1
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Puzzarini C, Alessandrini S. Carbamic acid and its dimer: A computational study. J Comput Chem 2024. [PMID: 38970400 DOI: 10.1002/jcc.27442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 07/08/2024]
Abstract
A recent work by Marks et al. on the formation of carbamic acid in NH3 $$ {}_3 $$ -CO2 $$ {}_2 $$ interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.
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Affiliation(s)
- Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| | - Silvia Alessandrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
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2
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Salta Z, Schaefer T, Tasinato N, Kieninger M, Katz A, Herrmann H, Ventura ON. Energetics of the OH radical H-abstraction reactions from simple aldehydes and their geminal diol forms. J Mol Model 2024; 30:253. [PMID: 38970670 DOI: 10.1007/s00894-024-06058-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
CONTEXT Carbonyl compounds, especially aldehydes, emitted to the atmosphere, may suffer hydration in aerosols or water droplets in clouds. At the same time, they can react with hydroxyl radicals which may add or abstract hydrogen atoms from these species. The interplay between hydration and hydrogen abstraction is studied using density functional and quantum composite theoretical methods, both in the gas phase and in simulated bulk water. The H-abstraction from the aldehydic and geminal diol forms of formaldehyde, acetaldehyde, glycolaldehyde, glyoxal, methylglyoxal, and acrolein is studied to determine whether the substituent has any noticeable effect in the preference for the abstraction of one form or another. It is found that abstraction of the H-atom adjacent to the carbonyl group gives a more stable radical than same abstraction from the geminal diol in the case of formaldehyde, acetaldehyde, and glycolaldehyde. The presence of a delocalizing group in the Cα (a carbonyl group in glyoxal and methylglyoxal, and a vinyl group in acrolein), reverts this trend, and now the abstraction of the H-atom from the geminal diol gives more stable radicals. A further study was conducted abstracting hydrogen atoms from the other different positions in the species considered, both in the aldehydic and geminal diol forms. Only in the case of glycolaldehyde, the radical formed by H-abstraction from the -CH2OH group is more stable than any of the other radical species. Abstraction of the hydrogen atom in one of the hydroxyl groups in the geminal diol is equivalent to the addition of the •OH radical to the aldehyde. It leads, in some cases, to decomposition into a smaller radical and a neutral molecule. In these cases, some interesting theoretical differences are observed between the results in gas phase and (simulated) bulk solvent, as well as with respect to the method of calculation chosen. METHODS DFT (M06-2X, B2PLYP, PW6B95), CCSD(T), and composite (CBS-QB3, jun-ChS, SCVECV-f12) methods using Dunning basis sets and extrapolation to the CBS limit were used to study the energetics of closed shell aldehydes in their keto and geminal-diol forms, as well as the radical derived from them by hydrogen abstraction. Both gas phase and simulated bulk solvent calculations were performed, in the last case using the Polarizable Continuum Model.
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Affiliation(s)
- Zoi Salta
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Thomas Schaefer
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), Permoserstr. 15, 04318, Leipzig, Germany
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Martina Kieninger
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay
| | - Aline Katz
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay
| | - Hartmut Herrmann
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), Permoserstr. 15, 04318, Leipzig, Germany
| | - Oscar N Ventura
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay.
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3
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Salta Z, Ventura ON, Rais N, Tasinato N, Barone V. A new chapter in the never ending story of cycloadditions: The puzzling case of SO 2 and acetylene. J Comput Chem 2024; 45:1587-1602. [PMID: 38517313 DOI: 10.1002/jcc.27350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
A comprehensive study of the different classes of cycloaddition reactions ([3+2], [2+2], and [2+1]) of SO2 to acetylene and ethylene has been performed using density functional theory (DFT) and composite wavefunction methods. The [3+2] cycloaddition reaction, that was previously explored in the context of the cycloaddition of thioformaldehyde S-methylide (TSM) to ethylene and acetylene, proceeds in a concerted way to the formation of stable heterocycles. In this paper, we extend our study to the [2+2] and [2+1] cycloadditions of SO2 to acetylene, which would produce 1,1-oxathiete-2-oxide and thiirene-1,1-dioxide, respectively. One of the main conclusions is that cyclic 1,1-oxathiete-2-oxide can open through a relatively easy breaking of the SO single bond and rearrange toward sulfinyl acetaldehyde (SA). The SA molecule can easily undergo several internal rearrangements, which eventually lead to sulfenic acid and sulfoxide derivatives of ethenone, 1,2,3-dioxathiole, and CO plus sulfinylmethane. The most probable path, however, produces 2-thioxoacetic acid, whose derivatives (or those of the corresponding acetate) are usually obtained by Willgerodt-Kindler-type sulfuration of acetates. This product can in turn decompose, leading to the final products CO2 and H2CS. Comparison of this decomposition path with that of 2-amino-2-thioxoacetic acid shows that the process occurs through different H-transfer processes.
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Affiliation(s)
- Zoi Salta
- Scuola Normale Superiore, Pisa, Italy
| | - Oscar N Ventura
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Nadjib Rais
- Scuola Normale Superiore, Pisa, Italy
- IUSS Scuola Universitaria Superiore, Pavia, Italy
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4
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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- 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
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5
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Tang Y, Yang Y, Cao Q, Wang K, Ma D, Liu B, Zhu Q, Ma J. Theoretical Study of the Temperature- and Pressure-Dependent Rate Constants for Nine Reactions between CO n ( n = 0-4), O m ( m = 1-3), C 2O, and C 3O 2 during the Radiolysis of Carbon Dioxide. J Phys Chem A 2024. [PMID: 38691833 DOI: 10.1021/acs.jpca.4c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
We investigate the reaction pathways of nine important CO2-related reactions using the revDSD-PBEP86-D3(BJ)/jun-cc-pV(T+d)Z level and simultaneously employ an accurate composite method (jun-Cheap) based on coupled-cluster (CC) theory. Subsequently, the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) is solved to calculate the temperature- and pressure-dependent rate constants. This work investigates reactions involving transition states that have been overlooked in previous literature, including the dissociation of singlet-state C3O2, the triple channel formation of C2O + CO to form C3O2, and the formation of O3 + CO. The results show that CO3 is highly prone to dissociation at high temperatures. Finally, the kinetic data show that over a wide temperature range, our calculations are consistent with previous experimental measurements. The majority of the reaction rate constants studied exhibit significant pressure dependence, while the O3 + CO reaction is pressure-independent at low temperatures. These results are instrumental in the development of detailed kinetic models for the CO2 radiolysis reaction network.
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Affiliation(s)
- Yuhong Tang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Yu Yang
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Qi Cao
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Keli Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Dandan Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Beibei Liu
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu 610065, PR China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu 610065, PR China
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6
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Mendolicchio M, Barone V. Unbiased Comparison between Theoretical and Experimental Molecular Structures and Properties: Toward an Accurate Reduced-Cost Evaluation of Vibrational Contributions. J Chem Theory Comput 2024; 20:2842-2857. [PMID: 38556752 DOI: 10.1021/acs.jctc.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The tremendous development of hardware and software is constantly increasing the role of quantum chemical (QC) computations in the assignment and interpretation of experimental results. However, an unbiased comparison between theory and experiment requires the proper account of vibrational averaging effects. In particular, high-resolution spectra in the gas phase are now available for molecules containing up to about 50 atoms, which are too large for a brute-force approach with the available QC methods of sufficient accuracy. In the present paper, we introduce hybrid approaches, which allow the accurate evaluation of vibrational averaging effects for molecules of this size beyond the harmonic approximation, with special attention being devoted to rotational constants. After the validation of new tools for relatively small molecules, the β-estradiol hormone and a prototypical molecular motor have been considered to witness the feasibility of accurate computations for large molecules.
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7
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Uribe L, Di Grande S, Crisci L, Lazzari F, Mendolicchio M, Barone V. Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol. J Phys Chem A 2024; 128:2629-2642. [PMID: 38530336 DOI: 10.1021/acs.jpca.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Lina Uribe
- 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
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, 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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8
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Lazzari F, Mendolicchio M, Barone V. Accurate Geometries of Large Molecules by Integration of the Pisa Composite Scheme and the Templating Synthon Approach. J Phys Chem A 2024; 128:1385-1395. [PMID: 38347709 DOI: 10.1021/acs.jpca.3c08382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
An effective yet reliable computational workflow is proposed, which permits the computation of accurate geometrical structures for large flexible molecules at an affordable cost thanks to the integration of machine learning tools and DFT models together with reduced scaling computations of vibrational averaging effects. After validation of the different components of the overall strategy, a panel of molecules of biological interest have been analyzed. The results confirm that very accurate geometrical parameters can be obtained at reasonable cost for molecules including up to about 50 atoms, which are the largest ones for which comparison with high-resolution rotational spectra is possible. Since the whole computational workflow can be followed employing standard electronic structure codes, accurate results for large-sized molecules can be obtained at DFT cost also by nonspecialists.
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Affiliation(s)
- 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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9
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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10
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Barone V, Lazzari F. Hunting for Complex Organic Molecules in the Interstellar Medium: The Role of Accurate Low-Cost Theoretical Geometries and Rotational Constants. J Phys Chem A 2023; 127:10517-10527. [PMID: 38033327 PMCID: PMC10726368 DOI: 10.1021/acs.jpca.3c06649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
A new approach to computation at affordable cost of accurate geometrical structures and rotational constants for medium-sized molecules in the gas phase is further improved and applied to a large panel of interstellar complex organic molecules. The most distinctive feature of the new model is the effective inclusion of core-valence correlation and vibrational averaging effects in the framework of density functional theory (DFT). In particular, a double-hybrid functional in conjunction with a quadruple-ζ valence/triple-ζ polarization basis set is employed for geometry optimizations, whereas a cheaper hybrid functional in conjunction with a split-valence basis set is used for the evaluation of vibrational corrections. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme approaches the accuracy of state-of-the-art wave function methods with the computational cost of the standard methods (DFT or MP2) routinely employed in the interpretation of microwave spectra. Since the whole computational workflow involves the postprocessing of the output of standard electronic structure codes by a new freely available web utility, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, di Pisa, Piazza dei Cavalieri 7, Pisa 56125, Italy
| | - Federico Lazzari
- Scuola Normale Superiore, di Pisa, Piazza dei Cavalieri 7, Pisa 56125, Italy
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11
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Melosso M, Alessandrini S, Spada L, Melli A, Wang X, Zheng Y, Duan C, Li J, Du W, Gou Q, Bizzocchi L, Dore L, Barone V, Puzzarini C. Rotational spectra and semi-experimental structures of furonitrile and its water cluster. Phys Chem Chem Phys 2023; 25:31281-31291. [PMID: 37955344 DOI: 10.1039/d3cp03984f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Rotational spectroscopy represents an invaluable tool for several applications: from the identification of new molecules in interstellar objects to the characterization of van der Waals complexes, but also for the determination of very accurate molecular structures and for conformational analyses. In this work, we used high-resolution rotational spectroscopic techniques in combination with high-level quantum-chemical calculations to address all these aspects for two isomers of cyanofuran, namely 2-furonitrile and 3-furonitrile. In particular, we have recorded and analyzed the rotational spectra of both of them from 6 to 320 GHz; rotational transitions belonging to several singly-substituted isotopologues have been identified as well. The rotational constants derived in this way have been used in conjunction with computed rotation-vibration interaction constants in order to derive a semi-experimental equilibrium structure for both isomers. Moreover, we observed the rotational spectra of four different intermolecular adducts formed by furonitrile and water, whose identification has been supported by a conformational analysis and a theoretical spectroscopic characterization. A semi-experimental determination of the intermolecular parameters has been achieved for all of them and the results have been compared with those obtained for the analogous system formed by benzonitrile and water.
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Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Alessio Melli
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Xiujuan Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Chunguo Duan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Jiayi Li
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Weiping Du
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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12
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Crisci L, Di Grande S, Cavallotti C, Barone V. Toward an Accurate Black-Box Tool for the Kinetics of Gas-Phase Reactions Involving Barrier-less Elementary Steps. J Chem Theory Comput 2023; 19:7626-7639. [PMID: 37880932 PMCID: PMC10653117 DOI: 10.1021/acs.jctc.3c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.
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Affiliation(s)
- Luigi Crisci
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Carlo Cavallotti
- Department
of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, I-20131 Milano, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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13
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Barone V, Crisci L, Di Grande S. Accurate Thermochemical and Kinetic Parameters at Affordable Cost by Means of the Pisa Composite Scheme (PCS). J Chem Theory Comput 2023; 19:7273-7286. [PMID: 37774410 PMCID: PMC10601482 DOI: 10.1021/acs.jctc.3c00817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 10/01/2023]
Abstract
A new strategy for the computation at an affordable cost of geometrical structures, thermochemical parameters, and rate constants for medium-sized molecules in the gas phase is proposed. The most distinctive features of the new model are the systematic use of cc-pVnZ-F12 basis sets, the addition of MP2 core-valence correlation in geometry optimizations by a double-hybrid functional, the separate extrapolation of MP2 and post-MP2 contributions, and the inclusion of anharmonic contributions in zero-point energies and thermodynamic functions. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme outperforms the most well-known model chemistries without the need for any empirical parameter. Additional tests show that the computed zero-point energies and thermal contributions can be confidently used for obtaining accurate thermochemical and kinetic parameters. Since the whole computational workflow is translated in a black-box procedure, which can be followed with standard electronic structure codes, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Luigi Crisci
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56125 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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14
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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: 0] [Impact Index Per Article: 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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15
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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: 0] [Impact Index Per Article: 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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16
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Nelson PM, Glick ZL, Sherrill CD. Approximating large-basis coupled-cluster theory vibrational frequencies using focal-point approximations. J Chem Phys 2023; 159:094104. [PMID: 37655773 DOI: 10.1063/5.0168608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
The focal-point approximation can be used to estimate a high-accuracy, slow quantum chemistry computation by combining several lower-accuracy, faster computations. We examine the performance of focal-point methods by combining second-order Møller-Plesset perturbation theory (MP2) with coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] for the calculation of harmonic frequencies and that of fundamental frequencies using second-order vibrational perturbation theory (VPT2). In contrast to standard CCSD(T), the focal-point CCSD(T) method approaches the complete basis set (CBS) limit with only triple-ζ basis sets for the coupled-cluster portion of the computation. The predicted harmonic and fundamental frequencies were compared with the experimental values for a set of 20 molecules containing up to six atoms. The focal-point method combining CCSD(T)/aug-cc-pV(T + d)Z with CBS-extrapolated MP2 has mean absolute errors vs experiment of only 7.3 cm-1 for the fundamental frequencies, which are essentially the same as the mean absolute error for CCSD(T) extrapolated to the CBS limit using the aug-cc-pV(Q + d)Z and aug-cc-pV(5 + d)Z basis sets. However, for H2O, the focal-point procedure requires only 3% of the computation time as the extrapolated CCSD(T) result, and the cost savings will grow for larger molecules.
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Affiliation(s)
- Philip M Nelson
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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17
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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: 0] [Impact Index Per Article: 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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18
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Ballotta B, Martínez-Núñez E, Rampino S, Barone V. New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations. Phys Chem Chem Phys 2023; 25:22840-22850. [PMID: 37584420 DOI: 10.1039/d3cp02571c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.
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Affiliation(s)
- Bernardo Ballotta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, Avenida das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Sergio Rampino
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Via Marzolo 1, 35131 Padova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
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19
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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: 0] [Impact Index Per Article: 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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20
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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: 0] [Impact Index Per Article: 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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21
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Czernek J, Brus J, Czerneková V, Kobera L. Quantifying the Intrinsic Strength of C-H⋯O Intermolecular Interactions. Molecules 2023; 28:molecules28114478. [PMID: 37298953 DOI: 10.3390/molecules28114478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
It has been recognized that the C-H⋯O structural motif can be present in destabilizing as well as highly stabilizing intermolecular environments. Thus, it should be of interest to describe the strength of the C-H⋯O hydrogen bond for constant structural factors so that this intrinsic strength can be quantified and compared to other types of interactions. This description is provided here for C2h-symmetric dimers of acrylic acid by means of the calculations that employ the coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] together with an extrapolation to the complete basis set (CBS) limit. Dimers featuring the C-H⋯O and O-H⋯O hydrogens bonds are carefully investigated in a wide range of intermolecular separations by the CCSD(T)/CBS approach, and also by the symmetry-adapted perturbation theory (SAPT) method, which is based on the density-functional theory (DFT) treatment of monomers. While the nature of these two types of hydrogen bonding is very similar according to the SAPT-DFT/CBS calculations and on the basis of a comparison of the intermolecular potential curves, the intrinsic strength of the C-H⋯O interaction is found to be about a quarter of its O-H⋯O counterpart that is less than one might anticipate.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
| | - Vladimíra Czerneková
- Institute of Physics, Czech Academy of Science, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Libor Kobera
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
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22
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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: 0] [Impact Index Per Article: 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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23
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Salta Z, Tasinato N, Ventura ON, Liebman JF. Paradigms and paradoxes: systematics in the study of the simplest sulfenic acids and sulfoxides, and a comparison between sulfur–oxygen and nitrogen–oxygen bonds. Struct Chem 2023. [DOI: 10.1007/s11224-023-02134-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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24
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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: 5] [Impact Index Per Article: 5.0] [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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25
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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: 0] [Impact Index Per Article: 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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26
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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: 17] [Impact Index Per Article: 17.0] [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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27
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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: 0] [Impact Index Per Article: 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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28
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Recio P, Alessandrini S, Vanuzzo G, Pannacci G, Baggioli A, Marchione D, Caracciolo A, Murray VJ, Casavecchia P, Balucani N, Cavallotti C, Puzzarini C, Barone V. Intersystem crossing in the entrance channel of the reaction of O( 3P) with pyridine. Nat Chem 2022; 14:1405-1412. [PMID: 36175514 DOI: 10.1038/s41557-022-01047-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/25/2022] [Indexed: 01/04/2023]
Abstract
Two quantum effects can enable reactions to take place at energies below the barrier separating reactants from products: tunnelling and intersystem crossing between coupled potential energy surfaces. Here we show that intersystem crossing in the region between the pre-reactive complex and the reaction barrier can control the rate of bimolecular reactions for weakly coupled potential energy surfaces, even in the absence of heavy atoms. For O(3P) plus pyridine, a reaction relevant to combustion, astrochemistry and biochemistry, crossed-beam experiments indicate that the dominant products are pyrrole and CO, obtained through a spin-forbidden ring-contraction mechanism. The experimental findings are interpreted-by high-level quantum-chemical calculations and statistical non-adiabatic computations of branching fractions-in terms of an efficient intersystem crossing occurring before the high entrance barrier for O-atom addition to the N-atom lone pair. At low to moderate temperatures, the computed reaction rates prove to be dominated by intersystem crossing.
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Affiliation(s)
- Pedro Recio
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica 'Giacomo Ciamician', University of Bologna, Bologna, Italy
| | - Gianmarco Vanuzzo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Giacomo Pannacci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Demian Marchione
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Adriana Caracciolo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- Department of Aerospace Engineering Sciences, University of Colorado, Boulder, CO, USA
| | - Vanessa J Murray
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- Montana State University, Bozeman, MT, USA
| | - Piergiorgio Casavecchia
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy.
| | - Carlo Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica 'Giulio Natta', Politecnico di Milano, Milan, Italy.
| | - Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', University of Bologna, Bologna, Italy.
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29
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Melli A, Melosso M, Bizzocchi L, Alessandrini S, Jiang N, Tonolo F, Boi S, Castellan G, Sapienza C, Guillemin JC, Dore L, Puzzarini C. Rotational Spectra of Unsaturated Carbon Chains Produced by Pyrolysis: The Case of Propadienone, Cyanovinylacetylene, and Allenylacetylene. J Phys Chem A 2022; 126:6210-6220. [PMID: 36044202 PMCID: PMC9483987 DOI: 10.1021/acs.jpca.2c05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Several interstellar molecules are highly reactive unsaturated
carbon chains, which are unstable under terrestrial conditions. Laboratory
studies in support of their detection in space thus face the issue
of how to produce these species and how to correctly model their rotational
energy levels. In this work, we introduce a general approach for producing
and investigating unsaturated carbon chains by means of selected test
cases. We report a comprehensive theoretical/experimental spectroscopic
characterization of three species, namely, propadienone, cyanovinylacetylene,
and allenylacetylene, all of them being produced by means of flash
vacuum pyrolysis of a suitable precursor. For each species, quantum-chemical
calculations have been carried out with the aim of obtaining accurate
predictions of the missing spectroscopic information required to guide
spectral analysis and assignment. Rotational spectra of the title
molecules have been investigated up to 400 GHz by using a frequency-modulation
millimeter-/submillimeter-wave spectrometer, thus significantly extending
spectral predictions over a wide range of frequency and quantum numbers.
A comparison between our results and those available in the literature
points out the clear need of the reported laboratory measurements
at higher frequencies for setting up accurate line catalogs for astronomical
searches.
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Affiliation(s)
- Alessio Melli
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Naples, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Salvatore Boi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Giorgia Castellan
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Carlotta Sapienza
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Jean-Claude Guillemin
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR6226, F-35000 Rennes, France
| | - Luca Dore
- 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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30
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Ventura ON, Segovia M, Vega-Teijido M, Katz A, Kieninger M, Tasinato N, Salta Z. Correcting the Experimental Enthalpies of Formation of Some Members of the Biologically Significant Sulfenic Acids Family. J Phys Chem A 2022; 126:6091-6109. [PMID: 36044372 DOI: 10.1021/acs.jpca.2c04235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfenic acids are important intermediates in the oxidation of cysteine thiol groups in proteins by reactive oxygen species. The mechanism is influenced heavily by the presence of polar groups, other thiol groups, and solvent, all of which determines the need to compute precisely the energies involved in the process. Surprisingly, very scarce experimental information exists about a very basic property of sulfenic acids, the enthalpies of formation. In this Article, we use high level quantum chemical methods to derive the enthalpy of formation at 298.15 K of methane-, ethene-, ethyne-, and benzenesulfenic acids, the only ones for which some experimental information exists. The methods employed were tested against well-known experimental data of related species and extensive CCSD(T) calculations. Our best results consistently point out to a much lower enthalpy of formation of methanesulfenic acid, CH3SOH (ΔfH0(298.15K) = -35.1 ± 0.4 kcal mol-1), than the one reported in the NIST thermochemical data tables. The enthalpies of formation derived for ethynesulfenic acid, HC≡CSOH, +32.9 ± 1.0 kcal/mol, and benzenesulfenic acid, C6H5SOH, -2.6 ± 0.6 kcal mol-1, also differ markedly from the experimental values, while the enthalpy of formation of ethenesulfenic acid CH2CHSOH, not available experimentally, was calculated as -11.2 ± 0.7 kcal mol-1.
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Affiliation(s)
- Oscar N Ventura
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Marc Segovia
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Mauricio Vega-Teijido
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Aline Katz
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Martina Kieninger
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Nicola Tasinato
- SMART Lab, Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Zoi Salta
- SMART Lab, Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
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31
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Nagy PR, Gyevi-Nagy L, Lőrincz BD, Kállay M. Pursuing the basis set limit of CCSD(T) non-covalent interaction energies for medium-sized complexes: case study on the S66 compilation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2109526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Péter R. Nagy
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - László Gyevi-Nagy
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - Balázs D. Lőrincz
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - Mihály Kállay
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
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32
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Salta Z, Vega-Teijido M, Katz A, Tasinato N, Barone V, Ventura ON. Dipolar 1,3-cycloaddition of thioformaldehyde S-methylide (CH 2 SCH 2 ) to ethylene and acetylene. A comparison with (valence) isoelectronic O 3 , SO 2 , CH 2 OO and CH 2 SO. J Comput Chem 2022; 43:1420-1433. [PMID: 35662073 DOI: 10.1002/jcc.26946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/08/2022]
Abstract
Methods rooted in the density functional theory and in the coupled cluster ansatz were employed to investigate the cycloaddition reactions to ethylene and acetylene of 1,3-dipolar species including ozone and the derivatives issued from replacement of the central oxygen atom by the valence-isoelectronic sulfur atom, and/or of one or both terminal oxygen atoms by the isoelectronic CH2 group. This gives rise to five different 1,3-dipolar compounds, namely ozone itself (O3 ), sulfur dioxide (SO2 ), the simplest Criegee intermediate (CH2 OO), sulfine (CH2 SO), and thioformaldehyde S-methylide (CH2 SCH2 , TSM). The experimental and accurate theoretical data available for some of those molecules were employed to assess the accuracy of two last-generation composite methods employing conventional or explicitly correlated post-Hartree-Fock contributions (jun-Cheap and SVECV-f12, respectively), which were then applied to investigate the reactivity of TSM. The energy barriers provided by both composite methods are very close (the average values for the two composite methods are 7.1 and 8.3 kcal mol-1 for the addition to ethylene and acetylene, respectively) and comparable to those ruling the corresponding additions of ozone (4.0 and 7.7 kcal mol-1 , respectively). These and other evidences strongly suggest that, at least in the case of cycloadditions, the reactivity of TSM is similar to that of O3 and very different from that of SO2 .
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Affiliation(s)
- Zoi Salta
- SMART Lab, Scuola Normale Superiore, Pisa, Italy
| | - Mauricio Vega-Teijido
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Aline Katz
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | | | | | - Oscar N Ventura
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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33
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Melli A, Melosso M, Lengsfeld KG, Bizzocchi L, Rivilla VM, Dore L, Barone V, Grabow JU, Puzzarini C. Spectroscopic Characterization of 3-Aminoisoxazole, a Prebiotic Precursor of Ribonucleotides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103278. [PMID: 35630755 PMCID: PMC9147597 DOI: 10.3390/molecules27103278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
The processes and reactions that led to the formation of the first biomolecules on Earth play a key role in the highly debated theme of the origin of life. Whether the first chemical building blocks were generated on Earth (endogenous synthesis) or brought from space (exogenous delivery) is still unanswered. The detection of complex organic molecules in the interstellar medium provides valuable support to the latter hypothesis. To gather more insight, here we provide the astronomers with accurate rotational frequencies to guide the interstellar search of 3-aminoisoxazole, which has been recently envisaged as a key reactive species in the scenario of the so-called RNA-world hypothesis. Relying on an accurate computational characterization, we were able to register and analyze the rotational spectrum of 3-aminoisoxazole in the 6–24 GHz and 80–320 GHz frequency ranges for the first time, exploiting a Fourier-transform microwave spectrometer and a frequency-modulated millimeter/sub-millimeter spectrometer, respectively. Due to the inversion motion of the −NH2 group, two states arise, and both of them were characterized, with more than 1300 lines being assigned. Although the fit statistics were affected by an evident Coriolis interaction, we were able to produce accurate line catalogs for astronomical observations of 3-aminoisoxazole.
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Affiliation(s)
- Alessio Melli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (A.M.); (V.B.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Mattia Melosso
- Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
- Correspondence: (M.M.); (C.P.)
| | - Kevin G. Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany; (K.G.L.); (J.-U.G.)
| | - Luca Bizzocchi
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Luca Dore
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (A.M.); (V.B.)
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany; (K.G.L.); (J.-U.G.)
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
- Correspondence: (M.M.); (C.P.)
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34
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Baiano C, Lupi J, Barone V, Tasinato N. Gliding on Ice in Search of Accurate and Cost-Effective Computational Methods for Astrochemistry on Grains: The Puzzling Case of the HCN Isomerization. J Chem Theory Comput 2022; 18:3111-3121. [PMID: 35446575 PMCID: PMC9097295 DOI: 10.1021/acs.jctc.1c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 11/28/2022]
Abstract
The isomerization of hydrogen cyanide to hydrogen isocyanide on icy grain surfaces is investigated by an accurate composite method (jun-Cheap) rooted in the coupled cluster ansatz and by density functional approaches. After benchmarking density functional predictions of both geometries and reaction energies against jun-Cheap results for the relatively small model system HCN···(H2O)2, the best performing DFT methods are selected. A large cluster containing 20 water molecules is then employed within a QM/QM' approach to include a realistic environment mimicking the surface of icy grains. Our results indicate that four water molecules are directly involved in a proton relay mechanism, which strongly reduces the activation energy with respect to the direct hydrogen transfer occurring in the isolated molecule. Further extension of the size of the cluster up to 192 water molecules in the framework of a three-layer QM/QM'/MM model has a negligible effect on the energy barrier ruling the isomerization. Computation of reaction rates by the transition state theory indicates that on icy surfaces, the isomerization of HNC to HCN could occur quite easily even at low temperatures thanks to the reduced activation energy that can be effectively overcome by tunneling.
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Affiliation(s)
- Carmen Baiano
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Jacopo Lupi
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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35
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Ceselin G, Salta Z, Bloino J, Tasinato N, Barone V. Accurate Quantum Chemical Spectroscopic Characterization of Glycolic Acid: A Route Toward its Astrophysical Detection. J Phys Chem A 2022; 126:2373-2387. [PMID: 35384666 PMCID: PMC9036519 DOI: 10.1021/acs.jpca.2c01419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The first step to
shed light on the abiotic synthesis of biochemical
building blocks, and their further evolution toward biological systems,
is the detection of the relevant species in astronomical environments,
including earthlike planets. To this end, the species of interest
need to be accurately characterized from structural, energetic, and
spectroscopic viewpoints. This task is particularly challenging when
dealing with flexible systems, whose spectroscopic signature is ruled
by the interplay of small- and large-amplitude motions (SAMs and LAMs,
respectively) and is further tuned by the conformational equilibrium.
In such instances, quantum chemical (QC) calculations represent an
invaluable tool for assisting the interpretation of laboratory measurements
or even observations. In the present work, the role of QC results
is illustrated with reference to glycolic acid (CH2OHCOOH),
a molecule involved in photosynthesis and plant respiration and a
precursor of oxalate in humans, which has been detected in the Murchison
meteorite but not yet in the interstellar medium or in planetary atmospheres.
In particular, the equilibrium structure of the lowest-energy conformer
is derived by employing the so-called semiexperimental approach. Then,
accurate yet cost-effective QC calculations relying on composite post-Hartree–Fock
schemes and hybrid coupled-cluster/density functional theory approaches
are used to predict the structural and ro-vibrational spectroscopic
properties of the different conformers within the framework of the
second-order vibrational perturbation theory. A purposely tailored
discrete variable representation anharmonic approach is used to treat
the LAMs related to internal rotations. The computed spectroscopic
data, particularly those in the infrared region, complement the available
experimental investigations, thus enhancing the possibility of an
astronomical detection of this molecule.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Zoi Salta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
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36
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow J, Feng G, Puzzarini C, Barone V. Gestapelt, nicht geklebt: Enthüllung der π→π*‐Wechselwirkung mithilfe des Benzofuran‐Formaldehyd‐Komplexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Lorenzo Spada
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
| | - Silvia Alessandrini
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Yang Zheng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Gang Feng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
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37
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Tonolo F, Bizzocchi L, Melosso M, Lique F, Dore L, Barone V, Puzzarini C. An improved study of HCO + and He system: Interaction potential, collisional relaxation, and pressure broadening. J Chem Phys 2021; 155:234306. [PMID: 34937352 DOI: 10.1063/5.0075929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In light of its ubiquitous presence in the interstellar gas, the chemistry and reactivity of the HCO+ ion requires special attention. The availability of up-to-date collisional data between this ion and the most abundant perturbing species in the interstellar medium is a critical resource in order to derive reliable values of its molecular abundance from astronomical observations. This work intends to provide improved scattering parameters for the HCO+ and He collisional system. We have tested the accuracy of explicitly correlated coupled-cluster methods for mapping the short- and long-range multi-dimensional potential energy surface of atom-ion systems. A validation of the methodology employed for the calculation of the potential well has been obtained from the comparison with experimentally derived bound-state spectroscopic parameters. Finally, by solving the close-coupling scattering equations, we have derived the pressure broadening and shift coefficients for the first six rotational transitions of HCO+ as well as inelastic state-to-state transition rates up to j = 5 in the 5-100 K temperature interval.
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Affiliation(s)
- F Tonolo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - L Bizzocchi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - M Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - F Lique
- Univ. Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, F-35000 Rennes, France
| | - L Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - V Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - C Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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38
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Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
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Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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39
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Melli A, Tonolo F, Barone V, Puzzarini C. Extending the Applicability of the Semi-experimental Approach by Means of "Template Molecule" and "Linear Regression" Models on Top of DFT Computations. J Phys Chem A 2021; 125:9904-9916. [PMID: 34752702 PMCID: PMC8607424 DOI: 10.1021/acs.jpca.1c07828] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Indexed: 11/28/2022]
Abstract
The accurate determination of equilibrium structures for isolated molecules plays a central role in the evaluation and interpretation of stereoelectronic, thermodynamic, and spectroscopic properties. For small semi-rigid systems, state-of-the-art quantum-chemical computations can rival the most sophisticated experimental results. For larger molecules, cheaper yet accurate approaches need to be defined. The double-hybrid rev-DSD-PBEP86 functional already delivers remarkable results that can be further improved by means of a "Lego brick" model. This is based on the idea that a molecular system can be seen as formed by different fragments (the "Lego bricks"), whose accurate semi-experimental (SE) equilibrium geometries are available. The template molecule (TM) approach can be used to account for the modifications occurring when going from the isolated fragment to the molecular system under investigation, with the linear regression (LR) model employed to correct the linkage between the different fragments. The resulting TM-SE_LR approach has been tested with respect to available SE equilibrium structures and rotational constants. Indeed, the latter parameters straightforwardly depend on the equilibrium geometry of the system under consideration. The main outcome of our study is the reliability, robustness, and accuracy of this novel approach. The molecular systems considered for benchmarking the TM-SE_LR scheme are those formally issued from addition/elimination reactions of nucleophilic unsaturated radicals (e.g., CN, C2H, and phenyl) to alkenes, imines, and aldehydes, whose rotational spectra have been investigated, but accurate structural determinations are not yet available.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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40
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Alessandrini S, Melosso M, Jiang N, Bizzocchi L, Dore L, Puzzarini C. Conformational stability of cyclopropanecarboxaldehyde is ruled by vibrational effects. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1955988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Silvia Alessandrini
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Luca Bizzocchi
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Luca Dore
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
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41
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Lupi J, Alessandrini S, Puzzarini C, Barone V. junChS and junChS-F12 Models: Parameter-free Efficient yet Accurate Composite Schemes for Energies and Structures of Noncovalent Complexes. J Chem Theory Comput 2021; 17:6974-6992. [PMID: 34677974 DOI: 10.1021/acs.jctc.1c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently developed model chemistry (denoted as junChS [Alessandrini, S.; et al. J. Chem. Theory Comput. 2020, 16, 988-1006]) has been extended to the employment of explicitly correlated (F12) methods. This led us to propose a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions. A thorough benchmark based on a wide range of interactions showed that the so-called junChS-F12 model, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms well-known model chemistries. Without employing any empirical parameter and at an affordable computational cost, junChS-F12 reaches subchemical accuracy. Accurate characterizations of molecular complexes are usually limited to energetics. To take a step forward, the conventional and F12 composite schemes developed for interaction energies have been extended to structural determinations. A benchmark study demonstrated that the most effective option is to add MP2-F12 core-valence correlation corrections to fc-CCSD(T)-F12/jun-cc-pVTZ geometries without the need of recovering the basis set superposition error and the extrapolation to the complete basis set.
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Affiliation(s)
- Jacopo Lupi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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42
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Ceselin G, Barone V, Tasinato N. Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry. J Chem Theory Comput 2021; 17:7290-7311. [PMID: 34666488 PMCID: PMC8582257 DOI: 10.1021/acs.jctc.1c00788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The determination
of accurate equilibrium molecular structures
plays a fundamental role for understanding many physical–chemical
properties of molecules, ranging from the precise evaluation of the
electronic structure to the analysis of the role played by dynamical
and environmental effects in tuning their overall behavior. For small
semi-rigid systems in the gas phase, state-of-the-art quantum chemical
computations rival the most sophisticated experimental (from, for
example, high-resolution spectroscopy) results. For larger molecules,
more effective computational approaches must be devised. To this end,
we have further enlarged the compilation of available semi-experimental
(SE) equilibrium structures, now covering the most important fragments
containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new
SE100 database. Next, comparison with geometries optimized by methods
rooted in the density functional theory showed that the already remarkable
results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals
can be further improved by a linear regression (LR) approach. Use
of template fragments (taken from the SE100 library) together with
LR estimates for the missing interfragment parameters paves the route
toward accurate structures of large molecules, as witnessed by the
very small deviations between computed and experimental rotational
constants. The whole approach has been implemented in a user-friendly
tool, termed nano-LEGO, and applied to a number of demanding case
studies.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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43
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow JU, Feng G, Puzzarini C, Barone V. Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex. Angew Chem Int Ed Engl 2021; 61:e202113737. [PMID: 34697878 PMCID: PMC9298890 DOI: 10.1002/anie.202113737] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/14/2022]
Abstract
The 1:1 benzofuran–formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint “rotational spectroscopy–quantum chemistry” strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low‐energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone‐pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi‐experimental equilibrium structure for a molecular complex of such a dimension.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Yang Zheng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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44
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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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45
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Sršeň Š, Slavíček P. Optimal Representation of the Nuclear Ensemble: Application to Electronic Spectroscopy. J Chem Theory Comput 2021; 17:6395-6404. [PMID: 34542278 DOI: 10.1021/acs.jctc.1c00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear densities are frequently represented by an ensemble of nuclear configurations or points in the phase space in various contexts of molecular simulations. The size of the ensemble directly affects the accuracy and computational cost of subsequent calculations of observable quantities. In the present work, we address the question of how many configurations do we need and how to select them most efficiently. We focus on the nuclear ensemble method in the context of electronic spectroscopy, where thousands of sampled configurations are usually needed for sufficiently converged spectra. The proposed representative sampling technique allows for a dramatic reduction of the sample size. By using an exploratory method, we model the density from a large sample in the space of transition properties. The representative subset of nuclear configurations is optimized by minimizing its Kullback-Leibler divergence to the full density with simulated annealing. High-level calculations are then performed only for the selected subset of configurations. We tested the algorithm on electronic absorption spectra of three molecules: (E)-azobenzene, the simplest Criegee intermediate, and hydrated nitrate anion. Typically, dozens of nuclear configurations provided sufficiently accurate spectra. A strongly forbidden transition of the nitrate anion presented the most challenging case due to rare geometries with disproportionately high transition intensities. This problematic case was easily diagnosed within the present approach. We also discuss various exploratory methods and a possible extension to dynamical simulations.
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Affiliation(s)
- Štěpán Sršeň
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
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46
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Barone V, Lupi J, Salta Z, Tasinato N. Development and Validation of a Parameter-Free Model Chemistry for the Computation of Reliable Reaction Rates. J Chem Theory Comput 2021; 17:4913-4928. [PMID: 34228935 PMCID: PMC8359010 DOI: 10.1021/acs.jctc.1c00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
A recently developed
model chemistry (jun-Cheap) has been slightly
modified and proposed as an effective, reliable, and parameter-free
scheme for the computation of accurate reaction rates with special
reference to astrochemical and atmospheric processes. Benchmarks with
different sets of state-of-the-art energy barriers spanning a wide
range of values show that, in the absence of strong multireference
contributions, the proposed model outperforms the most well-known
model chemistries, reaching a subchemical accuracy without any empirical
parameter and with affordable computer times. Some test cases show
that geometries, energy barriers, zero point energies, and thermal
contributions computed at this level can be used in the framework
of the master equation approach based on the ab initio transition-state
theory for obtaining accurate reaction rates.
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Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Jacopo Lupi
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Zoi Salta
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
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47
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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48
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Léon I, Tasinato N, Spada L, Alonso ER, Mata S, Balbi A, Puzzarini C, Alonso JL, Barone V. Looking for the Elusive Imine Tautomer of Creatinine: Different States of Aggregation Studied by Quantum Chemistry and Molecular Spectroscopy. Chempluschem 2021; 86:1374-1386. [PMID: 34255935 PMCID: PMC8519097 DOI: 10.1002/cplu.202100224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/22/2021] [Indexed: 01/06/2023]
Abstract
New spectroscopic experiments and state-of-the-art quantum-chemical computations of creatinine in different aggregation states unequivocally unveiled a significant tuning of tautomeric equilibrium by the environment: from the exclusive presence of the amine tautomer in the solid state and aqueous solution to a mixture of amine and imine tautomers in the gas phase. Quantum-chemical calculations predict the amine species as the most stable tautomer by about 30 kJ mol-1 in condensed phases. On the contrary, moving to the isolated forms, both Z and E imine isomers become more stable by about 7 kJ mol-1 . Since the imine isomers and one amine tautomer are separated by significant energy barriers, all of them should be present in the gas phase. This prediction has indeed been confirmed by high-resolution rotational spectroscopy, which provides the first experimental characterization of the elusive imine tautomer. The interpretation of the complicated hyperfine structure of the rotational spectrum, originated by three 14 N nuclei, makes it possible to use the spectral signatures as a sort of fingerprint for each individual tautomer in the complex sample.
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Affiliation(s)
- Iker Léon
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum -, Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Elena R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Alice Balbi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum -, Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Jose L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
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49
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Barone V, Alessandrini S, Biczysko M, Cheeseman JR, Clary DC, McCoy AB, DiRisio RJ, Neese F, Melosso M, Puzzarini C. Computational molecular spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00034-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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Melli A, Barone V, Puzzarini C. Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case. J Phys Chem A 2021; 125:2989-2998. [PMID: 33818109 PMCID: PMC8154618 DOI: 10.1021/acs.jpca.1c01679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Indexed: 11/30/2022]
Abstract
The ubiquitous role of water and its amphiprotic nature call for a deeper insight into the physical-chemical properties of hydrogen-bonded complexes formed with building blocks of biomolecules. In this work, the semiexperimental (SE) approach combined with the template model (TM) protocol allowed the accurate determination of the equilibrium structure of two isomeric forms of the imidazole-water complex. In this procedure, the integration of experiment (thanks to a recent rotational spectroscopy investigation) and theory is exploited, also providing the means of assessing the reliability and accuracy of different quantum-chemical approaches. Overall, this study demonstrated the robustness of the combined SE-TM approach, which can provide accurate results using affordable quantum-chemical methods. Finally, the structural and energetic characteristics of these complexes have been examined in detail and compared with those of analogous heterocycle-water adducts, also exploiting energy decomposition analyses.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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