed periodic implicit solvation model shows significantly improved accuracy compared to previous work (namely, solvation models in aqueous solution) and can be applied to simulate solvent effects in a wide range of surface and crystalline materials.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chong Teng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Elijah Begin
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mason Bussiere
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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3
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Fetoh A, Fantuzzi F, Lichtenberg C. The Chlorido-Bismuth Dication: A Potent Lewis Acid Captured in a Hepta-Coordinate Species with a Stereochemically Active Lone Pair. Inorg Chem 2024; 63:12089-12099. [PMID: 38900030 PMCID: PMC11220759 DOI: 10.1021/acs.inorgchem.4c01076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
The stabilization of simple, highly reactive cationic species in molecular complexes represents an important strategy to isolate and characterize compounds with uncommon or even unprecedented structural motifs and properties. Here we report the synthesis, isolation, and full characterization of chlorido-bismuth dications, stabilized only by monodentate dimethylsulfoxide (dmso) ligands: [BiCl(dmso)6][BF4]2 (1) and [BiCl(μ2-dmso)(dmso)4]2[BF4]4 (2). These compounds show unusual distorted pentagonal bipyramidal coordination geometries along with high Lewis acidities and have been analyzed by multinuclear NMR spectroscopy, elemental analysis, IR spectroscopy, single-crystal X-ray diffraction, and density functional theory calculations. Attempts to generate the bromido- and iodido-analogs gave dmso-stabilized tricationic bismuth species.
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Affiliation(s)
- Ahmed Fetoh
- Department
of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, Marburg 35032, Germany
- Department
of Chemistry, Faculty of Science, Mansoura
University, El Gomhouria,
Mansoura Qism 2, Dakahlia Governorate 11432 Mansoura, Egypt
| | - Felipe Fantuzzi
- School
of Chemistry and Forensic Science, University
of Kent, Park Wood Road, Canterbury CT2 7NH, U.K.
| | - Crispin Lichtenberg
- Department
of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, Marburg 35032, Germany
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4
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Lagardère L, Maurin L, Adjoua O, El Hage K, Monmarché P, Piquemal JP, Hénin J. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation. J Chem Theory Comput 2024; 20:4481-4498. [PMID: 38805379 DOI: 10.1021/acs.jctc.3c01249] [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
We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation of alchemical free-energy differences. We propose a software implementation and showcase it on biomolecular systems. The method arises from coupling multiple-walker adaptive biasing force with λ-dynamics. The sampling of the alchemical variable is continuous and converges toward a uniform distribution, making manual optimization of the λ schedule unnecessary. Contrary to most other approaches, alchemical free-energy estimates are obtained immediately without any postprocessing. Free diffusion of λ improves orthogonal relaxation compared to fixed-λ thermodynamic integration or free-energy perturbation. Furthermore, multiple walkers provide generic orthogonal space coverage with minimal user input and negligible computational overhead. We show that our high-performance implementations coupling the Colvars library with NAMD and Tinker-HP can address real-world cases including ligand-receptor binding with both fixed-charge and polarizable models, with a demonstrably richer sampling than fixed-λ methods. The implementation is fully open-source, publicly available, and readily usable by practitioners of current alchemical methods. Thanks to the portable Colvars library, lambda-ABF presents a unified user interface regardless of the back-end (NAMD, Tinker-HP, or any software to be interfaced in the future), sparing users the effort of learning multiple interfaces. Finally, the Colvars Dashboard extension of the visual molecular dynamics (VMD) software provides an interactive monitoring and diagnostic tool for lambda-ABF simulations.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, FR2622 CNRS, 75005 Paris, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Lise Maurin
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Krystel El Hage
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Pierre Monmarché
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Université Paris Cité, CNRS, UPR 9080, 75005 Paris, France
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5
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Kim Y, Jung H, Kumar S, Paton RS, Kim S. Designing solvent systems using self-evolving solubility databases and graph neural networks. Chem Sci 2024; 15:923-939. [PMID: 38239675 PMCID: PMC10793204 DOI: 10.1039/d3sc03468b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Designing solvent systems is key to achieving the facile synthesis and separation of desired products from chemical processes, so many machine learning models have been developed to predict solubilities. However, breakthroughs are needed to address deficiencies in the model's predictive accuracy and generalizability; this can be addressed by expanding and integrating experimental and computational solubility databases. To maximize predictive accuracy, these two databases should not be trained separately, and they should not be simply combined without reconciling the discrepancies from different magnitudes of errors and uncertainties. Here, we introduce self-evolving solubility databases and graph neural networks developed through semi-supervised self-training approaches. Solubilities from quantum-mechanical calculations are referred to during semi-supervised learning, but they are not directly added to the experimental database. Dataset augmentation is performed from 11 637 experimental solubilities to >900 000 data points in the integrated database, while correcting for the discrepancies between experiment and computation. Our model was successfully applied to study solvent selection in organic reactions and separation processes. The accuracy (mean absolute error around 0.2 kcal mol-1 for the test set) is quantitatively useful in exploring Linear Free Energy Relationships between reaction rates and solvation free energies for 11 organic reactions. Our model also accurately predicted the partition coefficients of lignin-derived monomers and drug-like molecules. While there is room for expanding solubility predictions to transition states, radicals, charged species, and organometallic complexes, this approach will be attractive to predictive chemistry areas where experimental, computational, and other heterogeneous data should be combined.
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Affiliation(s)
- Yeonjoon Kim
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
- Department of Chemistry, Pukyong National University Busan 48513 Republic of Korea
| | - Hojin Jung
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
| | - Sabari Kumar
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
| | - Robert S Paton
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
| | - Seonah Kim
- Department of Chemistry, Colorado State University Fort Collins CO 80523 USA
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6
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Islam SMR, Khezeli F, Ringe S, Plaisance C. An implicit electrolyte model for plane wave density functional theory exhibiting nonlinear response and a nonlocal cavity definition. J Chem Phys 2023; 159:234117. [PMID: 38112507 DOI: 10.1063/5.0176308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
We have developed and implemented an implicit electrolyte model in the Vienna Ab initio Simulation Package (VASP) that includes nonlinear dielectric and ionic responses as well as a nonlocal definition of the cavities defining the spatial regions where these responses can occur. The implementation into the existing VASPsol code is numerically efficient and exhibits robust convergence, requiring computational effort only slightly higher than the original linear polarizable continuum model. The nonlinear + nonlocal model is able to reproduce the characteristic "double hump" shape observed experimentally for the differential capacitance of an electrified metal interface while preventing "leakage" of the electrolyte into regions of space too small to contain a single water molecule or solvated ion. The model also gives a reasonable prediction of molecular solvation free energies as well as the self-ionization free energy of water and the absolute electron chemical potential of the standard hydrogen electrode. All of this, combined with the additional ability to run constant potential density functional theory calculations, should enable the routine computation of activation barriers for electrocatalytic processes.
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Affiliation(s)
- S M Rezwanul Islam
- Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Foroogh Khezeli
- Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Stefan Ringe
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Craig Plaisance
- Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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7
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Zheng JW, Green WH. Experimental Compilation and Computation of Hydration Free Energies for Ionic Solutes. J Phys Chem A 2023; 127:10268-10281. [PMID: 38010212 DOI: 10.1021/acs.jpca.3c05514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Although charged solutes are common in many chemical systems, traditional solvation models perform poorly in calculating solvation energies of ions. One major obstacle is the scarcity of experimental data for solvated ions. In this study, we release an experiment-based aqueous ionic solvation energy data set, IonSolv-Aq, that contains hydration free energies for 118 anions and 155 cations, more than 2 times larger than the set of hydration free energies for singly charged ions contained in the 2012 Minnesota Solvation Database commonly used in benchmarking studies. We discuss sources of systematic uncertainty in the data set and use the data to examine the accuracy of popular implicit solvation models COSMO-RS and SMD for predicting solvation free energies of singly charged ionic solutes in water. Our results indicate that most SMD and COSMO-RS modeling errors for ionic solutes are systematic and correctable with empirical parameters. We discuss two systematic offsets: one across all ions and one that depends on the functional group of the ionization site. After correcting for these offsets, solvation energies of singly charged ions are predicted using COSMO-RS to 3.1 kcal mol-1 MAE against a challenging test set and 1.7 kcal mol-1 MAE (about 3% relative error) with a filtered test set. The performance of SMD is similar, with MAE against those same test sets of 2.7 and 1.7 kcal mol-1. These results underscore the importance of compiling larger experimental data sets to improve solvation model parametrization and fairly assess performance.
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Affiliation(s)
- Jonathan W Zheng
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Lončarić D, Movahedifar F, Štoček JR, Dračínský M, Cvačka J, Guan S, Bythell BJ, Císařová I, Masson E, Kaleta J. Solvent-controlled formation of alkali and alkali-earth-secured cucurbituril/guest trimers. Chem Sci 2023; 14:9258-9266. [PMID: 37712024 PMCID: PMC10498720 DOI: 10.1039/d3sc02032k] [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: 04/19/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023] Open
Abstract
Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium oxide, addition of a selection of alkali and alkali-earth cations with van der Waals radii between 1.0 and 1.4 Å (Na+, K+, Ca2+, Sr2+, Ba2+ and Eu3+) to the CB[7]/guest complexes triggers their cation-mediated trimerization, a process that is very slow on the nuclear magnetic resonance (NMR) time scale. Smaller (Li+, Mg2+) or larger cations (Rb+, Cs+ or NH4+) are inert. The trimers display extensive CH-O interactions between the equatorial and pseudo-equatorial hydrogens of CB[7] and the carbonyl rim of the neighboring CB[7] unit in the trimer, and a deeply nested cation between the three interacting carbonylated CB[7] rims; a counteranion is likely perched in the shallow cavity formed by the three outer walls of CB[7] in the trimer. Remarkably, a guest must occupy the cavity of CB[7] for trimerization to take place. Using a combination of semi-empirical and density functional theory techniques in conjunction with continuum solvation models, we showed that trimerization is favored in DMSO, and not in water, because the penalty for the partial desolvation of three of the six CB[7] portals upon aggregation into a trimer is less unfavorable in DMSO compared to water.
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Affiliation(s)
- Doroteja Lončarić
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 160 00 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague 128 40 Prague 2 Czech Republic
| | - Fahimeh Movahedifar
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Jakub Radek Štoček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 160 00 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague 128 40 Prague 2 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 160 00 Prague 6 Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 160 00 Prague 6 Czech Republic
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague 128 40 Prague 2 Czech Republic
| | - Eric Masson
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Jiří Kaleta
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 160 00 Prague 6 Czech Republic
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9
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Jiang T, Luan N, Wang L, Leng J, Zhang Y. Theoretical Insights on the Sensing Performance for Newly-synthesized Two-photon Fluorescent N 2H 4 Probes Based on Spirobifluorence. J Fluoresc 2023; 33:1949-1959. [PMID: 36930342 DOI: 10.1007/s10895-023-03209-z] [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: 02/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The development of fluorescent probe for hydrazine (N2H4) detection has attracted much attention due to the important role of N2H4 plays in the fields of medicine, agriculture, biology and environments. In this paper, the optical properties and water solubility of two novel two-photon fluorescent molecular probes (Probe1 and Probe2) before and after the reaction with N2H4 are studied by using the density function theory. The results show that electronic distribution and transition dipole moment of the probes are obviously changed after the reaction with N2H4, thus the optical properties of the molecules are influenced and the detection of N2H4 are realized. In addition, photoinduced electron transfer processes for Probe1 and Probe2 in the presence of N2H4 are theoretically characterized, which explains the experimental observations from the microscopic mechanism. Special attention has been paid on the analysis of the two-photon absorption for the probes with the absence and presence of N2H4 by the response theory method. Both probes with good water solubility show large variation on the two-photon absorption cross section when reacts with N2H4. In particular, the two-photon absorption response of Probe2 is more obvious, so it possesses preferable two-photon fluorescence microscopic imaging ability. More importantly, the receptor effect on the sensing performances of the probes are demonstrated, providing a theoretical reference for the design and synthesis on more efficient two-photon fluorescence N2H4 probes. Our study provides necessary information on the response mechanism of the studied chemosensors and helps to establish the relationship between the structure and optical properties of two-photon fluorescence N2H4 probes.
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Affiliation(s)
- Tengfei Jiang
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Ni Luan
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Longping Wang
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Jiancai Leng
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Yujin Zhang
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
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10
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Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. J Chem Phys 2023; 159:054102. [PMID: 37526158 PMCID: PMC10396400 DOI: 10.1063/5.0158914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
Computational simulation of biomolecules can provide important insights into protein design, protein-ligand binding interactions, and ab initio biomolecular folding, among other applications. Accurate treatment of the solvent environment is essential in such applications, but the use of explicit solvents can add considerable cost. Implicit treatment of solvent effects using a dielectric continuum model is an attractive alternative to explicit solvation since it is able to describe solvation effects without the inclusion of solvent degrees of freedom. Previously, we described the development and parameterization of implicit solvent models for small molecules. Here, we extend the parameterization of the generalized Kirkwood (GK) implicit solvent model for use with biomolecules described by the AMOEBA force field via the addition of corrections to the calculation of effective radii that account for interstitial spaces that arise within biomolecules. These include element-specific pairwise descreening scale factors, a short-range neck contribution to describe the solvent-excluded space between pairs of nearby atoms, and finally tanh-based rescaling of the overall descreening integral. We then apply the AMOEBA/GK implicit solvent to a set of ten proteins and achieve an average coordinate root mean square deviation for the experimental structures of 2.0 Å across 500 ns simulations. Overall, the continued development of implicit solvent models will help facilitate the simulation of biomolecules on mechanistically relevant timescales.
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Affiliation(s)
- Rae A. Corrigan
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Jack R. Lynn
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Thomas L. Casavant
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas in Austin, Austin, Texas 78712, USA
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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11
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Tupikina EY, Korostelev VO, Krutin DV, Tolstoy PM. Evolution of vibrational bands upon gradual protonation/deprotonation of arsinic acid H 2As(O)OH in media of different polarity. Phys Chem Chem Phys 2023; 25:8664-8675. [PMID: 36891959 DOI: 10.1039/d2cp06060d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
This computational work is devoted to the investigation (MP2/def2-TZVP) of the geometry and IR parameters of arsinic acid H2AsOOH and its hydrogen-bonded complexes under vacuum and in media with different polarity. The medium effects were accounted for in two ways: (1) implicitly, using the IEFPCM model, varying the dielectric permittivity (ε) and (2) explicitly, by considering hydrogen-bonded complexes of H2As(O)OH with various hydrogen bond donors (41 complexes) or acceptors (38 complexes), imitating a gradual transition to the As(OH)2+ or AsO2- moiety, respectively. It was shown that the transition from vacuum to a medium with ε > 1 causes the As(O)OH fragment to lose its flatness. The solvent polar medium introduces significant changes in the geometry and IR spectral parameters of hydrogen-bonded complexes too: as the polarity of a medium increases, weak hydrogen bonds become weaker, and strong and medium hydrogen bonds become stronger; in the case of a complex with two hydrogen bonds cooperativity effects are observed. In almost all cases the driving force of these changes appears to be preferential solvation of charge-separated structures. In the limiting case of complete deprotonation (or conversely complete protonation) the vibrational frequencies of νAsO and νAs-O turn into νAs-O(asym) and νAs-O(sym), respectively. In the intermediate cases the distance between νAsO and νAs-O is sensitive to both implicit solvation and explicit solvation and the systematic changes of this distance can be used for estimation of the degree of proton transfer within the hydrogen bond.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
| | | | - Danil V Krutin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
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12
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Metal-Assisted Complexation of Fluorogenic Dyes by Cucurbit[7]uril and Cucurbit[8]uril: A DFT Evaluation of the Key Factors Governing the Host-Guest Recognition. Molecules 2023; 28:molecules28041540. [PMID: 36838524 PMCID: PMC9966945 DOI: 10.3390/molecules28041540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
With the emergence of host-guest systems, a novel branch of complexation chemistry has found wide application in industries such as food, pharmacy, medicine, environmental protection and cosmetics. Along with the extensively studied cyclodextrins and calixarenes, the innovative cucurbiturils (CB) have enjoyed increased popularity among the scientific community as they possess even better qualities as cavitands as compared to the former molecules. Moreover, their complexation abilities could further be enhanced with the assistance of metal cations, which can interestingly exert a dual effect on the complexation process: either by competitively binding to the host entity or cooperatively associating with the CB@guest structures. In our previous work, two metal species (Mg2+ and Ga3+) have been found to bind to CB molecules in the strongest fashion upon the formation of host-guest complexes. The current study focuses on their role in the complex formation with three dye molecules: thiazole orange, neutral red, and thioflavin T. Various key factors influencing the process have been recognized, such as pH and the dielectric constant of the medium, the cavity size of the host, Mn+ charge, and the presence/absence of hydration shell around the metal cation. A well-calibrated DFT methodology, solidly based and validated and presented in the literature experimental data, is applied. The obtained results shed new light on several aspects of the cucurbituril complexation chemistry.
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13
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Liu SC, Zhu XR, Liu DY, Fang DC. DFT calculations in solution systems: solvation energy, dispersion energy and entropy. Phys Chem Chem Phys 2023; 25:913-931. [PMID: 36519338 DOI: 10.1039/d2cp04720a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DFT calculations of reaction mechanisms in solution have always been a hot topic, especially for transition-metal-catalyzed reactions. The calculation of solvation energy is performed using either the polarizable continuum model (PCM) or the universal solvation model SMD. The PCM calculation is very sensitive to the choice of atomic radii to form a cavity, where the self-consistent isodensity PCM (SCI-PCM) has been recognized as the best choice and our IDSCRF radii can provide a similar cavity. Moving from a gas-phase case to a solution case, dispersion energy and entropy should be carefully treated. The solvent-solute dispersion is also important in solution systems, and it should be calculated together with the solute dispersion. Only half of the solvent-solute dispersion energy from the PCM calculation belongs to the solute molecules to maintain a thermal equilibrium between a solute molecule and its cavity, similar to the treatment of electrostatic energy. Relative solute dispersion energy should also be shared equally with the newly formed cavity. The entropy change from a gas phase to a liquid phase is quite large, but the modern quantum chemistry programs can only calculate the gas-phase translational entropy based on the idea-gas equation. In this review, we will provide an operable method to calculate the solution translational entropy, which has been coded in our THERMO program.
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Affiliation(s)
- Si-Cong Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xin-Rui Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Dan-Yang Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - De-Cai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
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14
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Fischer L, Hartmann SS, Maljusch A, Däschlein C, Prymak O, Ulbricht M. The influence of anion-exchange membrane nanostructure onto ion transport: Adjusting membrane performance through fabrication conditions. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Tran B, Cai Y, Janik MJ, Milner ST. Hydrogen Bond Thermodynamics in Aqueous Acid Solutions: A Combined DFT and Classical Force-Field Approach. J Phys Chem A 2022; 126:7382-7398. [PMID: 36190836 DOI: 10.1021/acs.jpca.2c04124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The thermodynamics of hydrogen bonds in aqueous and acidic solutions significantly impacts the kinetics and thermodynamics of acid reaction chemistry. We utilize in this work a multiscale approach, combining density functional theory (DFT) with classical molecular dynamics (MD) to model hydrogen bond thermodynamics in an acidic solution. Using thermodynamic cycles, we split the solution phase free energy into its gas phase counterpart plus solvation free energies. We validate this DFT/MD approach by calculating the aqueous phase hydrogen bond free energy between two water molecules (H2O-···-H2O), the free energy to transform an H3O+ cation into an H5O2+ cation, and the hydrogen bond free energy of protonated water clusters (H3O+-···-H2O and H5O2+-···-H2O). The computed equilibrium hydrogen bond free energy of H2O-···-H2O is remarkably accurate, especially considering the large individual contributions to the thermodynamic cycle. Turning to cations, we find the ion to be more stable than H3O+ by roughly 1-2 kBT. This small free energy difference allows for thermal fluctuation between the two idealized motifs, consistent with spectroscopic and simulation studies. Lastly, hydrogen bonding free energies between either H+ cation and H2O in solution were found to be stronger than between two H2O, though much less so than in vacuum because of dielectric screening in solution. Altogether, our results suggest the DFT/MD approach is promising for application in modeling hydrogen bonding and proton transfer thermodynamics in condensed phases.
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Affiliation(s)
- Bolton Tran
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania16801, United States
| | - Yusheng Cai
- Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Michael J Janik
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania16801, United States
| | - Scott T Milner
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania16801, United States
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16
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Paik D, Lee H, Kim H, Choi JM. Thermodynamics of π–π Interactions of Benzene and Phenol in Water. Int J Mol Sci 2022; 23:ijms23179811. [PMID: 36077201 PMCID: PMC9456204 DOI: 10.3390/ijms23179811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.
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Affiliation(s)
- Dooam Paik
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hankyul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Correspondence: (H.K.); (J.-M.C.)
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
- Correspondence: (H.K.); (J.-M.C.)
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17
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Sanad SG. Thermodynamic parameters of solvation and volumes of nano Cu(NO3)2·2.5H2O in different concentrations of DMF – Water mixed solvents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Vassetti D, Labat F. Towards a transferable nonelectrostatic model for continuum solvation: The electrostatic and nonelectrostatic energy correction model. J Comput Chem 2022; 43:1372-1387. [PMID: 35678272 DOI: 10.1002/jcc.26944] [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: 01/12/2022] [Revised: 03/24/2022] [Accepted: 05/01/2022] [Indexed: 11/09/2022]
Abstract
In this work, we introduce an electrostatic and non-electrostatic (ENE) correction to the solvation energy based on the Solvent-Accessible Surface Area (SASA) of the solute and the solvent static dielectric constant. The proposed correction was developed for neutral solutes in non-aqueous solvents, considering three different implicit solvation models based on a Self-Consistent Reaction Field treatment of solute-solvent mutual polarization using an Apparent Surface Charge formalism, namely the Integral Equation Formalism of the Polarizable Continuum Model using a continuous surface charge scheme (PCM), the Solvation Model based on solute electron density (SMD), and the generalized Finite-Difference Poisson-Boltzmann (FDPB) model. The proposed correction was parametrized on a diverse training set of 4980 solvation data from the Solv@tum database of experimental solvation energies, and validated on the non-aqueous subset of the MNSOL database comprising 2140 solvation energies. The performances of the proposed ENE models with minimal and extended parameters formulations have been analyzed and the latter variant has been further compared to the widely used Cavity, Dispersion, and Solvent structural effects (CDS) non-electrostatic model originally developed for the SMx family of implicit solvation models. Overall, a very good agreement between the computed solvation energies with the ENE correction and the reference experimental data has been found on both the training and test sets for all continuum solvation models considered. Furthermore, results for the ENE correction are on par with the reference CDS non-electrostatic model for both SMD and FDPB electrostatics, but with the advantage of using a lower number of parameters and thus an improved transferability between different electrostatics treatments.
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Affiliation(s)
- Dario Vassetti
- Chimie ParisTech, CNRS, Institute of Chemistry for Life and Health Sciences, Chemical Theory and Modelling Group, PSL University, Paris, France
| | - Frédéric Labat
- Chimie ParisTech, CNRS, Institute of Chemistry for Life and Health Sciences, Chemical Theory and Modelling Group, PSL University, Paris, France
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19
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Kircheva N, Dobrev S, Nikolova V, Angelova S, Dudev T. Theoretical Insight into the Phosphate-Targeted Silver's Antibacterial Action: Differentiation between Gram (+) and Gram (-) Bacteria. Inorg Chem 2022; 61:10089-10100. [PMID: 35724666 DOI: 10.1021/acs.inorgchem.2c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although silver is one of the first metals finding broad applications in everyday life, specific key points of the intimate mechanism of its bacteriostatic/bactericidal activity lack explanation. It is widely accepted that the antimicrobial potential of the silver cation depends on the composition and thickness of the bacterial external envelope: the outer membrane in Gram-negative bacteria is more prone to Ag+ attack than the cell wall in Gram-positive bacteria. The major cellular components able to interact strongly with Ag+ (teichoic acids, phospholipids, and lipopolysaccharides) contain mono/diesterified phosphate moieties. By applying a reliable DFT/SMD methodology, we modeled the reactions between the aforementioned constituents in typical Gram-positive and Gram-negative bacteria and hydrated Ag+ species, thus disclosing the factors that govern the process of metal-model ligand complexation. The conducted research indicates thermodynamically possible reactions in all cases but still a greater preference of the Ag+ toward the constituents in Gram-negative bacteria in comparison with their counterparts in Gram-positive bacteria. The observed tendencies shed light on the specific interactions of the silver cation with the modeled phosphate-containing units at the atomic level.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies ″Acad. J. Malinowski″, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies ″Acad. J. Malinowski″, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University ″St. Kl. Ohridski″, 1164 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies ″Acad. J. Malinowski″, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University ″St. Kl. Ohridski″, 1164 Sofia, Bulgaria
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20
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Fantuzzi F, Jiao Y, Dewhurst RD, Weinhold F, Braunschweig H, Engels B. Can a Wanzlick-like equilibrium exist between dicoordinate borylenes and diborenes? Chem Sci 2022; 13:5118-5129. [PMID: 35655568 PMCID: PMC9093173 DOI: 10.1039/d1sc05988b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/03/2022] [Indexed: 12/23/2022] Open
Abstract
Boron chemistry has experienced tremendous progress in the last few decades, resulting in the isolation of a variety of compounds with remarkable electronic structures and properties. Some examples are the singly Lewis-base-stabilised borylenes, wherein boron has a formal oxidation state of +I, and their dimers featuring a boron-boron double bond, namely diborenes. However, no evidence of a Wanzlick-type equilibrium between borylenes and diborenes, which would open a valuable route to the latter compounds, has been found. In this work, we combine DFT, coupled-cluster, multireference methods, and natural bond orbital/natural resonance theory analyses to investigate the electronic, structural, and kinetic factors controlling the reactivity of the transient CAAC-stabilised cyanoborylene, which spontaneously cyclotetramerises into a butterfly-type, twelve-membered (BCN)4 ring, and the reasons why its dimerisation through the boron atoms is hampered. The computations are also extended to the NHC-stabilised borylene counterparts. We reveal that the borylene ground state multiplicity dictates the preference for self-stabilising cyclooligomerisation over boron-boron dimerisation. Our comparison between NHC- vs. CAAC-stabilised borylenes provides a convincing rationale for why the reduction of the former always gives diborenes while a range of other products is found for the latter. Our findings provide a theoretical background for the rational design of base-stabilised borylenes, which could pave the way for novel synthetic routes to diborenes or alternatively non-dimerising systems for small-molecule activation.
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Affiliation(s)
- Felipe Fantuzzi
- Institute for Physical and Theoretical Chemistry, Julius-Maximilians-Universität Würzburg Emil-Fischer-Str. 42 97074 Würzburg Germany
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- School of Physical Sciences, Ingram Building, University of Kent Park Wood Road Canterbury CT2 7NH UK
| | - Yinchun Jiao
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Hunan University of Science and Technology Xiangtan 411201 China
| | - Rian D Dewhurst
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Holger Braunschweig
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Bernd Engels
- Institute for Physical and Theoretical Chemistry, Julius-Maximilians-Universität Würzburg Emil-Fischer-Str. 42 97074 Würzburg Germany
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21
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Fantuzzi F, Moral R, Dewhurst RD, Braunschweig H, Phukan AK. Probing the Potential of Hitherto Unexplored Base‐Stabilized Borylenes in Dinitrogen Binding. Chemistry 2022; 28:e202104123. [DOI: 10.1002/chem.202104123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Felipe Fantuzzi
- School of Physical Sciences Ingram Building University of Kent Park Wood Rd Canterbury CT2 7NH UK
- Institute for Inorganic Chemistry Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Rubi Moral
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
| | - Rian D. Dewhurst
- Institute for Inorganic Chemistry Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Holger Braunschweig
- Institute for Inorganic Chemistry Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
- Institute for Sustainable Chemistry & Catalysis with Boron Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Ashwini K. Phukan
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
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22
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Chellegui M, Champagne B, Trabelsi M. Lewis acid-catalyzed Diels–Alder cycloaddition of 2,5-dimethylfuran and ethylene: a density functional theory investigation. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02880-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Predicting the Solubility of Nonelectrolyte Solids Using a Combination of Molecular Simulation with the Solubility Parameter Method MOSCED: Application to the Wastewater Contaminants Monuron, Diuron, Atrazine and Atenolol. Processes (Basel) 2022. [DOI: 10.3390/pr10030538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Methods to predict the equilibrium solubility of nonelectrolyte solids are indispensable for early-stage process development, design, and feasibility studies. Conventional analytic methods typically require reference data to regress parameters, which may not be available or limited for novel systems. Molecular simulation is a promising alternative, but is computationally intensive. Here, we demonstrate the ability to use a small number of molecular simulation free energy calculations to generate reference data to regress model parameters for the analytical MOSCED (modified separation of cohesive energy density) model. The result is an efficient analytical method to predict the equilibrium solubility of nonelectrolyte solids. The method is demonstrated for the wastewater contaminants monuron, diuron, atrazine and atenolol. Predictions for monuron, diuron and atrazine are in reasonable agreement with MOSCED parameters regressed using experimental solubility data. Predictions for atenolol are inferior, suggesting a potential limitation in the adopted molecular models, or the solvents selected to generate the necessary reference data.
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24
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Carre-Burritt AE, Van Hoomissen DJ, Vyas S. Role of Explicit Hydration in Predicting the Aqueous Standard Reduction Potential of Sulfate Radical Anion by DFT and Insight into the Influence of pH on the Reduction Potential. J Phys Chem A 2022; 126:1422-1428. [PMID: 35171595 DOI: 10.1021/acs.jpca.1c09459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfate radical anion (SO4•-) is a potent oxidant capable of destroying recalcitrant environmental contaminants such as perfluoroalkyl carboxylic acids. In addition, it is thought to participate in important atmospheric reactions. Its standard reduction potential (E°) is fundamental to its reactivity. Using theoretical methods to accurately predict the aqueous phase E° requires solvation with explicit water molecules. Herein, using density functional theory, we calculated the aqueous E° of SO4•- and evaluated sensitivity to explicit water count. The E° increased considerably with more waters until ca. 24 were included, after which change in E° was small. When a proton was added to these systems, the E° was similar regardless of the explicit water count and this value was similar to the E° for systems with a large number of explicit waters but no proton. This result agrees with literature evidence that the E° is pH independent. Natural Bond Orbital natural population analysis indicated that in the case of both SO42- and SO4•-, considerable charge was donated from the SO4 center to the explicit solvation shells.
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Affiliation(s)
- Asa E Carre-Burritt
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Daniel J Van Hoomissen
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
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25
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Chang CW, Borne I, Lawler RM, Yu Z, Jang SS, Lively RP, Sholl DS. Accelerating Solvent Selection for Type II Porous Liquids. J Am Chem Soc 2022; 144:4071-4079. [PMID: 35170940 DOI: 10.1021/jacs.1c13049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II porous liquids, comprising intrinsically porous molecules dissolved in a liquid solvent, potentially combine the adsorption properties of porous adsorbents with the handling advantages of liquids. Previously, discovery of appropriate solvents to make porous liquids had been limited to direct experimental tests. We demonstrate an efficient screening approach for this task that uses COSMO-RS calculations, predictions of solvent pKa values from a machine-learning model, and several other features and apply this approach to select solvents from a library of more than 11,000 compounds. This method is shown to give qualitative agreement with experimental observations for two molecular cages, CC13 and TG-TFB-CHEDA, identifying solvents with higher solubility for these molecules than had previously been known. Ultimately, the algorithm streamlines the downselection of suitable solvents for porous organic cages to enable more rapid discovery of Type II porous liquids.
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Affiliation(s)
- Chao-Wen Chang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaiah Borne
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Robin M Lawler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhenzi Yu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Seung Soon Jang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ryan P Lively
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David S Sholl
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,Oak Ridge National Laboratory, Oak Ridge, Tennessee 37839, United States
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26
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Antonov L, Kawauchi S, Shirata K. Acid Dissociation Constants of the Benzimidazole Unit in the Polybenzimidazole Chain: Configuration Effects. Molecules 2022; 27:molecules27031064. [PMID: 35164328 PMCID: PMC8838992 DOI: 10.3390/molecules27031064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
The acid dissociation constant of three benzimidazoles, namely 2,2′-bibenzo[d]imidazole, 2,5′-bibenzo[d]imidazole, and 5,5′-bibenzo[d]imidazole, have been investigated by means of density functional theory calculations in gas phase and in aqueous solution. The theoretical approach was validated by the comparing of predicted and experimentally determined pKa values in imidazole, benzimidazole, and 2-phenylbenzimidazole. From the studied compounds, 2,2′-bibenzo[d]imidazole was found to be the most acidic, which made it a valuable candidate as a material for polymer electrolyte membrane fuel cells.
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Affiliation(s)
- Liudmil Antonov
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Central Scientific Research Laboratory, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
- Correspondence: (L.A.); (S.K.)
| | - Susumu Kawauchi
- Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
- Correspondence: (L.A.); (S.K.)
| | - Kei Shirata
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
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27
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Adjieufack AI, Liégeois V, Ndassa Mbouombouo I, Domingo LR, Champagne B. Unveiling the [3+2] cycloaddition between difluoromethyl diazomethane and 3-ylideneoxindole from the perspective of molecular electron density theory. NEW J CHEM 2022. [DOI: 10.1039/d2nj02685f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evolution of some key ELF basins along the IRC of the most favorable ortho/endo reaction path.
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Affiliation(s)
- Abel Idrice Adjieufack
- Laboratory of Theoretical Chemistry (LCT) and Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
- Physical and Theoretical Chemistry Laboratory, Faculty of Science, University of Yaoundé I, P.O. Box 812 Yaoundé, Cameroon
- Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé I, P. O. Box 47 Yaoundé, Cameroon
| | - Vincent Liégeois
- Laboratory of Theoretical Chemistry (LCT) and Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Ibrahim Ndassa Mbouombouo
- Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé I, P. O. Box 47 Yaoundé, Cameroon
| | - Luis Ramon Domingo
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Benoît Champagne
- Laboratory of Theoretical Chemistry (LCT) and Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
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Filser J, Reuter K, Oberhofer H. Piecewise Multipole-Expansion Implicit Solvation for Arbitrarily Shaped Molecular Solutes. J Chem Theory Comput 2021; 18:461-478. [PMID: 34935366 DOI: 10.1021/acs.jctc.1c00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric response still solves the electrostatic problem inefficiently or not at all for solutes larger than approximately ten non-hydrogen atoms. In existing MPE parametrizations, the resulting systematic underestimation of the electrostatic solute-solvent interaction is presently compensated for by a systematic overestimation of nonelectrostatic attractive interactions. Even though the MPE model can thus reproduce experimental free energies of solvation of small molecules remarkably well, the inherent error cancellation makes it hard to assign physical meaning to the individual free-energy terms in the model, raising concerns about transferability. Here we resolve this issue by solving the electrostatic problem piecewise in 3D regions centered around all non-hydrogen nuclei of the solute, ensuring reliable convergence of the multipole series. The resulting method thus allows for a much improved reproduction of the dielectric response of a medium to a solute. Employing a reduced nonelectrostatic model with a single free parameter, in addition to the density isovalue defining the solvation cavity, our method yields free energies of solvation of neutral, anionic, and cationic solutes in water in good agreement with experiment.
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Affiliation(s)
- Jakob Filser
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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29
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Ringe S, Hörmann NG, Oberhofer H, Reuter K. Implicit Solvation Methods for Catalysis at Electrified Interfaces. Chem Rev 2021; 122:10777-10820. [PMID: 34928131 PMCID: PMC9227731 DOI: 10.1021/acs.chemrev.1c00675] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Implicit solvation
is an effective, highly coarse-grained approach
in atomic-scale simulations to account for a surrounding liquid electrolyte
on the level of a continuous polarizable medium. Originating in molecular
chemistry with finite solutes, implicit solvation techniques are now
increasingly used in the context of first-principles modeling of electrochemistry
and electrocatalysis at extended (often metallic) electrodes. The
prevalent ansatz to model the latter electrodes and the reactive surface
chemistry at them through slabs in periodic boundary condition supercells
brings its specific challenges. Foremost this concerns the difficulty
of describing the entire double layer forming at the electrified solid–liquid
interface (SLI) within supercell sizes tractable by commonly employed
density functional theory (DFT). We review liquid solvation methodology
from this specific application angle, highlighting in particular its
use in the widespread ab initio thermodynamics approach
to surface catalysis. Notably, implicit solvation can be employed
to mimic a polarization of the electrode’s electronic density
under the applied potential and the concomitant capacitive charging
of the entire double layer beyond the limitations of the employed
DFT supercell. Most critical for continuing advances of this effective
methodology for the SLI context is the lack of pertinent (experimental
or high-level theoretical) reference data needed for parametrization.
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Affiliation(s)
- Stefan Ringe
- Department of Energy Science and Engineering, Daegu Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea.,Energy Science & Engineering Research Center, Daegu Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Nicolas G Hörmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.,Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching, Germany.,Chair for Theoretical Physics VII and Bavarian Center for Battery Technology (BayBatt), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Karsten Reuter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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30
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Kariyottu Kuniyil MJ, Padmanaban R. Anti‐Stokes Fluorescence and Nonlinear Optical Properties of the Functionalized Phenoxazine‐based Dye: A computational study. ChemistrySelect 2021. [DOI: 10.1002/slct.202103286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Muhammed Jeneesh Kariyottu Kuniyil
- Department of Chemistry School of Physical Chemical and Applied Sciences Pondicherry University, R. V. Nagar Kalapet, Puducherry 605 014 India
| | - Ramanathan Padmanaban
- Department of Chemistry School of Physical Chemical and Applied Sciences Pondicherry University, R. V. Nagar Kalapet, Puducherry 605 014 India
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31
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Guo XH, Yu LB, Hao XL, He TF, Guo JF, Wei X, Cui WB, Yu LY, Qu ZX, Ren AM. Theoretical Study of a Two-Photon Fluorescent Probe Based on Nile Red Derivatives with Controllable Fluorescence Wavelength and Water Solubility. J Chem Inf Model 2021; 61:5082-5097. [PMID: 34606272 DOI: 10.1021/acs.jcim.1c00635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hypochloric acid (HOCl) plays a vital role in the natural defense system, but abnormal levels of it can cause cell damage, accelerated human aging, and various diseases. It is of great significance to develop new probes for detecting HOCl in biosystems nondestructively and noninvasively. The purpose of this work is to explore new chemical modification strategies of two-photon excitation fluorescence (TPEF) probes to improve the poor water solubility and low efficiency in imaging applications. Nil-OH-6 has a two-photon absorption cross-section value as high as 243 GM and attains a good quantum yield of 0.49. In addition, the modification of terminal groups with different azetidine-heterospirocycles or N,N-dialkyl fused amino groups to Nile Red can effectively improve the fluorescence efficiency as well as increase the solubility to some extent. This study provides some strategies to simultaneously improve the fluorescence performance and solubility of these two-photon probes and, hence, reliable guidance and a foundation for the subsequent synthesis of TPEF probes based on Nile Red.
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Affiliation(s)
- Xue-Hui Guo
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Li-Bo Yu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Xue-Li Hao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Teng-Fei He
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Jing-Fu Guo
- School of Physics, Northeast Normal University, Changchun 10024, P.R. China
| | - Xue Wei
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Wei-Bo Cui
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Li-Ying Yu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Ze-Xing Qu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
| | - Ai-Min Ren
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road #2, Changchun 130061, P.R. China
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32
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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33
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Liu X, Liu C, Feng Z, Meng C. The Promoter Role of Amines in the Condensation of Silicic Acid: A First-Principles Investigation. ACS OMEGA 2021; 6:22811-22819. [PMID: 34514252 PMCID: PMC8427787 DOI: 10.1021/acsomega.1c03235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Though well-recognized, the molecular-level understanding of the multifunctional roles of amines in the condensation of polysilicic acids, which is one of the key processes in hydrothermal synthesis of zeolites, is still limited. Taking ethylamine as a prototype, we investigated the mechanism of polysilicic acid condensation in the existence of organic amines in aqueous solution with extensive first-principles-based calculations. Because of the high proton affinity, ethylamine exists as amine silicates and alters the subsequent condensation mechanisms from a 1-step lateral attack mechanism accompanied with simultaneous intermolecular proton transfer in neutral aqueous solution to a 2-step SN2-like mechanism. Specifically, the 5-coordinated Si species that were not observed on pathways of condensation in neutral solution are effectively stabilized by the ethylamine cations as intermediates, and the barriers for condensation of ortho-silicic acid are significantly reduced from 133 kJ/mol in neutral solution to 58 and 63 kJ/mol for formation of the 5-coordinated Si intermediate and proton transfer for water release, respectively. Similar variations of mechanisms and barriers for condensation were also observed in the formation of cyclic trimers as well as linear and cyclic tetramers of ortho-silicic acids. Based on these, it was proposed that apart from acting as structure-directing agents, pore fillers, and pH adjusters, organic amines can also function as promoters in the condensation of polysilicic acids.
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35
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 466] [Impact Index Per Article: 155.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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36
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Isegawa M, Matsumoto T, Ogo S. H 2 activation by hydrogenase-inspired NiFe catalyst using frustrated Lewis pair: effect of buffer and halide ion in the heterolytic H-H bond cleavage. RSC Adv 2021; 11:28420-28432. [PMID: 35480737 PMCID: PMC9038005 DOI: 10.1039/d1ra05928a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production. We investigate the reaction mechanism of H2 activation in an aqueous solution by the recently developed NiFe complex (Ogo et al. Sci. Adv. 2020, 6, eaaz8181) using density functional theory (DFT) calculation. Our computational results showed that H2 is activated using frustrated Lewis pair. That is, H2 binds to the Fe site of the NiFe complex, acting as a Lewis acid, while the added buffer, acting as Lewis base, abstracts protons to form a hydride complex. Furthermore, the higher basicity in the proton abstraction reaction characterises reaction more exergonic and lowers the reaction barrier. In addition, in the proton abstraction by the water molecule, the reaction barrier was lowered when anion such as Cl− is in the vicinity of the water. Understanding the chemical species that contribute to the catalytic process in cooperation with the metal catalyst at the atomic level should help to maximise the function of the catalyst. Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production.![]()
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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37
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Tam NM, Hieu LT, Thong NM, Hoa NT, Hoang LP, Nam PC, Quang DT, Mechler A, Vo QV. Mechanistic and kinetic studies of the radical scavenging activity of natural abietanes: A theoretical insight. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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38
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Mahaut D, Chardon A, Mineur L, Berionni G, Champagne B. Rational Development of a Metal-Free Bifunctional System for the C-H Activation of Methane: A Density Functional Theory Investigation. Chemphyschem 2021; 22:1958-1966. [PMID: 34309144 DOI: 10.1002/cphc.202100527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/10/2022]
Abstract
The activation or heterolytic splitting of methane, a challenging substrate usually restricted to transition metals, has so far proven elusive in experimental frustrated Lewis pair (FLP) chemistry. In this article, we demonstrate, using density functional theory (DFT), that 1-aza-9-boratriptycene is a conceptually simple intramolecular FLP for the activation of methane. Systematic comparison with other FLP systems allows to gain insight into their reactivity with methane. The thermodynamics and kinetics of methane activation are interpreted by referring to the analysis of the natural charges and by employing the distortion-interaction/activation strain (DIAS) model. These showed that the nature of the Lewis base influences the selectivity over the reaction pathway, with N Lewis bases favoring the deprotonation mechanism and P bases the hydride abstraction one. The lower barrier of activation for 1-aza-9-boratriptycene and the higher products stability are due to a better interaction energy than its counterparts, itself due to electrostatic interactions with the methane moiety, favorable orbital overlaps allowed by the side-attack, and space proximity between the B and N atoms.
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Affiliation(s)
- Damien Mahaut
- Department of Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Aurélien Chardon
- Department of Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Loïc Mineur
- Department of Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Guillaume Berionni
- Department of Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Benoît Champagne
- Department of Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000, Namur, Belgium
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39
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Ehlert S, Stahn M, Spicher S, Grimme S. Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods. J Chem Theory Comput 2021; 17:4250-4261. [PMID: 34185531 DOI: 10.1021/acs.jctc.1c00471] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a robust and efficient method to implicitly account for solvation effects in modern semiempirical quantum mechanics and force fields. A computationally efficient yet accurate solvation model based on the analytical linearized Poisson-Boltzmann (ALPB) model is parameterized for the extended tight binding (xTB) and density functional tight binding (DFTB) methods as well as for the recently proposed GFN-FF general force field. The proposed methods perform well over a broad range of systems and applications, from conformational energies over transition-metal complexes to large supramolecular association reactions of charged species. For hydration free energies of small molecules, GFN1-xTB(ALPB) is reaching the accuracy of sophisticated explicitly solvated approaches, with a mean absolute deviation of only 1.4 kcal/mol compared to the experiment. Logarithmic octanol-water partition coefficients (log Kow) are computed with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) compared to experimental values indicating a consistent description of differential solvent effects. Overall, more than twenty solvents for each of the six semiempirical methods are parameterized and tested. They are readily available in the xtb and dftb+ programs for diverse computational applications.
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Affiliation(s)
- Sebastian Ehlert
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Marcel Stahn
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Sebastian Spicher
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Stefan Grimme
- Mulliken Center of Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
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40
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Tomasini M, Duran J, Simon S, Azofra LM, Poater A. Towards mild conditions by predictive catalysis via sterics in the Ru-catalyzed hydrogenation of thioesters. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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41
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Janeček M, Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. J Chem Theory Comput 2021; 17:3495-3509. [PMID: 33999623 DOI: 10.1021/acs.jctc.0c00976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.
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Affiliation(s)
- Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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42
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Liu J, Li Y, Jiang J, Liu Y, Ke Z. Mechanism of Ir-Mediated Selective Pyridine o-C–H Activation: The Role of Lewis Acidic Boryl Group. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jiahao Liu
- School of Materials Science & Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Yinwu Li
- School of Materials Science & Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Jingxing Jiang
- School of Materials Science & Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Yan Liu
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, People’s Republic of China
| | - Zhuofeng Ke
- School of Materials Science & Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
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43
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Luque-Urrutia JA, Pèlachs T, Solà M, Poater A. Double-Carrousel Mechanism for Mn-Catalyzed Dehydrogenative Amide Synthesis from Alcohols and Amines. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00693] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jesús A. Luque-Urrutia
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Tània Pèlachs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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44
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Nam PC, Thong NM, Hoa NT, Quang DT, Hoang LP, Mechler A, Vo QV. Is natural fraxin an overlooked radical scavenger? RSC Adv 2021; 11:14269-14275. [PMID: 35423974 PMCID: PMC8697747 DOI: 10.1039/d1ra01360b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/02/2021] [Indexed: 01/08/2023] Open
Abstract
Fraxin (FX) (7-hydroxy-6-methoxycoumarin 8-glucoside) is a typical natural product of the coumarin family. This compound was shown to protect endothelial cells from oxidative stress; however, the nature of its antioxidant properties is still ambiguous. In this study, we report on a systematic evaluation of the radical scavenging activity of FX using a two-tier protocol based on thermodynamic and kinetic calculations. The results show that FX has moderate activity in the aqueous physiological environment against a range of radicals including HO˙, CCl3O˙, CCl3OO˙, NO2, , and HOO˙. The latter was examined in detail due to the prevalence of HOO˙ as a source of oxidative stress in biological systems. HOO˙ scavenging activity was promising in the gas phase but low in physiological environments with k overall = 1.57 × 106, 3.13 × 102 and 2.68 × 103 M-1 s-1 in the gas phase, pentyl ethanoate and water solvents, respectively. The formal hydrogen transfer mechanism at the O7-H bond dominates the hydroperoxyl radical scavenging of FX in the nonpolar media, whereas, in the polar environment, the activity is exerted by the single electron transfer mechanism of the anion state. This activity falls behind typical antioxidants such as Trolox, ascorbic acid, and trans-resveratrol under the studied conditions. Thus FX may have multiple health benefits, but it is not an outstanding natural antioxidant.
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Affiliation(s)
- Pham Cam Nam
- Department of Chemical Engineering, The University of Danang - University of Science and Technology Danang 550000 Vietnam
| | - Nguyen Minh Thong
- The University of Danang, Campus in Kon Tum 704 Phan Dinh Phung Kon Tum Vietnam
| | - Nguyen Thi Hoa
- The University of Danang - University of Technology and Education Danang 550000 Vietnam
| | | | - Loc Phuoc Hoang
- Institute of Research and Development, Duy Tan University Danang 550000 Vietnam
| | - Adam Mechler
- Department of Chemistry and Physics, La Trobe University Victoria 3086 Australia
| | - Quan V Vo
- The University of Danang - University of Technology and Education Danang 550000 Vietnam
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45
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Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021; 17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson-Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson-Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.
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Affiliation(s)
- Rae A Corrigan
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Andrew C Thiel
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jack R Lynn
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Brandon D Walker
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Thomas L Casavant
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Louis Lagardere
- Department of Chemistry, Sorbonne Université, F-75005 Paris, France
| | | | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Michael J Schnieders
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States.,Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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Tielker N, Eberlein L, Hessler G, Schmidt KF, Güssregen S, Kast SM. Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges? J Comput Aided Mol Des 2021; 35:453-472. [PMID: 33079358 PMCID: PMC8018924 DOI: 10.1007/s10822-020-00347-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/26/2020] [Indexed: 01/26/2023]
Abstract
Joint academic-industrial projects supporting drug discovery are frequently pursued to deploy and benchmark cutting-edge methodical developments from academia in a real-world industrial environment at different scales. The dimensionality of tasks ranges from small molecule physicochemical property assessment over protein-ligand interaction up to statistical analyses of biological data. This way, method development and usability both benefit from insights gained at both ends, when predictiveness and readiness of novel approaches are confirmed, but the pharmaceutical drug makers get early access to novel tools for the quality of drug products and benefit of patients. Quantum-mechanical and simulation methods particularly fall into this group of methods, as they require skills and expense in their development but also significant resources in their application, thus are comparatively slowly dripping into the realm of industrial use. Nevertheless, these physics-based methods are becoming more and more useful. Starting with a general overview of these and in particular quantum-mechanical methods for drug discovery we review a decade-long and ongoing collaboration between Sanofi and the Kast group focused on the application of the embedded cluster reference interaction site model (EC-RISM), a solvation model for quantum chemistry, to study small molecule chemistry in the context of joint participation in several SAMPL (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenges. Starting with early application to tautomer equilibria in water (SAMPL2) the methodology was further developed to allow for challenge contributions related to predictions of distribution coefficients (SAMPL5) and acidity constants (SAMPL6) over the years. Particular emphasis is put on a frequently overlooked aspect of measuring the quality of models, namely the retrospective analysis of earlier datasets and predictions in light of more recent and advanced developments. We therefore demonstrate the performance of the current methodical state of the art as developed and optimized for the SAMPL6 pKa and octanol-water log P challenges when re-applied to the earlier SAMPL5 cyclohexane-water log D and SAMPL2 tautomer equilibria datasets. Systematic improvement is not consistently found throughout despite the similarity of the problem class, i.e. protonation reactions and phase distribution. Hence, it is possible to learn about hidden bias in model assessment, as results derived from more elaborate methods do not necessarily improve quantitative agreement. This indicates the role of chance or coincidence for model development on the one hand which allows for the identification of systematic error and opportunities toward improvement and reveals possible sources of experimental uncertainty on the other. These insights are particularly useful for further academia-industry collaborations, as both partners are then enabled to optimize both the computational and experimental settings for data generation.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Gerhard Hessler
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany
| | - K Friedemann Schmidt
- R&D Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany
| | - Stefan Güssregen
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany.
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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Boulmokh Y, Belguidoum K, Meddour F, Amira-Guebailia H. Investigation of antioxidant activity of epigallocatechin gallate and epicatechin as compared to resveratrol and ascorbic acid: experimental and theoretical insights. Struct Chem 2021. [DOI: 10.1007/s11224-021-01763-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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49
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Fantuzzi F, Nascimento MAC, Ginovska B, Bullock RM, Raugei S. Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study. Dalton Trans 2021; 50:840-849. [PMID: 33237062 DOI: 10.1039/d0dt03411h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Splitting of molecular hydrogen (H2) into bridging and terminal hydrides is a common step in transition metal chemistry. Herein, we propose a novel organometallic platform for cleavage of multiple H2 molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(ii) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H2 molecules.
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Affiliation(s)
- Felipe Fantuzzi
- Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos 149, 21941.909, Rio de Janeiro, Brazil.
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50
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Towards a converged strategy for including microsolvation in reaction mechanism calculations. J Comput Aided Mol Des 2021; 35:473-492. [PMID: 33420644 DOI: 10.1007/s10822-020-00366-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/28/2020] [Indexed: 01/27/2023]
Abstract
A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pKa values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.
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