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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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Zimmermann C, Dorst AC, Suhm MA. Raising the benchmark potential of a simple alcohol-ketone intermolecular balance. Phys Chem Chem Phys 2022; 25:384-391. [PMID: 36477454 DOI: 10.1039/d2cp05141a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
2-Butanone offers two hydrogen bond docking variants to a solvating methanol which are cleanly separated by supersonic jet infrared absorption spectroscopy in the OH-stretching range, resolving earlier action spectroscopy indeterminacies for this elementary case of an intermolecular alcohol-ketone balance. The solvent preference for the shorter chain side is unambiguously derived from the spectra of homologous compounds. It is analysed in terms of competing steric and dispersion interactions and the resulting energy differences across a low interconversion barrier. Fortuitous cancellations are discussed and quantitative energy deficiencies of the employed DFT approaches are suggested. Some benchmarkable experimental observations: at low temperature, a single methanol molecule prefers the methyl-sided oxygen lone pair of 2-butanone over the ethyl-sided lone pair by 1-2 kJ mol-1, the trans butane backbone is conserved in both low-lying isomers, the OH-stretching fundamentals differ by 47(2) cm-1.
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Affiliation(s)
- Charlotte Zimmermann
- Institute of Physical Chemistry, Georg-August-University Göttingen, Tammannstr. 6, 37077, Göttingen, Germany.
| | - Arved C Dorst
- Institute of Physical Chemistry, Georg-August-University Göttingen, Tammannstr. 6, 37077, Göttingen, Germany.
| | - Martin A Suhm
- Institute of Physical Chemistry, Georg-August-University Göttingen, Tammannstr. 6, 37077, Göttingen, Germany.
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Parker SF, Silverwood IP, Hamilton NG, Lennon D. Structural and spectroscopic characterisation of C4 oxygenates relevant to structure/activity relationships of the hydrogenation of α,β-unsaturated carbonyls. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 153:289-297. [PMID: 26318704 DOI: 10.1016/j.saa.2015.08.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/11/2015] [Accepted: 08/16/2015] [Indexed: 06/04/2023]
Abstract
In the present work, we have investigated the conformational isomerism and calculated the vibrational spectra of the C4 oxygenates: 3-butyne-2-one, 3-butene-2-one, 2-butanone and 2-butanol using density functional theory. The calculations are validated by comparison to structural data where available and new, experimental inelastic neutron scattering and infrared spectra of the compounds. We find that for 3-butene-2-one and 2-butanol the spectra show clear evidence for the presence of conformational isomerism and this is supported by the calculations. Complete vibrational assignments for all four molecules are provided and this provides the essential information needed to generate structure/activity relationships for the sequential catalytic hydrogenation of 3-butyne-2-one to 2-butanol.
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Affiliation(s)
- Stewart F Parker
- ISIS Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK.
| | - Ian P Silverwood
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Neil G Hamilton
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - David Lennon
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
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Maekawa H, Ge NH. Picosecond Rotational Interconversion Adjacent to a C═O Bond Studied by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2012; 116:11292-301. [DOI: 10.1021/jp306201t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025,
United States
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025,
United States
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Marković S, Despotović A, Jovanović D, Đurović I. Enthalpy of formation of acyclic saturated ketones. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409090027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Analysis of the Temperature and Composition Dependence of Viscosimetric Properties of 2-Butanone + 2-Butanol Solvent Mixtures. J SOLUTION CHEM 2004. [DOI: 10.1007/s10953-004-7135-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Faranda S, Foca G, Marchetti A, Pályi G, Tassi L, Zucchi C. Density measurements of the binary mixtures of 2-butanone and 2-butanol at temperatures from −10 to 80 °C. J Mol Liq 2004. [DOI: 10.1016/j.molliq.2003.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Langley CH, Lii JH, Allinger NL. Molecular mechanics calculations on carbonyl compounds. II. Open-chain ketones. J Comput Chem 2001. [DOI: 10.1002/jcc.1099] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Langley CH, Lii JH, Allinger NL. Molecular mechanics calculations on carbonyl compounds. III. Cycloketones. J Comput Chem 2001. [DOI: 10.1002/jcc.1100] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Variation of volumic properties with temperature and composition of 2-butanone + 1,2-propanediol binary mixtures. J Mol Liq 2000. [DOI: 10.1016/s0167-7322(00)00153-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lecea B, Arrieta A, Cossío FP. Solvent Effects on the Conformer Distribution of 2-Methoxypropanal and Chloroacetaldehyde. A Model Case for the Conformational Analysis in Solution of Chiral Aldehydes Including Polar Groups. J Org Chem 1997. [DOI: 10.1021/jo970468t] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Begoña Lecea
- Farmazi Fakultatea, Euskal Herriko Unibertsitatea, P.K. 450, 01080 Vitoria-Gasteiz, Spain, and Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 San Sebastián-Donostia, Spain
| | - Ana Arrieta
- Farmazi Fakultatea, Euskal Herriko Unibertsitatea, P.K. 450, 01080 Vitoria-Gasteiz, Spain, and Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 San Sebastián-Donostia, Spain
| | - Fernando P. Cossío
- Farmazi Fakultatea, Euskal Herriko Unibertsitatea, P.K. 450, 01080 Vitoria-Gasteiz, Spain, and Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 San Sebastián-Donostia, Spain
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Kang YK, No KT, Scheraga HA. Intrinsic Torsional Potential Parameters for Conformational Analysis of Peptides and Proteins. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9611434] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Korea, Department of Chemistry, Soong Sil University, Sang Do 5 Dong 1-1, Dong Jak Gu, Seoul 156-743, Korea, and Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301
| | - Kyoung Tai No
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Korea, Department of Chemistry, Soong Sil University, Sang Do 5 Dong 1-1, Dong Jak Gu, Seoul 156-743, Korea, and Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301
| | - Harold A. Scheraga
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Korea, Department of Chemistry, Soong Sil University, Sang Do 5 Dong 1-1, Dong Jak Gu, Seoul 156-743, Korea, and Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301
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13
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Gas-phase structure and conformation of diethyl ketone studied by molecular orbital constrained electron diffraction. J Mol Struct 1996. [DOI: 10.1016/0022-2860(95)09081-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gundertofte K, Palm J, Pettersson I, Stamvik A. A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods. J Comput Chem 1991. [DOI: 10.1002/jcc.540120209] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Molecular structure and conformation of 3-methyl-2-butanone: A gas electron diffraction investigation combined with ab initio calculation and vibrational spectroscopy. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)85125-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Fausto R, Teixeira-Dias J, Carey P. A molecular mechanics force field for conformational analysis of simple thiocarbonyl compounds. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)85068-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Wiberg KB, Murcko MA. Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures, and of electron correlation on relative energies. J Comput Chem 1988. [DOI: 10.1002/jcc.540090507] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Green R, Horsewill A. A study of methyl group dynamics and barrier heights in a homologous series of unbranched ketones. Mol Phys 1986. [DOI: 10.1080/00268978600100631] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ohta S. The Solvent Effects on the Optical Rotatory Properties of 1,7-Diaryl-5-hydroxy-3-heptanones and Related Compounds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1986. [DOI: 10.1246/bcsj.59.1181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Carbonyles tres decales par rapport a l'eclipse dans les aldehydes et les cetones aliphatiques satures: analyse conformationnelle theorique. J Mol Struct 1978. [DOI: 10.1016/0022-2860(78)87016-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Oyanagi K, Kuchitsu K. Molecular Structure and Conformation of Ethyl Methyl Ether as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1978. [DOI: 10.1246/bcsj.51.2237] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Oyanagi K, Kuchitsu K. Molecular Structure and Conformation of Ethyl Methyl Sulfide as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1978. [DOI: 10.1246/bcsj.51.2243] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Calculation of Molecular Structure and Energy by Force-Field Methods. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 1976. [DOI: 10.1016/s0065-3160(08)60212-9] [Citation(s) in RCA: 227] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Buric Z, Krueger P. Vibrational analysis of diethyl ketone and its deuterated analogues. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/0584-8539(74)80059-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kitano M, Kuchitsu K. Molecular Structure ofN-Methylformamide as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1974. [DOI: 10.1246/bcsj.47.631] [Citation(s) in RCA: 93] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Haller R, Schneider HJ. [Conformation of diphenyl acetaldehyde and of homologous diphenylmethyl alkyl ketones (author's transl)]. Arch Pharm (Weinheim) 1974; 307:116-22. [PMID: 4825987 DOI: 10.1002/ardp.19743070208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Kitano M, Kuchitsu K. Molecular Structure of Formamide as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1974. [DOI: 10.1246/bcsj.47.67] [Citation(s) in RCA: 129] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kitano M, Fukuyama T, Kuchitsu K. Molecular Structure ofN-Methylacetamide as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1973. [DOI: 10.1246/bcsj.46.384] [Citation(s) in RCA: 129] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yokozeki A, Kuchitsu K. Structure and Rotational Isomerism of Ethylenediamine as Studied by Gas Electron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1971. [DOI: 10.1246/bcsj.44.2926] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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