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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [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: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
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Mališ M, Loquais Y, Gloaguen E, Biswal HS, Piuzzi F, Tardivel B, Brenner V, Broquier M, Jouvet C, Mons M, Došlić N, Ljubić I. Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue. J Am Chem Soc 2012; 134:20340-51. [DOI: 10.1021/ja3054942] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Yohan Loquais
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Eric Gloaguen
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Himansu S. Biswal
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - François Piuzzi
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Benjamin Tardivel
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Valérie Brenner
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Michel Broquier
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Christophe Jouvet
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Michel Mons
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Ivan Ljubić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
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