1
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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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2
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Demaison J, Liévin J. Equilibrium Values for the Si-H Bond Length and Equilibrium Structures of Silyl Iodide and Halosilylenes. Molecules 2024; 29:3101. [PMID: 38999053 PMCID: PMC11243611 DOI: 10.3390/molecules29133101] [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: 05/30/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
The equilibrium structures of silyl iodide, SiH3I, and silylene halides, SiHX (X = F, Cl, Br, I), were determined by using the mixed regression method, where approximate values of the rotational constants are supplemented by the structural parameters of a different origin. For this goal, it is shown that the r(Si-H) bond length can be determined by using the isolated SiH stretching frequency and that an accurate estimation of the bond angles is obtained by an MP2 calculation with a basis set of triple zeta quality. To check the accuracy of the experimental structures, they were also optimized by means of all electron CCSD(T) calculations using basis sets of quadruple zeta quality.
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Affiliation(s)
- Jean Demaison
- Physique des Lasers, Atomes et Molécules, Université de Lille, Bât. P5, 59655 Villeneuve d'Ascq cedex, France
| | - Jacques Liévin
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), CP160/09, Faculté des Sciences, Université Libre de Bruxelles (U.L.B.), Ave. Roosevelt, 50, B-1050 Brussels, Belgium
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3
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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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4
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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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5
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Tikhonov DS, Vishnevskiy YV. Describing nuclear quantum effects in vibrational properties using molecular dynamics with Wigner sampling. Phys Chem Chem Phys 2023. [PMID: 37401424 DOI: 10.1039/d3cp01007d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
In this work we discuss the generally applicable Wigner sampling and introduce a new, simplified Wigner sampling method, for computationally effective modeling of molecular properties containing nuclear quantum effects and vibrational anharmonicity. For various molecular systems test calculations of (a) vibrationally averaged rotational constants, (b) vibrational IR spectra and (c) photoelectron spectra have been performed. The performance of Wigner sampling has been assessed by comparing with experimental data and with results of other theoretical models, including harmonic and VPT2 approximations. The developed simplified Wigner sampling method shows advantages in application to large and flexible molecules.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Yury V Vishnevskiy
- 2Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany.
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6
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Semiexperimental equilibrium molecular structure of phthalic anhydride. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Demaison J, Vogt N, Ksenafontov DN. Accuracy of semiexperimental equilibrium structures: Sulfine as an example. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Vogt N, Nair KPR, Grabow JU, Demaison J. Microwave rotational spectrum and ab initio computations on 4-cyanopyridine: molecular structure and hyperfine interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1467053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - K. P. Rajappan Nair
- Institut für Physikalische Chemie und Elektrochemie, Wilhelm-Gottfried-Leibniz-Universität Hannover, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Wilhelm-Gottfried-Leibniz-Universität Hannover, Hannover, Germany
| | - Jean Demaison
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
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9
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Vogt N, Demaison J, Rudolph HD, Juanes M, Fernández J, Lesarri A. Semiexperimental and mass-dependent structures by the mixed regression method: Accurate equilibrium structure and failure of the Kraitchman method for ethynylcyclohexane. J Chem Phys 2018; 148:064306. [DOI: 10.1063/1.5018053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, University of Ulm, Albert-Einstein-Allee 47, 89081 Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Jean Demaison
- Section of Chemical Information Systems, University of Ulm, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Heinz Dieter Rudolph
- Section of Chemical Information Systems, University of Ulm, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Jairo Fernández
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
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10
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Demaison J, Craig NC, Gurusinghe R, Tubergen MJ, Rudolph HD, Coudert LH, Szalay PG, Császár AG. Fourier Transform Microwave Spectrum of Propene-3-d 1 (CH 2═CHCH 2D), Quadrupole Coupling Constants of Deuterium, and a Semiexperimental Equilibrium Structure of Propene. J Phys Chem A 2017; 121:3155-3166. [PMID: 28368600 DOI: 10.1021/acs.jpca.7b01470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ground-state rotational spectrum of propene-3-d1, CH2═CHCH2D, was measured by Fourier transform microwave spectroscopy. Transitions were assigned for the two conformers, one with the D atom in the symmetry plane (S) and the other with the D atom out of the plane (A). The energy difference between the two conformers was calculated to be 6.5 cm-1, the S conformer having lower energy. The quadrupole hyperfine structure due to deuterium was resolved and analyzed for both conformers. The experimental quadrupole coupling and the centrifugal distortion constants compared favorably to their ab initio counterparts. Ground-state rotational constants for the S conformer are 40582.157(9), 9067.024(1), and 7766.0165(12) MHz. Ground-state rotational constants for the A conformer are 43403.75(3), 8658.961(2), and 7718.247(2) MHz. For the A conformer, a small tunneling splitting (19 MHz) due to internal rotation was observed and analyzed. Using the new rotational constants of this work as well as those previously determined for the 13C species and for some deuterium-substituted species from the literature, a new semiexperimental equilibrium structure was determined and its high accuracy was confirmed. The difficulty in obtaining accurate coordinates for the out-of-plane hydrogen atom is discussed.
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Affiliation(s)
- Jean Demaison
- Section of Chemical Information Systems, University of Ulm , Albert Einstein Allee 47, 89069 Ulm, Germany
| | - Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College , Oberlin, Ohio 44074, United States
| | - Ranil Gurusinghe
- Department of Chemistry, Kent State University , Kent, Ohio 44242, United States
| | - Michael J Tubergen
- Department of Chemistry, Kent State University , Kent, Ohio 44242, United States
| | - Heinz Dieter Rudolph
- Section of Chemical Information Systems, University of Ulm , Albert Einstein Allee 47, 89069 Ulm, Germany
| | - Laurent H Coudert
- Institut des Sciences Moléculaires d'Orsay, UMR 8214, Bâtiment 210, Université Paris-Sud , 91405 Orsay, France
| | - Péter G Szalay
- Institute of Chemistry, Eötvös Loránd University , Budapest H-1053, Hungary
| | - Attila G Császár
- MTA-ELTE Complex Chemical Systems Research Group , Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
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11
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Vogt N, Demaison J, Cocinero EJ, Écija P, Lesarri A, Rudolph HD, Vogt J. The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations. Phys Chem Chem Phys 2016; 18:15555-63. [PMID: 27212641 DOI: 10.1039/c6cp01842d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mixed estimation method yields very accurate equilibrium structures, as observed in deoxyribose and fructose.
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Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Jean Demaison
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
| | - Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Heinz Dieter Rudolph
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Jürgen Vogt
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
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12
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Benchmark study of molecules with large-amplitude ring-twisting motion: accurate equilibrium structure of succinic anhydride from gas electron diffraction data and coupled-cluster computations. Struct Chem 2015. [DOI: 10.1007/s11224-015-0654-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Craig NC, Demaison J, Groner P, Rudolph HD, Vogt N. Electron delocalization in polyenes: a semiexperimental equilibrium structure for (3E)-1,3,5-hexatriene and theoretical structures for (3Z,5Z)-, (3E,5E)-, and (3E,5Z)-1,3,5,7-octatetraene. J Phys Chem A 2015; 119:195-204. [PMID: 25465856 DOI: 10.1021/jp510237h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electronic structure theory reveals that π-electron delocalization increases with the chain length in polyenes. To analyze quantitatively this effect a semiexperimental equilibrium structure has been determined for trans-hexatriene by the mixed estimation method. For this fit rotational constants for a number of carbon and hydrogen isotopologues as well as a high-level ab initio structure have been used. The accuracy is 0.001 Å for bond lengths and 0.1° for bond angles. For the three isomers of octatetraene, high-level ab initio calculations have given a comparably accurate structure. These structures have been used in comparison with the structure of s-trans-butadiene to show that "C═C" bonds increase in length and "C-C" bonds decrease in length as the polyene chain lengthens. These structural effects of π-electron delocalization increase toward the center of polyenes. Most likely, π-π conjugation in the molecules studied plays a large part in their planarity that, in turn, forces the hydrogen atoms of cis fragments in bay regions to be in a close contact. Their distance is indeed shorter than the sum of their van der Waals radii, and they seem to participate in a six-membered ring.
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Affiliation(s)
- Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College , Oberlin, Ohio 44074, United States
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14
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Vogt N, Marochkin II, Rykov AN. From the Determination of the Accurate Equilibrium Structure of 1-Methylthymine by Gas Electron Diffraction and Coupled Cluster Computations to the Observation of Methylation and Flexibility Effects in Pyrimidine Nucleobases. J Phys Chem A 2014; 119:152-9. [DOI: 10.1021/jp508500z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalja Vogt
- Chemieinformationssysteme, University of Ulm, 89069 Ulm, Germany
- Department
of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Ilya I. Marochkin
- Chemieinformationssysteme, University of Ulm, 89069 Ulm, Germany
- Department
of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anatolii N. Rykov
- Department
of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
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15
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Császár AG, Demaison J, Rudolph HD. Equilibrium Structures of Three-, Four-, Five-, Six-, and Seven-Membered Unsaturated N-Containing Heterocycles. J Phys Chem A 2014; 119:1731-46. [DOI: 10.1021/jp5084168] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Attila G. Császár
- Laboratory
of Molecular Structure and Dynamics, Eötvös University, H-1117 Budapest,
Pázmány Péter sétány 1/A, Budapest, Hungary
- MTA-ELTE Research Group on Complex Chemical Systems, H-1518 Budapest 112, P.O. Box
32, Budapest, Hungary
| | - Jean Demaison
- Laboratoire
de Physique des Lasers, Atomes et Molécules, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
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16
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Vogt N, Demaison J, Ksenafontov DN, Rudolph HD. A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of thymine from microwave rotational constants and coupled-cluster computations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Vogt N, Demaison J, Vogt J, Rudolph HD. Why it is sometimes difficult to determine the accurate position of a hydrogen atom by the semiexperimental method: Structure of molecules containing the OH or the CH3group. J Comput Chem 2014; 35:2333-42. [DOI: 10.1002/jcc.23758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Natalja Vogt
- Department of Theoretical Chemistry; Chemical Information Systems, University of Ulm; D-89069 Ulm Germany
- Department of Chemistry; Lomonosov Moscow State University; Moscow 119992 Russia
| | - Jean Demaison
- Department of Theoretical Chemistry; Chemical Information Systems, University of Ulm; D-89069 Ulm Germany
| | - Jürgen Vogt
- Department of Theoretical Chemistry; Chemical Information Systems, University of Ulm; D-89069 Ulm Germany
| | - Heinz Dieter Rudolph
- Department of Theoretical Chemistry; Chemical Information Systems, University of Ulm; D-89069 Ulm Germany
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18
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Demaison J, Craig NC, Groner P, Écija P, Cocinero EJ, Lesarri A, Rudolph HD. Accurate Equilibrium Structures for Piperidine and Cyclohexane. J Phys Chem A 2014; 119:1486-93. [DOI: 10.1021/jp505765t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire
de Physique des Lasers, Atomes et Molécules, Université de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Norman C. Craig
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Peter Groner
- Department
of Chemistry, University of Missouri—Kansas City, Kansas City, Missouri 64110-2499, United States
| | - Patricia Écija
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Ap. 644, E-48080 Bilbao, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Ap. 644, E-48080 Bilbao, Spain
| | - Alberto Lesarri
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
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19
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Vogt N, Demaison J, Rudolph HD. Accurate equilibrium structures of fluoro- and chloroderivatives of methane. Mol Phys 2014. [DOI: 10.1080/00268976.2014.915067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Demaison J, Császár AG, Groner P, Rudolph HD, Craig NC. Semiexperimental Equilibrium Structures for cis, cis- and trans, trans-1,4-Difluorobutadiene by the Mixed Estimation Method and Definitive Relative Energies of the Isomers. J Phys Chem A 2013; 117:13166-75. [DOI: 10.1021/jp4098183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire
de Physique des Lasers, Atomes et Molécules, Université de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Attila G. Császár
- Laboratory of Molecular Structure and Dynamics,
Institute of Chemistry, Eötvös University, Pázmány
Péter sétány 1/A, H-1117 Budapest, Hungary
- MTA-ELTE
Research Group on Complex Chemical Systems, P.O. Box
32, H-1518 Budapest, Hungary
| | - Peter Groner
- Department of Chemistry, University of Missouri—Kansas City, Kansas City, Missouri 64110-2499, United States
| | | | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
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21
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Rudolph HD, Demaison J, Császár AG. Accurate determination of the deformation of the benzene ring upon substitution: equilibrium structures of benzonitrile and phenylacetylene. J Phys Chem A 2013; 117:12969-82. [PMID: 24160689 DOI: 10.1021/jp408208s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accurate equilibrium, re, structures of the monosubstituted benzene molecules benzonitrile, C6H5CN, and phenylacetylene, C6H5CCH, have been determined using two different, to some extent complementary techniques. The semiexperimental, r(e)(SE), structural parameters are the result of a least-squares fit to equilibrium rotational constants derived from experimental effective ground-state rotational constants and rovibrational corrections based principally on an ab initio cubic force field. The composite ab initio Born-Oppenheimer, r(e)(BO), structural parameters are obtained from frozen-core and all-electron MP2 and the CCSD(T) geometry optimizations using Gaussian basis sets up to quintuple-zeta quality. The DFT(B3LYP) method, with two different Gaussian basis sets, 6-31G* and 6-311+G(3df,2pd), was used to calculate the cubic force field employed during the r(e)(SE) structure determination. With the 6-31G* basis set, the error of the rovibrational correction is to a large extent random, whereas with the 6-311+G(3df,2pd) basis set it is mainly systematic. As shown here, systematic errors do not have a significant effect on the accuracy of the derived structure; the quality of the structural fit, however, is sensitive to the true accuracy of the ground-state rotational constants. An even more important general conclusion of this study is that the addition of extra rotational constants from multisubstituted species does not seem to improve the accuracy of the r(e)(SE) structures, quite in contrast to the highly desirable availability of data corresponding to all singly substituted species.
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22
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Vogt N, Marochkin II, Rykov AN, Dorofeeva OV. Interplay of experiment and theory: determination of an accurate equilibrium structure of 1-methyluracil by the gas electron diffraction method and coupled-cluster computations. J Phys Chem A 2013; 117:11374-81. [PMID: 24168752 DOI: 10.1021/jp408297f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.
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Affiliation(s)
- Natalja Vogt
- Chemieinformationssysteme, University of Ulm , 89069 Ulm, Germany
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23
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Craig NC, Chen Y, Fuson HA, Tian H, van Besien H, Conrad AR, Tubergen MJ, Rudolph HD, Demaison J. Microwave spectra of the deuterium isotopologues of cis-hexatriene and a semiexperimental equilibrium structure. J Phys Chem A 2013; 117:9391-400. [PMID: 23237234 DOI: 10.1021/jp311035c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microwave transitions and ground state rotational constants are reported for five newly synthesized deuterium isotopologues of cis-1,3,5-hexatriene (cHTE). These rotational constants along with those of the parent and the three (13)C species are used with vibration-rotation constants calculated from an MP2/cc-pVTZ model to derive an equilibrium structure. That structure is improved by the mixed estimation method. In this method, internal coordinates from good-quality quantum chemical calculations (with appropriate uncertainties) are fit simultaneously with moments of inertia of the full set of isotopologues. The new structure of cHTE is confirmed to be planar and is stabilized by an interaction between the hydrogen atoms H2 and H5, which form a bond and participate in a six-membered ring. cHTE shows larger structural effects of π-electron delocalization than does butadiene with the effects being magnified in the center of the molecule. Thus, strong structural evidence now exists for an increase in π-electron delocalization as the polyene chain lengthens.
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Affiliation(s)
- Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College , Oberlin, Ohio 44074, United States
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24
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Vogt N, Khaikin LS, Grikina OE, Rykov AN. A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of uracil from gas-phase electron diffraction data and coupled-cluster calculations. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.07.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Demaison J, Rudolph HD, Császár AG. Deformation of the benzene ring upon fluorination: equilibrium structures of all fluorobenzenes. Mol Phys 2013. [DOI: 10.1080/00268976.2013.793843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jean Demaison
- a Laboratoire de Physique des Lasers, Atomes et Molécules , Université de Lille I , France
| | | | - Attila G. Császár
- c Laboratory of Molecular Structure and Dynamics, Institute of Chemistry , Eötvös University , Budapest , Hungary
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26
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Abstract
Rotational spectroscopy is known to be a technique that is widely used to infer information on molecular structure and dynamics. In the last few decades, its role in the field of atmospheric and astrophysical investigations has rapidly grown. However, several are the challenging aspects in rotational spectroscopy, since the detection and analysis of spectra as well as interpretation of obtained results are not at all straightforward. Quantum chemistry has reached such an accuracy that can be used to disentangle these challenging situations by guiding the experimental investigation, assisting in the determination of the spectroscopic parameters, and extracting information of chemical interest. This perspective provides an overview of the theoretical background and computational requirements needed for the accurate evaluation of the spectroscopic parameters of relevance to rotational spectroscopy. The role of theory in guiding and supporting experiment is detailed through a few examples, and the interplay of experiment and theory is discussed in terms of the information of physical and chemical interest that can be derived.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica Giacomo Ciamician, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy.
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27
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Demaison J, Jahn MK, Cocinero EJ, Lesarri A, Grabow JU, Guillemin JC, Rudolph HD. Accurate Semiexperimental Structure of 1,3,4-Oxadiazole by the Mixed Estimation Method. J Phys Chem A 2013; 117:2278-84. [DOI: 10.1021/jp400505v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire de Physique des
Lasers, Atomes et Molécules, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
| | - Michaela K. Jahn
- Institut für Physikalische Chemie & Elektrochemie, Lehrgebiet A, Gottfried-Wilhelm-Leibniz Universität, Callinstraße 3A, D-30167 Hannover, Germany
| | - Emilio J. Cocinero
- Departamento de Quı́mica
Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV-EHU),
Ap. 644, E-48080 Bilbao, Spain
| | - Alberto Lesarri
- Departamento de Quı́mica
Fı́sica y Quı́mica Inorgánica, Facultad
de Ciencias, Universidad de Valladolid,
E-47011 Valladolid, Spain
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie, Lehrgebiet A, Gottfried-Wilhelm-Leibniz Universität, Callinstraße 3A, D-30167 Hannover, Germany
| | - Jean-Claude Guillemin
- Institut
des Sciences Chimiques de
Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc,
CS 50837, 35708 Rennes Cedex 7, France
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28
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Demaison J, Craig NC, Conrad AR, Tubergen MJ, Rudolph HD. Semiexperimental Equilibrium Structure of the Lower Energy Conformer of Glycidol by the Mixed Estimation Method. J Phys Chem A 2012; 116:9116-22. [PMID: 22894798 DOI: 10.1021/jp305504x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jean Demaison
- Laboratoire de Physique des
Lasers, Atomes et Molécules, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
| | - Norman C. Craig
- Department of Chemistry and
Biochemistry, Oberlin College, Oberlin,
Ohio 44074, United States
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29
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Demaison J, Craig NC, Cocinero EJ, Grabow JU, Lesarri A, Rudolph HD. Semiexperimental Equilibrium Structures for the Equatorial Conformers of N-Methylpiperidone and Tropinone by the Mixed Estimation Method. J Phys Chem A 2012; 116:8684-92. [PMID: 22861349 DOI: 10.1021/jp304178n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire de Physique des
Lasers, Atomes et Molécules, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
| | - Norman C. Craig
- Department of Chemistry and
Biochemistry, Oberlin College, Oberlin,
Ohio 44074, United States
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, E-48080 Bilbao, Spain
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie, Lehrgebiet A, Gottfried-Wilhelm-Leibniz-Universität, Callinstraße 3A, D-30167 Hannover, Germany
| | - Alberto Lesarri
- Departamento de Química
Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
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30
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Demaison J, Császár AG, Margulès LD, Rudolph HD. Equilibrium Structures of Heterocyclic Molecules with Large Principal Axis Rotations upon Isotopic Substitution. J Phys Chem A 2011; 115:14078-91. [DOI: 10.1021/jp2063595] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire de Physique des Lasers, Atomes et Molécules, UMR CNRS 8523, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
| | - Attila G. Császár
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Laurent D. Margulès
- Laboratoire de Physique des Lasers, Atomes et Molécules, UMR CNRS 8523, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
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31
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Demaison JF, Craig NC. Semiexperimental Equilibrium Structure for cis,trans-1,4-Difluorobutadiene by the Mixed Estimation Method. J Phys Chem A 2011; 115:8049-54. [DOI: 10.1021/jp203575r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jean F. Demaison
- Laboratoire de Physique des Lasers, Atomes et Molécules, Université de Lille I, 59655 Villeneuve d’Ascq Cedex, France
| | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
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