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Chan B, Dawson W, Nakajima T. Sorting drug conformers in enzyme active sites: the XTB way. Phys Chem Chem Phys 2024; 26:12610-12618. [PMID: 38597505 DOI: 10.1039/d4cp00930d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan.
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - William Dawson
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
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Mészáros D, Matejčík Š, Papp P. Formation of negative ions from cobalt tricarbonyl nitrosyl Co(CO) 3NO clusters. Phys Chem Chem Phys 2024; 26:7522-7533. [PMID: 38357994 DOI: 10.1039/d3cp05601e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Electron attachment and corresponding dissociative electron attachment (DEA) to cobalt tricarbonyl nitrosyl (Co(CO)3NO) clusters have been studied by co-expansion with Ar gas into a high vacuum. A monochromatic electron beam was utilized to generate negative ions and the resulting reaction products were identified using mass spectrometry. The ion fragments corresponding to Co(CO)3NO monomers closely resemble results from earlier gas phase experiments and studies conducted on Co(CO)3NO in He nanodroplets. However, contrary to the gas phase or He nanodroplet ion yields, a resonance structure comprising several peaks at energies above ∼4 eV was observed both in the case of molecular clusters [Co(CO)3NO]n- (with n = 1, 2, 3) and clusters comprising DEA fragments. Additionally, the ion yields of numerous other clusters such as ions without nitrosyl ([Co(CO)4]-, [Co2(CO)5]-), clusters consisting of two fragments such as ([Co2(CO)NO]-, [Co2(CO)(NO)2]-, [Co2(CO)2NO]-, [Co2(CO)2(NO)2]-, [Co3(CO)(NO)3]-, [Co3(CO)8(NO)3]-, [Co3(CO)(NO)2]-, [Co3(CO)3(NO)2]-, and [Co3(CO)5(NO)2]-) were recorded. Moreover, NO bond dissociation was confirmed with the [Co(CO)2N]-ion and with N- or O-retaining cluster ions, such as [Co2(CO)(NO)N]-, [Co2(CO)2(NO)N]-, [Co3(CO)2(NO)N]-, [Co3(CO)3(NO)N]- and [Co3(CO)(NO)2N]-, or [Co2(CO)2O]-, [Co2(CO)3O]-, [Co3(CO)3O]-, [Co3(CO)4O]-and [Co3(CO)2(NO)O]- respectively.
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Affiliation(s)
- Dušan Mészáros
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
| | - Štefan Matejčík
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
| | - Peter Papp
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
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Chan B. DAPD Set of Pd-Containing Diatomic Molecules: Accurate Molecular Properties and the Great Lengths to Obtain Them. J Chem Theory Comput 2023; 19:9260-9268. [PMID: 38096563 DOI: 10.1021/acs.jctc.3c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
In the present study, we obtained reliable bond energy, bond length, and zero-point vibrational frequency for a set of diatomic Pd species (the DAPD set). It includes PdH, Pd2, and PdX (X = B, C, N, O, F, Al, Si, P, S, and Cl). Our highest-level protocol (W4X-L) represents scalar and spin-orbit relativistic, valence- and inner-valence correlated, extrapolated CCSDTQ(5) energy. The DAPD set of molecules is challenging for computational chemistry methods in different manners; for Pd2, the spin-orbit contribution to the bond energy is fairly large, whereas for PdC and PdSi, the post-CCSD(T) correlation components are considerable. The diverse range of requirements represents a significant challenge for lower-level methods. While density functional theory (DFT) methods generally yield good agreements for bond lengths and vibrational frequencies, large deviations are found for bond energies. In general, hybrid DFT methods are more accurate than nonhybrid functionals, but the agreement in individual cases varies. This illustrates the critical role that new high-quality reference data would play in the continual development of lower-cost methods.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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Akhmetshina ES, Khursan SL. Theoretical determination of the standard enthalpies of formation of alkyl radicals using the concept of a complete set of homodesmotic reactions. J Mol Graph Model 2023; 125:108615. [PMID: 37647723 DOI: 10.1016/j.jmgm.2023.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
The complete sets of homodesmotic reactions (HDR) for 107 acyclic alkyl free radicals С4-С9 of normal and branched structure were constructed using the graph-theoretic representation and analysis of a tested compound. The absolute enthalpies of the studied compounds and HDR reference structures were calculated using the M062X/cc-pVTZ level of theory. Based on these data, the thermal effects of HDRs were calculated and then applied to determine the standard enthalpies of formation of the studied radicals using the known enthalpies of formation of reference structures. The dissociation energies of BDE C-H and C-CH3 bonds were also calculated. The effect of radical structure on the BDE value is discussed, and a new effect of stabilization of the radical center in the skewed conformation of free radical is established; this effect has not been previously described in the scientific literature.
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Affiliation(s)
- Ekaterina S Akhmetshina
- Institution of Russian Academy of Sciences Institute of Organic Chemistry, Ufa Scientific Centre of the RAS, 71 Prospect Oktyabrya, 450054, Ufa, Russian Federation
| | - Sergey L Khursan
- Institution of Russian Academy of Sciences Institute of Organic Chemistry, Ufa Scientific Centre of the RAS, 71 Prospect Oktyabrya, 450054, Ufa, Russian Federation.
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Mukeba CT, Isamura BK, Mudogo V, Katshiatshia HM, Muya JT. Bond dissociation energies of ethyl valerate and tripropionin. J Mol Model 2023; 29:261. [PMID: 37482544 DOI: 10.1007/s00894-023-05666-6] [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: 05/12/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
CONTEXT Due to the expected decrease in the availability of conventional oils, numerous studies are currently underway to find complementary sources of energy. Among the explored avenue is that of biofuels. Ethyl valerate (ETV) and tripropionin (TPP) are two biofuels whose thermal decomposition has not received the attention it deserves. Herein, we have evaluated the bond dissociation enthalpies (BDHs) to predict how easy it is to break some bonds in these compounds, and subsequently contribute to revealing the initiation step in their combustion reactions. Our computations consistently predict C4-C5 and C1-C2 bonds in ETV and TPP as the weakest bonds, likely to break first and initiate the thermal decomposition of these two compounds, respectively. The conformational changes in ETV and TPP have only a small influence on the BDHs of 1 kcal/mol at M06-2X/6-311 + G(3df,2p). B3LYP and ωB97XD appear to be the most affordable methods for estimating BDHs at 6-31G(d,p) as they give good results for ETV (RMSD: 2.94 kcal/mol and 3.22 kcal/mol) and performed better than CBS-QB3 (RMSD: 3.64 kcal/mol). Using a larger basis set, the M06-2X (RMSD: 3.61 kcal/mol) and ωB97XD (RMSD: 3.51 kcal/mol) functionals are found to provide the most accurate predictions at 6-311 + G(3df,2p) as compared to G4MP2. METHODS BDHs of ETV and TPP are computed using density functional theory (DFT) and quantum chemistry composite methods at 6-31G(d,p) and 6-311 + G(3df,2p) levels. Because of its reliability and accuracy in thermochemical calculations, the G4MP2 theory is used as a reference to gauge the performance of DFT methods. All the calculations were carried out using the Gaussian 09 program.
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Affiliation(s)
- Christian Tshikala Mukeba
- Department of Chemistry, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Bienfait Kabuyaya Isamura
- Department of Chemistry, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Department of Chemistry, University of Manchester, M13 9PL, Manchester, Great Britain
| | - Virima Mudogo
- Department of Chemistry, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Research Center for Applied Sciences and Technologies, Kinshasa, B.P. 8401, Democratic Republic of the Congo
| | - Haddy Mbuyi Katshiatshia
- Research Center for Renewable Energy, Polytechnics Faculty, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.
| | - Jules Tshishimbi Muya
- Department of Chemistry, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.
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Kříž K, Schmidt L, Andersson AT, Walz MM, van der Spoel D. An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J Chem Inf Model 2023; 63:412-431. [PMID: 36630710 PMCID: PMC9875315 DOI: 10.1021/acs.jcim.2c01127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 01/12/2023]
Abstract
Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.
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Affiliation(s)
- Kristian Kříž
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Lisa Schmidt
- Faculty
of Biosciences, University of Heidelberg, Heidelberg69117, Germany
| | - Alfred T. Andersson
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Marie-Madeleine Walz
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - David van der Spoel
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
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