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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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Toumi I, Dalbouha S, Al-Mogren MM, Yazidi O, Jaïdane NE, Carvajal M, Senent ML. Theoretical Spectroscopic Study of Two Ketones of Atmospheric Interest: Methyl Glyoxal (CH 3COCHO) and Methyl Vinyl Ketone (CH 3COCH═CH 2). J Phys Chem A 2022; 126:7230-7241. [PMID: 36178377 PMCID: PMC9574920 DOI: 10.1021/acs.jpca.2c05653] [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: 11/28/2022]
Abstract
Two ketones of atmospheric interest, methyl glyoxal and methyl vinyl ketone, are studied using explicitly correlated coupled cluster theory and core-valence correlation-consistent basis sets. The work focuses on the far-infrared region. At the employed level of theory, the rotational constants can be determined to within a few megahertz of the experimental data. Both molecules present two conformers, trans/cis and antiperiplanar (Ap)/synperiplanar (Sp), respectively. trans-Methyl glyoxal and Ap-methyl vinyl ketone are the preferred structures. cis-Methyl glyoxal is a secondary minimum of very low stability, which justifies the unavailability of experimental data in this form. In methyl vinyl ketone, the two conformers are almost isoenergetic, but the interconversion implies a relatively high torsional barrier of 1798 cm-1. A very low methyl torsional barrier was estimated for trans-methyl glyoxal (V3 = 273.6 cm-1). Barriers of 429.6 and 380.7 cm-1 were computed for Ap- and Sp-methyl vinyl ketone. Vibrational second-order perturbation theory was applied to determine the rovibrational parameters. The far-infrared region was explored using a variational procedure of reduced dimensionality. For trans-methyl glyoxal, the ground vibrational state was estimated to split by 0.067 cm-1, and the two low excited energy levels (1 0) and (0 1) were found to lie at 89.588 cm-1/88.683 cm-1 (A2/E) and 124.636 cm-1/123.785 cm-1 (A2/E). For Ap- and Sp-methyl vinyl ketone, the ground vibrational state splittings were estimated to be 0.008 and 0.017 cm-1, respectively.
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Affiliation(s)
- Insaf Toumi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Samira Dalbouha
- Laboratoire de Spectroscopie, Modélisation Moléculaire, Matériaux, Nanomatériaux, Eau et Environnement, LS3MN2E/CERNE2D, Faculté des Sciences Rabat, Université Mohammed V de Rabat, BP 1014 Rabat, Morocco.,Laboratoire de Chimie Organique et de Chimie Physique, Equipe de recherche: Modélisation Moléculaire, Matériaux et Environnement, Département de chimie, Faculté des Sciences d'Agadir, Université Ibn Zohr d'Agadir, BP 8106 Agadir, Morocco
| | - Muneerah Mogren Al-Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Ounaies Yazidi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia.,Institut Préparatoire aux Etudes d'Ingénieurs el Manar, Université de Tunis El Manar, BP 244, 2092 Tunis, Tunisia
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Miguel Carvajal
- Departamento de Ciencias Integradas, Centro de Estudios Avanzados en Física, Matemática y Computación, Unidad Asociada GIFMAN, CSIC-UHU, Universidad de Huelva, 21071 Huelva, Spain.,Instituto Universitario Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071 Granada, Spain
| | - María Luisa Senent
- Departamento de Química y Física Teóricas, Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.,Unidad Asociada GIFMAN, CSIC-UHU, Universidad de Huelva, 21071 Huelva, Spain
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Park SM, Choi J, Kim HL, Kwon CH. Conformer-specific VUV-MATI spectroscopy of methyl vinyl ketone: stabilities and cationic structures of the s- trans and s- cis conformers. Phys Chem Chem Phys 2020; 22:28383-28392. [PMID: 33300923 DOI: 10.1039/d0cp05782g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methyl vinyl ketone (MVK), a volatile compound with photochemical activity, has received considerable attention in the fields of environmental chemistry and atmospheric chemistry. We explored the conformational stabilities of MVK in the neutral S0 and the cationic D0 states using conformer-specific vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy, which provided identifiable vibrational spectra for cationic MVK conformers. Based on the origin bands of the two individual conformers of MVK identified in the MATI spectra under different supersonic expansion conditions, the accurate adiabatic ionization energies of the s-trans and the s-cis conformers were determined to be 77 867 ± 4 (9.6543 ± 0.0005 eV) and 78 222 ± 4 cm-1 (9.6983 ± 0.0005 eV), respectively. The identifiable vibrational spectra of the two cationic conformers were further confirmed using vibrational assignments based on the Franck-Condon fit. Accordingly, precise cationic structures of the MVK conformers could be determined. The structural changes of the two conformers upon ionization could be attributed to the removal of an electron from the highest occupied molecular orbital of each conformer, which consists of nonbonding molecular orbitals on the oxygen atom in the carbonyl group interacting with the σ orbitals in the molecular plane. Consequently, the s-trans conformer was preferred by 48 ± 18 and 403 ± 18 cm-1 in the neutral ground S0 and the cationic D0 states, respectively, which was supported by density-corrected density functional theory calculations and natural bond orbital analysis.
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Affiliation(s)
- Sung Man Park
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Korea.
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Passos MO, Lins IA, Alves TV. Rate coefficients and product branching ratios for (E)-2-butenal + H reactions. Phys Chem Chem Phys 2020; 22:14246-14254. [PMID: 32555895 DOI: 10.1039/d0cp02142c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for the hydrogen abstraction reactions of (E)-2-butenal by hydrogen atoms were calculated, for the first time, using the multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). After a torsional potential energy surface exploration, ten conformations of the transition states (including the mirror images) were found and separated into four conformational reaction channels (CRCs). Individual energy paths of each CRC were built, recrossing and quantum tunneling effects estimated, and the thermal rate constants obtained. Due to the hindered rotors, the torsional anharmonicity was incorporated in the rate coefficient through the calculations of the rovibrational partition functions using the extended two-dimensional torsional method (E2DT). For comparison, the one-well (1W-CVT/SCT) and harmonic multipath (MP-CVT/SCT) thermal rate constants were also estimated. In addition, kinetic Monte Carlo (KMC) simulations were performed to predict the product branching ratios. For all kinetic approaches, the formation of products of (R1) is predominant. Compared to the harmonic multipath estimation, the percentage of reaction (R4) increases by approximately 9% when the torsional anharmonicity is taken into account. For the reactions (R2) and (R3), the product branching ratio is slightly decreased when compared with the harmonic simulation.
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Affiliation(s)
- Maiara Oliveira Passos
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Igor Araujo Lins
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
| | - Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química - Universidade Federal da Bahia, Rua Barão de Jeremoabo, 147, Salvador, Bahia, 40170-115, Brazil.
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Gu Z, Wang Y, Ren Y, Zhang B. Unraveling electronic states and relaxation dynamics in ultraviolet excited crotonaldehyde via femtosecond time-resolved photoelectron imaging. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bokareva O, Bataev V, Godunov I. Structures and conformational dynamics of trans- and cis-crotonaldehydes in excited electronic states: A quantum-chemical study. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Park SM, Kim HL, Kwon CH. Identification and composition of conformational isomers and their cations in crotonaldehyde by VUV-MATI spectroscopy. Phys Chem Chem Phys 2018; 20:27162-27168. [DOI: 10.1039/c8cp05577g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Composition of the crotonaldehyde sample at ambient temperature was determined as 93.0%, 3.4%, 3.4%, and 0.2% for the tt-/tc-/ct-/cc-conformers, respectively, for the first time.
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Affiliation(s)
- Sung Man Park
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University
- Chuncheon 24341
- Korea
| | - Hong Lae Kim
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University
- Chuncheon 24341
- Korea
| | - Chan Ho Kwon
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University
- Chuncheon 24341
- Korea
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Zakharenko O, Motiyenko RA, Aviles Moreno JR, Huet TR. Conformational Landscape and Torsion–Rotation–Vibration Effects in the Two Conformers of Methyl Vinyl Ketone, a Major Oxidation Product of Isoprene. J Phys Chem A 2017; 121:6420-6428. [DOI: 10.1021/acs.jpca.7b06360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olena Zakharenko
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Roman A. Motiyenko
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Juan Ramon Aviles Moreno
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Thérèse R. Huet
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers Atomes et Molécules, F-59000 Lille, France
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Calow ADJ, Carbó JJ, Cid J, Fernández E, Whiting A. Understanding α,β-Unsaturated Imine Formation from Amine Additions to α,β-Unsaturated Aldehydes and Ketones: An Analytical and Theoretical Investigation. J Org Chem 2014; 79:5163-72. [DOI: 10.1021/jo5007366] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam D. J. Calow
- Centre
for Sustainable Chemical Processes, Department of Chemistry, Science
Laboratories, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jorge J. Carbó
- Departament
Química Física I Inorgànica, University Rovira I Virgili, C/Marcel.lí Domingo s/n, 43007 Tarragona, Spain
| | - Jessica Cid
- Departament
Química Física I Inorgànica, University Rovira I Virgili, C/Marcel.lí Domingo s/n, 43007 Tarragona, Spain
| | - Elena Fernández
- Departament
Química Física I Inorgànica, University Rovira I Virgili, C/Marcel.lí Domingo s/n, 43007 Tarragona, Spain
| | - Andrew Whiting
- Centre
for Sustainable Chemical Processes, Department of Chemistry, Science
Laboratories, Durham University, South Road, Durham DH1 3LE, U.K
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Chang SW, Witek HA. Choice of Optimal Shift Parameter for the Intruder State Removal Techniques in Multireference Perturbation Theory. J Chem Theory Comput 2012; 8:4053-61. [DOI: 10.1021/ct2006924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shu-Wei Chang
- Department of Applied Chemistry and Institute of Molecular
Science, National Chiao Tung University, Hsinchu, Taiwan
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular
Science, National Chiao Tung University, Hsinchu, Taiwan
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Krenske EH, Petter RC, Zhu Z, Houk KN. Transition States and Energetics of Nucleophilic Additions of Thiols to Substituted α,β-Unsaturated Ketones: Substituent Effects Involve Enone Stabilization, Product Branching, and Solvation. J Org Chem 2011; 76:5074-81. [DOI: 10.1021/jo200761w] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Elizabeth H. Krenske
- School of Chemistry, University of Melbourne, and Australian Research Council Centre of Excellence for Free Radical Chemistry and Biotechnology, VIC 3010, Australia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Russell C. Petter
- Avila Therapeutics, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Zhendong Zhu
- Avila Therapeutics, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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Sitzmann M, Ihlenfeldt WD, Nicklaus MC. Tautomerism in large databases. J Comput Aided Mol Des 2010; 24:521-51. [PMID: 20512400 PMCID: PMC2886898 DOI: 10.1007/s10822-010-9346-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 03/17/2010] [Indexed: 11/29/2022]
Abstract
We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS's tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection.
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Affiliation(s)
- Markus Sitzmann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles St., Frederick, MD 21702, USA
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