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Tripathi MK, Paul A, Ramanathan V. Revisiting structure and conformational stability of ethanethiol. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.128997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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Tourchi AE, Benabdelkrim A, Hammoutène D, Ben Yaghlane S, Abdallah HH, Ben Said R, Linguerri R, Hochlaf M. Theoretical Characterization of the Structure and Spectroscopy of HCNO 2 Isomers and Applications. J Phys Chem A 2020; 124:11061-11071. [PMID: 33347316 DOI: 10.1021/acs.jpca.0c09027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We carried out a theoretical, fully ab initio, investigation of the stable forms of the [H,C,N,O,O] pentatomic molecular system, whose isomers are involved in fundamental combustion and atmospheric processes and are of potential interest for astrophysics. By adopting the MP2 and CCSD(T) electronic structure methods, combined with extrapolations to the complete basis set (CBS) limit, we characterized 20 low-energy isomers, excluding weak van der Waals complexes. For these molecules, we determined a set of geometrical parameters, relative energies, anharmonic vibrational frequencies, IR intensities, and fragmentation/formation energies from various atomic and/or molecular fragments. We discuss the relevance of the present findings for the search of new molecular species in astrophysical and atmospheric media and give suggestions for their possible detection in laboratory experiments. The set of data provided by the present work should facilitate the identification of these species from their gas-phase and low-temperature solid matrix spectra, whenever measured.
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Affiliation(s)
- Ala Eddine Tourchi
- Faculty of Chemistry, Laboratory of Thermodynamics and Molecular Modeling, USTHB, BP 32, El Alia, 16111, Bab Ezzouar, Algiers, Algeria.,COSYS/LISIS, Université Gustave Eiffel, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Aicha Benabdelkrim
- Faculty of Chemistry, Laboratory of Thermodynamics and Molecular Modeling, USTHB, BP 32, El Alia, 16111, Bab Ezzouar, Algiers, Algeria.,COSYS/LISIS, Université Gustave Eiffel, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Dalila Hammoutène
- Faculty of Chemistry, Laboratory of Thermodynamics and Molecular Modeling, USTHB, BP 32, El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Saida Ben Yaghlane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - Hassan H Abdallah
- Department of Chemistry, Salahaddin University-Erbil, Erbil 44001, Iraq
| | - Ridha Ben Said
- Department of Chemistry, College of Science and Arts, Qassim University, Ar Rass, Saudi Arabia
| | - Roberto Linguerri
- COSYS/LISIS, Université Gustave Eiffel, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Majdi Hochlaf
- COSYS/LISIS, Université Gustave Eiffel, 5 Bd Descartes 77454, Champs sur Marne, France
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Barone V, Ceselin G, Fusè M, Tasinato N. Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals. Front Chem 2020; 8:584203. [PMID: 33195078 PMCID: PMC7645164 DOI: 10.3389/fchem.2020.584203] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.
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Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Giorgia Ceselin
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
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Benabdelkrim A, Tourchi AE, Hammoutène D, Ben Yaghlane S, Abdallah HH, Linguerri R, Hochlaf M. Characterization of the simplest sulfenyl thiocyanate: isomers, spectroscopy and implications of astrophysical and biological relevance. Phys Chem Chem Phys 2020; 22:17052-17061. [PMID: 32658239 DOI: 10.1039/d0cp02382e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sulfenyl thiocyanate compounds, RSSCN, are involved in the human immune system biochemical processes. They are also the routes for the synthesis of complex S-containing species such as polypeptides, or symmetrical (RSSR) and unsymmetrical disulfides (RSSR'). At present, we have characterized the stable forms of the simplest sulfenyl thiocyanate compound, HSSCN, at the coupled cluster level. We found twenty-three isomers, for which we determined a set of structural parameters, anharmonic frequencies and reaction energies for the formation of the corresponding diatomic + triatomic and atomic + tetratomic fragments. We also discussed the implications of the present findings for biological entities containing a disulfide bridge, where we identified three isomers that may serve as prototypes. Similarities and differences with other S/N hybrid bioactive molecules are also discussed. From an astrophysical point of view, we expect HSSCN isomers to be present in astrophysical media, since several of their molecular fragments have already been detected. In sum, the present set of data can be used for the identification of HSSCN compounds and understanding the physical chemistry of sulfur containing molecules in vivo, in the laboratory and in astrophysical media.
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Affiliation(s)
- Aicha Benabdelkrim
- USTHB, Faculty of Chemistry, Laboratory of Thermodynamics and Molecular Modeling, BP 32, Al Alia, 16111, Bab Ezzouar, Algiers, Algeria
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DFT meets the segmented polarization consistent basis sets: Performances in the computation of molecular structures, rotational and vibrational spectroscopic properties. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127886] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Boussessi R, Tasinato N, Pietropolli Charmet A, Stoppa P, Barone V. Sextic centrifugal distortion constants: interplay of density functional and basis set for accurate yet feasible computations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1734678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | - Paolo Stoppa
- Università Ca’ Foscari Venezia, Dipartimento di Scienze Molecolari e Nanosistemi, Mestre Venezia, Italy
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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Alloui M, Belaidi S, Othmani H, Jaidane NE, Hochlaf M. Imidazole derivatives as angiotensin II AT1 receptor blockers: Benchmarks, drug-like calculations and quantitative structure-activity relationships modeling. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Den T, Menzi S, Frey HM, Leutwyler S. Accurate gas-phase structure of para-dioxane by fs Raman rotational coherence spectroscopy and ab initio calculations. J Chem Phys 2017; 147:074306. [PMID: 28830173 DOI: 10.1063/1.4997633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
p-Dioxane is non-polar, hence its rotational constants cannot be determined by microwave rotational coherence spectroscopy (RCS). We perform high-resolution gas-phase rotational spectroscopy of para-dioxane-h8 and -d8 using femtosecond time-resolved Raman RCS in a gas cell at T = 293 K and in a pulsed supersonic jet at T∼130 K. The inertial tensor of p-dioxane-h8 is strongly asymmetric, leading to a large number of asymmetry transients in its RCS spectrum. In contrast, the d8-isotopomer is a near-oblate symmetric top that exhibits a much more regular RCS spectrum with few asymmetry transients. Fitting the fs Raman RCS transients of p-dioxane-h8 to an asymmetric-top model yields the ground-state rotational constants A0 = 5084.4(5) MHz, B0 = 4684(1) MHz, C0 = 2744.7(8) MHz, and (A0 + B0)/2 = 4884.5(7) MHz (±1σ). The analogous values for p-dioxane-d8 are A0 = 4083(2) MHz, B0 = 3925(4) MHz, C0 = 2347.1(6) MHz, and (A0 + B0)/2 = 4002.4(6) MHz. We determine the molecular structure with a semi-experimental approach involving the highly correlated coupled-cluster singles, doubles and iterated triples method and the cc-pCVXZ basis set series from double- to quadruple-zeta (X = D, T, Q). Combining the calculated vibrationally averaged rotational constants A0calc(X),B0calc(X),C0calc(X) for increasing basis-set size X with non-linear extrapolation to the experimental constants A0exp,B0exp,C0exp allows to determine the equilibrium ground state structure of p-dioxane. For instance, the equilibrium C-C and C-O bond lengths are re(CC) = 1.5135(3) Å and re(CO) = 1.4168(4) Å, and the four axial C-H bond lengths are 0.008 Å longer than the four equatorial ones. The latter is ascribed to the trans-effect (anomeric effect), i.e., the partial delocalization of the electron lone-pairs on the O atoms that are oriented trans, relative to the axial CH bonds.
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Affiliation(s)
- Takuya Den
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Samuel Menzi
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
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Linguerri R, Puzzarini C, Al Mogren MM, Francisco JS, Hochlaf M. Benchmark study of the structural and spectroscopic parameters of the hydroxymethyl peroxy (HOCH2OO) radical and its decomposition reaction to HO2 and H2CO. J Chem Phys 2017; 146:144303. [DOI: 10.1063/1.4979573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Roberto Linguerri
- Laboratorie Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 Blvd. Descartes, 77454 Marne-la-Vallée, France
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician,” Universitá di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Muneerah Mogren Al Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Joseph S. Francisco
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Majdi Hochlaf
- Laboratorie Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 Blvd. Descartes, 77454 Marne-la-Vallée, France
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Hochlaf M. Advances in spectroscopy and dynamics of small and medium sized molecules and clusters. Phys Chem Chem Phys 2017; 19:21236-21261. [DOI: 10.1039/c7cp01980g] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics.
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Affiliation(s)
- Majdi Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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