Emerging Conformational-Analysis Protocols from the RTCONF55-16K Reaction Thermochemistry Conformational Benchmark Set

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2024 Jun 20

PMID 38899777

Authors

Bence Balazs Meszaros

Karoly Kubicsko

David Dorian Nemeth

Janos Daru

Affiliations

Soon will be listed here.

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. , 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.

Citing Articles

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PMID: 39723648 PMC: 11726553. DOI: 10.1021/jacs.4c14596.

References

Bursch M, Mewes J, Hansen A, Grimme S . Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. Angew Chem Int Ed Engl. 2022; 61(42):e202205735. PMC: 9826355. DOI: 10.1002/anie.202205735. View

Grimme S . Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations. J Chem Theory Comput. 2019; 15(5):2847-2862. DOI: 10.1021/acs.jctc.9b00143. View

Bannwarth C, Ehlert S, Grimme S . GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions. J Chem Theory Comput. 2019; 15(3):1652-1671. DOI: 10.1021/acs.jctc.8b01176. View

Verteramo M, Stenstrom O, Misini Ignjatovic M, Caldararu O, Olsson M, Manzoni F . Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. J Am Chem Soc. 2019; 141(5):2012-2026. DOI: 10.1021/jacs.8b11099. View

Liu X, Bai F, Ouyang S, Wang X, Li H, Jiang H . Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinformatics. 2009; 10:101. PMC: 2678094. DOI: 10.1186/1471-2105-10-101. View

Agrafiotis D, Gibbs A, Zhu F, Izrailev S, Martin E . Conformational sampling of bioactive molecules: a comparative study. J Chem Inf Model. 2007; 47(3):1067-86. DOI: 10.1021/ci6005454. View

Yepes D, Neese F, List B, Bistoni G . Unveiling the Delicate Balance of Steric and Dispersion Interactions in Organocatalysis Using High-Level Computational Methods. J Am Chem Soc. 2020; 142(7):3613-3625. PMC: 7307905. DOI: 10.1021/jacs.9b13725. View

Nagy P, Samu G, Kallay M . Optimization of the Linear-Scaling Local Natural Orbital CCSD(T) Method: Improved Algorithm and Benchmark Applications. J Chem Theory Comput. 2018; 14(8):4193-4215. DOI: 10.1021/acs.jctc.8b00442. View

Gorges J, Grimme S, Hansen A, Pracht P . Towards understanding solvation effects on the conformational entropy of non-rigid molecules. Phys Chem Chem Phys. 2022; 24(20):12249-12259. DOI: 10.1039/d1cp05805c. View

10.

Karplus M, Ichiye T, Pettitt B . Configurational entropy of native proteins. Biophys J. 1987; 52(6):1083-5. PMC: 1330109. DOI: 10.1016/S0006-3495(87)83303-9. View

11.

Santra G, Martin J . Do Double-Hybrid Functionals Benefit from Regularization in the PT2 Term? Observations from an Extensive Benchmark. J Phys Chem Lett. 2022; 13(15):3499-3506. PMC: 9036584. DOI: 10.1021/acs.jpclett.2c00718. View

12.

Perdew J, Ruzsinszky A, Tao J, Staroverov V, Scuseria G, Csonka G . Prescription for the design and selection of density functional approximations: more constraint satisfaction with fewer fits. J Chem Phys. 2005; 123(6):62201. DOI: 10.1063/1.1904565. View

13.

Ehlert S, Grimme S, Hansen A . Conformational Energy Benchmark for Longer -Alkane Chains. J Phys Chem A. 2022; 126(22):3521-3535. DOI: 10.1021/acs.jpca.2c02439. View

14.

Pracht P, Grimme S . Calculation of absolute molecular entropies and heat capacities made simple. Chem Sci. 2021; 12(19):6551-6568. PMC: 8139639. DOI: 10.1039/d1sc00621e. View

15.

Chang C, Chen W, Gilson M . Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A. 2007; 104(5):1534-9. PMC: 1780070. DOI: 10.1073/pnas.0610494104. View

16.

Iribarren I, Trujillo C . Efficiency and Suitability when Exploring the Conformational Space of Phase-Transfer Catalysts. J Chem Inf Model. 2022; 62(22):5568-5580. PMC: 9709918. DOI: 10.1021/acs.jcim.2c00934. View

17.

Haworth N, Wang Q, Coote M . Modeling Flexible Molecules in Solution: A pK Case Study. J Phys Chem A. 2017; 121(27):5217-5225. DOI: 10.1021/acs.jpca.7b04133. View

18.

Bursch M, Hansen A, Pracht P, Kohn J, Grimme S . Theoretical study on conformational energies of transition metal complexes. Phys Chem Chem Phys. 2020; 23(1):287-299. DOI: 10.1039/d0cp04696e. View

19.

Mardirossian N, Head-Gordon M . ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation. J Chem Phys. 2016; 144(21):214110. DOI: 10.1063/1.4952647. View

20.

Angyal P, Hegedus K, Meszaros B, Daru J, Dudas A, Galambos A . Total Synthesis and Structural Plasticity of Kratom Pseudoindoxyl Metabolites. Angew Chem Int Ed Engl. 2023; 62(35):e202303700. DOI: 10.1002/anie.202303700. View