1
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Sahoo NP, Franke PR, Stanton JF. On the performance of composite schemes in determining equilibrium molecular structures. J Comput Chem 2024; 45:1419-1427. [PMID: 38450778 DOI: 10.1002/jcc.27312] [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: 10/15/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 03/08/2024]
Abstract
Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.
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Affiliation(s)
- Nitai P Sahoo
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
| | - Peter R Franke
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
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2
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Franke PR, Stanton JF. Influence of fourth-order vibrational corrections on semi-experimental (reSE) structures of linear molecules. J Chem Phys 2024; 160:014102. [PMID: 38174791 DOI: 10.1063/5.0177694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Semi-experimental structures (reSE) are derived from experimental ground state rotational constants combined with theoretical vibrational corrections. They permit a meaningful comparison with equilibrium structures based on high-level ab initio calculations. Typically, the vibrational corrections are evaluated with second-order vibrational perturbation theory (VPT2). The amount of error introduced by this approximation is generally thought to be small; however, it has not been thoroughly quantified. Herein, we assess the accuracy of theoretical vibrational corrections by extending the treatment to fourth order (VPT4) for a series of small linear molecules. Typical corrections to bond distances are on the order of 10-5 Å. Larger corrections, nearly 0.0002 Å, are obtained to the bond lengths of NCCN and CNCN. A borderline case is CCCO, which will likely require variational computations for a satisfactory answer. Treatment of vibrational effects beyond VPT2 will thus be important when one wishes to know bond distances confidently to four decimal places (10-4 Å). Certain molecules with shallow bending potentials, e.g., HOC+, are not amenable to a VPT2 description and are not improved by VPT4.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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3
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Ríos P, See MS, Handford RC, Cooper JK, Don Tilley T. Tetracopper σ-Bound μ-Acetylide and -Diyne Units Stabilized by a Naphthyridine-based Dinucleating Ligand. Angew Chem Int Ed Engl 2023; 62:e202310307. [PMID: 37705304 DOI: 10.1002/anie.202310307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023]
Abstract
Reactions of a dicopper(I) tert-butoxide complex with alkynes possessing boryl or silyl capping groups resulted in formation of unprecedented tetracopper(I) μ-acetylide/diyne complexes that were characterized by NMR and UV/Vis spectroscopy, mass spectrometry and single-crystal X-ray diffraction. These compounds possess an unusual μ4 -η1 :η1 :η1 :η1 coordination mode for the bridging organic fragment, enforced by the rigid and dinucleating nature of the ligand utilized. Thus, the central π system remains unperturbed and accessible for subsequent reactivity and modification. This has been corroborated by addition of a fifth copper atom, giving rise to a pentacopper acetylide complex. This work may provide a new approach by which metal-metal cooperativity can be exploited in the transformation of acetylide and diyne groups to a variety of substrates, or as a starting point for the controlled synthesis of copper(I) alkyne-containing clusters.
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Affiliation(s)
- Pablo Ríos
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica, Centro de Innovación en Química Avanzada (ORFEO-CINQA), CSIC and Universidad de Sevilla, 41092, Sevilla, Spain
- Department of Chemistry, University of California, Berkeley, USA
| | - Matthew S See
- Department of Chemistry, University of California, Berkeley, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rex C Handford
- Department of Chemistry, University of California, Berkeley, USA
| | - Jason K Cooper
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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Esselman BJ, Zdanovskaia MA, Owen AN, Stanton JF, Woods RC, McMahon RJ. Precise Equilibrium Structure of Benzene. J Am Chem Soc 2023; 145:21785-21797. [PMID: 37774420 DOI: 10.1021/jacs.3c03109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Recent advances in gas-phase structure determination afford outstanding agreement between the CCSD(T)/cc-pCVTZ-corrected semi-experimental (reSE) equilibrium structures and their corresponding best theoretical estimates (BTEs) of the equilibrium structures (re) based upon corrections to the CCSD(T)/cc-pCV5Z geometries for the aromatic heterocycles pyrimidine and pyridazine. Herein, that same analysis is extended to the fundamental aromatic molecule benzene, using published experimental spectroscopic data for a total of 11 available isotopologues. The incorporation of rotational constants from all of these isotopologues and CCSD(T) corrections to address the impacts of both the vibration-rotation interaction and electron-mass distribution results in a highly precise and accurate reSE structure. The CCSD(T)/cc-pCV5Z optimized geometry has been further corrected to address a finite basis set, untreated electron correlation, relativistic effects, and a breakdown of the Born-Oppenheimer approximation. This analysis achieves outstanding agreement between the re (BTE) and reSE structural parameters of benzene to a highly satisfying level (0.0001 Å), an agreement that surpasses our recently published structures of the aforementioned nitrogen-substituted benzene analogues. The D6h geometry of benzene is now known to an unprecedented precision: RC-C = 1.3913 (1) Å and RC-H = 1.0809 (1) Å. The mutual agreement between theory and experiment presented in this work validates both, substantially resolving all discrepancies between the reSE and theoretical re structures available in the literature.
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Affiliation(s)
- Brian J Esselman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Maria A Zdanovskaia
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Andrew N Owen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - John F Stanton
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - R Claude Woods
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Robert J McMahon
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
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5
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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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6
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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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7
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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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8
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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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9
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Varvarezos L, Delgado-Guerrero J, Di Fraia M, Kelly TJ, Palacios A, Callegari C, Cavalieri AL, Coffee R, Danailov M, Decleva P, Demidovich A, DiMauro L, Düsterer S, Giannessi L, Helml W, Ilchen M, Kienberger R, Mazza T, Meyer M, Moshammer R, Pedersini C, Plekan O, Prince KC, Simoncig A, Schletter A, Ueda K, Wurzer M, Zangrando M, Martín F, Costello JT. Controlling Fragmentation of the Acetylene Cation in the Vacuum Ultraviolet via Transient Molecular Alignment. J Phys Chem Lett 2023; 14:24-31. [PMID: 36562987 PMCID: PMC9841558 DOI: 10.1021/acs.jpclett.2c03354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
An open-loop control scheme of molecular fragmentation based on transient molecular alignment combined with single-photon ionization induced by a short-wavelength free electron laser (FEL) is demonstrated for the acetylene cation. Photoelectron spectra are recorded, complementing the ion yield measurements, to demonstrate that such control is the consequence of changes in the electronic response with molecular orientation relative to the ionizing field. We show that stable C2H2+ cations are mainly produced when the molecules are parallel or nearly parallel to the FEL polarization, while the hydrogen fragmentation channel (C2H2+ → C2H+ + H) predominates when the molecule is perpendicular to that direction, thus allowing one to distinguish between the two photochemical processes. The experimental findings are supported by state-of-the art theoretical calculations.
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Affiliation(s)
- L. Varvarezos
- School
of Physical Sciences and National Centre for Plasma Science and Technology, Dublin City University, Dublin 9, Ireland
| | - J. Delgado-Guerrero
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Instituto
Madrileño de Estudios Advanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - M. Di Fraia
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - T. J. Kelly
- Department
of Computer Science and Applied Physics, Atlantic Technological University, T91 T8NW Galway, Ireland
| | - A. Palacios
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chimical Sciences, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - C. Callegari
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - A. L. Cavalieri
- Institute
of Applied Physics, University of Bern, 3012 Bern, Switzerland
- Paul
Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - R. Coffee
- Linac
Coherent Light Source/SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - M. Danailov
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - P. Decleva
- Istituto
Officina dei Materiali IOM-CNR and Dipartimento di Scienze Chimiche
e Farmaceutiche, Università degli
Studi di Trieste, 34121 Trieste, Italy
| | - A. Demidovich
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - L. DiMauro
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - S. Düsterer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - L. Giannessi
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - W. Helml
- Fakultät
Physik, Technische Universität Dortmund, Maria-Goeppert-Mayer-Str. 2, 44227 Dortmund, Germany
| | - M. Ilchen
- Institut
fur Physik und CINSaT, Universitat Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
- European XFEL, Holzkoppel
4, 22869 Schenefeld, Germany
| | - R. Kienberger
- Physics
Department, Technische Universität
München, 85748 Garching, Germany
| | - T. Mazza
- European XFEL, Holzkoppel
4, 22869 Schenefeld, Germany
| | - M. Meyer
- European XFEL, Holzkoppel
4, 22869 Schenefeld, Germany
| | - R. Moshammer
- Max-Planck Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - C. Pedersini
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - O. Plekan
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - K. C. Prince
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
- Department
of Chemistry and Biotechnology, Swinburne
University of Technology, Melbourne, Victoria 3122, Australia
| | - A. Simoncig
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - A. Schletter
- Physics
Department, Technische Universität
München, 85748 Garching, Germany
| | - K. Ueda
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - M. Wurzer
- Physics
Department, Technische Universität
München, 85748 Garching, Germany
| | - M. Zangrando
- Elettra-Sincrotrone
Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
- Istituto
Officina dei Materiali, Consiglio Nazionale
delle Ricerche, 34149 Trieste, Italy
| | - F. Martín
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Instituto
Madrileño de Estudios Advanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
- Condensed
Matter Physics Center, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - J. T. Costello
- School
of Physical Sciences and National Centre for Plasma Science and Technology, Dublin City University, Dublin 9, Ireland
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10
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Bunn HA, Esselman BJ, Franke PR, Kougias SM, McMahon RJ, Stanton JF, Widicus Weaver SL, Woods RC. Millimeter/Submillimeter-wave Spectroscopy and the Semi-experimental Equilibrium ( reSE) Structure of 1 H-1,2,4-Triazole ( c-C 2H 3N 3). J Phys Chem A 2022; 126:8196-8210. [DOI: 10.1021/acs.jpca.2c06038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hayley A. Bunn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Brian J. Esselman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Peter R. Franke
- Department of Chemistry, University of Florida, Gainesville, Florida32611-7200, United States
| | - Samuel M. Kougias
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Robert J. McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - John F. Stanton
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida32611-7200, United States
| | | | - R. Claude Woods
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
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11
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Noonikara-Poyil A, Ridlen SG, Fernández I, Dias HVR. Isolable acetylene complexes of copper and silver. Chem Sci 2022; 13:7190-7203. [PMID: 35799825 PMCID: PMC9214850 DOI: 10.1039/d2sc02377f] [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: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
Copper and silver play important roles in acetylene transformations but isolable molecules with acetylene bonded to Cu(i) and Ag(i) ions are scarce. This report describes the stabilization of π-acetylene complexes of such metal ions supported by fluorinated and non-fluorinated, pyrazole-based chelators. These Cu(i) and Ag(i) complexes were formed readily in solutions under an atmosphere of excess acetylene and the appropriate ligand supported metal precursor, and could be isolated as crystalline solids, enabling complete characterization using multiple tools including X-ray crystallography. Molecules that display κ2-or κ3-ligand coordination modes and trigonal planar or tetrahedral metal centers have been observed. Different trends in coordination shifts of the acetylenic carbon resonance were revealed by 13C NMR spectroscopy for the Cu(i) and Ag(i) complexes. The reduction in acetylene
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C
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C due to metal ion coordination is relatively large for copper adducts. Computational tools were also used to quantitatively understand in detail the bonding situation in these species. It is found that the interaction between the transition metal fragment and the acetylene ligand is significantly stronger in the copper complexes, which is consistent with the experimental findings. The CC distance of these copper and silver acetylene complexes resulting from routine X-ray models suffers due to incomplete deconvolution of thermal smearing and anisotropy of the electron density in acetylene, and is shorter than expected. A method to estimate the CC distance of these metal complexes based on their experimental CC is also presented. Gaseous acetylene can be trapped on copper(i) and silver(i) sites supported by pyrazole-based scorpionates to produce isolable molecules for detailed investigations and the study of metal-acetylene bonding.![]()
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Affiliation(s)
- Anurag Noonikara-Poyil
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Shawn G. Ridlen
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040-Madrid, Spain
| | - H. V. Rasika Dias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA
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12
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Melli A, Tonolo F, Barone V, Puzzarini C. Extending the Applicability of the Semi-experimental Approach by Means of "Template Molecule" and "Linear Regression" Models on Top of DFT Computations. J Phys Chem A 2021; 125:9904-9916. [PMID: 34752702 PMCID: PMC8607424 DOI: 10.1021/acs.jpca.1c07828] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Indexed: 11/28/2022]
Abstract
The accurate determination of equilibrium structures for isolated molecules plays a central role in the evaluation and interpretation of stereoelectronic, thermodynamic, and spectroscopic properties. For small semi-rigid systems, state-of-the-art quantum-chemical computations can rival the most sophisticated experimental results. For larger molecules, cheaper yet accurate approaches need to be defined. The double-hybrid rev-DSD-PBEP86 functional already delivers remarkable results that can be further improved by means of a "Lego brick" model. This is based on the idea that a molecular system can be seen as formed by different fragments (the "Lego bricks"), whose accurate semi-experimental (SE) equilibrium geometries are available. The template molecule (TM) approach can be used to account for the modifications occurring when going from the isolated fragment to the molecular system under investigation, with the linear regression (LR) model employed to correct the linkage between the different fragments. The resulting TM-SE_LR approach has been tested with respect to available SE equilibrium structures and rotational constants. Indeed, the latter parameters straightforwardly depend on the equilibrium geometry of the system under consideration. The main outcome of our study is the reliability, robustness, and accuracy of this novel approach. The molecular systems considered for benchmarking the TM-SE_LR scheme are those formally issued from addition/elimination reactions of nucleophilic unsaturated radicals (e.g., CN, C2H, and phenyl) to alkenes, imines, and aldehydes, whose rotational spectra have been investigated, but accurate structural determinations are not yet available.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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13
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Affiliation(s)
- Jean Demaison
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), CP160/09, Faculté des Sciences, Université Libre de Bruxelles (U.L.B.) Brussels, Belgium
| | - Jacques Liévin
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), CP160/09, Faculté des Sciences, Université Libre de Bruxelles (U.L.B.) Brussels, Belgium
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14
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Melli A, Barone V, Puzzarini C. Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case. J Phys Chem A 2021; 125:2989-2998. [PMID: 33818109 PMCID: PMC8154618 DOI: 10.1021/acs.jpca.1c01679] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Indexed: 11/30/2022]
Abstract
The ubiquitous role of water and its amphiprotic nature call for a deeper insight into the physical-chemical properties of hydrogen-bonded complexes formed with building blocks of biomolecules. In this work, the semiexperimental (SE) approach combined with the template model (TM) protocol allowed the accurate determination of the equilibrium structure of two isomeric forms of the imidazole-water complex. In this procedure, the integration of experiment (thanks to a recent rotational spectroscopy investigation) and theory is exploited, also providing the means of assessing the reliability and accuracy of different quantum-chemical approaches. Overall, this study demonstrated the robustness of the combined SE-TM approach, which can provide accurate results using affordable quantum-chemical methods. Finally, the structural and energetic characteristics of these complexes have been examined in detail and compared with those of analogous heterocycle-water adducts, also exploiting energy decomposition analyses.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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15
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Müller HS, Thorwirth S, Lewen F. Rotational spectroscopy of singly 13C substituted isotopomers of propyne and determination of a semi-empirical equilibrium structure. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Pavošević F, Culpitt T, Hammes-Schiffer S. Multicomponent Quantum Chemistry: Integrating Electronic and Nuclear Quantum Effects via the Nuclear–Electronic Orbital Method. Chem Rev 2020; 120:4222-4253. [DOI: 10.1021/acs.chemrev.9b00798] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabijan Pavošević
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Tanner Culpitt
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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17
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Puzzarini C, Barone V. The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy. Phys Chem Chem Phys 2020; 22:6507-6523. [PMID: 32163090 DOI: 10.1039/d0cp00561d] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
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18
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Bakowies D. Estimating Systematic Error and Uncertainty in Ab Initio Thermochemistry: II. ATOMIC(hc) Enthalpies of Formation for a Large Set of Hydrocarbons. J Chem Theory Comput 2019; 16:399-426. [DOI: 10.1021/acs.jctc.9b00974] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dirk Bakowies
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstr. 80, CH 4056 Basel, Switzerland
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19
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Schneider PE, Pavošević F, Hammes-Schiffer S. Diagonal Born-Oppenheimer Corrections within the Nuclear-Electronic Orbital Framework. J Phys Chem Lett 2019; 10:4639-4643. [PMID: 31347849 DOI: 10.1021/acs.jpclett.9b01803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The nuclear-electronic orbital (NEO) method treats specified nuclei, typically protons, quantum mechanically on the same level as the electrons. This approach invokes the Born-Oppenheimer separation between the quantum and classical nuclei, as well as the conventional separation between the electrons and classical nuclei. To test the validity of this additional adiabatic approximation, herein the diagonal Born-Oppenheimer correction (DBOC) within the NEO framework is derived, analyzed, and calculated numerically for a set of eight molecules. Inclusion of the NEO DBOC is found to change the equilibrium bond lengths by only ∼10-4 Å and the heavy atom vibrational stretching frequencies by ∼1-2 cm-1 per quantum proton bonded to an atom participating in the vibrational mode. These results imply that the DBOC does not significantly impact molecular properties computed with the NEO approach, although it can be included when necessary. Understanding the physical characteristics and quantitative contributions of the DBOC has broad implications for applications of multicomponent density functional theory and wave function methods.
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Affiliation(s)
- Patrick E Schneider
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Fabijan Pavošević
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
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20
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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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21
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Reimers JR, Hush NS. The critical role of the transition-state cusp diameter in understanding adiabatic and non-adiabatic electron transfer. RUSS J ELECTROCHEM+ 2017. [DOI: 10.1134/s1023193517090105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Timár M, Barcza G, Gebhard F, Veis L, Legeza Ö. Hückel-Hubbard-Ohno modeling of π-bonds in ethene and ethyne with application to trans-polyacetylene. Phys Chem Chem Phys 2016; 18:18835-45. [PMID: 27348188 DOI: 10.1039/c6cp00726k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantum chemistry calculations provide the potential energy between two carbon atoms in ethane (H3C-CH3), ethene (H2C[double bond, length as m-dash]CH2), and ethyne (HC[triple bond, length as m-dash]CH) as a function of the atomic distance. Based on the energy function for the σ-bond in ethane, Vσ(r), we use the Hückel model with Hubbard-Ohno interaction for the π electrons to describe the energies Vσπ(r) and Vσππ(r) for the σπ double bond in ethene and the σππ triple bond in ethyne, respectively. The fit of the force functions shows that the electron transfer matrix element and the Peierls coupling can be estimated with some precision whereas the Hubbard-Ohno parameters are insignificant at the distances under consideration. We apply the Hückel-Hubbard-Ohno model to describe the bond lengths and the energies of elementary electronic excitations of trans-polyacetylene, (CH)n, whereby we adjust the σ-bond potential for conjugated polymers.
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Affiliation(s)
- Máté Timár
- Strongly Correlated Systems Lendület Research Group, Institute for Solid State Physics and Optics, MTA Wigner Research Centre for Physics, P. O. Box 49, H-1525 Budapest, Hungary.
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23
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Imafuku Y, Abe M, Schmidt MW, Hada M. Heavy Element Effects in the Diagonal Born-Oppenheimer Correction within a Relativistic Spin-Free Hamiltonian. J Phys Chem A 2016; 120:2150-9. [PMID: 27003510 DOI: 10.1021/acs.jpca.6b01507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Most previous evaluations of the BO correction are, however, focused on light-element molecules and based on a nonrelativistic Hamiltonian, so no information about the BO approximation (BOA) breakdown in heavy-element molecules is available. The present work is the first to investigate the BOA breakdown for the entire periodic table, by considering scalar relativistic effects in the Diagonal BO correction (DBOC). In closed shell atoms, the relativistic EDBOC scales as Z(1.25) and the nonrelativistic EDBOC scales as Z(1.17), where Z is the atomic number. Hence, we found that EDBOC becomes larger in heavy element atoms and molecules, and the relativistic EDBOC increases faster than nonrelativistic EDBOC. We have further investigated the DBOC effects on properties such as potential energy curves, spectroscopic parameters, and various energetic properties. The DBOC effects for these properties are mostly affected by the lightest atom in the molecule. Hence, in X2 or XAt molecule (X = H, Li, Na, K, Rb, and Cs) the effect of DBOC systematically decreases when X becomes heavier but in HX molecules, the effect of DBOC seems relatively similar among all the molecules.
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Affiliation(s)
- Yuji Imafuku
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University , Tokyo 192-0397, Japan
| | - Minori Abe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University , Tokyo 192-0397, Japan
| | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory (US-DOE), Iowa State University , Ames, Iowa 50011, United States
| | - Masahiko Hada
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University , Tokyo 192-0397, Japan
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24
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Tamassia F, Cané E, Fusina L, Di Lonardo G. The experimental equilibrium structure of acetylene. Phys Chem Chem Phys 2016; 18:1937-44. [PMID: 26687993 DOI: 10.1039/c5cp05997f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The empirical equilibrium structure of acetylene has been derived by exploiting the very precise experimental rotational constants available in the literature for the 10 isotopologues relative to all the possible combinations of H, D, (12)C and (13)C atoms. The geometry obtained when data for all species are fitted together is: re(CH) = 106.167(14) pm and re(CC) = 120.2866(72) pm. This determination shows some systematic residuals due to the singly D-substituted isotopologues. If we exclude such species from the fit, we obtain our most precise evaluation: re(CH) = 106.1689(23) pm and re(CC) = 120.2817(12) pm. The possibility of a breakdown of the Born-Oppenheimer approximation has also been tested.
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Affiliation(s)
- Filippo Tamassia
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
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25
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Zaleski DP, Stephens SL, Tew DP, Bittner DM, Walker NR, Legon AC. Distortions of ethyne when complexed with a cuprous or argentous halide: the rotational spectrum of C2H2CuF. Phys Chem Chem Phys 2015; 17:18857. [PMID: 26134582 PMCID: PMC4672754 DOI: 10.1039/c5cp02248g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/17/2015] [Indexed: 11/25/2022]
Abstract
A new molecule C2H2···CuF has been synthesized in the gas phase by means of the reaction of laser-ablated metallic copper with a pulse of gas consisting of a dilute mixture of ethyne and sulfur hexafluoride in argon.
A new molecule C2H2···CuF has been synthesized in the gas phase by means of the reaction of laser-ablated metallic copper with a pulse of gas consisting of a dilute mixture of ethyne and sulfur hexafluoride in argon. The ground-state rotational spectrum was detected by two types of Fourier-transform microwave spectroscopy, namely that conducted in a microwave Fabry–Perot cavity and the chirped-pulse broadband technique. The spectroscopic constants of the six isotopologues 12C2H2···63Cu19F, 12C2H2···65Cu19F, 13C2H2···63Cu19F, 13C2H2···65Cu19F, 12C2D2···63Cu19F and 12C2D2···65Cu19F were determined and interpreted to show that the molecule has a planar, T-shaped geometry belonging to the molecular point group C2v, with CuF forming the stem of the T. Quantitative interpretation reveals that the ethyne molecule is distorted when subsumed into the complex in such manner that the C
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C bond lengthens (by δr) and the two H atoms cease to be collinear with the CC internuclear line. The H atoms move symmetrically away from the approaching Cu atom of CuF, to increase each *C–H angle by δA = 14.65(2)°, from 180° to 194.65(2)°. Ab initio calculations at the explicitly-correlated level of theory CCSD(T)(F12*)/aug-cc-pVTZ lead to good agreement with the experimental geometry. It is shown that similar distortions δr and δA, similarly determined, for four complexes C2H2···MX (M = Cu or Ag; X = F, Cl or CCH) are approximately linearly related to the energies De for the dissociation process C2H2···MX = C2H2 + MX.
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Affiliation(s)
- Daniel P Zaleski
- School of Chemistry, Newcastle University, Bedson Building, Newcastle-upon-Tyne, NE1 7RU, UK.
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26
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Zaleski DP, Tew DP, Walker NR, Legon AC. Chemistry in laser-induced plasmas: formation of M-C≡C-Cl (M = Ag or Cu) and their characterization by rotational spectroscopy. J Phys Chem A 2015; 119:2919-25. [PMID: 25732940 PMCID: PMC4578364 DOI: 10.1021/acs.jpca.5b01861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The new linear molecule Ag-C≡C-Cl has been detected and fully characterized by means of rotational spectroscopy. It was synthesized by laser ablation of a silver rod in the presence of a gaseous sample containing a low concentration of CCl4 in argon, cooled to a rotational temperature approaching ∼1-3 K through supersonic expansion, and analyzed by chirped-pulse, Fourier transform microwave spectroscopy. Six isotopologues were investigated, and for each the spectroscopic constants B0, D(J) and χ(aa)(Cl) were determined. The B0 values were interpreted to give the following bond lengths: r(Ag-C) = 2.015(14) Å and r(C-Cl) = 1.635(6) Å, with r(C≡C) = 1.2219 Å assumed from an ab initio calculation at the CCSD(T)/aug-cc-pV5Z level of theory. The Cu analogue Cu-C≡C-Cl was similarly identified and characterized.
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Affiliation(s)
- Daniel P Zaleski
- †School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, Tyne and Wear NE1 7RU, United Kingdom
| | - David P Tew
- ‡School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8 1TS, United Kingdom
| | - Nicholas R Walker
- †School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne, Tyne and Wear NE1 7RU, United Kingdom
| | - Anthony C Legon
- ‡School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8 1TS, United Kingdom
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27
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Piccardo M, Penocchio E, Puzzarini C, Biczysko M, Barone V. Semi-Experimental Equilibrium Structure Determinations by Employing B3LYP/SNSD Anharmonic Force Fields: Validation and Application to Semirigid Organic Molecules. J Phys Chem A 2015; 119:2058-82. [DOI: 10.1021/jp511432m] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Matteo Piccardo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Emanuele Penocchio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca CNR,
UOS di Pisa, Via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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28
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Paytakov G, Dinadayalane T, Leszczynski J. Toward Selection of Efficient Density Functionals for van der Waals Molecular Complexes: Comparative Study of C–H···π and N–H···π Interactions. J Phys Chem A 2015; 119:1190-200. [DOI: 10.1021/jp511450u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Guvanchmyrat Paytakov
- Interdisciplinary Center for
Nanotoxicity, Department of Chemistry
and Biochemistry, Jackson State University, J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Tandabany Dinadayalane
- Department
of Chemistry, Clark Atlanta University, 223 James P. Brawley Drive, S.W., Atlanta, Georgia 30314, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for
Nanotoxicity, Department of Chemistry
and Biochemistry, Jackson State University, J. R. Lynch Street, Jackson, Mississippi 39217, United States
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29
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Møllendal H, Samdal S, Guillemin JC. Microwave and quantum-chemical study of conformational properties and intramolecular hydrogen bonding of 2-hydroxy-3-butynenitrile (HC≡CCH(OH)C≡N). J Phys Chem A 2015; 119:634-40. [PMID: 25560047 DOI: 10.1021/jp5112923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microwave spectra of 2-hydroxy-3-butynenitrile, HC≡CCH(OH)C≡N, and a deuterated species, HC≡CCH(OD)C≡N, have been investigated in the 38-120 GHz spectral region. Three rotameric forms, each stabilized by intramolecular hydrogen bonds, are possible for this compound. The hydrogen atom of the hydroxyl group is hydrogen-bonded to the π electrons of the alkynyl group in one of these conformers, to the π electrons of the cyano group in the second rotamer, and to both of these groups simultaneously in the third conformer. The microwave spectra of the parent and deuterated species of last-mentioned form have been assigned, and accurate values of the rotational and quartic centrifugal distortion constants of these species have been determined. The spectra of two vibrational excited states of this conformer have also been assigned, and their frequencies have been determined by relative intensity measurements. Quantum-chemical calculations at the MP2/cc-pVTZ and CCSD/cc-pVQZ levels were performed to assist the microwave work. The theoretical predictions were generally found to be in good agreement with observations.
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Affiliation(s)
- Harald Møllendal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo , P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
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30
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Reimers JR, McKemmish LK, McKenzie RH, Hush NS. Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born–Oppenheimer breakdown corrections. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp02238j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analytical and numerical solutions describing Born–Oppenheimer breakdown in a simple, widely applicable, model depict shortcomings in modern computational methods.
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Affiliation(s)
- Jeffrey R. Reimers
- International Centre for Quantum and Molecular Structure
- College of Sciences, Shanghai University
- Shanghai 200444
- China
- School of Mathematical and Physical Sciences
| | - Laura K. McKemmish
- Department of Physics and Astronomy
- University College London
- London
- UK
- School of Chemistry
| | - Ross H. McKenzie
- School of Mathematics and Physics
- The University of Queensland
- Australia
| | - Noel S. Hush
- School of Chemistry
- The University of Sydney
- Sydney
- Australia
- School of Molecular Biosciences
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31
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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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32
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Stephens SL, Bittner DM, Mikhailov VA, Mizukami W, Tew DP, Walker NR, Legon AC. Changes in the geometries of C₂H₂ and C₂H₄ on coordination to CuCl revealed by broadband rotational spectroscopy and ab-initio calculations. Inorg Chem 2014; 53:10722-30. [PMID: 25233123 DOI: 10.1021/ic501899c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular geometries of isolated complexes in which a single molecule of C2H4 or C2H2 is bound to CuCl have been determined through pure rotational spectroscopy and ab-initio calculations. The C2H2···CuCl and C2H4···CuCl complexes are generated through laser vaporization of a copper rod in the presence of a gas sample undergoing supersonic expansion and containing C2H2 (or C2H4), CCl4, and Ar. Results are presented for five isotopologues of C2H2···CuCl and six isotopologues of C2H4···CuCl. Both of these complexes adopt C(2v), T-shaped geometries in which the hydrocarbon binds to the copper atom through its π electrons such that the metal is equidistant from all H atoms. The linear and planar geometries of free C2H2 and C2H4, respectively, are observed to distort significantly on attachment to the CuCl unit, and the various changes are quantified. The ∠(*-C-H) parameter in C2H2 (where * indicates the midpoint of the C≡C bond) is measured to be 192.4(7)° in the r0 geometry of the complex representing a significant change from the linear geometry of the free molecule. This distortion of the linear geometry of C2H2 involves the hydrogen atoms moving away from the copper atom within the complex. Ab-initio calculations at the CCSD(T)(F12*)/AVTZ level predict a dihedral ∠(HCCCu) angle of 96.05° in C2H4···CuCl, and the experimental results are consistent with such a distortion from planarity. The bonds connecting the carbon atoms within each of C2H2 and C2H4, respectively, extend by 0.027 and 0.029 Å relative to the bond lengths in the isolated molecules. Force constants, k(σ), and nuclear quadrupole coupling constants, χ(aa)(Cu), [χ(bb)(Cu) - χ(cc)(Cu)], χ(aa)(Cl), and [χ(bb)(Cl) - χ(cc)(Cl)], are independently determined for all isotopologues of C2H2···CuCl studied and for four isotopologues of C2H4···CuCl.
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Affiliation(s)
- Susanna L Stephens
- School of Chemistry, Bedson Building, Newcastle University , Newcastle upon Tyne, Tyne and Wear NE1 7RU, United Kingdom
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Møllendal H, Samdal S, Gauss J, Guillemin JC. Synthesis, Microwave Spectrum, Quantum Chemical Calculations, and Conformational Composition of a Novel Primary Phosphine, Cyclopropylethynylphosphine, (C3H5C≡CPH2). J Phys Chem A 2014; 118:9419-28. [DOI: 10.1021/jp506169g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harald Møllendal
- Centre for Theoretical
and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O.
Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Svein Samdal
- Centre for Theoretical
and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O.
Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Jürgen Gauss
- Institut für
Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jean-Claude Guillemin
- Institut
des Sciences
Chimiques de Rennes, École Nationale Supérieure de Chimie
de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837 35708 Rennes Cedex
7, France
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Stephens SL, Zaleski DP, Mizukami W, Tew DP, Walker NR, Legon AC. Distortion of ethyne on coordination to silver acetylide, C2H2⋅⋅⋅AgCCH, characterised by broadband rotational spectroscopy and ab initio calculations. J Chem Phys 2014; 140:124310. [DOI: 10.1063/1.4868035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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Samdal S, Møllendal H, Guillemin JC. Microwave spectrum and conformational properties of 4-isocyano-1-butyne (HC≡CCH2CH2N≡C). J Phys Chem A 2013; 117:10304-10. [PMID: 24003874 DOI: 10.1021/jp407126x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microwave spectrum of 4-isocyano-1-butyne (HC≡CCH2CH2N≡C) has been investigated in the 12.4-77.6 GHz spectral region. The spectra of two rotamers denoted ap and sc were assigned. ap has an antiperiplanar arrangement for the C-C-C-N chain of atoms, whereas sc has synclinal conformation for this link. The ground state spectrum and three vibrationally excited state spectra of the lowest torsional vibration were assigned for ap, while the ground vibrational state spectrum was assigned for sc. The C-C-C-N dihedral angle was found to be 64.5(30)° in sc and exactly 180° in ap. ap was determined to be 2.9(6) kJ/mol lower in energy than sc from relative intensity measurements. The microwave study has been augmented with ab initio and DFT calculations employing the CCSD(T), MP2, and B3LYP methods with the cc-pVTZ basis set. A Natural Bond Order analysis has also been performed. Most, but not all, of the quantum chemical predictions agree satisfactorily with the experimental results.
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Affiliation(s)
- Svein Samdal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo , P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
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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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38
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Herman M, Perry DS. Molecular spectroscopy and dynamics: a polyad-based perspective. Phys Chem Chem Phys 2013; 15:9970-93. [DOI: 10.1039/c3cp50463h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Stephens SL, Mizukami W, Tew DP, Walker NR, Legon AC. Distortion of ethyne on formation of a π complex with silver chloride: C2H2⋯Ag–Cl characterised by rotational spectroscopy and ab initio calculations. J Chem Phys 2012; 137:174302. [DOI: 10.1063/1.4761895] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Cauët E, Carette T, Lauzin C, Li JG, Loreau J, Delsaut M, Nazé C, Verdebout S, Vranckx S, Godefroid M, Liévin J, Vaeck N. From atoms to biomolecules: a fruitful perspective. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1254-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Coccia E, Chernomor O, Barborini M, Sorella S, Guidoni L. Molecular Electrical Properties from Quantum Monte Carlo Calculations: Application to Ethyne. J Chem Theory Comput 2012; 8:1952-62. [DOI: 10.1021/ct300171q] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emanuele Coccia
- Dipartimento di Scienze Fisiche
e Chimiche, Universitá degli Studi dell'Aquila, via Vetoio (Coppito), 67100, L'Aquila, Italy
| | - Olga Chernomor
- Università Degli Studi de L’Aquila, Dipartimento di Matematica
Pura ed Applicata, via Vetoio (Coppito 1), 67100 L’Aquila,
Italy
| | - Matteo Barborini
- Università Degli Studi de L’Aquila, Dipartimento di Matematica
Pura ed Applicata, via Vetoio (Coppito 1), 67100 L’Aquila,
Italy
| | - Sandro Sorella
- Scuola Internazionale
Superiore
di Studi Avanzati (SISSA) and Democritos National Simulation Center, Istituto Officina dei Materiali del CNR, via Bonomea
265, 34136 Trieste, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche
e Chimiche, Universitá degli Studi dell'Aquila, via Vetoio (Coppito), 67100, L'Aquila, Italy
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Rivera-Rivera LA, McElmurry BA, Wang Z, Leonov II, Lucchese RR, Bevan JW. Morphed intermolecular potential of OC:HCCH complex based on infrared quantum cascade laser spectroscopy. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.11.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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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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Botschwina P, Oswald R. Explicitly Correlated Coupled Cluster Calculations for the Benzenium Ion (C6H7+) and Its Complexes with Ne and Ar. J Phys Chem A 2011; 115:13664-72. [DOI: 10.1021/jp207905t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Botschwina
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Rainer Oswald
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
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