1
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Schultz T. Correlated rotational alignment spectroscopy: a new tool for high-resolution spectroscopy and the analysis of heterogeneous samples. Phys Chem Chem Phys 2024; 26:25287-25313. [PMID: 39328147 DOI: 10.1039/d4cp00994k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Correlated rotational alignment spectroscopy correlates observables of ultrafast gas-phase spectroscopy with high-resolution, broad-band rotational Raman spectra. This article reviews the measurement principle of CRASY, existing implementations for mass-correlated measurements, and the potential for future developments. New spectroscopic capabilities are discussed in detail: signals for individual sample components can be separated even in highly heterogeneous samples. Isotopologue rotational spectra can be observed at natural isotope abundance. Fragmentation channels are readily assigned in molecular and cluster mass spectra. And finally, rotational Raman spectra can be measured with sub-MHz resolution, an improvement of several orders-of-magnitude as compared to preceding experiments.
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Affiliation(s)
- Thomas Schultz
- UNIST (Ulsan National Institute of Science and Technology), Advanced Materials Research, Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, South Korea.
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2
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Di Grande S, Lazzari F, Barone V. Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments. J Chem Theory Comput 2024. [PMID: 39373710 DOI: 10.1021/acs.jctc.4c00900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.
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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
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Xie F, Mendolicchio M, Omarouayache W, Murugachandran SI, Lei J, Gou Q, Sanz ME, Barone V, Schnell M. Structural and Electronic Evolution of Ethanolamine upon Microhydration: Insights from Hyperfine Resolved Rotational Spectroscopy. Angew Chem Int Ed Engl 2024; 63:e202408622. [PMID: 38982982 DOI: 10.1002/anie.202408622] [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: 05/07/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024]
Abstract
Ethanolamine hydrates containing from one to seven water molecules were identified via rotational spectroscopy with the aid of accurate quantum chemical methods considering anharmonic vibrational corrections. Ethanolamine undergoes significant conformational changes upon hydration to form energetically favorable hydrogen bond networks. The final structures strongly resemble the pure (H2O)3-9 complexes reported before when replacing two water molecules by ethanolamine. The 14N nuclear quadrupole coupling constants of all the ethanolamine hydrates have been determined and show a remarkable correlation with the strength of hydrogen bonds involving the amino group. After addition of the seventh water molecule, both hydrogen atoms of the amino group actively contribute to hydrogen bond formation, reinforcing the network and introducing approximately 21-27 % ionicity towards the formation of protonated amine. These findings highlight the critical role of microhydration in altering the electronic environment of ethanolamine, enhancing our understanding of amine hydration dynamics.
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Affiliation(s)
- Fan Xie
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | | | | | - Juncheng Lei
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, 401331, Chongqing, China
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, 401331, Chongqing, China
| | - M Eugenia Sanz
- Department of Chemistry, King's College London, London, SE1 1DB, U.K
| | | | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
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4
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Xu Y, Biczysko M. Toward the identification of cyano-astroCOMs via vibrational features: benzonitrile as a test case. Front Chem 2024; 12:1439194. [PMID: 39296366 PMCID: PMC11408737 DOI: 10.3389/fchem.2024.1439194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/12/2024] [Indexed: 09/21/2024] Open
Abstract
The James Webb Space Telescope (JWST) opened a new era for the identification of molecular systems in the interstellar medium (ISM) by vibrational features. One group of molecules of increasing interest is cyano-derivatives of aromatic organic molecules, which have already been identified in the ISM on the basis of the analysis of rotational signatures, and so, are plausible candidates for the detection by the JWST. Benzonitrile considered in this work represents a suitable example for the validation of a computational strategy, which can be further applied for different, larger, and not-yet observed molecules. For this purpose, anharmonic simulations of infrared (IR) spectra have been compared with recent FTIR experimental studies. The anharmonic computations using the generalized second-order vibrational perturbation theory (GVPT2) in conjunction with a hybrid force field combining the harmonic part of revDSD-PBEP86-D3/jun-cc-pVTZ with anharmonic corrections from B3LYP-D3/SNSD show very good agreement with those in the experiment, with a mean error of 11 c m - 1 for all fundamental transitions overall and only 2 c m - 1 for the C ≡ N stretching fundamental at 4.49 μ m . The inclusion of overtones up to three-quanta transitions also allowed the prediction of spectra in the near-infrared region, which shows distinct features due to C ≡ N overtones at the 2.26 μ m and 1.52 μ m . The remarkable accuracy of the GVPT2 results opens a pathway for the reliable prediction of spectra for a broader range of cyano-astroCOMs.
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Affiliation(s)
- Yanting Xu
- International Centre for Quantum and Molecular Structures, Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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5
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Alessandrini S, Melosso M, Bizzocchi L, Barone V, Puzzarini C. The Semiexperimental Approach at Work: Equilibrium Structure of Radical Species. J Phys Chem A 2024; 128:5833-5855. [PMID: 38991181 DOI: 10.1021/acs.jpca.4c01758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The so-called semiexperimental (SE) approach is a powerful technique for obtaining highly accurate equilibrium structures for isolated systems. This Featured Article describes its extension to open-shell species, thus providing the first systematic investigation on radical equilibrium geometries to be used for benchmarking purposes. The small yet significant database obtained demonstrates that there is no reduction in accuracy when moving from closed-shell species to radicals. We also provide an extension of the applicability of the SE approach to medium-/large-sized radicals by exploiting the so-called "Lego-brick" approach, which is based on the assumption that a molecular system can be seen as formed by smaller fragments for which the SE equilibrium structure is available. In this Featured Article we show that this model can be successfully applied also to open-shell species.
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Affiliation(s)
- Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Luca Bizzocchi
- 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
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6
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Rais N, Salta Z, Tasinato N. Theoretical investigation of the OH-initiated atmospheric degradation mechanism of CX 2CHX (X = H, F, Cl) by advanced quantum chemical and transition state theory methods. Phys Chem Chem Phys 2024; 26:19976-19991. [PMID: 38995148 DOI: 10.1039/d4cp01453g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Halogenated olefins are anthropogenic compounds with many industrial applications but at the same time raising many environmental and health concerns. Gas-phase electrophilic addition of the OH radical to the olefinic CC bond represents the primary sink for these chemicals in the atmosphere, with the degree and type of halogenation playing a significant role in their overall reactivity. In this work, we present a theoretical investigation of the reaction mechanisms and kinetics for the reactions between the OH radical and CH2CH2 (ethylene, ETH), CF2CHF (trifluoroethylene, TFE) and CCl2CHCl (trichloroethylene, TCE), simulated by state-of-the-art protocols and methods, with the aim of providing a detailed interpretation of the available experimental results, as well as new data of relevance to tropospheric chemistry. Specifically, potential energy surfaces (PESs) are obtained using the jun-Cheap (jChS) composite scheme, whereas temperature and pressure dependent rate coefficients and product distributions in the 100-600 K temperature range are calculated within the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) framework. The rates for barrierless channels are obtained from variable reaction coordinate-variational transition state theory (VRC-VTST) combined with the two transition state model. While the reactions with ETH and TFE proceed mainly via the formation of addition adducts at P = 1 atm and T = 298 K, the dominant channel for TCE is the Cl-elimination reaction. Global rate constants for the two halogenated olefins, TFE and TCE, are found to be pressure-independent, contrary to the case of ETH. The computed rate constants, as well as their temperature and pressure dependence, are in remarkable agreement with the available experimental data, and they are used to derive atmospheric lifetimes (τ) for both TFE and TCE as a function of altitude (h) in the atmosphere, by taking into account variations in the rate coefficients (k (T, P)) and [OH] concentration.
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Affiliation(s)
- Nadjib Rais
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
- IUSS Scuola Universitaria Superiore, Piazza della Vittoria 15, I-27100, Pavia, Italy
| | - Zoi Salta
- 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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7
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Uribe L, Lazzari F, Di Grande S, Crisci L, Mendolicchio M, Barone V. Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS). J Chem Phys 2024; 161:014307. [PMID: 38958160 DOI: 10.1063/5.0216384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.
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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
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, 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
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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8
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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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9
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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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10
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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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11
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Li H, Brémond E, Sancho-García JC, Pérez-Jiménez ÁJ, Scalmani G, Frisch MJ, Adamo C. Axial-equatorial equilibrium in substituted cyclohexanes: a DFT perspective on a small but complex problem. Phys Chem Chem Phys 2024; 26:8094-8105. [PMID: 38384253 DOI: 10.1039/d3cp06141h] [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
In Chemistry, complexity is not necessarily associated to large systems, as illustrated by the textbook example of axial-equatorial equilibrium in mono-substituted cyclohexanes. The difficulty in modelling such a simple isomerization is related to the need for reproducing the delicate balance between two forces, with opposite effects, namely the attractive London dispersion and the repulsive steric interactions. Such balance is a stimulating challenge for density-functional approximations and it is systematically explored here by considering 20 mono-substituted cyclohexanes. In comparison to highly accurate CCSD(T) reference calculations, their axial-equatorial equilibrium is studied with a large set of 48 exchange-correlation approximations, spanning from semilocal to hybrid to more recent double hybrid functionals. This dataset, called SAV20 (as Steric A-values for 20 molecules), allows to highlight the difficulties encountered by common and more original DFT approaches, including those corrected for dispersion with empirical potentials, the 6-31G*-ACP model, and our cost-effective PBE-QIDH/DH-SVPD protocol, in modeling these challenging interactions. Interestingly, the performance of the approaches considered in this contribution on the SAV20 dataset does not correlate with that obtained with other more standard datasets, such as S66, IDISP or NC15, thus indicating that SAV20 covers physicochemical features not already considered in previous noncovalent interaction benchmarks.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
| | - Eric Brémond
- Université Paris Cité, ITODYS, CNRS, F-75006 Paris, France
| | | | | | | | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
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12
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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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13
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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: 7] [Impact Index Per Article: 7.0] [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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14
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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: 7] [Impact Index Per Article: 7.0] [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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15
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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: 6] [Impact Index Per Article: 6.0] [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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16
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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: 6] [Impact Index Per Article: 6.0] [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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17
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Di Grande S, Kállay M, Barone V. Accurate thermochemistry at affordable cost by means of an improved version of the JunChS-F12 model chemistry. J Comput Chem 2023; 44:2149-2157. [PMID: 37432050 DOI: 10.1002/jcc.27187] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
The junChS-F12 composite method has been improved by means of the latest implementation of the CCSD(F12*)(T+) ansatz and validated for the thermochemistry of molecules containing atoms of the first three rows of the periodic table. A thorough benchmark showed that this model, in conjunction with cost-effective revDSD-PBEP86-D3(BJ) reference geometries, offers an optimal compromise between accuracy and computational cost. If improved geometries are sought, the most effective option is to add MP2-F12 core-valence correlation corrections to CCSD(T)-F12b/jun-cc-pVTZ geometries without the need of performing any extrapolation to the complete basis set limit. In the same vein, CCSD(T)-F12b/jun-cc-pVTZ harmonic frequencies are remarkably accurate without any additional contribution. Pilot applications to noncovalent intermolecular interactions, conformational landscapes, and tautomeric equilibria confirm the effectiveness and reliability of the model.
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Affiliation(s)
- S Di Grande
- Classe di Scienze, Scuola Normale Superiore di Pisa, Pisa, Italy
- Scuola Superiore Meridionale, Napoli, Italy
| | - M Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Budapest, Hungary
| | - V Barone
- Classe di Scienze, Scuola Normale Superiore di Pisa, Pisa, Italy
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18
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Puzzarini C, Alessandrini S, Bizzocchi L, Melosso M. Hunting for interstellar molecules: rotational spectra of reactive species. Faraday Discuss 2023; 245:309-326. [PMID: 37318358 DOI: 10.1039/d3fd00052d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Interstellar molecules are often highly reactive species, which are unstable under terrestrial conditions, such as radicals, ions and unsaturated carbon chains. Their detection in space is usually based on the astronomical observation of their rotational fingerprints. However, laboratory investigations have to face the issue of efficiently producing these molecules and preserving them during rotational spectroscopy measurements. A general approach for producing and investigating unstable/reactive species is presented by means of selected case-study molecules. The overall strategy starts from quantum-chemical calculations that aim at obtaining accurate predictions of the missing spectroscopic information required to guide spectral analysis and assignment. Rotational spectra of these species are then recorded by exploiting the approach mentioned above, and their subsequent analysis leads to accurate spectroscopic parameters. These are then used for setting up accurate line catalogs for astronomical searches.
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Affiliation(s)
- Cristina Puzzarini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Silvia Alessandrini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Luca Bizzocchi
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Mattia Melosso
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
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19
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Barone V, Uribe Grajales LM, Di Grande S, Lazzari F, Mendolicchio M. DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline. J Phys Chem A 2023; 127:7534-7543. [PMID: 37665117 PMCID: PMC10510395 DOI: 10.1021/acs.jpca.3c04227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Indexed: 09/05/2023]
Abstract
A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lina Marcela Uribe Grajales
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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20
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Thimmakondu VS, Karton A. CCSD(T) Rotational Constants for Highly Challenging C 5H 2 Isomers-A Comparison between Theory and Experiment. Molecules 2023; 28:6537. [PMID: 37764314 PMCID: PMC10537648 DOI: 10.3390/molecules28186537] [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: 07/30/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
We evaluate the accuracy of CCSD(T) and density functional theory (DFT) methods for the calculation of equilibrium rotational constants (Ae, Be, and Ce) for four experimentally detected low-lying C5H2 isomers (ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 2-cyclopropen-1-ylidenethenylidene (8)). The calculated rotational constants are compared to semi-experimental rotational constants obtained by converting the vibrationally averaged experimental rotational constants (A0, B0, and C0) to equilibrium values by subtracting the vibrational contributions (calculated at the B3LYP/jun-cc-pVTZ level of the theory). The considered isomers are closed-shell carbenes, with cumulene, acetylene, or strained cyclopropene moieties, and are therefore highly challenging from an electronic structure point of view. We consider both frozen-core and all-electron CCSD(T) calculations, as well as a range of DFT methods. We find that calculating the equilibrium rotational constants of these C5H2 isomers is a difficult task, even at the CCSD(T) level. For example, at the all-electron CCSD(T)/cc-pwCVTZ level of the theory, we obtain percentage errors ≤0.4% (Ce of isomer 3, Be and Ce of isomer 5, and Be of isomer 8) and 0.9-1.5% (Be and Ce of isomer 2, Ae of isomer 5, and Ce of isomer 8), whereas for the Ae rotational constant of isomers 2 and 8 and Be rotational constant of isomer 3, high percentage errors above 3% are obtained. These results highlight the challenges associated with calculating accurate rotational constants for isomers with highly challenging electronic structures, which is further complicated by the need to convert vibrationally averaged experimental rotational constants to equilibrium values. We use our best CCSD(T) rotational constants (namely, ae-CCSD(T)/cc-pwCVTZ for isomers 2 and 5, and ae-CCSD(T)/cc-pCVQZ for isomers 3 and 8) to evaluate the performance of DFT methods across the rungs of Jacob's Ladder. We find that the considered pure functionals (BLYP-D3BJ, PBE-D3BJ, and TPSS-D3BJ) perform significantly better than the global and range-separated hybrid functionals. The double-hybrid DSD-PBEP86-D3BJ method shows the best overall performance, with percentage errors below 0.5% in nearly all cases.
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Affiliation(s)
- Venkatesan S Thimmakondu
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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21
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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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22
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Barone V, Di Grande S, Lazzari F, Mendolicchio M. Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12). J Phys Chem A 2023; 127:6771-6778. [PMID: 37535450 PMCID: PMC10440789 DOI: 10.1021/acs.jpca.3c03999] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Indexed: 08/05/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, Napoli 80138, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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23
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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24
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Barone V, Fusè M. Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods. J Phys Chem A 2023; 127:3648-3657. [PMID: 37052318 PMCID: PMC10150396 DOI: 10.1021/acs.jpca.3c01174] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- DMMT-sede Europa, Università di Brescia, Viale Europa 11, 25121 Brescia, Italy
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25
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Sutikdja LW, Nguyen HVL, Jelisavac D, Stahl W, Mouhib H. Benchmarking quantum chemical methods for accurate gas-phase structure predictions of carbonyl compounds: the case of ethyl butyrate. Phys Chem Chem Phys 2023; 25:7688-7696. [PMID: 36857713 PMCID: PMC10015624 DOI: 10.1039/d2cp05774c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
High-resolution spectroscopy techniques play a pivotal role to validate and efficiently benchmark available methods from quantum chemistry. In this work, we analyzed the microwave spectrum of ethyl butyrate within the scope of a systematic investigation to benchmark state-of-the-art exchange-correlation functionals and ab initio methods, to accurately predict the lowest energy conformers of carbonyl compounds in their isolated state. Under experimental conditions, we observed two distinct conformers, one of Cs and one of C1 symmetry. As reported earlier in the cases of some ethyl and methyl alkynoates, structural optimizations of the most abundant conformer that exhibits a C1 symmetry proved extremely challenging for several quantum chemical levels. To probe the sensitivity of different methods and basis sets, we use the identified soft-degree of freedom in proximity to the carbonyl group as an order parameter. The results of our study provide useful insight for spectroscopists to select an adapted method for structure prediction of carbonyl compounds based on their available computational resources, suggesting a reasonable trade-off between accuracy and CPU cost. At the same time, our observations and the resulting sets of highly accurate experimental constants from high-resolution spectroscopy experiments give an appeal to theoretical groups to look further into this seemingly simple family of chemical compounds, which may prove useful for the further development and parametrization of theoretical methods in computational chemistry.
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Affiliation(s)
- Lilian W Sutikdja
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52074, Aachen, Germany
| | - Ha Vinh Lam Nguyen
- Univ Paris Est Creteil and Université Paris Cité, CNRS, LISA, F-94010, Créteil, France.
- Institut Universitaire de France (IUF), F-75231, Paris cedex 05, France
| | - Dragan Jelisavac
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52074, Aachen, Germany
| | - Wolfgang Stahl
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52074, Aachen, Germany
| | - Halima Mouhib
- Department of Computer Science, VU Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1111, 1081 HV, Amsterdam, The Netherlands.
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26
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Spaniol JT, Lee KLK, Pirali O, Puzzarini C, Martin-Drumel MA. A rotational investigation of the three isomeric forms of cyanoethynylbenzene (HCC-C 6H 4-CN): benchmarking experiments and calculations using the "Lego brick" approach. Phys Chem Chem Phys 2023; 25:6397-6405. [PMID: 36779600 DOI: 10.1039/d2cp04825f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report the study of three structural isomers of phenylpropiolonitrile (3-phenyl-2-propynenitrile, C6H5-C3N) containing an alkyne function and a cyano group, namely ortho-, meta-, and para-cyanoethynylbenzene (HCC-C6H4-CN). The pure rotational spectra of these species have been recorded at room temperature in the millimeter-wave domain using a chirped-pulse spectrometer (75-110 GHz) and a source-frequency modulation spectrometer (140-220 GHz). Assignments of transitions in the vibrational ground state and several vibrationally excited states were supported by quantum chemical calculations using the so-called "Lego brick" approach [A. Melli, F. Tonolo, V. Barone and C. Puzzarini, J. Phys. Chem. A, 2021, 125, 9904-9916]. From these assignments, accurate spectroscopic (rotational and centrifugal distortion) constants have been derived: for all species and all observed vibrational states, predicted rotational constants show relative accuracy better than 0.1%, and often of the order of 0.01%, compared to the experimental values. The present work hence further validates the use of the "Lego brick" approach for predicting spectroscopic constants with high precision.
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Affiliation(s)
- Jean-Thibaut Spaniol
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Kin Long Kelvin Lee
- Intel Accelerated Computing Systems and Graphics Group, Intel JF5 2111 NE 25th Ave, Hillsboro, OR 97124, USA
| | - Olivier Pirali
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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27
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Barone V, Fusè M, Aguado R, Potenti S, León I, Alonso ER, Mata S, Lazzari F, Mancini G, Spada L, Gualandi A, Cozzi PG, Puzzarini C, Alonso JL. Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine. Chemistry 2023; 29:e202203990. [PMID: 36734519 DOI: 10.1002/chem.202203990] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.
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Affiliation(s)
- V Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - M Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - R Aguado
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Potenti
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - F Lazzari
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - G Mancini
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - L Spada
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - A Gualandi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - P G Cozzi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - C Puzzarini
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
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28
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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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29
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Puzzarini C, Stanton JF. Connections between the accuracy of rotational constants and equilibrium molecular structures. Phys Chem Chem Phys 2023; 25:1421-1429. [PMID: 36562443 DOI: 10.1039/d2cp04706c] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126, Bologna, Italy.
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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30
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Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
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31
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Teale AM, Helgaker T, Savin A, Adamo C, Aradi B, Arbuznikov AV, Ayers PW, Baerends EJ, Barone V, Calaminici P, Cancès E, Carter EA, Chattaraj PK, Chermette H, Ciofini I, Crawford TD, De Proft F, Dobson JF, Draxl C, Frauenheim T, Fromager E, Fuentealba P, Gagliardi L, Galli G, Gao J, Geerlings P, Gidopoulos N, Gill PMW, Gori-Giorgi P, Görling A, Gould T, Grimme S, Gritsenko O, Jensen HJA, Johnson ER, Jones RO, Kaupp M, Köster AM, Kronik L, Krylov AI, Kvaal S, Laestadius A, Levy M, Lewin M, Liu S, Loos PF, Maitra NT, Neese F, Perdew JP, Pernal K, Pernot P, Piecuch P, Rebolini E, Reining L, Romaniello P, Ruzsinszky A, Salahub DR, Scheffler M, Schwerdtfeger P, Staroverov VN, Sun J, Tellgren E, Tozer DJ, Trickey SB, Ullrich CA, Vela A, Vignale G, Wesolowski TA, Xu X, Yang W. DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science. Phys Chem Chem Phys 2022; 24:28700-28781. [PMID: 36269074 PMCID: PMC9728646 DOI: 10.1039/d2cp02827a] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 12/13/2022]
Abstract
In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.
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Affiliation(s)
- Andrew M. Teale
- School of Chemistry, University of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andreas Savin
- Laboratoire de Chimie Théorique, CNRS and Sorbonne University, 4 Place Jussieu, CEDEX 05, 75252 Paris, France.
| | - Carlo Adamo
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany.
| | - Alexei V. Arbuznikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7Straße des 17. Juni 13510623Berlin
| | | | - Evert Jan Baerends
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.
| | - Patrizia Calaminici
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Eric Cancès
- CERMICS, Ecole des Ponts and Inria Paris, 6 Avenue Blaise Pascal, 77455 Marne-la-Vallée, France.
| | - Emily A. Carter
- Department of Mechanical and Aerospace Engineering and the Andlinger Center for Energy and the Environment, Princeton UniversityPrincetonNJ 08544-5263USA
| | | | - Henry Chermette
- Institut Sciences Analytiques, Université Claude Bernard Lyon1, CNRS UMR 5280, 69622 Villeurbanne, France.
| | - Ilaria Ciofini
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - T. Daniel Crawford
- Department of Chemistry, Virginia TechBlacksburgVA 24061USA,Molecular Sciences Software InstituteBlacksburgVA 24060USA
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | | | - Claudia Draxl
- Institut für Physik and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany. .,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany. .,Beijing Computational Science Research Center (CSRC), 100193 Beijing, China.,Shenzhen JL Computational Science and Applied Research Institute, 518110 Shenzhen, China
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France.
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
| | - Giulia Galli
- Pritzker School of Molecular Engineering and Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. .,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Nikitas Gidopoulos
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK.
| | - Peter M. W. Gill
- School of Chemistry, University of SydneyCamperdown NSW 2006Australia
| | - Paola Gori-Giorgi
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Andreas Görling
- Chair of Theoretical Chemistry, University of Erlangen-Nuremberg, Egerlandstrasse 3, 91058 Erlangen, Germany.
| | - Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Gold Coast, Qld 4222, Australia.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany.
| | - Oleg Gritsenko
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie UniversityHalifaxNova ScotiaB3H 4R2Canada
| | - Robert O. Jones
- Peter Grünberg Institut PGI-1, Forschungszentrum Jülich52425 JülichGermany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin.
| | - Andreas M. Köster
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav)CDMX07360Mexico
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth, 76100, Israel.
| | - Anna I. Krylov
- Department of Chemistry, University of Southern CaliforniaLos AngelesCalifornia 90089USA
| | - Simen Kvaal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andre Laestadius
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Mel Levy
- Department of Chemistry, Tulane University, New Orleans, Louisiana, 70118, USA.
| | - Mathieu Lewin
- CNRS & CEREMADE, Université Paris-Dauphine, PSL Research University, Place de Lattre de Tassigny, 75016 Paris, France.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, France.
| | - Neepa T. Maitra
- Department of Physics, Rutgers University at Newark101 Warren StreetNewarkNJ 07102USA
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany.
| | - John P. Perdew
- Departments of Physics and Chemistry, Temple UniversityPhiladelphiaPA 19122USA
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland.
| | - Pascal Pernot
- Institut de Chimie Physique, UMR8000, CNRS and Université Paris-Saclay, Bât. 349, Campus d'Orsay, 91405 Orsay, France.
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Elisa Rebolini
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Lucia Reining
- Laboratoire des Solides Irradiés, CNRS, CEA/DRF/IRAMIS, École Polytechnique, Institut Polytechnique de Paris, F-91120 Palaiseau, France. .,European Theoretical Spectroscopy Facility
| | - Pina Romaniello
- Laboratoire de Physique Théorique (UMR 5152), Université de Toulouse, CNRS, UPS, France.
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA.
| | - Dennis R. Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary2500 University Drive NWCalgaryAlbertaT2N 1N4Canada
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, D-14195, Germany.
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0632 Auckland, New Zealand.
| | - Viktor N. Staroverov
- Department of Chemistry, The University of Western OntarioLondonOntario N6A 5B7Canada
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA.
| | - Erik Tellgren
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - David J. Tozer
- Department of Chemistry, Durham UniversitySouth RoadDurhamDH1 3LEUK
| | - Samuel B. Trickey
- Quantum Theory Project, Deptartment of Physics, University of FloridaGainesvilleFL 32611USA
| | - Carsten A. Ullrich
- Department of Physics and Astronomy, University of MissouriColumbiaMO 65211USA
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Giovanni Vignale
- Department of Physics, University of Missouri, Columbia, MO 65203, USA.
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, Université de Genève30 Quai Ernest-Ansermet1211 GenèveSwitzerland
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Weitao Yang
- Department of Chemistry and Physics, Duke University, Durham, NC 27516, USA.
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32
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Falbo E, Fusè M, Lazzari F, Mancini G, Barone V. Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents. J Chem Theory Comput 2022; 18:6203-6216. [PMID: 36166322 PMCID: PMC9558374 DOI: 10.1021/acs.jctc.2c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 11/30/2022]
Abstract
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces. Next accurate variational computations are performed for a representative point of each cluster, whereas intracluster fluctuations are taken into account by a cheap yet reliable perturbative approach. A number of methodological improvements have been introduced including, e.g., more realistic reaction field effects at the outer boundary of the simulation sphere, automatic definition of the feature space by continuous perception of solute-solvent interactions, full account of polarization and charge transfer in the first solvation shell, and inclusion of vibronic contributions. After its validation, this new approach has been applied to the challenging case of solvatochromic effects on the UV-vis spectra of a prototypical nitroxide radical (TEMPO) in different solvents. The reliability, effectiveness, and robustness of the new platform is demonstrated by the remarkable agreement with experiment of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional quantum mechanics and molecular mechanics models without any accuracy reduction.
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Affiliation(s)
- Emanuele Falbo
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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33
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Heo I, Lee JC, Özer BR, Schultz T. Mass-Correlated High-Resolution Spectra and the Structure of Benzene. J Phys Chem Lett 2022; 13:8278-8283. [PMID: 36036614 DOI: 10.1021/acs.jpclett.2c02035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass-correlated rotational alignment spectroscopy resolved the rotational Raman spectra for 5 benzene isotopologues with unprecedented resolution. 13-C isotopologues were characterized at natural abundance. Fitted rotational constants allowed the analysis of effective and equilibrium bond lengths for benzene with sub-mÅ uncertainties. We found that previously reported experimental structures were wrong by multiple mÅ, due to unrecognized H/D isotope effects. Our results also refute recent experimental and theoretical literature claims of identical effective C-H and C-D bond lengths in benzene and reveal an isotope effect similar to that in other small molecules.
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Affiliation(s)
- In Heo
- Advanced Materials Research Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
| | - Jong Chan Lee
- Advanced Materials Research Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
| | - Begüm Rukiye Özer
- Advanced Materials Research Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
| | - Thomas Schultz
- Advanced Materials Research Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
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34
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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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35
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Tasinato N, Pietropolli Charmet A, Ceselin G, Salta Z, Stoppa P. In Vitro and In Silico Vibrational-Rotational Spectroscopic Characterization of the Next-Generation Refrigerant HFO-1123. J Phys Chem A 2022; 126:5328-5342. [PMID: 35930010 PMCID: PMC9393866 DOI: 10.1021/acs.jpca.2c04680] [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: 07/04/2022] [Revised: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Very short-lived substances have recently been proposed as replacements for hydrofluorocarbons (HFCs), in turn being used in place of ozone-depleting substances, in refrigerant applications. In this respect, hydro-fluoro-olefins (HFOs) are attracting particular interest because, due to their reduced global warming potential, they are supposed to be environmentally friendlier. Notwithstanding this feature, they represent a new class of compounds whose spectroscopic properties and reactivity need to be characterized to allow their atmospheric monitoring and to understand their environmental fate. In the present work, the structural, vibrational, and ro-vibrational properties of trifluorothene (HFO-1123, F2C = CHF) are studied by state-of-the-art quantum chemical calculations. The equilibrium molecular structure has an expected error within 2 mÅ and 0.2° for bond lengths and angles, respectively. This represents the first step toward the computation of highly accurate rotational constants for both the ground and first excited fundamental vibrational levels, which reproduce the available experimental data well within 0.1%. Centrifugal distortion parameters and vibrational-rotational coupling terms are computed as well and used to solve some conflicting experimental results. Simulation of the vibrational transition frequencies and intensities beyond the double harmonic approximation and up to three quanta of vibrational excitation provides insights into the couplings ruling the vibrational dynamics and guides the characterization of the gas-phase infrared spectrum experimentally recorded in the range of 200-5000 cm-1. The full characterization of the IR features is completed with the experimental determination of the absorption cross sections over the 400-5000 cm-1 region from which the radiative forcing and global warming potential of HFO-1123 are derived.
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Affiliation(s)
- Nicola Tasinato
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Andrea Pietropolli Charmet
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari Venezia, Via Torino 155, I-30172 Mestre, Italy
| | - Giorgia Ceselin
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Zoi Salta
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Paolo Stoppa
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari Venezia, Via Torino 155, I-30172 Mestre, Italy
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36
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León I, Fusè M, Alonso ER, Mata S, Mancini G, Puzzarini C, Alonso JL, Barone V. Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine. J Chem Phys 2022; 157:074107. [DOI: 10.1063/5.0102841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.
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Affiliation(s)
- Iker León
- Universidad de Valladolid - Campus Miguel Delibes, Spain
| | | | - Elena R. Alonso
- Química Física y Química Inorgánica, Universidad de Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia. Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Spain
| | | | | | - Jose L. Alonso
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid Departamento Química Física y Química Inorgánica, Spain
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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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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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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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40
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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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [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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Mancini G, Fusè M, Lipparini F, Nottoli M, Scalmani G, Barone V. Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters. J Chem Theory Comput 2022; 18:2479-2493. [PMID: 35257572 PMCID: PMC9009096 DOI: 10.1021/acs.jctc.2c00046] [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: 12/01/2022]
Abstract
![]()
Multiscale methods
combining quantum mechanics and molecular mechanics
(QM/MM) have become the most suitable and effective strategies for
the investigation of the spectroscopic properties of medium-to-large
size chromophores in condensed phases. In this context, we are developing
a novel workflow aimed at improving the generality, reliability, and
ease of use of the available computational tools. In this paper, we
report our latest developments with specific reference to a general
protocol based on atomistic simulations, carried out under nonperiodic
boundary conditions (NPBC). In particular, we add to our in house
MD engine a new efficient treatment of mean field electrostatic contributions
to energy and forces, together with the capability of performing the
simulations either in the canonical (NVT) or in the
isothermal–isobaric (NPT) ensemble. Next,
we provide convincing evidence that the NBPC approach enhanced by
specific tweaks for rigid body propagation, allows for the simulation
of solute–solvent systems with a minimum number of degrees
of freedom and large integration time step. After its validation,
this new approach is applied to the challenging case of solvatochromic
effects on the electron paramagnetic resonance (EPR) spectrum of a
prototypical nitroxide radical. To this end, we propose and validate
also an automated protocol to extract and weight simulation snapshots,
making use of a continuous description of the strength of solute–solvent
hydrogen bridges. While further developments are being worked on,
the effectiveness of our approach, even in its present form, is demonstrated
by the accuracy of the results obtained through an unsupervised approach
characterized by a strongly reduced computational cost as compared
to that of conventional QM/MM models, without any appreciable deterioration
of accuracy.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Universitaá di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Universitaá di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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The Spectroscopic Characterization of Halogenated Pollutants through the Interplay between Theory and Experiment: Application to R1122. Molecules 2022; 27:molecules27030748. [PMID: 35164013 PMCID: PMC8839295 DOI: 10.3390/molecules27030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 01/30/2023] Open
Abstract
In the last decade, halogenated ethenes have seen an increasing interest for different applications; in particular, in refrigeration, air-conditioning and heat pumping. At the same time, their adverse effects as atmospheric pollutants require environmental monitoring, especially by remote sensing spectroscopic techniques. For this purpose, an accurate characterization of the spectroscopic fingerprint—in particular, those of relevance for rotational–vibrational spectroscopy—of the target molecules is strongly needed. This work provides an integrated computational–theoretical investigation on R1122 (2-Chloro-1,1-difluoro-ethylene, ClHC=CF2), a compound widely employed as a key intermediate in different chemical processes. State-of-the-art quantum chemical calculations relying on CCSD(T)-based composite schemes and hybrid CCSD(T)/DFT approaches are used to obtain an accurate prediction of the structural, rotational and vibrational spectroscopic properties. In addition, the equilibrium geometry is obtained by exploiting the semi-experimental method. The theoretical predictions are used to guide the analysis of the experimentally recorded gas-phase infrared spectrum, which is assigned in the 400–6500 cm−1 region. Furthermore, absorption cross sections are accurately determined over the same spectral range. Finally, by using the obtained spectroscopic data, a first estimate of the global warming potential of R1122 vibrational spectra is obtained.
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Ye H, Alessandrini S, Melosso M, Puzzarini C. Exploiting the “Lego brick” approach to predict accurate molecular structures of PAHs and PANHs. Phys Chem Chem Phys 2022; 24:23254-23264. [DOI: 10.1039/d2cp03294e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are important and ubiquitous species in space. However, their accurate structural and spectroscopic characterization is often missing. To fill this...
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Barone V, Fusè M, Pinto SMV, Tasinato N. A Computational Journey across Nitroxide Radicals: From Structure to Spectroscopic Properties and Beyond. Molecules 2021; 26:molecules26237404. [PMID: 34885980 PMCID: PMC8659111 DOI: 10.3390/molecules26237404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Nitroxide radicals are characterized by a long-lived open-shell electronic ground state and are strongly sensitive to the chemical environment, thus representing ideal spin probes and spin labels for paramagnetic biomolecules and materials. However, the interpretation of spectroscopic parameters in structural and dynamic terms requires the aid of accurate quantum chemical computations. In this paper we validate a computational model rooted into double-hybrid functionals and second order vibrational perturbation theory. Then, we provide reference quantum chemical results for the structures, vibrational frequencies and other spectroscopic features of a large panel of nitroxides of current biological and/or technological interest.
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45
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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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