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Friede M, Hölzer C, Ehlert S, Grimme S. dxtb-An efficient and fully differentiable framework for extended tight-binding. J Chem Phys 2024; 161:062501. [PMID: 39120026 DOI: 10.1063/5.0216715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
Automatic differentiation (AD) emerged as an integral part of machine learning, accelerating model development by enabling gradient-based optimization without explicit analytical derivatives. Recently, the benefits of AD and computing arbitrary-order derivatives with respect to any variable were also recognized in the field of quantum chemistry. In this work, we present dxtb-an open-source, fully differentiable framework for semiempirical extended tight-binding (xTB) methods. Developed entirely in Python and leveraging PyTorch for array operations, dxtb facilitates extensibility and rapid prototyping while maintaining computational efficiency. Through comprehensive code vectorization and optimization, we essentially reach the speed of compiled xTB programs for high-throughput calculations of small molecules. The excellent performance also scales to large systems, and batch operability yields additional benefits for execution on parallel hardware. In particular, energy evaluations are on par with existing programs, whereas the speed of automatically differentiated nuclear derivatives is only 2 to 5 times slower compared to their analytical counterparts. We showcase the utility of AD in dxtb by calculating various molecular and spectroscopic properties, highlighting its capacity to enhance and simplify such evaluations. Furthermore, the framework streamlines optimization tasks and offers seamless integration of semiempirical quantum chemistry in machine learning, paving the way for physics-inspired end-to-end differentiable models. Ultimately, dxtb aims to further advance the capabilities of semiempirical methods, providing an extensible foundation for future developments and hybrid machine learning applications. The framework is accessible at https://github.com/grimme-lab/dxtb.
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Affiliation(s)
- Marvin Friede
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Christian Hölzer
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118CZ Schiphol, Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
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2
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Wittmann L, Gordiy I, Friede M, Helmich-Paris B, Grimme S, Hansen A, Bursch M. Extension of the D3 and D4 London dispersion corrections to the full actinides series. Phys Chem Chem Phys 2024; 26:21379-21394. [PMID: 39092890 DOI: 10.1039/d4cp01514b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 and D4 London dispersion corrections to the full actinides series, francium, and radium. To keep consistency with the existing versions, the original parameterization strategy of the D4 model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at the ωB97M-V/ma-def-TZVP level to fit the required electronegativity equilibration charge (EEQ) model. In this context, we developed a new actinide data set called AcQM, which covers the most common molecular actinide compound space. Furthermore, the efficient calculation of dynamic polarizabilities that are needed to construct CAB6 dispersion coefficients was implemented into the ORCA program package. The extended models are assessed for the computation of dissociation curves of actinide atoms and ions, geometry optimizations of crystal structure cutouts, gas-phase structures of small uranium compounds, and an example extracted from a small actinide complex protein assembly. We found that the novel parameterizations perform on par with the computationally more demanding density-dependent VV10 dispersion correction. With the presented extension, the excellent cost-accuracy ratio of the D3 and D4 models can now be utilized in various fields of computational actinide chemistry and, e.g., in efficient composite DFT methods such as r2SCAN-3c. They are implemented in our freely available standalone codes (dftd4, s-dftd3) and the D4 version will be also available in the upcoming ORCA 6.0 program package.
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Affiliation(s)
- Lukas Wittmann
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Igor Gordiy
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Marvin Friede
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- FACCTs GmbH, 50677, Köln, Germany
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3
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Gross IP, Lima AL, Bedogni GR, Sa-Barreto L, Gratieri T, Gelfuso GM, Salomon CJ, Cunha-Filho M. Conformational analysis and spectroscopic properties of antichagasic nifurtimox. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124346. [PMID: 38692105 DOI: 10.1016/j.saa.2024.124346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/27/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Considering the health relevance of Chagas' disease, recent research efforts have focused on developing more efficient drug delivery systems containing nifurtimox (NFX). This paper comprehensively investigates NFX through conformational analysis and spectroscopic characterization. Using a conformer-rotamer ensemble sampling tool (CREST-xtb), five distinct conformers of NFX were sampled within a 3.0 kcal mol-1 relative energy window. Subsequently, such structures were used as inputs for geometry optimization by density functional theory (DFT) at B3LYP-def2-TZVP level of theory. Notably, harmonic vibrational frequencies were calculated to establish an in-depth comparison with experimental results and existing literature for the NFX or similar molecules and functional groups, thereby achieving a widely reasoned assignment of the mid-infrared band absorptions for the first time. Moreover, UV-VIS spectra of NFX were obtained in several solvents, enabling the determination of the molar absorptivity coefficient for the two electronic transitions observed for NFX. Among the aprotic solvents, a bathochromic effect was observed in the function of the dielectric constants. Furthermore, a hypochromic effect was observed when the drug was dissolved in protic solvents. These findings offer crucial support for new drug delivery systems containing NFX while demonstrating the potential of spectrophotometric studies in establishing quality control assays for NFX drug products.
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Affiliation(s)
- Idejan P Gross
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil.
| | - Ana Luiza Lima
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil
| | - Giselle R Bedogni
- Pharmaceutical Technical Area, Department of Pharmacy, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina; National Council for Scientific and Technical Research, Godoy Cruz, Argentina
| | - Livia Sa-Barreto
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil
| | - Tais Gratieri
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil
| | - Guilherme M Gelfuso
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil
| | - Claudio J Salomon
- Pharmaceutical Technical Area, Department of Pharmacy, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina; National Council for Scientific and Technical Research, Godoy Cruz, Argentina.
| | - Marcílio Cunha-Filho
- Laboratory of Food, Drug, and Cosmetics (LTMAC), School of Health Sciences, University of Brasilia, 70.910-900 Brasília, DF, Brazil
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4
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Ermakova E, Tsyrendorzhieva I, Mareev A, Pavlov D, Maslova O, Shayapov V, Maksimovskiy E, Yushina I, Kosinova M. Carbon-Rich Plasma-Deposited Silicon Oxycarbonitride Films Derived from 4-(Trimethylsilyl)morpholine as a Novel Single-Source Precursor. Chempluschem 2024; 89:e202400094. [PMID: 38659085 DOI: 10.1002/cplu.202400094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
4-(trimethylsilyl)morpholine O(CH2CH2)2NSi(CH3)3 (TMSM) was investigated as a single-source precursor for SiCNO films synthesis. Optical emission spectroscopy of plasma generated from TMSM/He, TMSM/H2, and TMSM/NH3 gas mixtures revealed the presence of N2, CH, H, CN, and CO species. The last two are suggested to be responsible for the lowering of carbon concentration in the films in comparison with the precursor. The refractive index ranged from 1.5 to 2.0, and bandgap varied from 2.0 to 4.6 eV, which pointed that some of the films can be used as antireflective coatings in silicon photovoltaic cell technologies and dielectric layers in electronic devices.
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Affiliation(s)
- Evgeniya Ermakova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Irina Tsyrendorzhieva
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Alexander Mareev
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Dmitry Pavlov
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Olga Maslova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Vladimir Shayapov
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Eugene Maksimovskiy
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Irina Yushina
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Marina Kosinova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
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Korb M, Ghazvini SMBH, Low PJ. Migration of Condensed Aromatic Hydrocarbons During Alkyne-Vinylidene Rearrangements. Chemistry 2024; 30:e202400930. [PMID: 38780030 DOI: 10.1002/chem.202400930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Diarylacetylenes ArC≡CAr featuring condensed aromatic hydrocarbon fragments (Ar) such as naphthalene, anthracene, phenanthrene and pyrene were converted into vinylidene ligands by 1,2-migration reactions within the coordination sphere of half-sandwich complexes [MII(dppe)Cp]+ (MII = RuII, FeII). Comparison of the extent of conversion of the alkyne substrates to the vinylidene complexes [Ru{=C=CAr2}(dppe)Cp]+ with those obtained from acetylenes functionalized by smaller groups (H, CH3, Ph) show that the molecular volume (VM) of the migrating group and relief of steric congestion plays a role during the rearrangement process. Conversely, the H-atoms from the larger condensed ring aryl groups that are in close proximity to the migrating sites also have a significant influence on the efficacy and extent of the reaction by restricting access of the alkyne to the metal center, resulting in a less effective migration reaction. This combination of competing steric factors (acceleration due to relief of steric congestion and restricted access of the alkyne moiety to the reaction site) is exemplified by the facile migration of 1-pyryl entities and the low yields of vinylidene products formed from 1,2-bis(9-anthryl)acetylene.
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Affiliation(s)
- Marcus Korb
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Seyed M B H Ghazvini
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Paul J Low
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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Marques BDS, de Andrade KN, Peixoto BP, Dos Santos FM, Pedrosa LF, Fiorot RG, Costa de Souza M. Sequential nucleophilic aromatic substitutions on cyanuric chloride: synthesis of BODIPY derivatives and mechanistic insights. Org Biomol Chem 2024; 22:5987-5998. [PMID: 38989906 DOI: 10.1039/d4ob00683f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Herein we report a study on the sequential substitution of different nucleophiles on cyanuric chloride to obtain potential candidates for metal sensors (5a-c). The set of nucleophiles on the 1,3,5-triazine ring includes a phenolic BODIPY, an aminoalkyl pyridine and aminoalkyl phosphoramidates, each one designed to play a specific role in the final fluoroionophore. Three new triazine triads were synthesized in similar yields: 5a (45%), 5b (43%) and 5c (52%) after a methodical sequential combination of the nucleophiles via thermodependent nucleophilic aromatic substitution of the three chlorine atoms of cyanuric chloride. To ratify the synthetic results we simulated the reaction mechanisms for the different nucleophiles, aiming to address the distinctive orthogonality and temperature control inherent in this process, identifying and providing a sound rationale for any preferential sequence of nucleophiles inserted into the triazine core. According to our experimental and computational analysis (thermo- and kinetic preferences), we have identified the following preferential order for the sequential substitution: p-hydroxybenzaldehyde > 2-(pyridin-2-yl)ethanamine > aminoalkyl phosphoramidate, indicating that all steps follow a single-step process (concerted) in two stages, where nucleophilic addition precedes leaving group dissociation. The Meisenheimer σ-complex was identified as a transition state structure, with insufficient stability to exist as an intermediate. We observed a consistent and progressive increase in barrier height: 2-8 kcal mol-1 for the first step, 9-15 kcal mol-1 for the second step, and >15 kcal mol-1 for the third substitution. These findings align with the experimental observation of thermodependency in the sequential substitution.
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Affiliation(s)
- Bruno da Silva Marques
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
| | - Karine Nascimento de Andrade
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
| | - Bárbara Pereira Peixoto
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
| | - Fernando Martins Dos Santos
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
| | - Leandro Ferreira Pedrosa
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, 27213-145, Volta Redonda, RJ, Brazil
| | - Rodolfo Goetze Fiorot
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
| | - Marcos Costa de Souza
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141, Niterói, RJ, Brazil.
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Kalisch T, Brehm PC, Streubel R. Tricyclic 1,4-Diphosphinines: Local vs. Global Aromaticity. Chemphyschem 2024:e202400417. [PMID: 38986024 DOI: 10.1002/cphc.202400417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/11/2024] [Indexed: 07/12/2024]
Abstract
1D and 2DNICS π . zz SOM ${{{\rm { NICS}}}_{{\rm { {\rm \pi}{}}}{\rm { .zz}}}^{{\rm { SOM}}}}$ (Sigma only model) calculations were performed on recently established tricyclic 1,4-diphosphinines as well as related benzene and pyrazine derivatives. The study was extended to evaluate the effect of the fused rings on the overall aromatic properties with a special focus on functional groups such as carbenes. The effect of non-aromatic heterocycles on the local ring current of the central ring is small, while aromatic heterocycles (e. g. NHC, imidazolium) lead to a global aromaticity. A higher sulfur content of the adjacent five-membered rings reduces the central ring current. The comparison to related tricyclic benzene and pyrazine derivatives showed that the 1,4-diphosphinine systems resemble more closely the situation in the benzene derivatives than the pyrazines. The effect of charged systems was studied using bis(TTF)-fused 1,4-diphosphinines and, according toNICS π . zz SOM ${{{\rm { NICS}}}_{{\rm { {\rm \pi}{}}}{\rm { .zz}}}^{{\rm { SOM}}}}$ values, the neutral form doesn't possess significant aromaticity but the tetracation resembles the global aromatic situation observed for other heterocycles in this study.
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Affiliation(s)
- Tim Kalisch
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany) E-mail: E-mai
| | - Philipp C Brehm
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany) E-mail: E-mai
| | - Rainer Streubel
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany) E-mail: E-mai
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8
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Spiegel M. Unveiling the Antioxidative Potential of Galangin: Complete and Detailed Mechanistic Insights through Density Functional Theory Studies. J Org Chem 2024; 89:8676-8690. [PMID: 38861646 PMCID: PMC11197094 DOI: 10.1021/acs.joc.4c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
A comprehensive quantum mechanical investigation delved into the antioxidative activity of galangin (Glg). Thermochemical and kinetic data were used to assess antiradical, chelating, and renewal potential under physiological conditions. A brief comparison with reference antioxidants and other flavonoids characterized Glg as a moderate antioxidative agent. The substance showed significantly lower performance in lipid compared to aqueous solvent─the reaction rates for scavenging •OOH in both media were established at 3.77 × 103 M-1 s-1 and 6.21 × 104 M-1 s-1, respectively, accounting for the molar fraction of both interacting molecules at the given pH. The impact of pH value on the kinetics was assessed. Although efficient at chelating Cu(II) ions, the formed complexes can still undergo the Fenton reaction. On the other hand, they persistently scavenge •OH in statu nascendi. The flavonoid effectively repairs oxidatively damaged biomolecules except model lipid acids. All Glg radicals are readily restored by physiologically prevailing O2•-. Given this, the polyphenol is expected to participate in antiradical and regenerating activities multiple times, amplifying its antioxidative potential.
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Affiliation(s)
- Maciej Spiegel
- Department of Organic Chemistry and
Pharmaceutical Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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Westberry BP, Rio M, Waterland MR, Williams MAK. On the origin of optical rotation changes during the κ-carrageenan disorder-to-order transition. Carbohydr Polym 2024; 333:121975. [PMID: 38494229 DOI: 10.1016/j.carbpol.2024.121975] [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: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
It is well established that solutions of both polymeric and oligomeric κ-carrageenan exhibit a clear change in optical rotation (OR), in concert with gel-formation for polymeric samples, as the solution is cooled in the presence of certain ions. The canonical interpretation - that this OR change reflects a 'coil-to-helix transition' in single chains - has seemed unambiguous; the solution- or 'disordered'-state structure has ubiquitously been assumed to be a 'random coil', and the helical nature of carrageenan in the solid-state was settled in the 1970s. However, recent work has found that κ-carrageenan contains substantial helical secondary structure elements in the disordered-state, raising doubts over the validity of this interpretation. To investigate the origins of the OR, density-functional theory calculations were conducted using atomic models of κ-carrageenan oligomers. Changes were found to occur in the predicted OR owing purely to dimerization of chains, and - together with the additional effects of slight changes in conformation that occur when separated helical chains form double-helices - the predicted OR changes are qualitatively consistent with experimental results. These findings contribute to a growing body of evidence that the carrageenan 'disorder-to-order' transition is a cooperative process, and have further implications for the interpretation of OR changes demonstrated by macromolecules in general.
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Affiliation(s)
- B P Westberry
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand; Fonterra Research and Development Centre, Private Bag 11029, Dairy Farm Road, Palmerston North, New Zealand.
| | - M Rio
- National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand; Science Infrastructure (NeSI), Auckland, New Zealand
| | - M R Waterland
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - M A K Williams
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
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de Barros Leite NF, Marques RB, Macedo-Filho A, Rocha GB, Martins EPS. Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties. J Mol Model 2024; 30:177. [PMID: 38775913 DOI: 10.1007/s00894-024-05969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
CONTEXT Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals. METHODS Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).
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Affiliation(s)
| | | | | | - Gerd Bruno Rocha
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Evandro P S Martins
- Graduate Program in Chemistry, State University of Piaui, Teresina, PI, Brazil.
- State University of Piauí, Piripiri, PI, 64260-000, Brazil.
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11
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M Zahir FZ, Hay MA, Janetzki JT, Gable RW, Goerigk L, Boskovic C. Predicting valence tautomerism in diverse cobalt-dioxolene complexes: elucidation of the role of ligands and solvent. Chem Sci 2024; 15:5694-5710. [PMID: 38638213 PMCID: PMC11023039 DOI: 10.1039/d3sc04493a] [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: 08/27/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
The ability of molecular switches to reversibly interconvert between different forms promises potential applications at the scale of single molecules up to bulk materials. One type of molecular switch comprises cobalt-dioxolene compounds that exhibit thermally-induced valence tautomerism (VT) interconversions between low spin Co(iii)-catecholate (LS-CoIII-cat) and high spin Co(ii)-semiquinonate (HS-CoII-sq) forms. Two families of these compounds have been investigated for decades but have generally been considered separately: neutral [Co(diox)(sq)(N2L)] and cationic [Co(diox)(N4L)]+ complexes (diox = generic dioxolene, N2L/N4L = bidentate/tetradentate N-donor ancillary ligand). Computational identification of promising new candidate compounds prior to experimental exploration is beneficial for environmental and cost considerations but requires a thorough understanding of the underlying thermochemical parameters that influence the switching. Herein, we report a robust approach for the analysis of both cobalt-dioxolene families, which involved a quantitative density functional theory-based study benchmarked with reliable quasi-experimental references. The best-performing M06L-D4/def2-TZVPP level of theory has subsequently been verified by the synthesis and experimental investigation of three new complexes, two of which exhibit thermally-induced VT, while the third remains in the LS-CoIII-cat form across all temperatures, in agreement with prediction. Valence tautomerism in solution is markedly solvent-dependent, but the origin of this has not been definitively established. We have extended our computational approach to elucidate the correlation of VT transition temperature with solvent stabilisation energy and change in dipole moment. This new understanding may inform the development of VT compounds for applications in soft materials including films, gels, and polymers.
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Affiliation(s)
- F Zahra M Zahir
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Moya A Hay
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Jett T Janetzki
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Robert W Gable
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Lars Goerigk
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Colette Boskovic
- School of Chemistry, University of Melbourne Victoria 3010 Australia
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12
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Villard J, Bircher MP, Rothlisberger U. Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder. Chem Sci 2024; 15:4434-4451. [PMID: 38516095 PMCID: PMC10952088 DOI: 10.1039/d3sc05828j] [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: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.
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Affiliation(s)
- Justin Villard
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
| | - Martin P Bircher
- Computational and Soft Matter Physics, Universität Wien Wien A-1090 Austria
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
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13
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Ghosh S, Hassan SH, Das A. Role of Explicit Solvation in Computational Modeling of Chemical Reactions: Mechanism of Cu(I) Transfer Between Thiolate-Based Chelators in Water. J Phys Chem B 2024. [PMID: 38503566 DOI: 10.1021/acs.jpcb.3c07327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Solvation plays important roles in controlling the thermodynamic and kinetic aspects of chemical reactions. The conventional approaches to treat solvation via electronic structure methods are likely to become inadequate, when the reacting solutes have strong electrostatic and hydrogen bonding interactions with the solvent and undergo significant structural changes during the course of the reaction. In this article, we present evidence of such solvent and structural effects in the computational study of the Cu(I) transfer reaction between thiolate-based chelators dithiobutylamine (DTBA) and dithiotheritol (DTT) in water, inspired from biological copper trafficking phenomena. We propose a general solution to the problem by combining classical molecular dynamics (MD) simulations of the bulk system and static quantum chemistry calculations. The fluctuating solvation shell was estimated from MD, and energetics was assessed by averaging QM energies of a series of molecular clusters constructed from the MD snapshots. Applying this approach, we propose a reaction pathway with estimates of relative intermediate stabilities and barriers, which suggest the overall reaction to be reversible in nature and likely to go through both two and three coordinated intermediates, confirming previous studies of similar protein analogues. An interesting fact that emerged from our study was the strong indication that the rate-determining step is the deprotonation of initial thiol bound Cu(I) complex, without involving any Cu(I)-S bonds. The proposed method will lead to a better treatment of solvations, and these mechanistic insights will aid our understanding of biological copper(I) trafficking.
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Affiliation(s)
- Soumak Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sk Hasibo Hassan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Avisek Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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14
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Gasevic T, Kleine Büning JB, Grimme S, Bursch M. Benchmark Study on the Calculation of 207Pb NMR Chemical Shifts. Inorg Chem 2024; 63:5052-5064. [PMID: 38446045 PMCID: PMC10951955 DOI: 10.1021/acs.inorgchem.3c04539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
A benchmark set for the computation of 207Pb nuclear magnetic resonance (NMR) chemical shifts is presented. The PbS50 set includes conformer ensembles of 50 lead-containing molecular compounds and their experimentally measured 207Pb NMR chemical shifts. Various bonding motifs at the Pb center with up to seven bonding partners are included. Six different solvents were used in the measurements. The respective shifts lie in the range between +10745 and -5030 ppm. Several calculation settings are assessed by evaluating computed 207Pb NMR shifts for the use with different density functional approximations (DFAs), relativistic approaches, treatment of the conformational space, and levels for geometry optimization. Relativistic effects were included explicitly with the zeroth order regular approximation (ZORA), for which only the spin-orbit variant was able to yield reliable results. In total, seven GGAs and three hybrid DFAs were tested. Hybrid DFAs significantly outperform GGAs. The most accurate DFAs are mPW1PW with a mean absolute deviation (MAD) of 429 ppm and PBE0 with an MAD of 446 ppm. Conformational influences are small as most compounds are rigid, but more flexible structures still benefit from Boltzmann averaging. Including explicit relativistic treatments such as SO-ZORA in the geometry optimization does not show any significant improvement over the use of effective core potentials (ECPs).
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Affiliation(s)
- Thomas Gasevic
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Julius B. Kleine Büning
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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15
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Lupi J, Ayarde-Henríquez L, Kelly M, Dooley S. Ab Initio and Kinetic Modeling of β-d-Xylopyranose under Fast Pyrolysis Conditions. J Phys Chem A 2024; 128:1009-1024. [PMID: 38299300 PMCID: PMC10875674 DOI: 10.1021/acs.jpca.3c07063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Lignocellulosic biomass is an abundant renewable resource that can be upgraded to chemical and fuel products through a range of thermal conversion processes. Fast pyrolysis is a promising technology that uses high temperatures and fast heating rates to convert lignocellulose into bio-oils in high yields in the absence of oxygen. Hemicellulose is one of the three major components of lignocellulosic biomass and is a highly branched heteropolymer structure made of pentose, hexose sugars, and sugar acids. In this study, β-d-xylopyranose is proposed as a model structural motif for the essential chemical structure of hemicellulose. The gas-phase pyrolytic reactivity of β-d-xylopyranose is thoroughly investigated using computational strategies rooted in quantum chemistry. In particular, its thermal degradation potential energy surfaces are computed employing Minnesota global hybrid functional M06-2X in conjunction with the 6-311++G(d,p) Pople basis set. Electronic energies are further refined by performing DLPNO-CCSD(T)-F12 single-point calculations on top of M06-2X geometries using the cc-pVTZ-F12 basis set. Conformational analysis for minima and transition states is performed with state-of-the-art semiempirical quantum chemical methods coupled with metadynamics simulations. Key thermodynamic quantities (free energies, barrier heights, enthalpies of formation, and heat capacities) are computed. Rate coefficients for the initial steps of thermal decomposition are computed by means of reaction rate theory. For the first time, a detailed elementary reaction kinetic model for β-d-xylopyranose is developed by utilizing the thermodynamic and kinetic information acquired from the aforementioned calculations. This model specifically targets the initial stages of β-d-xylopyranose pyrolysis in the high-pressure limit, aiming to gain a deeper understanding of its reaction kinetics. This approach establishes a systematic strategy for exploring reactive pathways, evaluating competing parallel reactions, and selectively accepting or discarding pathways based on the analysis. The findings suggest that acyclic d-xylose plays a significant role as an intermediary in the production of key pyrolytic compounds during the pyrolysis of xylose. These compounds include furfural, anhydro-d-xylopyranose, glycolaldehyde, and dihydrofuran-3(2H)-one.
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Affiliation(s)
- Jacopo Lupi
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Leandro Ayarde-Henríquez
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Mark Kelly
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Stephen Dooley
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
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16
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Friede M, Ehlert S, Grimme S, Mewes JM. Do Optimally Tuned Range-Separated Hybrid Functionals Require a Reparametrization of the Dispersion Correction? It Depends. J Chem Theory Comput 2023; 19:8097-8107. [PMID: 37955590 DOI: 10.1021/acs.jctc.3c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
For ground- and excited-state studies of large molecules, it is the state of the art to combine (time-dependent) DFT with dispersion-corrected range-separated hybrid functionals (RSHs), which ensures an asymptotically correct description of exchange effects and London dispersion. Specifically for studying excited states, it is common practice to tune the range-separation parameter ω (optimal tuning), which can further improve the accuracy. However, since optimal tuning essentially changes the functional, it is unclear if and how much the parameters used for the dispersion correction depend on the chosen ω value. To answer this question, we explore this interdependency by refitting the DFT-D4 dispersion model for six established RSHs over a wide range of ω values (0.05-0.45 a0-1) using a set of noncovalently bound molecular complexes. The results reveal some surprising differences among the investigated functionals: While PBE-based RSHs and ωB97M-D4 generally exhibit a weak interdependency and robust performance over a wide range of ω values, B88-based RSHs, specifically LC-BLYP, are strongly affected. For these, even a minor reduction of ω from the default value manifests in strong systematic overbinding and poor performance in the typical range of optimally tuned ω values. Finally, we discuss strategies to mitigate these issues and reflect the results in the context of the employed D4 parameter optimization algorithm and fit set, outlining strategies for future improvements.
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Affiliation(s)
- Marvin Friede
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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17
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Scheele T, Neudecker T. Investigating the accuracy of density functional methods for molecules in electric fields. J Chem Phys 2023; 159:124111. [PMID: 38127387 DOI: 10.1063/5.0164372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/05/2023] [Indexed: 12/23/2023] Open
Abstract
The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical reactions has gained traction in recent years. Electronic structure calculations using OEEFs are commonly done using methods based on density functional theory (DFT), but until now, the performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more general scope. Looking at the accuracy of molecular geometries, electronic energies, and electric dipole moments compared to accurate coupled-cluster with perturbative triples data, we have investigated a wide variety of density functionals using different basis sets to determine how well the individual functionals perform on various types of chemical bonds. We found that most functionals accurately calculate geometries in OEEFs and that small basis sets are sufficient in many cases. Calculations of electronic energies show a significant error introduced by the OEEF, which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages that they bring.
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Affiliation(s)
- Tarek Scheele
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359 Bremen, Germany
| | - Tim Neudecker
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359 Bremen, Germany
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany
- MAPEX Center for Materials and Processes, University of Bremen, Bibliothekstraße 1, D-28359 Bremen, Germany
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18
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Cuomo A, Ibarraran S, Sreekumar S, Li H, Eun J, Menzel JP, Zhang P, Buono F, Song JJ, Crabtree RH, Batista VS, Newhouse TR. Feed-Forward Neural Network for Predicting Enantioselectivity of the Asymmetric Negishi Reaction. ACS CENTRAL SCIENCE 2023; 9:1768-1774. [PMID: 37780365 PMCID: PMC10540279 DOI: 10.1021/acscentsci.3c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 10/03/2023]
Abstract
Density functional theory (DFT) is a powerful tool to model transition state (TS) energies to predict selectivity in chemical synthesis. However, a successful multistep synthesis campaign must navigate energetically narrow differences in pathways that create some limits to rapid and unambiguous application of DFT to these problems. While powerful data science techniques may provide a complementary approach to overcome this problem, doing so with the relatively small data sets that are widespread in organic synthesis presents a significant challenge. Herein, we show that a small data set can be labeled with features from DFT TS calculations to train a feed-forward neural network for predicting enantioselectivity of a Negishi cross-coupling reaction with P-chiral hindered phosphines. This approach to modeling enantioselectivity is compared with conventional approaches, including exclusive use of DFT energies and data science approaches, using features from ligands or ground states with neural network architectures.
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Affiliation(s)
- Abbigayle
E. Cuomo
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Sebastian Ibarraran
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Sanil Sreekumar
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Haote Li
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Jungmin Eun
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Jan Paul Menzel
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Pengpeng Zhang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Frederic Buono
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Jinhua J. Song
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Robert H. Crabtree
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Timothy R. Newhouse
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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19
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Stahn M, Ehlert S, Grimme S. Extended Conductor-like Polarizable Continuum Solvation Model (CPCM-X) for Semiempirical Methods. J Phys Chem A 2023; 127:7036-7043. [PMID: 37567769 DOI: 10.1021/acs.jpca.3c04382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
We have developed a new method to accurately account for solvation effects in semiempirical quantum mechanics based on a polarizable continuum model (PCM). The extended conductor-like polarizable continuum model (CPCM-X) incorporates a computationally efficient domain decomposition conductor-like screening model (ddCOSMO) for extended tight binding (xTB) methods and uses a post-processing approach based on established solvation models, like the conductor-like screening model for real solvents (COSMO-RS) and the universal solvent model based on solute electron density (SMD). According to various benchmarks, the approach performs well across a broad range of systems and applications, including hydration free energies, non-aqueous solvation free energies, and large supramolecular association reactions of neutral and charged species. Our method for computing solvation free energies is much more accurate than the current methods in the xtb program package. It improves the accuracy of solvation free energies by up to 40% for larger supramolecular association reactions to match even the accuracy of higher-level DFT-based solvation models like COSMO-RS and SMD while being computationally more than 2 orders of magnitude faster. The proposed method and the underlying ddCOSMO model are readily available for a wide variety of solvents and are accessible in xtb for use in various computational applications.
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Affiliation(s)
- Marcel Stahn
- Mulliken Center of Theoretical Chemistry, 53115 Bonn, Germany
| | | | - Stefan Grimme
- Mulliken Center of Theoretical Chemistry, 53115 Bonn, Germany
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20
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Marco J, Dávalos-Prado JZ, Hnyk D, Holub J, Oña OB, Alcoba DR, Ferrer M, Elguero J, Lain L, Torre A, Oliva-Enrich JM. Two Shared Icosahedral Metallacarboranes through Iron: A Joint Experimental and Theoretical Refinement of Mössbauer Spectrum in [Fe(1,2-C 2B 9H 11) 2]Cs. ACS OMEGA 2023; 8:13993-14004. [PMID: 37091389 PMCID: PMC10116535 DOI: 10.1021/acsomega.3c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Mössbauer and X-ray photoelectron spectroscopies (XPS) are complemented with high-level quantum-chemical computations in the study of the geometric and electronic structure of the paramagnetic salt of the metallacarborane sandwich complex [Fe(1,2-C2B9H11)2]Cs = FeSanCs. Experimental 57Fe isomer shifts and quadrupole splitting parameters are compared with the theoretical prediction, with good agreement. The appearance of two sets of Cs(3d) doublets in the XPS spectrum, separated by 2 eV, indicates that Cs has two different chemical environments due to ease of the Cs(+) cation moving around the sandwich complex with low-energy barriers, as confirmed by quantum-chemical computations. Several minimum-energy geometries of the FeSanCs structure with the corresponding energies and Mössbauer parameters are discussed, in particular the atomic charges and spin population and the surroundings of the Fe atom in the complex. The Mössbauer spectra were taken at different temperatures showing the presence of a low-spin Fe atom with S = 1/2 and thus confirming a paramagnetic FeIII species.
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Affiliation(s)
- José
F. Marco
- Instituto
de Química-Física “Rocasolano”, CSIC, E-28006 Madrid, Spain
| | | | - Drahomír Hnyk
- Institute
of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68 Řež
near Prague, Czech Republic
| | - Josef Holub
- Institute
of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68 Řež
near Prague, Czech Republic
| | - Ofelia B. Oña
- Instituto
de Investigaciones Fisicoquímicas Teóricas y Aplicadas,
Universidad Nacional de La Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (S/N), Sucursal 4,
CC 16, 1900 La Plata, Argentina
| | - Diego R. Alcoba
- Departamento
de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
- Instituto
de Física de Buenos Aires, Consejo
Nacional de Investigaciones Científicas y Técnicas,
Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Maxime Ferrer
- Instituto
de Química Médica, CSIC, E-28006 Madrid, Spain
- Theoretical
Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica, CSIC, E-28006 Madrid, Spain
| | - Luis Lain
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado Postal 644, E-48080 Bilbao, Spain
| | - Alicia Torre
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado Postal 644, E-48080 Bilbao, Spain
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21
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Li C, Huang H, Sun L, Huang M, Ding H, Bai J, Cao BP, Xiao Q. Three-Component Synthesis of Dioxaphosphorane-Fused Diphosphacycles Exhibiting Unique Dynamic Fluorescence "On/Off" Properties. Angew Chem Int Ed Engl 2023; 62:e202215436. [PMID: 36524991 DOI: 10.1002/anie.202215436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Rigidly planar polycyclic phosphacycles featuring an internal dioxaphosphorane are promising photofunctional materials. However, the lack of efficient synthetic methods resulted in limited structural diversities which significantly hampered extensive study. Herein, we report a straightforward three-component synthesis of novel dioxaphosphorane-fused diphosphacycles with distinctive photophysical properties. Control experiments and theory calculations were performed to account for a plausible reaction mechanism. We also systematically investigated the structure-property relationships of these unprecedented platforms by combining experiments (X-ray analysis, optical and redox properties) and theoretical computations. Based on their unique structure and properties, a novel fluorescent switch for pH sensing was revealed by a dynamic ring-opening/ring-closing process.
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Affiliation(s)
- Chenchen Li
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Haiyang Huang
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Longgen Sun
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Mingqing Huang
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Haixin Ding
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Jiang Bai
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Ban-Peng Cao
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Qiang Xiao
- Key Laboratory of Organic Chemistry in Jiangxi Province, Institute of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
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22
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Weickgenannt N, Maaß F, Kueckmann T, Su X, Tobey S. Angewandte Chemie: A Team Effort. Angew Chem Int Ed Engl 2023; 62:e202217572. [PMID: 36543360 DOI: 10.1002/anie.202217572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Indexed: 12/24/2022]
Abstract
While the number of submissions to the journal continued to increase in 2022, the Editorial Team also implemented a number of changes with support of the GDCh and the journal's advisory bodies. For example, "Team Profiles" are author profiles that celebrate joint efforts as the basis of an inclusive research culture. In looking forward, two new members will join the International Advisory Board in 2023.
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Affiliation(s)
| | - Frank Maaß
- Executive Committee, Angewandte Chemie , Germany
| | | | - Xin Su
- Executive Committee, Angewandte Chemie , Germany
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23
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Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
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Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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24
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Weickgenannt N, Maaß F, Kueckmann T, Su X, Tobey S. Angewandte Chemie
: A Team Effort. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202217572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Frank Maaß
- Executive Committee Angewandte Chemie Germany
| | | | - Xin Su
- Executive Committee Angewandte Chemie Germany
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25
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Wang Y, Walker BD, Liu C, Ren P. An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules 2022; 27:8567. [PMID: 36500658 PMCID: PMC9738817 DOI: 10.3390/molecules27238567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization.
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Affiliation(s)
| | | | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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26
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Gómez S, Giovannini T, Cappelli C. Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution. ACS PHYSICAL CHEMISTRY AU 2022; 3:1-16. [PMID: 36718266 PMCID: PMC9881242 DOI: 10.1021/acsphyschemau.2c00050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
In this Perspective, we outline the essential physicochemical aspects that need to be considered when building a reliable approach to describe absorption properties of solvated systems. In particular, we focus on how to properly model the complexity of the solvation phenomenon, arising from dynamical aspects and specific, strong solute-solvent interactions. To this end, conformational and configurational sampling techniques, such as Molecular Dynamics, have to be coupled to accurate fully atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) methodologies. By exploiting different illustrative applications, we show that an effective reproduction of experimental spectral signals can be achieved by delicately balancing exhaustive sampling, hydrogen bonding, mutual polarization, and nonelectrostatic effects.
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Barravecchia L, Blanco-Gómez A, Neira I, Skackauskaite R, Vila A, Rey-Rico A, Peinador C, García MD. "Vermellogens" and the Development of CB[8]-Based Supramolecular Switches Using pH-Responsive and Non-Toxic Viologen Analogues. J Am Chem Soc 2022; 144:19127-19136. [PMID: 36206443 DOI: 10.1021/jacs.2c08575] [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
We present herein the "vermellogens", a new class of pH-responsive viologen analogues, which replace the direct linking between para-substituted pyridinium moieties within those by a hydrazone functional group. A series of such compounds have been efficiently synthesized in aqueous media by hydrazone exchange reactions, displaying a marked pH-responsivity. Furthermore, the parent N,N'-dimethylated "vermellogen": the "red thread", an analogue of the herbicide paraquat and used herein as a representative model of the series, showed anion-recognition abilities, non-reversible electrochemical behavior, and non-toxicity of the modified bis-pyridinium core. The host-guest chemistry for the "red thread" with the CB[7,8] macrocyclic receptors has been extensively studied experimentally and by dispersion corrected density functional theory methods, showing a parallel behavior to that previously described for the herbicide but, crucially, swapping the well-known redox reactive capabilities of the viologen-based inclusion complexes by acid-base supramolecular responsiveness.
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Affiliation(s)
- Liliana Barravecchia
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Arturo Blanco-Gómez
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Iago Neira
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Raminta Skackauskaite
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Alejandro Vila
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Ana Rey-Rico
- Gene & Cell Therapy Research Group (G-CEL), Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071A Coruña, Spain
| | - Carlos Peinador
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
| | - Marcos D García
- Departamento de Química and Centro de Investigaciones Científicas Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, 15071A Coruña, Spain
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