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Medrano Sandonas L, Van Rompaey D, Fallani A, Hilfiker M, Hahn D, Perez-Benito L, Verhoeven J, Tresadern G, Kurt Wegner J, Ceulemans H, Tkatchenko A. Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules. Sci Data 2024; 11:742. [PMID: 38972891 PMCID: PMC11228031 DOI: 10.1038/s41597-024-03521-8] [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: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.
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Affiliation(s)
- Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany.
| | - Dries Van Rompaey
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Alessio Fallani
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Mathias Hilfiker
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - David Hahn
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jonas Verhoeven
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Joerg Kurt Wegner
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
- Drug Discovery Data Sciences (D3S), Johnson & Johnson Innovative Medicine, 301 Binney Street, MA 02142, Cambridge, USA
| | - Hugo Ceulemans
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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2
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Mészáros BB, Kubicskó K, Németh DD, Daru J. Emerging Conformational-Analysis Protocols from the RTCONF55-16K Reaction Thermochemistry Conformational Benchmark Set. J Chem Theory Comput 2024. [PMID: 38899777 DOI: 10.1021/acs.jctc.4c00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
RTCONF55-16K is a new, reactive conformational data set based on cost-efficient methods to assess different conformational analysis protocols. Our reference calculations underpinned the accuracy of the CENSO (Grimme et al. J. Phys. Chem. A, 2021, 125, 4039) procedure and resulted in alternative recipes with different cost-accuracy compromises. Our general-purpose and economical protocols (CENSO-light and zero, respectively) were found to be 10-30 times faster than the original algorithm, adding only 0.4-0.7 kcal/mol absolute error to the relative free energy estimates.
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Affiliation(s)
- Bence Balázs Mészáros
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Károly Kubicskó
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Dávid Dorián Németh
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - János Daru
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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3
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Burda H, Hsieh I, Burda C, Parson WW. Entropy-Enthalpy Compensation in Electron-Transfer Processes. J Phys Chem Lett 2024; 15:3946-3952. [PMID: 38568867 DOI: 10.1021/acs.jpclett.4c00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Solvent reorganization energies, free energies, and entropies are obtained for photoexcitation of three molecules that exhibit strong solvatochromism [Nile red, 5-(dimethylamino)-5'-nitro-2,2-bisthiophene, and Reichardt's dye B30] by measuring their optical absorption spectra at temperatures between 150 and 300 K in solvents with a range of polarities. Energies, free energies, and entropies of solvent reorganization are also obtained from computer simulations of three intramolecular electron-transfer reactions (charge separation and recombination in Zn-porphyrin-quinone cyclophane and charge transfer in a bis-biphenylandrostane radical anion). Entropy-enthalpy compensation in the solvent reorganization free energy for photoexcitation or electron transfer is found to be essentially complete (having nearly equal and opposite contributions from entropic and enthalpic effects) for all of the processes with solvent reorganization energies less than about 0.1 eV. Compensation becomes less complete as the reorganization energy becomes larger. A semiclassical treatment of the solvent reorganization entropy can rationalize these results.
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Affiliation(s)
- Henrik Burda
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Isabelle Hsieh
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Clemens Burda
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - William W Parson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Wesołowski P, Wales DJ, Pracht P. Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation. J Phys Chem B 2024; 128:3145-3156. [PMID: 38512062 PMCID: PMC11000224 DOI: 10.1021/acs.jpcb.4c00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
In this study, a three-layered multicenter ONIOM approach is implemented to characterize the naive folding pathway of bovine pancreatic trypsin inhibitor (BPTI). Each layer represents a distinct level of theory, where the initial layer, encompassing the entire protein, is modeled by a general all-atom force-field GFN-FF. An intermediate electronic structure layer consisting of three multicenter fragments is introduced with the state-of-the-art semiempirical tight-binding method GFN2-xTB. Higher accuracy, specifically addressing the breaking and formation of the three disulfide bonds, is achieved at the innermost layer using the composite DFT method r2SCAN-3c. Our analysis sheds light on the structural stability of BPTI, particularly the significance of interlinking disulfide bonds. The accuracy and efficiency of the multicenter QM/SQM/MM approach are benchmarked using the oxidative formation of cystine. For the folding pathway of BPTI, relative stabilities are investigated through the calculation of free energy contributions for selected intermediates, focusing on the impact of the disulfide bond. Our results highlight the intricate trade-off between accuracy and computational cost, demonstrating that the multicenter ONIOM approach provides a well-balanced and comprehensive solution to describe electronic structure effects in biomolecular systems. We conclude that multiscale energy landscape exploration provides a robust methodology for the study of intriguing biological targets.
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Affiliation(s)
- Patryk
A. Wesołowski
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Philipp Pracht
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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5
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Pracht P, Grimme S, Bannwarth C, Bohle F, Ehlert S, Feldmann G, Gorges J, Müller M, Neudecker T, Plett C, Spicher S, Steinbach P, Wesołowski PA, Zeller F. CREST-A program for the exploration of low-energy molecular chemical space. J Chem Phys 2024; 160:114110. [PMID: 38511658 DOI: 10.1063/5.0197592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.
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Affiliation(s)
- Philipp Pracht
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and 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
| | - Gereon Feldmann
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Marcel Müller
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Tim Neudecker
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Christoph Plett
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | | | - Pit Steinbach
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Patryk A Wesołowski
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Felix Zeller
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
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6
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Rummel L, Schreiner PR. Advances and Prospects in Understanding London Dispersion Interactions in Molecular Chemistry. Angew Chem Int Ed Engl 2024; 63:e202316364. [PMID: 38051426 DOI: 10.1002/anie.202316364] [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: 10/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
London dispersion (LD) interactions are the main contribution of the attractive part of the van der Waals potential. Even though LD effects are the driving force for molecular aggregation and recognition, the role of these omnipresent interactions in structure and reactivity had been largely underappreciated over decades. However, in the recent years considerable efforts have been made to thoroughly study LD interactions and their potential as a chemical design element for structures and catalysis. This was made possible through a fruitful interplay of theory and experiment. This review highlights recent results and advances in utilizing LD interactions as a structural motif to understand and utilize intra- and intermolecularly LD-stabilized systems. Additionally, we focus on the quantification of LD interactions and their fundamental role in chemical reactions.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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7
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Plett C, Grimme S, Hansen A. Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules. J Comput Chem 2024; 45:419-429. [PMID: 37982322 DOI: 10.1002/jcc.27248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1 . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.
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Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
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Pattanaik L, Menon A, Settels V, Spiekermann KA, Tan Z, Vermeire FH, Sandfort F, Eiden P, Green WH. ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents. J Phys Chem B 2023; 127:10151-10170. [PMID: 37966798 DOI: 10.1021/acs.jpcb.3c05904] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Predicting Gibbs free energy of solution is key to understanding the solvent effects on thermodynamics and reaction rates for kinetic modeling. Accurately computing solution free energies requires the enumeration and evaluation of relevant solute conformers in solution. However, even after generation of relevant conformers, determining their free energy of solution requires an expensive workflow consisting of several ab initio computational chemistry calculations. To help address this challenge, we generate a large data set of solution free energies for nearly 44,000 solutes with almost 9 million conformers calculated in 41 different solvents using density functional theory and COSMO-RS and quantify the impact of solute conformers on the solution free energy. We then train a message passing neural network to predict the relative solution free energies of a set of solute conformers, enabling the identification of a small subset of thermodynamically relevant conformers. The model offers substantial computational time savings with predictions usually substantially within 1 kcal/mol of the free energy of the solution calculated by using computational chemical methods.
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Affiliation(s)
- Lagnajit Pattanaik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Angiras Menon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Volker Settels
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - Kevin A Spiekermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zipei Tan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Florence H Vermeire
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Frederik Sandfort
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - Philipp Eiden
- BASF SE, Scientific Modeling, Group Research, Ludwigshafen am Rhein 67056, Germany
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Sepulveda-Montaño LX, Galindo JF, Kuroda DG. Infrared Spectroscopy of Liquid Solutions as a Benchmarking Tool of Semiempirical QM Methods: The Case of GFN2-xTB. J Phys Chem B 2023; 127:7955-7963. [PMID: 37676972 DOI: 10.1021/acs.jpcb.3c03174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The accurate description of large molecular systems has triggered the development of new computational methods. Due to the computational cost of modeling large systems, the methods usually require a trade-off between accuracy and speed. Therefore, benchmarking to test the accuracy and precision of the method is an important step in their development. The typical gold standard for evaluating these methods is isolated molecules, because of the low computational cost. However, the advent of high-performance computing has made it possible to benchmark computational methods using observables from more complex systems such as liquid solutions. To this end, infrared spectroscopy provides a suitable set of observables (i.e., vibrational transitions) for liquid systems. Here, IR spectroscopy observables are used to benchmark the predictions of the newly developed GFN2-xTB semiempirical method. Three different IR probes (i.e., N-methylacetamide, benzonitrile, and semiheavy water) in solution are selected for this purpose. The work presented here shows that GFN2-xTB predicts central frequencies with errors of less than 10% in all probes. In addition, the method captures detailed properties of the molecular environment such as weak interactions. Finally, the GFN2-xTB correctly assesses the vibrational solvatochromism for N-methylacetamide and semiheavy water but does not have the accuracy needed to properly describe benzonitrile. Overall, the results indicate not only that GFN2-xTB can be used to predict the central frequencies and their dependence on the molecular environment with reasonable accuracy but also that IR spectroscopy data of liquid solutions provide a suitable set of observables for the benchmarking of computational methods.
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Affiliation(s)
| | - Johan Fabian Galindo
- Department of Chemistry, Universidad Nacional de Colombia sede Bogotá, 111321 Bogotá, Colombia
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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10
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Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
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Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
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11
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Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
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Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Rummel L, König HF, Hausmann H, Schreiner PR. Silyl Groups Are Strong Dispersion Energy Donors. J Org Chem 2022; 87:13168-13177. [PMID: 36166406 DOI: 10.1021/acs.joc.2c01633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an experimental and computational study to investigate noncovalent interactions between silyl groups that are often employed as "innocent" protecting groups. We chose an extended cyclooctatetraene (COT)-based molecular balance comprising unfolded (1,4-disubstituted) and folded (1,6-disubstituted) valance bond isomers that typically display remote and close silyl group contacts, respectively. The thermodynamic equilibria were determined using nuclear magnetic resonance measurements. Additionally, we utilized Boltzmann weighted symmetry-adapted perturbation theory (SAPT) at the sSAPT0/aug-cc-pVDZ level of theory to dissect and quantify noncovalent interactions. Apart from the extremely bulky tris(trimethylsilyl)silyl "supersilyl" group, there is a preference for the folded 1,6-COT valence isomer, with London dispersion interactions being the main stabilizing factor. This makes silyl groups excellent dispersion energy donors, a finding that needs to be taken into account in synthesis planning.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Henrik F König
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Heike Hausmann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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13
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Abstract
Differences in entropies of competing transition states can direct kinetic selectivity. Understanding and modeling such entropy differences at the molecular level is complicated by the fact that entropy is statistical in nature; i.e., it depends on multiple vibrational states of transition structures, the existence of multiple dynamically accessible pathways past these transition structures, and contributions from multiple transition structures differing in conformation/configuration. The difficulties associated with modeling each of these contributors are discussed here, along with possible solutions, all with an eye toward the development of portable qualitative models of use to experimentalists aiming to design reactions that make use of entropy to control kinetic selectivity.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
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14
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Gorges J, Grimme S, Hansen A. Reliable prediction of association (free) energies of supramolecular complexes with heavy main group elements – the HS13L benchmark set. Phys Chem Chem Phys 2022; 24:28831-28843. [DOI: 10.1039/d2cp04049b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We introduce a set of 13 supramolecular complexes featuring diverse non-covalent interactions with heavy main group elements (Zn, As, Se, Te, Br, I), high charges (−2 up to +4), and large systems with up to 266 atoms (HS13L).
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Affiliation(s)
- Johannes Gorges
- 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
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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