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Mun H, Lorpaiboon W, Ho J. In Search of the Best Low-Cost Methods for Efficient Screening of Conformers. J Phys Chem A 2024; 128:4391-4400. [PMID: 38754085 DOI: 10.1021/acs.jpca.4c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Locating the lowest energy conformer is crucial for the accurate computation of equilibrium properties of molecular systems. This paper examines the performance of efficient low-cost methods in terms of the alignment and relative energies of their energy minima against the benchmark revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ potential energy surface. The low-cost methods considered include GFN-FF, GFN2-xTB, DFTB3, HF-3c, B97-3c, PBEh-3c, and r2SCAN-3c composite methods against a diverse test set of 20 compounds including alkanes, perfluoroalkyl molecules, peptides, open-shell radicals, and Zn(II) complexes of varying sizes. The "3c" composite methods are generally more accurate, but are at least 2-3 orders of magnitude more expensive than tight-binding methods which have energy minima that align well with the benchmark potential energy surface. The findings of this paper were further exploited to introduce a simple strategy involving Grimme's CENSO energy-sorting algorithm that resulted in up to an order of magnitude reduction in computational time for locating the lowest energy conformer on the revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ surface.
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Affiliation(s)
- Haedam Mun
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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2
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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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3
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Jorgensen WL, Ghahremanpour MM, Saar A, Tirado-Rives J. OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers. J Phys Chem B 2024; 128:250-262. [PMID: 38127719 DOI: 10.1021/acs.jpcb.3c06602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The OPLS all-atom force field was updated and applied to modeling unsaturated hydrocarbons, alcohols, and ethers. Testing has included gas-phase conformational energetics, properties of pure liquids, and free energies of hydration. Monte Carlo statistical mechanics (MC) calculations were used to model 60 liquids. In addition, a robust, automated procedure was devised to compute the free energies of hydration with high precision via free-energy perturbation (FEP) calculations using double annihilation. Testing has included larger molecules than in the past, and parameters are reported for the first time for some less common groups including alkynes, allenes, dienes, and acetals. The average errors in comparison with experimental data for the computed properties of the pure liquids were improved with the modified force field (OPLS/2020). For liquid densities and heats of vaporization, the average unsigned errors are 0.01 g/cm3 and 0.2 kcal/mol. The average error and signed error for free energies of hydration are both 1.2 kcal/mol. As noted before, this reflects a systematic overestimate of the hydrophobicity of organic molecules when the parametrization is done to minimize the errors for properties of pure liquids. Implications for the modeling of biomolecular systems with standard force fields are considered.
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Affiliation(s)
- William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | | | - Anastasia Saar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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4
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Corzo HH, Hillers-Bendtsen AE, Barnes A, Zamani AY, Pawłowski F, Olsen J, Jørgensen P, Mikkelsen KV, Bykov D. Corrigendum: Coupled cluster theory on modern heterogeneous supercomputers. Front Chem 2023; 11:1256510. [PMID: 37654900 PMCID: PMC10466216 DOI: 10.3389/fchem.2023.1256510] [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: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fchem.2023.1154526.].
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Affiliation(s)
| | | | | | - Abdulrahman Y. Zamani
- Department of Chemistry and Biochemistry and Center for Chemical Computation and Theory, University of California, Merced, CA, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, United States
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Dmytro Bykov
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
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5
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Müller M, Hansen A, Grimme S. ωB97X-3c: A composite range-separated hybrid DFT method with a molecule-optimized polarized valence double-ζ basis set. J Chem Phys 2023; 158:014103. [PMID: 36610980 DOI: 10.1063/5.0133026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A new composite density functional theory (DFT) method is presented. It is based on ωB97X-V as one of the best-performing density functionals for the GMTKN55 thermochemistry database and completes the family of "3c" methods toward range-separated hybrid DFT. This method is consistently available for all elements up to Rn (Z = 1-86). Its further key ingredients are a polarized valence double-ζ (vDZP) Gaussian basis set, which was fully optimized in molecular DFT calculations, in combination with large-core effective core potentials and a specially adapted D4 dispersion correction. Unlike most existing double-ζ atomic orbital sets, vDZP shows only small basis set superposition errors (BSSEs) and can compete with standard sets of triple-ζ quality. Small residual BSSE effects are efficiently absorbed by the D4 damping scheme, which overall eliminates the need for an explicit treatment or empirical corrections for BSSE. Thorough tests on a variety of thermochemistry benchmark sets show that the new composite method, dubbed ωB97X-3c, is on par with or even outperforms standard hybrid DFT methods in a quadruple-zeta basis set at a small fraction of the computational cost. Particular strengths of this method are the description of non-covalent interactions and barrier heights, for which it is among the best-performing density functionals overall.
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Affiliation(s)
- Marcel Müller
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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6
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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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7
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Otlyotov AA, Minenkov Y. Conformational energies of microsolvated Na + clusters with protic and aprotic solvents from GFNn-xTB methods. J Comput Chem 2022; 43:1856-1863. [PMID: 36053781 DOI: 10.1002/jcc.26988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022]
Abstract
Performance of contemporary tight-binding semiempirical GFNn-xTB methods for the conformational energies of singly charged sodium clusters Na+ (S)n (n = 4-8) with 3 protic and 8 aprotic solvents is examined against the reference RI-MP2/CBS method. The median Pearson correlation coefficients of ρ = 0.84 (GFN2-xTB) and ρ = 0.82 (GFN1-xTB) do not give the clear preference to any tested approach. GFN1-xTB method demonstrates more stable performance than its GFN2-xTB successor with the average mean absolute errors (MAEs)/mean signed errors (MSEs) of 1.2/0.2 and 2.3/1.6 kcal mol-1 , respectively. Conformational energies produced by the computationally efficient DFT functional PBE and double-ζ basis set complemented with -D3(BJ) dispersion correction are suitable for the preliminary sampling (median ρ = 0.93), but should be used with a caution for the calculations of the average ensemble properties (MAE/MSE = 1.7/1.1 kcal mol-1 ). Higher-ranking PBE0-D3(BJ) and ωB97M-V with triple-ζ basis sets yield significantly lower MAEs/MSEs of 0.55/0.20 and 0.51/0.23 kcal mol-1 , respectively.
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Affiliation(s)
- Arseniy A Otlyotov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation
| | - Yury Minenkov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation.,Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russian Federation
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8
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Gasevic T, Stückrath JB, Grimme S, Bursch M. Optimization of the r 2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets. J Phys Chem A 2022; 126:3826-3838. [PMID: 35654439 PMCID: PMC9255700 DOI: 10.1021/acs.jpca.2c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "Swiss army knife" composite density functional electronic-structure method r2SCAN-3c (J. Chem. Phys. 2021, 154, 064103) is extended and optimized for the use with Slater-type orbital basis sets. The meta generalized-gradient approximation (meta-GGA) functional r2SCAN by Furness et al. is combined with a tailor-made polarized triple-ζ Slater-type atomic orbital (STO) basis set (mTZ2P), the semiclassical London dispersion correction (D4), and a geometrical counterpoise (gCP) correction. Relativistic effects are treated explicitly with the scalar-relativistic zeroth-order regular approximation (SR-ZORA). The performance of the new implementation is assessed on eight geometry and 74 energy benchmark sets, including the extensive GMTKN55 database as well as recent sets such as ROST61 and IONPI19. In geometry optimizations, the STO-based r2SCAN-3c is either on par with or more accurate than the hybrid density functional approximation M06-2X-D3(0)/TZP. In energy calculations, the overall accuracy is similar to the original implementation of r2SCAN-3c with Gaussian-type atomic orbitals (GTO), but basic properties, intermolecular noncovalent interactions, and barrier heights are better described with the STO approach, resulting in a lower weighted mean absolute deviation (WTMAD-2(STO) = 7.15 vs 7.50 kcal mol-1 with the original method) for the GMTKN55 database. The STO-optimized r2SCAN-3c outperforms many conventional hybrid/QZ approaches in most common applications at a fraction of their cost. The reliable, robust, and accurate r2SCAN-3c implementation with STOs is a promising alternative to the original implementation with GTOs and can be generally used for a broad field of quantum chemical problems.
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Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Julius B Stückrath
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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9
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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10
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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11
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Pescitelli G. ECD exciton chirality method today: a modern tool for determining absolute configurations. Chirality 2021; 34:333-363. [PMID: 34791704 PMCID: PMC9299504 DOI: 10.1002/chir.23393] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 02/02/2023]
Abstract
The application of the exciton chirality method (ECM) to interpret electronic circular dichroism (ECD) spectra is a well‐established and still popular approach to assign the absolute configuration (AC) of natural products, chiral organic compounds, and organometallic species. The method applies to compounds containing at least two chromophores with electric dipole allowed transitions (e.g., π–π* transitions). The exciton chirality rule correlates the sign of an exciton couplet (two ECD bands with opposite sign and similar intensity) with the overall molecular stereochemistry, including the AC. A correct application of the ECM requires three main prerequisites: (a) the knowledge of the molecular conformation, (b) the knowledge of the directions of the electric transition moments (TDMs), and (c) the assumption that the exciton coupling mechanism must be the major source of the observed ECD signals. All these prerequisites can be easily verified by means of quantum‐mechanical (QM) calculations. In the present review, we shortly introduce the general principles that underpin the use of the ECM for configurational assignments and survey its applications, both classic ones and some reported in the recent literature. Based on these examples, we will stress the advantages of the ECM but also the key requisites for its correct application. Additionally, we will discuss the dependence of the couplet sign on geometrical parameters (angles α,β,γ between TDMs), which can be helpful for discerning the sign of exciton chirality in ambiguous situations. Finally, we will present a molecular orbital (MO) description of the exciton coupling phenomenon.
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Affiliation(s)
- Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
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12
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Gaston JJ, Tague AJ, Smyth JE, Butler NM, Willis AC, van Eikema Hommes N, Yu H, Clark T, Keller PA. The Detosylation of Chiral 1,2-Bis(tosylamides). J Org Chem 2021; 86:9163-9180. [PMID: 34153182 DOI: 10.1021/acs.joc.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The deprotection of chiral 1,2-bis(tosylamides) to their corresponding 1,2-diamines is mostly unsuccessful under standard conditions. In a new methodology, the use of Mg/MeOH with sufficient steric additions allows the facile synthesis of 1,2-diamines in 78-98% yields. These results are rationalized using density functional theory and the examination of inner and outer-sphere reduction mechanisms.
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Affiliation(s)
- Jayden J Gaston
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Andrew J Tague
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jamie E Smyth
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Nicholas M Butler
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Anthony C Willis
- School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Nico van Eikema Hommes
- Computer Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Timothy Clark
- Computer Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Paul A Keller
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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Santra G, Semidalas E, Martin JML. Exploring Avenues beyond Revised DSD Functionals: II. Random-Phase Approximation and Scaled MP3 Corrections. J Phys Chem A 2021; 125:4628-4638. [PMID: 34019413 PMCID: PMC8279643 DOI: 10.1021/acs.jpca.1c01295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
For revDSD double
hybrids, the Görling–Levy second-order
perturbation theory component is an Achilles’ heel when applied
to systems with significant near-degeneracy (“static”)
correlation. We have explored its replacement by the direct random
phase approximation (dRPA), inspired by the SCS-dRPA75 functional
of Kállay and co-workers. The addition to the final energy
of both a D4 empirical dispersion correction and of a semilocal correlation
component lead to significant improvements, with DSD-PBEdRPA75-D4 approaching the performance of revDSD-PBEP86-D4 and the Berkeley
ωB97M(2). This form appears to be fairly insensitive to the
choice of the semilocal functional but does exhibit stronger basis
set sensitivity than the PT2-based double hybrids (due to much larger
prefactors for the nonlocal correlation). As an alternative, we explored
adding an MP3-like correction term (in a medium-sized basis set) to
a range-separated ωDSD-PBEP86-D4 double hybrid and found it
to have significantly lower WTMAD2 (weighted mean absolute deviation)
for the large and chemically diverse GMTKN55 benchmark suite; the
added computational cost can be mitigated through density fitting
techniques.
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Affiliation(s)
- Golokesh Santra
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Emmanouil Semidalas
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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14
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Grimme S, Bohle F, Hansen A, Pracht P, Spicher S, Stahn M. Efficient Quantum Chemical Calculation of Structure Ensembles and Free Energies for Nonrigid Molecules. J Phys Chem A 2021; 125:4039-4054. [PMID: 33688730 DOI: 10.1021/acs.jpca.1c00971] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The application of quantum chemical, automatic multilevel modeling workflows for the determination of thermodynamic (e.g., conformation equilibria, partition coefficients, pKa values) and spectroscopic properties of relatively large, nonrigid molecules in solution is described. Key points are the computation of rather complete structure (conformer) ensembles with extremely fast but still reasonable GFN2-xTB or GFN-FF semiempirical methods in the CREST searching approach and subsequent refinement at a recently developed, accurate r2SCAN-3c DFT composite level. Solvation effects are included in all steps by accurate continuum solvation models (ALPB, (D)COSMO-RS). Consistent inclusion of thermostatistical contributions in the framework of the modified rigid-rotor-harmonic-oscillator approximation (mRRHO) based on xTB/FF computed PES is also recommended.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Marcel Stahn
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
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15
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Grimme S, Hansen A, Ehlert S, Mewes JM. r 2SCAN-3c: A "Swiss army knife" composite electronic-structure method. J Chem Phys 2021; 154:064103. [PMID: 33588555 DOI: 10.1063/5.0040021] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The recently proposed r2SCAN meta-generalized-gradient approximation (mGGA) of Furness and co-workers is used to construct an efficient composite electronic-structure method termed r2SCAN-3c. To this end, the unaltered r2SCAN functional is combined with a tailor-made triple-ζ Gaussian atomic orbital basis set as well as with refitted D4 and geometrical counter-poise corrections for London-dispersion and basis set superposition error. The performance of the new method is evaluated for the GMTKN55 database covering large parts of chemical space with about 1500 data points, as well as additional benchmarks for non-covalent interactions, organometallic reactions, and lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r2SCAN-3c: It by far surpasses its predecessor B97-3c at only twice the cost and provides one of the best results of all semi-local density-functional theory (DFT)/QZ methods ever tested for the GMTKN55 database at one-tenth of the cost. Specifically, for reaction and conformational energies as well as non-covalent interactions, it outperforms prominent hybrid-DFT/QZ approaches at two to three orders of magnitude lower cost. Perhaps, the most relevant remaining issue of r2SCAN-3c is self-interaction error (SIE), owing to its mGGA nature. However, SIE is slightly reduced compared to other (m)GGAs, as is demonstrated in two examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous composite DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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16
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Polynski MV, Sapova MD, Ananikov VP. Understanding the solubilization of Ca acetylide with a new computational model for ionic pairs. Chem Sci 2020; 11:13102-13112. [PMID: 34094492 PMCID: PMC8163204 DOI: 10.1039/d0sc04752j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/07/2020] [Indexed: 01/05/2023] Open
Abstract
The unique reactivity of the acetylenic unit in DMSO gives rise to ubiquitous synthetic methods. We theoretically consider CaC2 solubility and protolysis in DMSO and formulate a strategy for CaC2 activation in solution-phase chemical transformations. For this, we use a new strategy for the modeling of ionic compounds in strongly coordinating solvents combining Born-Oppenheimer molecular dynamics with the DFTB3-D3(BJ) Hamiltonian and static DFT computations at the PBE0-D3(BJ)/pob-TZVP-gCP level. We modeled the thermodynamics of CaC2 protolysis under ambient conditions, taking into account its known heterogeneity and considering three polymorphs of CaC2. We give a theoretical basis for the existence of the elusive intermediate HC[triple bond, length as m-dash]C-Ca-OH and show that CaC2 insolubility in DMSO is of thermodynamic nature. We confirm the unique role of water and specific properties of DMSO in CaC2 activation and explain how the activation is realized. The proposed strategy for the utilization of CaC2 in sustainable organic synthesis is outlined.
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Affiliation(s)
- Mikhail V Polynski
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
| | - Mariia D Sapova
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Valentine P Ananikov
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
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17
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Bermesheva EV, Wozniak AI, Andreyanov FA, Karpov GO, Nechaev MS, Asachenko AF, Topchiy MA, Melnikova EK, Nelyubina YV, Gribanov PS, Bermeshev MV. Polymerization of 5-Alkylidene-2-norbornenes with Highly Active Pd–N-Heterocyclic Carbene Complex Catalysts: Catalyst Structure–Activity Relationships. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04686] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Evgeniya V. Bermesheva
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
- I. M. Sechenov First Moscow State Medical University, Trubetskaya str., 8, building 2, 119991 Moscow, Russia
| | - Alyona I. Wozniak
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
| | - Fedor A. Andreyanov
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
| | - Gleb O. Karpov
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
| | - Mikhail S. Nechaev
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskiye gory, Moscow 119991, Russia
| | - Andrey F. Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
| | - Maxim A. Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
| | - Elizaveta K. Melnikova
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskiye gory, Moscow 119991, Russia
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov Street 28, Moscow 119991, Russia
| | - Yulia V. Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov Street 28, Moscow 119991, Russia
| | - Pavel S. Gribanov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov Street 28, Moscow 119991, Russia
| | - Maxim V. Bermeshev
- A. V. Topchiev Institute of Petrochemical Synthesis, RAS, 29 Leninsky pr., 119991 Moscow, Russia
- D. I. Mendeleyev University of Chemical Technology of Russia, 9 Miusskaya sq., 125047 Moscow, Russia
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18
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Matczak P, Mlostoń G, Hamera-Fałdyga R, Görls H, Weigand W. Structure of Diferrocenyl Thioketone: From Molecule to Crystal. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24213950. [PMID: 31683693 PMCID: PMC6864675 DOI: 10.3390/molecules24213950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023]
Abstract
Ferrocenyl-functionalized thioketones have recently been recognized as useful building blocks for sulfur-containing compounds with potential applications in materials chemistry. This work is devoted to a single representative of such thioketones, namely diferrocenyl thioketone (Fc2CS), whose structure has been determined here for the first time. Both X-ray crystallography and a wide variety of quantum-chemical methods were used to explore the structure of Fc2CS. In addition to the X-ray structure determination, intermolecular interactions occurring in the crystal structure of Fc2CS were examined in detail by quantum-chemical methods. These methods were also an invaluable tool in studying the molecular structure of Fc2CS, from the gas phase to solutions and to its crystal. Intramolecular interactions governing the conformational behavior of an isolated Fc2CS molecule were deduced from quantum-chemical analyses carried out in orbital space and real space. Our experimental and theoretical results indicate that the main structural features of an isolated Fc2CS molecule in its lowest-energy geometry are retained both upon solvation and in the crystal. The tilt of ferrocenyl groups is only slightly affected by crystal packing forces that are dominated by dispersion. Nonetheless, a network of intermolecular interactions, such as H···H, C···H and S···H, was detected in the Fc2CS crystal but each of them is fairly weak.
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Affiliation(s)
- Piotr Matczak
- Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90236 Lodz, Poland.
| | - Grzegorz Mlostoń
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91403 Lodz, Poland.
| | - Róża Hamera-Fałdyga
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91403 Lodz, Poland.
| | - Helmar Görls
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Humboldtstrasse 8, 07743 Jena, Germany.
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Humboldtstrasse 8, 07743 Jena, Germany.
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