51
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Di Grande S, Kállay M, Barone V. Accurate thermochemistry at affordable cost by means of an improved version of the JunChS-F12 model chemistry. J Comput Chem 2023; 44:2149-2157. [PMID: 37432050 DOI: 10.1002/jcc.27187] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
The junChS-F12 composite method has been improved by means of the latest implementation of the CCSD(F12*)(T+) ansatz and validated for the thermochemistry of molecules containing atoms of the first three rows of the periodic table. A thorough benchmark showed that this model, in conjunction with cost-effective revDSD-PBEP86-D3(BJ) reference geometries, offers an optimal compromise between accuracy and computational cost. If improved geometries are sought, the most effective option is to add MP2-F12 core-valence correlation corrections to CCSD(T)-F12b/jun-cc-pVTZ geometries without the need of performing any extrapolation to the complete basis set limit. In the same vein, CCSD(T)-F12b/jun-cc-pVTZ harmonic frequencies are remarkably accurate without any additional contribution. Pilot applications to noncovalent intermolecular interactions, conformational landscapes, and tautomeric equilibria confirm the effectiveness and reliability of the model.
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Affiliation(s)
- S Di Grande
- Classe di Scienze, Scuola Normale Superiore di Pisa, Pisa, Italy
- Scuola Superiore Meridionale, Napoli, Italy
| | - M Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Budapest, Hungary
| | - V Barone
- Classe di Scienze, Scuola Normale Superiore di Pisa, Pisa, Italy
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52
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Chun Y, Remmerswaal WA, Codée JDC, Woerpel KA. Neighboring-Group Participation by C-2 Acyloxy Groups: Influence of the Nucleophile and Acyl Group on the Stereochemical Outcome of Acetal Substitution Reactions. Chemistry 2023; 29:e202301894. [PMID: 37410662 PMCID: PMC10592418 DOI: 10.1002/chem.202301894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
A single acyloxy group at C-2 can control the outcome of nucleophilic substitution reactions of pyran-derived acetals, but the extent of the neighboring-group participation depends on a number of factors. We show here that neighboring-group participation does not necessarily control the stereochemical outcome of acetal substitution reactions with weak nucleophiles. The 1,2-trans selectivity increased with increasing reactivity of the incoming nucleophile. This trend suggests the intermediacy of both cis-fused dioxolenium ions and oxocarbenium ions in the stereochemistry-determining step. In addition, as the electron-donating ability of the neighboring group decreased, the preference for the 1,2-trans products increased. Computational studies show how the barriers for the ring-opening reaction on the dioxolenium ions and the transition states to provide the oxocarbenium ions change with the electron-donating capacity of the C-2-acyloxy group and the reactivity of the nucleophile.
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Affiliation(s)
- Yuge Chun
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - K A Woerpel
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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53
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Lorpaiboon W, Ho J. High-Level Quantum Chemical Prediction of C-F Bond Dissociation Energies of Perfluoroalkyl Substances. J Phys Chem A 2023; 127:7943-7953. [PMID: 37722129 DOI: 10.1021/acs.jpca.3c04750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
In this study, 550 C-F bond dissociation energies (BDEs) of a variety of per- and polyfluoroalkyl substances (PFASs) obtained from high-level DLPNO-CCSD(T)/CBS calculations were used to assess the accuracy of contemporary density functional theory (DFT) and semiempirical methods. DLPNO-CCSD(T)/CBS gas phase C-F BDEs fall between 404.9-550.7 kJ mol-1 and M06-2X and ωB97M-V in conjunction with the aug-cc-pVTZ basis set predicted BDEs closest to the benchmark level with a mean absolute deviation (MAD) of 7.3 and 8.3 kJ mol-1, respectively. It was observed that DFT prediction errors increase with the degree of fluorination and system size. As such, previous model chemistry recommendations based on smaller nonfluorinated systems may not be carried over to modeling the energetics of PFASs and related systems.
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Affiliation(s)
- Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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54
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Daas KJ, Kooi DP, Peters NC, Fabiano E, Della Sala F, Gori-Giorgi P, Vuckovic S. Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost. J Phys Chem Lett 2023; 14:8448-8459. [PMID: 37721318 DOI: 10.1021/acs.jpclett.3c01832] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.
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Affiliation(s)
- Kimberly J Daas
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Derk P Kooi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Nina C Peters
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Eduardo Fabiano
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Fabio Della Sala
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Paola Gori-Giorgi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Stefan Vuckovic
- Department of Chemistry, Faculty of Science and Medicine, Université de Fribourg/Universität Freiburg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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55
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Puzzarini C, Alessandrini S, Bizzocchi L, Melosso M. Hunting for interstellar molecules: rotational spectra of reactive species. Faraday Discuss 2023; 245:309-326. [PMID: 37318358 DOI: 10.1039/d3fd00052d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Interstellar molecules are often highly reactive species, which are unstable under terrestrial conditions, such as radicals, ions and unsaturated carbon chains. Their detection in space is usually based on the astronomical observation of their rotational fingerprints. However, laboratory investigations have to face the issue of efficiently producing these molecules and preserving them during rotational spectroscopy measurements. A general approach for producing and investigating unstable/reactive species is presented by means of selected case-study molecules. The overall strategy starts from quantum-chemical calculations that aim at obtaining accurate predictions of the missing spectroscopic information required to guide spectral analysis and assignment. Rotational spectra of these species are then recorded by exploiting the approach mentioned above, and their subsequent analysis leads to accurate spectroscopic parameters. These are then used for setting up accurate line catalogs for astronomical searches.
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Affiliation(s)
- Cristina Puzzarini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Silvia Alessandrini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Luca Bizzocchi
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Mattia Melosso
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
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56
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Manna S, Paul S, Kong WY, Aich D, Sahoo R, Tantillo DJ, Panda S. Stereodivergent Zweifel Olefination and its Mechanistic Dichotomy. Angew Chem Int Ed Engl 2023; 62:e202309136. [PMID: 37495925 DOI: 10.1002/anie.202309136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/28/2023]
Abstract
Stereoselective Zweifel olefination using boronate complexes carrying two different reactive π-systems was achieved to synthesize vinyl heteroarenes and conjugated 1,3-dienes in good yield and up to 100 % stereoselectivity, which remains unexplored until now. Most importantly, we report the unprecedented formation of E vs. Z-vinyl heteroarenes for different heteroarenes under identical conditions. Density functional theory (DFT) investigations unveil the mechanistic dichotomy between olefin and heteroarene activation followed by 1,2-migration, leading to E or Z-vinyl heteroarenes respectively. We also report a previously unknown reversal of stereoselectivity by using 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electrophile. The Zweifel olefination using a boronate complex that carries two different olefins was previously unexplored due to significant challenges associated with the site-selective activation of olefins. We have solved this problem and reported the site-selective activation of olefins for the stereoselective synthesis of 1,3-dienes.
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Affiliation(s)
- Samir Manna
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Swagata Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Debasis Aich
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Rupam Sahoo
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Santanu Panda
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
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57
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Barone V, Uribe Grajales LM, Di Grande S, Lazzari F, Mendolicchio M. DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline. J Phys Chem A 2023; 127:7534-7543. [PMID: 37665117 PMCID: PMC10510395 DOI: 10.1021/acs.jpca.3c04227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Indexed: 09/05/2023]
Abstract
A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lina Marcela Uribe Grajales
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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58
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Cusumano AQ, Zhang T, Goddard WA, Stoltz BM. Origins of Enhanced Enantioselectivity in the Pd-Catalyzed Decarboxylative Allylic Alkylation of N-Benzoyl Lactams. Catalysts 2023; 13:1258. [PMID: 37990660 PMCID: PMC10662798 DOI: 10.3390/catal13091258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
We explore the origins of the marked improvement in enantioselectivity in the inner-sphere (PHOX)Pd-catalyzed allylic alkylation of N-benzoyl lactam nucleophiles over their carbocyclic counterparts. We employ density functional theory calculations to aid in the interpretation of experimental results. Ultimately, we propose that the enhancement in enantioselectivity arises primarily from noncovalent interactions between the substrate and ligand rather than secondary substrate chelation, as previously hypothesized.
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Affiliation(s)
- Alexander Q. Cusumano
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tianyi Zhang
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William A. Goddard
- Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brian M. Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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59
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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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60
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Barone V, Di Grande S, Lazzari F, Mendolicchio M. Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12). J Phys Chem A 2023; 127:6771-6778. [PMID: 37535450 PMCID: PMC10440789 DOI: 10.1021/acs.jpca.3c03999] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Indexed: 08/05/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, Napoli 80138, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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61
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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62
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Vysotskiy VP, Torbjörnsson M, Jiang H, Larsson ED, Cao L, Ryde U, Zhai H, Lee S, Chan GKL. Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods. J Chem Phys 2023; 159:044106. [PMID: 37486046 DOI: 10.1063/5.0152611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (∆E) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ∆E estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree-Fock included (0%-54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ∆E is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn-Sham orbitals gives results within 4-11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ∼5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.
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Affiliation(s)
- Victor P Vysotskiy
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Magne Torbjörnsson
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Ernst D Larsson
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Lili Cao
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, SE-221 00 Lund, Sweden
| | - Huanchen Zhai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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63
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Wang M, He X, Taylor M, Lorpaiboon W, Mun H, Ho J. Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets. J Chem Theory Comput 2023. [PMID: 37463146 DOI: 10.1021/acs.jctc.3c00388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol-1, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes. Our analysis indicates that for many organic molecules and their transition states, high-level revDSD-PBEP86-D4 and DLPNO-CCSD(T)/(aug-)cc-pVTZ single-point energies usually vary by less than 2 kJ mol-1 on density functional theory geometries optimized using basis sets ranging from 6-31+G(d) to aug-pcseg-2 and aug-cc-pVTZ. In cases where these single-point energies vary significantly, indicating sensitivity of molecular geometries to the choice of basis set, there is often substantial cancellation of errors when the reaction energy or barrier is calculated. The study concludes that the choice of basis set for molecular geometry and frequencies, particularly those considered in this study, is not critical for the accuracy of thermochemistry calculations in the gas or solution phase.
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Affiliation(s)
- Minzhi Wang
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Xinlan He
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Haedam Mun
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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64
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Unimuke TO, Louis H, Ikenyirimba OJ, Mathias GE, Adeyinka AS, Nasr CB. High throughput computations of the effective removal of liquified gases by novel perchlorate hybrid material. Sci Rep 2023; 13:10837. [PMID: 37407702 PMCID: PMC10322887 DOI: 10.1038/s41598-023-38091-z] [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: 09/19/2022] [Accepted: 07/03/2023] [Indexed: 07/07/2023] Open
Abstract
The utilization of hybrid materials in separation technology, sorbents, direct air capture (DAC) technology, sensors, adsorbents, and chiral material recognition has increased in the past decade due to the recognized impact of atmospheric pollutants and hazardous industrial gases on climate change. A novel hybrid material, perchlorate hybrid (PClH), has been proposed in this study for the effective sensory detection and trapping of atmospheric pollutants and industrial hazardous gases. The study evaluated the structural properties, adsorption mechanism, electronic sensitivity, and topological analysis of PClH using highly accurate computational methods (M062X-D3BJ/def2-ccpVTZ and DSDPBEP86/def2-ccpVTZ). The computational analysis demonstrated that PClH has considerable adsorption energies and favorable interaction with CO2, NO2, SO2, COCl2, and H2S. PClH is more suitable for detecting liquefiable gases such as COCl2, CO2, and SO2, and can be easily recovered under ambient conditions. Developing such materials can contribute to reducing hazardous gases and pollutants in the atmosphere, leading to a cleaner and safer environment.
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Affiliation(s)
- Tomsmith O Unimuke
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria.
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria.
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria.
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria.
| | - Onyinye J Ikenyirimba
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria
| | - Gideon E Mathias
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria
| | - Adedapo S Adeyinka
- Department of Chemical Sciences, Research Centre for Synthesis and Catalysis, University of Johannesburg, Johannesburg, 2006, South Africa
| | - Chérif Ben Nasr
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna, Tunisie
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65
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Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
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Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
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66
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Wang B, Rong C, Lei M, Liu S, De Proft F. Mechanistic Study and Conceptual Chemical Reactivity Analysis of Hydroboration of Carbon Dioxide Catalyzed by a Manganese(I)-PNP-Pincer Complex. Inorg Chem 2023; 62:7366-7375. [PMID: 37129648 DOI: 10.1021/acs.inorgchem.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Designing efficient and selective catalysts for carbon dioxide reduction is an intensive research area in the recent literature on homogeneous catalysis. In this work, we study the catalytic activity of a newly reported Mn(I)-PNP-pincer catalyst with an embedded aromatic ring. First, we systematically examine its capability to yield different products and highlight the importance of ligand aromaticity and steric effects on metal-ligand cooperativity. We then further conceptually probe its reactivity with descriptors from both conceptual density functional theory and an information-theoretic approach, thereby proposing a novel partitioning of the reaction coordinate into three relevant regions. Our results show that the reactivity in these different regions is governed by different properties such as steric effects, electrophilicity/nucleophilicity, or aromaticity. We anticipate that this methodology, with the analytical tools employed in this study, can be generalized and extended to other catalytic systems and find applications in designing better catalysts.
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Affiliation(s)
- Bin Wang
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, Hunan, P. R. China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, Hunan, P. R. China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
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67
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Li X, Yang SL, He HK, Zhang QR, Zhang N, Wang SJ. Aromatic diglycosides from Sophora tonkinensis and a multi-step conformer filtering procedure for TDDFT calculation of flexible glycoside. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:411-421. [PMID: 35880466 DOI: 10.1080/10286020.2022.2100359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Three previously undescribed aromatic diglycosides (1, 5, and 8) and six known analogs (2-4, 6, 7, and 9) were isolated from the roots and rhizomes of Sophora tonkinensis Gagnep. Their structures were elucidated by detailed spectroscopic analysis. The absolute configuration of compound 8 was determined by comparing the experimental and TDDFT calculated ECD spectra of 8 and aglycone 8a. Furthermore, a multistep conformer filtering procedure for TDDFT calculation of flexible glycoside was proposed, which afforded high accuracy with acceptable computing cost in determining the absolute configuration of glycosides using quantum calculated ECD.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Sheng-Li Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hao-Ke He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qian-Ru Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ning Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Su-Juan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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68
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Xu Y, Xu J, Chen X, Fan YL, Wu H. Structural confirmation of synthetic cannabinoids in seized electronic cigarette oil: A combined mass spectrometric and computational study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9485. [PMID: 36735629 DOI: 10.1002/rcm.9485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
RATIONALE Synthetic cannabinoids are some of the most used and abused new psychoactive substances, because they can produce a stronger intense pleasure than natural cannabis. Most of the new synthetic cannabinoids are structurally similar to existing synthetic cannabinoids and can be obtained by modifying partial structures of the latter without changing their effects. Therefore, the derivatization rules and common fragmentation patterns of synthetic cannabinoids could be used for rapid screening and structural identification of them. METHODS The derivatization rules of synthetic cannabinoids are summarized, and the common fragmentation pattern of synthetic cannabinoids including three typical cleavage pathways was explored and extended in this work based on combined mass spectrometry (MS) and density functional theory studies. Five synthetic cannabinoids in electronic cigarette oil from a drug case were separated and characterized using gas chromatography with MS and liquid chromatography coupled to high-resolution quadrupole Orbitrap MS. RESULTS The structures of five synthetic cannabinoids in seized electronic cigarette oil were deduced from electron impact ion source (EI) MS and high-resolution electrospray ionization (ESI) MSn data, along with the derivatization rules and common fragmentation pattern of synthetic cannabinoids. The proposed structures of these synthetic cannabinoids were further verified via reference substances. Computational study showed that selective cleavage of these compounds was mainly controlled by spin population in EI-MS, but a tunneling effect arose from proton transfer in ESI-MSn detection, which has been rarely reported in previous works. CONCLUSIONS Our results showed that EI-MS was suitable for identifying synthetic cannabinoids with aromatic ketone structure, which could also be extended to adamantane linked group. Nevertheless, synthetic cannabinoids with carbamoyl linked group were better characterized by high-resolution ESI-MSn compared to EI-MS. This study demonstrated a method with promising potential for rapid and reliable screening of synthetic cannabinoids in mixtures with enhanced detection throughput and operation simplicity.
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Affiliation(s)
- Yu Xu
- Key Laboratory of Drug Monitoring and Control of Zhejiang Province, National Anti-Drug Laboratory Zhejiang Regional Center, Hangzhou, Zhejiang, China
| | - Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, China
- School of Chemical Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xianxin Chen
- Key Laboratory of Drug Monitoring and Control of Zhejiang Province, National Anti-Drug Laboratory Zhejiang Regional Center, Hangzhou, Zhejiang, China
| | - Yi Lei Fan
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Hao Wu
- Dian Regional Forensic Science Institute·Zhejiang, Hangzhou, Zhejiang, China
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69
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Becke AD, Santra G, Martin JML. A double-hybrid density functional based on good local physics with outstanding performance on the GMTKN55 database. J Chem Phys 2023; 158:2882268. [PMID: 37094004 DOI: 10.1063/5.0141238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023] Open
Abstract
In two recent papers [A. D. Becke, J. Chem. Phys. 156, 214101 (2022) and A. D. Becke, J. Chem. Phys. 157, 234102 (2022)], we compared two Kohn-Sham density functionals based on physical modeling and theory with the best density-functional power-series fits in the literature. The best error statistics reported to date for a hybrid functional on the general main-group thermochemistry, kinetics, and noncovalent interactions (GMTKN55) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)] were obtained. In the present work, additional second-order perturbation-theory terms are considered. The result is a 12-parameter double-hybrid density functional with the lowest GMTKN55 WTMAD2 "weighted total mean absolute deviation" error (1.76 kcal/mol) yet seen for any hybrid or double-hybrid density-functional approximation. We call it "DH23."
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Affiliation(s)
- Axel D Becke
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
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70
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Barone V, Fusè M. Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods. J Phys Chem A 2023; 127:3648-3657. [PMID: 37052318 PMCID: PMC10150396 DOI: 10.1021/acs.jpca.3c01174] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- DMMT-sede Europa, Università di Brescia, Viale Europa 11, 25121 Brescia, Italy
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71
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Alessandrini S, Melosso M, Rivilla VM, Bizzocchi L, Puzzarini C. Computational Protocol for the Identification of Candidates for Radioastronomical Detection and Its Application to the C3H3NO Family of Isomers. Molecules 2023; 28:molecules28073226. [PMID: 37049990 PMCID: PMC10096335 DOI: 10.3390/molecules28073226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
The C3H3NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C3H3NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol−1 above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol−1 higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps.
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Affiliation(s)
- Silvia Alessandrini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir km. 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Luca Bizzocchi
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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72
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Li Y, Fan WX, Luo S, Trofimova A, Liu Y, Xue JH, Yang L, Li Q, Wang H, Yudin AK. β-Boron Effect Enables Regioselective and Stereospecific Electrophilic Addition to Alkenes. J Am Chem Soc 2023; 145:7548-7558. [PMID: 36947220 DOI: 10.1021/jacs.3c00860] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Electrophilic addition to alkenes is a textbook-taught reaction, yet it is not always possible to control the regioselectivity of addition to unsymmetrical 1,2-disubstituted substrates. We report the observation and applications of the β-boron effect that accounts for high regioselectivity in electrophilic addition reactions to allylic MIDA (N-methyliminodiacetic acid) boronates. While the well-established β-silicon effect bears partial resemblance to the observed reactivity, the silyl group is typically lost during functionalization. In contrast, the boryl moiety is retained in the product when B(MIDA) is used as the nucleophilic stabilizer. Mechanistic studies elucidate the origin of this effect and demonstrate how σ(C-B) hyperconjugation helps stabilize the incipient carbocation. This transformation represents a rare example of the stereospecific hydrohalogenation of secondary allyl MIDA-boronates that proceeds in a syn-fashion.
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Affiliation(s)
- Yin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wen-Xin Fan
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shuang Luo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Alina Trofimova
- Davenport Research Laboratories, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6 Canada
| | - Yuan Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jiang-Hao Xue
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Ling Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qingjiang Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Honggen Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Andrei K Yudin
- Davenport Research Laboratories, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6 Canada
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73
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Spadetto E, Philipsen PHT, Förster A, Visscher L. Toward Pair Atomic Density Fitting for Correlation Energies with Benchmark Accuracy. J Chem Theory Comput 2023; 19:1499-1516. [PMID: 36787494 PMCID: PMC10018742 DOI: 10.1021/acs.jctc.2c01201] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Pair atomic density fitting (PADF) has been identified as a promising strategy to reduce the scaling with system size of quantum chemical methods for the calculation of the correlation energy like the direct random-phase approximation (RPA) or second-order Møller-Plesset perturbation theory (MP2). PADF can however introduce large errors in correlation energies as the two-electron interaction energy is not guaranteed to be bounded from below. This issue can be partially alleviated by using very large fit sets, but this comes at the price of reduced efficiency and having to deal with near-linear dependencies in the fit set. One posibility is to use global density fitting (DF), but in this work, we introduce an alternative methodology to overcome this problem that preserves the intrinsically favorable scaling of PADF. We first regularize the Fock matrix by projecting out parts of the basis set which gives rise to orbital products that are hard to describe by PADF. After having thus obtained a reliable self-consistent field solution, we then also apply this projector to the orbital coefficient matrix to improve the precision of PADF-MP2 and PADF-RPA. We systematically assess the accuracy of this new approach in a numerical atomic orbital framework using Slater type orbitals (STO) and correlation consistent Gaussian type basis sets up to quintuple-ζ quality for systems with more than 200 atoms. For the small and medium systems in the S66 database we show the maximum deviation of PADF-MP2 and PADF-RPA relative correlation energies to DF-MP2 and DF-RPA reference results to be 0.07 and 0.14 kcal/mol, respectively. When the new projector method is used, the errors only slightly increase for large molecules and also when moderately sized fit sets are used the resulting errors are well under control. Finally, we demonstrate the computational efficiency of our algorithm by calculating the interaction energies of large, non-covalently bound complexes with more than 1000 atoms and 20000 atomic orbitals at the RPA@PBE/CC-pVTZ level of theory.
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Affiliation(s)
- Edoardo Spadetto
- Software for Chemistry and Materials NV, NL-1081HV Amsterdam, The Netherlands
| | | | - Arno Förster
- Software for Chemistry and Materials NV, NL-1081HV Amsterdam, The Netherlands.,Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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74
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Kee CW. Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities. Molecules 2023; 28:molecules28041715. [PMID: 36838703 PMCID: PMC9966076 DOI: 10.3390/molecules28041715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/25/2023] Open
Abstract
Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.
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Affiliation(s)
- Choon Wee Kee
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
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75
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Barone V, Fusè M, Aguado R, Potenti S, León I, Alonso ER, Mata S, Lazzari F, Mancini G, Spada L, Gualandi A, Cozzi PG, Puzzarini C, Alonso JL. Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine. Chemistry 2023; 29:e202203990. [PMID: 36734519 DOI: 10.1002/chem.202203990] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.
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Affiliation(s)
- V Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - M Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - R Aguado
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Potenti
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - F Lazzari
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - G Mancini
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - L Spada
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - A Gualandi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - P G Cozzi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - C Puzzarini
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
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76
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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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77
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Sandoval-Salinas ME, Brémond E, Pérez-Jiménez AJ, Adamo C, Sancho-García JC. Excitation energies of polycylic aromatic hydrocarbons by double-hybrid functionals: Assessing the PBE0-DH and PBE-QIDH models and their range-separated versions. J Chem Phys 2023; 158:044105. [PMID: 36725511 DOI: 10.1063/5.0134946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A family of non-empirical double-hybrid (DH) density functionals, such as Perdew-Burke-Ernzerhof (PBE)0-DH, PBE-QIDH, and their range-separated exchange (RSX) versions RSX-0DH and RSX-QIDH, all using Perdew-Burke-Ernzerhof(PBE) exchange and correlationfunctionals, is applied here to calculate the excitation energies for increasingly longer linear and cyclic acenes as part of their intense benchmarking for excited states of all types. The energies for the two lowest-lying singlet 1La and 1Lb states of linear oligoacenes as well as the triplet 3La and 3Lb states, are calculated and compared with experimental results. These functionals clearly outperform the results obtained from hybrid functionals and favorably compare with other double-hybrid expressions also tested here, such as B2-PLYP, B2GP-PLYP, ωB2-PLYP, and ωB2GP-PLYP. The study is complemented by the computation of adiabatic S0-T1 singlet-triplet energy difference for linear acenes as well as the extension of the study to strained cyclic oligomers, showing how the family of non-empirical expressions robustly leads to competitive results.
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Affiliation(s)
- M E Sandoval-Salinas
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - E Brémond
- ITODYS, CNRS, Université Paris Cité, F-75006 Paris, France
| | - A J Pérez-Jiménez
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - C Adamo
- Chimie ParisTech, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), UMR8060, PSL Research University, F-75005 Paris, France
| | - J C Sancho-García
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
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78
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Kreienborg NM, Yang Q, Pollok CH, Bloino J, Merten C. Matrix-isolation and cryosolution-VCD spectra of α-pinene as benchmark for anharmonic vibrational spectra calculations. Phys Chem Chem Phys 2023; 25:3343-3353. [PMID: 36633064 DOI: 10.1039/d2cp04782a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The inclusion of anharmonicity in vibrational spectral analyis remains associated to small molecular systems with up to a dozen of atoms, with half a dozen of non-hydrogen atoms, typically thesize of propylene oxide. One may see two reasons for this: first of all, larger systems are often thought to be computationally too demanding (high computational costs) for a full anharmonic vibrational analysis. Second, the identification of resonances and their correction is often considered something only expert theoreticians could address because of the lack of unequivocal criteria. In this contribution, we illustrate that resonances can indeed become a complex problem, which can be handled almost transparently thanks to recent advances in vibrational perturbation theory (VPT2). The study also emphasizes the importance and the central role played by experiment in benchmarking novel theoretical approaches. In fact, we herein provide the currently highest resolution VCD spectra available for α- and β-pinene obtained under matrix-isolation conditions and in liquid Xenon as solvent. They are interpreted by VPT2 with novel tests for the identification of resonances. Hence, the study demonstrates the mutual stimulation of advances in both experimental techniques and computational models.
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Affiliation(s)
- Nora M Kreienborg
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Qin Yang
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Corina H Pollok
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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79
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Wilming FM, Marazzi B, Debes PP, Becker J, Schreiner PR. Probing the Size Limit of Dispersion Energy Donors with a Bifluorenylidene Balance: Magic Cyclohexyl. J Org Chem 2023; 88:1024-1035. [PMID: 36576961 DOI: 10.1021/acs.joc.2c02444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report the synthesis of 14 2,2'-disubstituted 9,9'-bifluorenylidenes as molecular balances for the quantification of London dispersion interactions between various dispersion energy donors. For all balances, we measured ΔGZ/E at 333 K using 1H NMR in seven organic solvents. For various alkyl and aryl substituents, we generally observe a preference for the "folded" Z-isomer due to attractive London dispersion interactions. The cyclohexyl-substituted system shows the largest Z-preference in this study with ΔGZ/E = -0.6 ± 0.05 kcal mol-1 in all solvents, owing to the rotational freedom of cyclohexyl groups paired with their large polarizability that maximizes London dispersion interactions. On the other hand, rigid and sterically more demanding substituents like tert-butyl unexpectedly favor the unfolded E-isomer. This is a result of the close relative position in which the functional groups are positioned in this molecular balance. This close proximity is the reason for the increase of Pauli repulsion in the Z-isomers with large rigid substituents (tert-butyl, adamantyl, and diamantyl) which leads to an equilibrium shift toward the unfolded E-form. While we were able to reproduce most of our experimental trends qualitatively using contemporary computational chemistry methods, quantitative accuracy of the employed methods still needs further improvement.
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Affiliation(s)
- Finn M Wilming
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Benito Marazzi
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Paul P Debes
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
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80
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de Oliveira MT, Alves JMA, Vrech NL, Braga AAC, Barboza CA. A comprehensive benchmark investigation of quantum chemical methods for carbocations. Phys Chem Chem Phys 2023; 25:1903-1922. [PMID: 36541431 DOI: 10.1039/d2cp04603b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The application of various density functional approximations (DFAs) and an emphasis on popular methods without any consensus have prevailed in computational studies dedicated to carbocations. More importantly, an extensive and rigorous benchmark investigation on density functionals for the class is still lacking. To close this gap, we present a comprehensive benchmark study of quantum chemical methods on a series of classical and nonclassical carbocations, the CARBO33 dataset. We evaluate a total of 107 DFT methods from all rungs giving particular attention to double hybrid density functionals as the potential of the class has been largely undermined in the context of carbocations. To support our findings, DLPNO-CCSD(T) at the complete basis set (CBS) limit and W1-F12 are used as reference methods. Our results indicate that the composite CBS-QB3 method performs poorly and should not be adopted for target energies. Oftentimes, the tested DFAs of a lower rung perform better than several DFAs in a higher rung of Perdew's "Jacob's ladder". Nonetheless, double hybrids DSD-PBEP86-NL and ωB97X-2-D3(BJ) stand out by showing the overall best performance. Among the hybrids evaluated, about half of them show mean absolute deviation (MAD) below 1.1 kcal mol-1, including the popular hybrids M06-2X and mPW1PW91. In this family, MN15-D3(BJ) performs particularly well (MAD = 0.77 kcal mol-1) displaying reliable results across various tests. Highly popular B3LYP exhibited one of the worst performances (MAD = 4.74 kcal mol-1), and we do not recommend its application to carbocations. We also assess the 24 general-purpose basis sets of single- up to quadruple-ζ quality. The best compromise between accuracy and computational cost is achieved with cc-pVTZ followed by def2-TZVP. Computations on larger structures of general interest, including terpene carbocations, are also presented for selected DFT methods confirming general trends in the results.
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Affiliation(s)
- Marcelo T de Oliveira
- Department of Chemistry and Physics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia. .,Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Júlia M A Alves
- Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Natália L Vrech
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Ataualpa A C Braga
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Cristina A Barboza
- Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw, Poland
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81
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Puzzarini C, Stanton JF. Connections between the accuracy of rotational constants and equilibrium molecular structures. Phys Chem Chem Phys 2023; 25:1421-1429. [PMID: 36562443 DOI: 10.1039/d2cp04706c] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126, Bologna, Italy.
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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82
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Medvedko S, Ströbele M, Wagner JP. Synthesis of Sterically Encumbered Thiourea S-Oxides through Direct Thiourea Oxidation. Chemistry 2023; 29:e202203005. [PMID: 36279187 PMCID: PMC10107457 DOI: 10.1002/chem.202203005] [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: 09/26/2022] [Indexed: 11/07/2022]
Abstract
Thiourea S-oxides can be viewed as formal analogs of the currently unknown diamino-substituted Criegee intermediates (urea O-oxides). However, the preparation of such S-oxides is rather challenging, and the direct oxidation of thioureas typically only leads to formation of desulfurized products. Employing the accurate revDSD-PBEP86-D4 double hybrid density functional, it was found that the peracid mediated oxidation of thiourea S-oxides exhibits a lower reaction barrier than the oxidation of the corresponding thiourea itself in contrast to most other ordinary thioketones. The undesired overoxidation reactivity, which is associated with strong π-donation from the thiourea's nitrogen atoms, can be partially suppressed by introduction of bulky substituents and the utilization of protic solvents. In this regard, we managed to prepare two sterically encumbered thiourea S-oxides in isolated yields of 35-40 %. The S-oxides are stable in the solid state and in alcoholic solutions at room temperature for extended periods of time, but swiftly decompose in aprotic solvents by disproportionation. A dimesityl-substituted thiourea S-oxide complexed with residual mCBA could be characterized by means of X-ray crystallography, confirming the importance of hydrogen bonding in the stabilization of the amino-substituted C=S+ -O- moiety.
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Affiliation(s)
- Serhii Medvedko
- Institut für Organische Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.,Department of Organic Chemistry, National Technical University of Ukraine, Igor Sikorsky Kyiv Polytechnic Institute, Peremohy Ave 37, 03056, Kyiv, Ukraine
| | - Markus Ströbele
- Institut für Anorganische Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - J Philipp Wagner
- Institut für Organische Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
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83
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Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
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84
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Curtis K, Adeyiga O, Suleiman O, Odoh SO. Building on the strengths of a double-hybrid density functional for excitation energies and inverted singlet-triplet energy gaps. J Chem Phys 2023; 158:024116. [PMID: 36641391 DOI: 10.1063/5.0133727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is demonstrated that a double hybrid density functional approximation, ωB88PTPSS, that incorporates equipartition of density functional theory and the non-local correlation, however with a meta-generalized gradient approximation correlation functional, as well as with the range-separated exchange of ωB2PLYP, provides accurate excitation energies for conventional systems, as well as correct prescription of negative singlet-triplet gaps for non-conventional systems with inverted gaps, without any necessity for parametric scaling of the same-spin and opposite-spin non-local correlation energies. Examined over "safe" excitations of the QUESTDB set, ωB88PTPSS performs quite well for open-shell systems, correctly and fairly accurately [relative to equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) reference] predicts negative gaps for 50 systems with inverted singlet-triplet gaps, and is one of the leading performers for intramolecular charge-transfer excitations and achieves near-second-order approximate coupled cluster (CC2) and second-order algebraic diagrammatic construction quality for the Q1 and Q2 subsets. Subsequently, we tested ωB88PTPSS on two sets of real-life examples from recent computational chemistry literature-the low energy bands of chlorophyll a (Chl a) and a set of thermally activated delayed fluorescence (TADF) systems. For Chl a, ωB88PTPSS qualitatively and quantitatively achieves DLPNO-STEOM-CCSD-level performance and provides excellent agreement with experiment. For TADF systems, ωB88PTPSS agrees quite well with spin-component-scaled CC2 (SCS-CC2) excitation energies, as well as experimental values, for the gaps between the S1 and T1 excited states.
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Affiliation(s)
- Kevin Curtis
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Olajumoke Adeyiga
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Olabisi Suleiman
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel O Odoh
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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85
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Santra G, Martin JM. Performance of Localized-Orbital Coupled-Cluster Approaches for the Conformational Energies of Longer n-Alkane Chains. J Phys Chem A 2022; 126:9375-9391. [PMID: 36508714 PMCID: PMC9791657 DOI: 10.1021/acs.jpca.2c06407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report an update and enhancement of the ACONFL (conformer energies of large alkanes [J. Phys. Chem. A2022,126, 3521-3535]) dataset. For the ACONF12 (n-dodecane) subset, we report basis set limit canonical coupled-cluster with singles, doubles, and perturbative triples [i.e., CCSD(T)] reference data obtained from the MP2-F12/cc-pV{T,Q}Z-F12 extrapolation, [CCSD(F12*)-MP2-F12]/aug-cc-pVTZ-F12, and a (T) correction from conventional CCSD(T)/aug-cc-pV{D,T}Z calculations. Then, we explored the performance of a variety of single and composite localized-orbital CCSD(T) approximations, ultimately finding an affordable localized natural orbital CCSD(T) [LNO-CCSD(T)]-based post-MP2 correction that agrees to 0.006 kcal/mol mean absolute deviation with the revised canonical reference data. In tandem with canonical MP2-F12 complete basis set extrapolation, this was then used to re-evaluate the ACONF16 and ACONF20 subsets for n-hexadecane and n-icosane, respectively. Combining those with the revised canonical reference data for the dodecane conformers (i.e., ACONF12 subset), a revised ACONFL set was obtained. It was then used to assess the performance of different localized-orbital coupled-cluster approaches, such as pair natural orbital localized CCSD(T) [PNO-LCCSD(T)] as implemented in MOLPRO, DLPNO-CCSD(T0) and DLPNO-CCSD(T1) as implemented in ORCA, and LNO-CCSD(T) as implemented in MRCC, at their respective "Normal", "Tight", "vTight", and "vvTight" accuracy settings. For a given accuracy threshold and basis set, DLPNO-CCSD(T1) and DLPNO-CCSD(T0) perform comparably. With "VeryTightPNO" cutoffs, explicitly correlated DLPNO-CCSD(T1)-F12/VDZ-F12 is the best pick among all the DLPNO-based methods tested. To isolate basis set incompleteness from localized-orbital-related truncation errors (domain, LNOs), we have also compared the localized coupled-cluster approaches with canonical DF-CCSD(T)/aug-cc-pVTZ for the ACONF12 set. We found that gradually tightening the cutoffs improves the performance of LNO-CCSD(T), and using a composite scheme such as vTight + 0.50[vTight - Tight] improves things further. For DLPNO-CCSD(T1), "TightPNO" and "VeryTightPNO" offer a statistically similar accuracy, which gets slightly better when TCutPNO is extrapolated to the complete PNO space limit. Similar to Brauer et al.'s [Phys. Chem. Chem. Phys.2016,18 (31), 20905-20925] previous report for the S66x8 noncovalent interactions, the dispersion-corrected direct random phase approximation (dRPA)-based double hybrids perform remarkably well for the ACONFL set. While the revised reference data do not affect any conclusions on the less accurate methods, they may upend orderings for more accurate methods with error statistics on the same order as the difference between reference datasets.
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86
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Mendolicchio M, Bloino J, Barone V. Perturb-Then-Diagonalize Vibrational Engine Exploiting Curvilinear Internal Coordinates. J Chem Theory Comput 2022; 18:7603-7619. [PMID: 36322968 DOI: 10.1021/acs.jctc.2c00773] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The present paper is devoted to the implementation and validation of a second-order perturbative approach to anharmonic vibrations, followed by variational treatment of strong couplings (GVPT2) based on curvilinear internal coordinates. The main difference with respect to the customary Cartesian-based formulation is that the kinetic energy operator is no longer diagonal, and has to be expanded as well, leading to additional terms which have to be taken into proper account. It is, however, possible to recast all the equations as well-defined generalizations of the corresponding Cartesian-based counterparts, thus achieving a remarkable simplification of the new implementation. Particular attention is paid to the treatment of Fermi resonances with significant number of test cases analyzed fully, validating the new implementation. The results obtained in this work confirm that curvilinear coordinates strongly reduce the strength of inter-mode couplings compared to their Cartesian counterparts. This increases the reliability of low-order perturbative treatments for semi-rigid molecules and paves the way toward the reliable representation of more flexible molecules where small- and large-amplitude motions can be safely decoupled and treated at different levels of theory.
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Affiliation(s)
- Marco Mendolicchio
- Scuola Superiore Meridionale, Largo S. Marcellino 10, Napoli I-80138, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa I-56126, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa I-56126, Italy
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87
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Jiang Y, Supuran CT, Ho J. Quantum Chemical Prediction of the Acidities of Sulfonamide Inhibitors of Carbonic Anhydrase. J Phys Chem A 2022; 126:9207-9217. [DOI: 10.1021/acs.jpca.2c06358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Yuhong Jiang
- School of Chemistry, The University of New South Wales, Sydney, NSW2052, Australia
| | - Claudiu T. Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019Florence, Italy
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW2052, Australia
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88
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Liu S, Lian Z, Zhang M, Zhang S, Zhong Q. Intensification of NO2 removal in sulfite solutions with reusable copper chloride: Mechanism and Process parameters. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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89
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Yang Q, Bloino J. An Effective and Automated Processing of Resonances in Vibrational Perturbation Theory Applied to Spectroscopy. J Phys Chem A 2022; 126:9276-9302. [DOI: 10.1021/acs.jpca.2c06460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Qin Yang
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610Prague, Czech Republic
| | - Julien Bloino
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
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90
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Zhang YL, Li B. Reliability of Computing van der Waals Bond Lengths of Some Rare Gas Diatomics. Int J Mol Sci 2022; 23:ijms232213944. [PMID: 36430420 PMCID: PMC9696166 DOI: 10.3390/ijms232213944] [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: 10/25/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
When the bond lengths of 11 molecules containing van der Waals bonds are optimized by 572 methods and 20 basis sets, it is found that the best mean absolute deviations (MADs) of density-functional theory (DFT) methods are 0.005 Å (shown by APFD/6-311++G**), 0.007 Å (B2PLYPD3(Full)/aug-cc-pVQZ), and 0.010 Å (revDSDPBEP86/aug-cc-pVQZ), while the best MADs of ab initio methods are 0.008 Å (BD(T)/aug-cc-pVTZ) and 0.016 Å (MP4/aug-cc-pVQZ). Moreover, the best MADs calculated by 54 selected methods in combination with 60 other basis sets (such as 6-311++G, 6-31++G(3d'f,3p'd), and UGBS1V++) are not better. Therefore, these bond lengths can be calculated with extremely high accuracy by some special methods and basis sets, and CCSD(T) is also not as good as expected because its best MAD is only 0.023 Å (CCSD(T)/aug-cc-pVQZ).
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91
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Phatake RS, Averdunk A, Würtele C, Gellrich U. Piers’ Borane-Catalyzed Dimerization of Arylallenes via Transborylation: A Synthetic and Mechanistic Study. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ravindra S. Phatake
- Institut für Organische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392Gießen, Germany
| | - Arthur Averdunk
- Institut für Organische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392Gießen, Germany
| | - Christian Würtele
- Institut für Anorganische und Analytische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392Gießen, Germany
| | - Urs Gellrich
- Institut für Organische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392Gießen, Germany
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92
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Demkiw KM, Remmerswaal WA, Hansen T, van der Marel GA, Codée JDC, Woerpel KA. Halogen Atom Participation in Guiding the Stereochemical Outcomes of Acetal Substitution Reactions. Angew Chem Int Ed Engl 2022; 61:e202209401. [PMID: 35980341 PMCID: PMC9561118 DOI: 10.1002/anie.202209401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Indexed: 01/11/2023]
Abstract
Acetal substitution reactions of α-halogenated five- and six-membered rings can be highly stereoselective. Erosion of stereoselectivity occurs as nucleophilicity increases, which is consistent with additions to a halogen-stabilized oxocarbenium ion, not a three-membered-ring halonium ion. Computational investigations confirmed that the open-form oxocarbenium ions are the reactive intermediates involved. Kinetic studies suggest that hyperconjugative effects and through-space electrostatic interactions can both contribute to the stabilization of halogen-substituted oxocarbenium ions.
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Affiliation(s)
- Krystyna M. Demkiw
- Department of ChemistryNew York University100 Washington Square EastNew YorkNY 10003USA
| | - Wouter A. Remmerswaal
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - Thomas Hansen
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | | | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - K. A. Woerpel
- Department of ChemistryNew York University100 Washington Square EastNew YorkNY 10003USA
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93
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Bursch M, Mewes J, Hansen A, Grimme S. Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. Angew Chem Int Ed Engl 2022; 61:e202205735. [PMID: 36103607 PMCID: PMC9826355 DOI: 10.1002/anie.202205735] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 01/11/2023]
Abstract
Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.
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Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Andreas Hansen
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
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94
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Mehta N, Martin JML. Reduced-Scaling Double Hybrid Density Functional Theory with Rapid Basis Set Convergence through Localized Pair Natural Orbital F12. J Phys Chem Lett 2022; 13:9332-9338. [PMID: 36178852 PMCID: PMC9575149 DOI: 10.1021/acs.jpclett.2c02620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Following earlier work [Mehta, N.; Martin, J. M. L. J. Chem. Theory Comput.2022, 10.1021/acs.jctc.2c00426] that showed how the slow basis set convergence of the double hybrid density functional theory can be obviated by the use of F12 explicit correlation in the GLPT2 step (second order Görling-Levy perturbation theory), we demonstrate here for the very large and chemically diverse GMTKN55 benchmark suite that the CPU time scaling of this step can be reduced (asymptotically linearized) using the localized pair natural orbital (PNO-L) approximation at negligible cost in accuracy.
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95
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Rummel L, König HF, Hausmann H, Schreiner PR. Silyl Groups Are Strong Dispersion Energy Donors. J Org Chem 2022; 87:13168-13177. [PMID: 36166406 DOI: 10.1021/acs.joc.2c01633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an experimental and computational study to investigate noncovalent interactions between silyl groups that are often employed as "innocent" protecting groups. We chose an extended cyclooctatetraene (COT)-based molecular balance comprising unfolded (1,4-disubstituted) and folded (1,6-disubstituted) valance bond isomers that typically display remote and close silyl group contacts, respectively. The thermodynamic equilibria were determined using nuclear magnetic resonance measurements. Additionally, we utilized Boltzmann weighted symmetry-adapted perturbation theory (SAPT) at the sSAPT0/aug-cc-pVDZ level of theory to dissect and quantify noncovalent interactions. Apart from the extremely bulky tris(trimethylsilyl)silyl "supersilyl" group, there is a preference for the folded 1,6-COT valence isomer, with London dispersion interactions being the main stabilizing factor. This makes silyl groups excellent dispersion energy donors, a finding that needs to be taken into account in synthesis planning.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Henrik F König
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Heike Hausmann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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96
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Falbo E, Fusè M, Lazzari F, Mancini G, Barone V. Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents. J Chem Theory Comput 2022; 18:6203-6216. [PMID: 36166322 PMCID: PMC9558374 DOI: 10.1021/acs.jctc.2c00654] [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: 11/30/2022]
Abstract
![]()
The ongoing integration of quantum chemistry, statistical
mechanics,
and artificial intelligence is paving the route toward more effective
and accurate strategies for the investigation of the spectroscopic
properties of medium-to-large size chromophores in condensed phases.
In this context we are developing a novel workflow aimed at improving
the generality, reliability, and ease of use of the available computational
tools. In this paper we report our latest developments with specific
reference to unsupervised atomistic simulations employing non periodic
boundary conditions (NPBC) followed by clustering of the trajectories
employing optimized feature spaces. Next accurate variational computations
are performed for a representative point of each cluster, whereas
intracluster fluctuations are taken into account by a cheap yet reliable
perturbative approach. A number of methodological improvements have
been introduced including, e.g., more realistic reaction field effects
at the outer boundary of the simulation sphere, automatic definition
of the feature space by continuous perception of solute–solvent
interactions, full account of polarization and charge transfer in
the first solvation shell, and inclusion of vibronic contributions.
After its validation, this new approach has been applied to the challenging
case of solvatochromic effects on the UV–vis spectra of a prototypical
nitroxide radical (TEMPO) in different solvents. The reliability,
effectiveness, and robustness of the new platform is demonstrated
by the remarkable agreement with experiment of the results obtained
through an unsupervised approach characterized by a strongly reduced
computational cost as compared to that of conventional quantum mechanics
and molecular mechanics models without any accuracy reduction.
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Affiliation(s)
- Emanuele Falbo
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy.,Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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97
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Förster A. Assessment of the Second-Order Statically Screened Exchange Correction to the Random Phase Approximation for Correlation Energies. J Chem Theory Comput 2022; 18:5948-5965. [PMID: 36150190 PMCID: PMC9558381 DOI: 10.1021/acs.jctc.2c00366] [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: 11/30/2022]
Abstract
![]()
With increasing interelectronic distance, the screening
of the
electron–electron interaction by the presence of other electrons
becomes the dominant source of electron correlation. This effect is
described by the random phase approximation (RPA) which is therefore
a promising method for the calculation of weak interactions. The success
of the RPA relies on the cancellation of errors, which can be traced
back to the violation of the crossing symmetry of the 4-point vertex,
leading to strongly overestimated total correlation energies. By the
addition of second-order screened exchange (SOSEX) to the correlation
energy, this issue is substantially reduced. In the adiabatic connection
(AC) SOSEX formalism, one of the two electron–electron interaction
lines in the second-order exchange term is dynamically screened (SOSEX(W, vc)). A
related SOSEX expression in which both electron–electron interaction
lines are statically screened (SOSEX(W(0), W(0))) is obtained from the G3W2 contribution to the electronic self-energy. In contrast to SOSEX(W, vc), the
evaluation of this correlation energy expression does not require
an expensive numerical frequency integration and is therefore advantageous
from a computational perspective. We compare the accuracy of the statically
screened variant to RPA and RPA+SOSEX(W, vc) for a wide range of chemical
reactions. While both methods fail for barrier heights, SOSEX(W(0), W(0)) agrees very well with SOSEX(W, vc) for
charged excitations and noncovalent interactions where they lead to
major improvements over RPA.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
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98
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Fusè M, Longhi G, Mazzeo G, Stranges S, Leonelli F, Aquila G, Bodo E, Brunetti B, Bicchi C, Cagliero C, Bloino J, Abbate S. Anharmonic Aspects in Vibrational Circular Dichroism Spectra from 900 to 9000 cm -1 for Methyloxirane and Methylthiirane. J Phys Chem A 2022; 126:6719-6733. [PMID: 36126273 PMCID: PMC9527749 DOI: 10.1021/acs.jpca.2c05332] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Vibrational circular dichroism (VCD) spectra and the
corresponding
IR spectra of the chiral isomers of methyloxirane and of methylthiirane
have been reinvestigated, both experimentally and theoretically, with
particular attention to accounting for anharmonic corrections, as
calculated by the GVPT2 approach. De novo recorded VCD spectra in
the near IR (NIR) range regarding CH-stretching overtone transitions,
together with the corresponding NIR absorption spectra, were also
considered and accounted for, both with the GVPT2 and with the local
mode approaches. Comparison of the two methods has permitted us to
better describe the nature of active “anharmonic” modes
in the two molecules and the role of mechanical and electrical anharmonicity
in determining the intensities of VCD and IR/NIR data. Finally, two
nonstandard IR/NIR regions have been investigated: the first one about
≈2000 cm–1, involving mostly two-quanta bending
mode transitions, the second one between 7000 and 7500 cm–1 involving three-quanta transitions containing CH-stretching overtones
and HCC/HCH bending modes.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123 Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Stefano Stranges
- Dipartimento di Chimica e Tecnologia del Farmaco, Università"La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.,IOM-CNR, Laboratorio TASC, Basovizza, 34149 Trieste, Italy
| | - Francesca Leonelli
- Dipartimento di Chimica, Università"La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Giorgia Aquila
- Dipartimento di Chimica, Università"La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Enrico Bodo
- Dipartimento di Chimica, Università"La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Bruno Brunetti
- ISMN-CNR, Università La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9,00124 Torino, Italy
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9,00124 Torino, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, 56125, Pisa, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123 Brescia, Italy
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99
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Bursch M, Mewes J, Hansen A, Grimme S. Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
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100
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Mehta N, Martin JML. Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database. J Chem Theory Comput 2022; 18:5978-5991. [PMID: 36099641 PMCID: PMC9558368 DOI: 10.1021/acs.jctc.2c00426] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Double-hybrid density functional theory (DHDFT) offers
a pathway
to accuracy approaching composite wavefunction approaches such as
G4 theory. However, the Görling–Levy second-order perturbation
theory (GLPT2) term causes them to partially inherit the slow ∝L–3 (with L the maximum
angular momentum) basis set convergence of correlated wavefunction
methods. This could potentially be remedied by introducing F12 explicit
correlation: we investigate the basis set convergence of both DHDFT
and DHDFT-F12 (where GLPT2 is replaced by GLPT2-F12) for the large
and chemically diverse general main-group thermochemistry, kinetics,
and noncovalent interactions (GMTKN55) benchmark suite. The B2GP-PLYP-D3(BJ)
and revDSD-PBEP86-D4 DHDFs are investigated as test cases, together
with orbital basis sets as large as aug-cc-pV5Z and F12 basis sets
as large as cc-pVQZ-F12. We show that F12 greatly accelerates basis
set convergence of DHDFs, to the point that even the modest cc-pVDZ-F12
basis set is closer to the basis set limit than cc-pV(Q+d)Z or def2-QZVPPD
in orbital-based approaches, and in fact comparable in quality to
cc-pV(5+d)Z. Somewhat surprisingly, aug-cc-pVDZ-F12 is not required
even for the anionic subsets. In conclusion, DHDF-F12/VDZ-F12 eliminates
concerns about basis set convergence in both the development and applications
of double-hybrid functionals. Mass storage and I/O bottlenecks for
larger systems can be circumvented by localized pair natural orbital
approximations, which also exhibit much gentler system size scaling.
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Affiliation(s)
- Nisha Mehta
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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