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Dvores MP, Çarçabal P, Maître P, Simons JP, Gerber RB. Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside. Phys Chem Chem Phys 2020; 22:4144-4157. [PMID: 32039431 DOI: 10.1039/c9cp06572e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.
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Affiliation(s)
- M P Dvores
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - P Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - J P Simons
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
| | - R B Gerber
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel. and Department of Chemistry, University of California Irvine, CA 92697, USA
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2
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Brickel S, Meuwly M. OH-Stretching Overtone Induced Dynamics in HSO3F from Reactive Molecular Dynamics Simulations. J Phys Chem A 2017; 121:5079-5087. [DOI: 10.1021/acs.jpca.7b02950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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3
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Hirshberg B, Sagiv L, Gerber RB. Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications. J Chem Theory Comput 2017; 13:982-991. [DOI: 10.1021/acs.jctc.6b01129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barak Hirshberg
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - Lior Sagiv
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - R. Benny Gerber
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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4
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Verdes M, Paniagua M. Facet shapes and thermo-stabilities of H₂SO₄•HNO₃ hydrates involved in polar stratospheric clouds. J Mol Model 2015; 21:238. [PMID: 26287119 DOI: 10.1007/s00894-015-2782-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/31/2015] [Indexed: 11/24/2022]
Abstract
The nucleation, ice crystal shapes and thermodynamic stability of polar stratospheric clouds particles are interesting concerns owing to their implication in the ozone layer destruction. Some of these particles are formed by conformers of H2O, HNO3, and H2SO4. We carried out calculations using density functional theory (DFT) to obtain optimized structures. Several stable trimers are achieved -divided in two groups, one with HNO3 moiety, second with H2SO4 moiety- after pre-optimization at B3LYP/6-31G and subsequently optimization at B3LYP/aug-cc-pVTZ level of theory. For both most stable conformers five H2O molecules are added to their optimized trimers to calculate hydrated geometries. The OH stretching harmonic frequencies are provided for all aggregates. The zero-point energy correction (ZEPC), relative electronic energies (∆E), relative reaction Gibbs free energies ∆(∆G)k-relative, and cooling constant (K cooling ) are reported at three temperatures: 188 K, 195 K, and 210 K. Shapes given in our calculations are compared with various experimental shapes as well as comparisons with their thermo-stabilities.
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Affiliation(s)
- Marian Verdes
- Departamento de Química Física Aplicada, Facultad de Ciencias, C-14, Universidad Autónoma de Madrid, Cantoblanco, E-28049, Madrid, Spain,
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Pavlyuchko AI, Yurchenko SN, Tennyson J. A hybrid variational-perturbation calculation of the ro-vibrational spectrum of nitric acid. J Chem Phys 2015; 142:094309. [DOI: 10.1063/1.4913741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. I. Pavlyuchko
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Physics, Moscow State University of Civil Engineering (MGSU), Moscow, Russia
| | - S. N. Yurchenko
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Jonathan Tennyson
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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6
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The performance of RI-MP2 based potential energy surfaces in a vibrational self-consistent field treatment. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Largely reduced grid densities in a vibrational self-consistent field treatment do not significantly impact the resultingwavenumbers. Molecules 2014; 19:21253-75. [PMID: 25525825 PMCID: PMC6270979 DOI: 10.3390/molecules191221253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/25/2014] [Accepted: 12/09/2014] [Indexed: 11/16/2022] Open
Abstract
Especially for larger molecules relevant to life sciences, vibrational self-consistent field (VSCF) calculations can become unmanageably demanding even when only first and second order potential coupling terms are considered. This paper investigates to what extent the grid density of the VSCF’s underlying potential energy surface can be reduced without sacrificing accuracy of the resulting wavenumbers. Including single-mode and pair contributions, a reduction to eight points per mode did not introduce a significant deviation but improved the computational efficiency by a factor of four. A mean unsigned deviation of 1.3% from the experiment could be maintained for the fifteen molecules under investigation and the approach was found to be applicable to rigid, semi-rigid and soft vibrational problems likewise. Deprotonated phosphoserine, stabilized by two intramolecular hydrogen bonds, was investigated as an exemplary application.
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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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9
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Roy TK, Carrington T, Gerber RB. Approximate first-principles anharmonic calculations of polyatomic spectra using MP2 and B3LYP potentials: comparisons with experiment. J Phys Chem A 2014; 118:6730-9. [PMID: 24977304 DOI: 10.1021/jp5060155] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.
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Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University , Jerusalem 91904, Israel
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10
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Vaida V, Donaldson DJ. Red-light initiated atmospheric reactions of vibrationally excited molecules. Phys Chem Chem Phys 2014; 16:827-36. [DOI: 10.1039/c3cp53543f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Larsen MC, Vaida V. Near Infrared Photochemistry of Pyruvic Acid in Aqueous Solution. J Phys Chem A 2012; 116:5840-6. [DOI: 10.1021/jp2087972] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Molly C. Larsen
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder,
Colorado 80309, United States
| | - Veronica Vaida
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder,
Colorado 80309, United States
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12
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Kołaski M, Zakharenko AA, Karthikeyan S, Kim KS. Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study. J Chem Theory Comput 2011; 7:3447-59. [DOI: 10.1021/ct100428z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maciej Kołaski
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Aleksey A. Zakharenko
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - S. Karthikeyan
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
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13
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Affiliation(s)
- Veronica Vaida
- Department of Chemistry and Biochemistry, CIRES, University of Colorado, Boulder, Colorado 80309-0215, USA
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15
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Affiliation(s)
- Kenneth R. Leopold
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455;
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16
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Brauer B, Pincu M, Buch V, Bar I, Simons JP, Gerber RB. Vibrational Spectra of α-Glucose, β-Glucose, and Sucrose: Anharmonic Calculations and Experiment. J Phys Chem A 2011; 115:5859-72. [DOI: 10.1021/jp110043k] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Victoria Buch
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - John. P. Simons
- Chemistry Department, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, U.K
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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17
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Meng K, Wang J. Anharmonic overtone and combination states of glycine and two model peptides examined by vibrational self-consistent field theory. Phys Chem Chem Phys 2011; 13:2001-13. [DOI: 10.1039/c0cp01177k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Xantheas SS. Anharmonic vibrational spectra of hydrogen bonded clusters: comparison between higher energy derivative and mean-field grid based methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350600922564] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sotiris S. Xantheas
- a Chemical Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard, PO Box 999, MS K1-83, Richland , WA, 99352 , USA
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19
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Kowal AT. Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d4. J Comput Chem 2010; 32:718-29. [DOI: 10.1002/jcc.21665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 07/07/2010] [Accepted: 08/07/2010] [Indexed: 11/10/2022]
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20
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Gonzalez J, Anglada JM. Gas Phase Reaction of Nitric Acid with Hydroxyl Radical without and with Water. A Theoretical Investigation. J Phys Chem A 2010; 114:9151-62. [DOI: 10.1021/jp102935d] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Javier Gonzalez
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya, IQAC - CSIC, c/Jordi Girona 18, E-08034 Barcelona, Spain
| | - Josep M. Anglada
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya, IQAC - CSIC, c/Jordi Girona 18, E-08034 Barcelona, Spain
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21
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Gupta P, Lane JR, Kjaergaard HG. Molecular dynamic simulations of OH-stretching overtone induced photodissociation of fluorosulfonic and chlorosulfonic acid. Phys Chem Chem Phys 2010; 12:8277-84. [PMID: 20526505 DOI: 10.1039/c003073m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the OH-stretching overtone dynamics of fluorosulfonic acid (FSO(3)H) and chlorosulfonic acid (ClSO(3)H) using classical trajectory simulations. The initial nuclear coordinates and momenta for the trajectories are sampled from anharmonic correlation-corrected vibrational self consistent field (CC-VSCF) wavefunctions. We consider both OH-stretching overtone states and combination states containing a mix of OH-stretching overtones and SOH-bending or OSOH-torsional modes. Our molecular dynamics simulations confirm that photodissociation of these sulfonic acids to form the corresponding hydrogen halides and sulfur trioxide (HF + SO(3) and HCl + SO(3)), is possible via highly vibrationally excited states on a picosecond timescale. Hydrogen-hopping events are also observed in the trajectories whereby the hydrogen atom of the excited OH group is found to migrate to one of the adjacent S=O groups. The transition states, activation energies and dissociation dynamics of FSO(3)H and ClSO(3)H are found to be similar to those of H(2)SO(4). We suggest that these halogenated sulfonic acids should be suitable proxy molecules for an experimental investigation of the OH-stretching overtone induced photodissociation of H(2)SO(4) thought to be important in Earths' atmosphere.
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Affiliation(s)
- Priyanka Gupta
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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22
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Yekutiel M, Lane JR, Gupta P, Kjaergaard HG. Calculated Spectroscopy and Atmospheric Photodissociation of Phosphoric Acid. J Phys Chem A 2010; 114:7544-52. [DOI: 10.1021/jp1007957] [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)
- Mivsam Yekutiel
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Joseph R. Lane
- Department of Chemistry, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Priyanka Gupta
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø
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23
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Kowal AT. Computational study of the equilibrium geometry and anharmonic vibrational spectra of PbX 2··· NO and PbX 2··· ON (X = F, Cl, Br, I) complexes. Mol Phys 2010. [DOI: 10.1080/00268976.2010.489519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Lauvergnat D, Nauts A. Torsional energy levels of nitric acid in reduced and full dimensionality with ElVibRot and Tnum. Phys Chem Chem Phys 2010; 12:8405-12. [DOI: 10.1039/c001944e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Maroń MK, Shultz MJ, Vaida V. Characterization of the nitric acid–water complex in the infrared and near-infrared region at ambient temperatures in carbon tetrachloride. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Torrent-Sucarrat M, Anglada JM, Luis JM. Role of vibrational anharmonicity in atmospheric radical hydrogen-bonded complexes. Phys Chem Chem Phys 2009; 11:6377-88. [DOI: 10.1039/b904736k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Spectroscopic identification and stability of the intermediate in the OH + HONO2 reaction. Proc Natl Acad Sci U S A 2008; 105:12678-83. [PMID: 18678905 DOI: 10.1073/pnas.0800320105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction of nitric acid with the hydroxyl radical influences the residence time of HONO(2) in the lower atmosphere. Prior studies [Brown SS, Burkholder JB, Talukdar RK, Ravishankara AR (2001) J Phys Chem A 105:1605-1614] have revealed unusual kinetic behavior for this reaction, including a negative temperature dependence, a complex pressure dependence, and an overall reaction rate strongly affected by isotopic substitution. This behavior suggested that the reaction occurs through an intermediate, theoretically predicted to be a hydrogen-bonded OH-HONO(2) complex in a six-membered ring-like configuration. In this study, the intermediate is generated directly by the association of photolytically generated OH radicals with HONO(2) and stabilized in a pulsed supersonic expansion. Infrared action spectroscopy is used to identify the intermediate by the OH radical stretch (nu(1)) and OH stretch of nitric acid (nu(2)) in the OH-HONO(2) complex. Two vibrational features are attributed to OH-HONO(2): a rotationally structured nu(1) band at 3516.8 cm(-1) and an extensively broadened nu(2) feature at 3260 cm(-1), both shifted from their respective monomers. These same transitions are identified for OD-DONO(2). Assignments of the features are based on their vibrational frequencies, analysis of rotational band structure, and comparison with complementary high level ab initio calculations. In addition, the OH (v = 0) product state distributions resulting from nu(1) and nu(2) excitation are used to determine the binding energy of OH-HONO(2), D(0) <or= 5.3 kcal x mol(-1), which is in good accord with ab initio predictions.
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28
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Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(100)-2×1 surface. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Pele L, Gerber RB. On the number of significant mode-mode anharmonic couplings in vibrational calculations: Correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides. J Chem Phys 2008; 128:165105. [DOI: 10.1063/1.2909558] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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30
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Kjaergaard HG, Garden AL, Chaban GM, Gerber RB, Matthews DA, Stanton JF. Calculation of Vibrational Transition Frequencies and Intensities in Water Dimer: Comparison of Different Vibrational Approaches. J Phys Chem A 2008; 112:4324-35. [DOI: 10.1021/jp710066f] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Galina M. Chaban
- NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, California 94035-1000
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697 and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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31
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Miller Y, Gerber RB. Dynamics of proton recombination with NO3- anion in water clusters. Phys Chem Chem Phys 2008; 10:1091-3. [PMID: 18270608 DOI: 10.1039/b717338p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recombination events of a proton with NO3- at (H2O)8 clusters are studied by molecular dynamics, using "on-the-fly" reliable ab initio MP2 potentials. The main findings are: (1) the lifetime of the ions is less than 1.2 picoseconds; (2) the recombination step invariably involves H3O+, not H5O2+; and (3) an essentially unique transition-state structure of H3O+/NO3- for recombination is found in all cases. Proton migration involves both H3O+ and H5O2+ species: Grotthuss and other mechanisms contribute.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem, 91904, Israel
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32
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Kamboures MA, Raff JD, Miller Y, Phillips LF, Finlayson-Pitts BJ, Gerber RB. Complexes of HNO3 and NO3− with NO2 and N2O4, and their potential role in atmospheric HONO formation. Phys Chem Chem Phys 2008; 10:6019-32. [DOI: 10.1039/b805330h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Miller Y, Gerber RB. Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O: hydrogen-hopping and photodissociation processes. J Am Chem Soc 2007; 128:9594-5. [PMID: 16866489 DOI: 10.1021/ja062890+] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photochemical processes of sulfuric acid (H2SO4) and sulfuric acid monohydrate (H2SO4-H2O) following overtone excitation of the OH stretching mode are studied by classical trajectory simulations using the semiempirical PM3 potential suface in "on the fly" calculations. The main results are the following: (1) In the excitation of H2SO4 to the fifth OH-stretch overtone, hopping of the H atom between oxygen atoms is found to take place in 22% of the trajectories, only once during simulations of 400 ps. (2) All the trajectories for H2SO4 show a rapid cis-trans isomerization. (3) The photolysis of H2SO4 into SO3 + H2O takes place in 5% of the trajectories on a time scale of approximately 9 ps. (4) Only low overtone levels of H2SO4-H2O have sufficiently long lifetimes to be spectroscopically relevant. Excitation to these OH stretching overtones is found to result in the dissociation of the cluster. H hopping or dissociation of H2SO4 does not take place.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Miller Y, Chaban GM, Zhou J, Asmis KR, Neumark DM, Gerber RB. Vibrational spectroscopy of (SO42−)∙(H2O)n clusters, n=1–5: Harmonic and anharmonic calculations and experiment. J Chem Phys 2007; 127:094305. [PMID: 17824737 DOI: 10.1063/1.2764074] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n<or=5.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel
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Miller Y, Chaban GM, Finlayson-Pitts BJ, Gerber RB. Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O. J Phys Chem A 2007; 110:5342-54. [PMID: 16623461 DOI: 10.1021/jp0559940] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in "on-the-fly" simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO, isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these OH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.
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Affiliation(s)
- Y Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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36
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Anharmonic vibrational spectroscopy calculations with electronic structure potentials: comparison of MP2 and DFT for organic molecules. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0299-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Isayev O, Gorb L, Leszczynski J. Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately? J Comput Chem 2007; 28:1598-1609. [PMID: 17340602 DOI: 10.1002/jcc.20696] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.
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Affiliation(s)
- Olexandr Isayev
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
| | - Leonid Gorb
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
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38
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The vibrational spectra of N-phenylpyrrole in the gas phase, in argon matrices and in single crystals. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Christiansen O. Vibrational structure theory: new vibrational wave function methods for calculation of anharmonic vibrational energies and vibrational contributions to molecular properties. Phys Chem Chem Phys 2007; 9:2942-53. [PMID: 17551617 DOI: 10.1039/b618764a] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of recently developed theoretical methods for the calculation of vibrational energies and wave functions are reviewed. Methods for constructing the appropriate quantum mechanical Hamilton operator are briefly described before reviewing a particular branch of theoretical methods for solving the nuclear Schrödinger equation. The main focus is on wave function methods using the vibrational self-consistent field (VSCF) as starting point, and includes vibrational configuration interaction (VCI), vibrational Møller-Plesset (VMP) theory, and vibrational coupled cluster (VCC) theory. The convergence of the different methods towards the full vibrational configuration interaction (FVCI) result is discussed. Finally, newly developed vibrational response methods for calculation of vibrational contributions to properties, energies, and transition probabilities are discussed.
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Affiliation(s)
- Ove Christiansen
- The Lundbeck Foundation Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, DK-8000 Arhus C, Denmark
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Njegic B, Gordon MS. Exploring the effect of anharmonicity of molecular vibrations on thermodynamic properties. J Chem Phys 2006; 125:224102. [PMID: 17176129 DOI: 10.1063/1.2395940] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermodynamic properties of selected small and medium size molecules were calculated using harmonic and anharmonic vibrational frequencies. Harmonic vibrational frequencies were obtained by normal mode analysis, whereas anharmonic ones were calculated using the vibrational self-consistent field (VSCF) method. The calculated and available experimental thermodynamic data for zero point energy, enthalpy, entropy, and heat capacity are compared. It is found that the anharmonicity and coupling of molecular vibrations can play a significant role in predicting accurate thermodynamic quantities. Limitations of the current VSCF method for low frequency modes have been partially removed by following normal mode displacements in internal, rather than Cartesian, coordinates.
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Affiliation(s)
- Bosiljka Njegic
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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Feierabend KJ, Havey DK, Varner ME, Stanton JF, Vaida V. A comparison of experimental and calculated spectra of HNO3 in the near-infrared using Fourier transform infrared spectroscopy and vibrational perturbation theory. J Chem Phys 2006; 124:124323. [PMID: 16599690 DOI: 10.1063/1.2180248] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work combines new laboratory studies of the near-infrared vibrational spectra of HNO3 with theoretical predictions of these spectra as a means to understand the properties of this molecule at energies well above the fundamental region. Trends in overtone and combination band energy levels and intensities are compiled and examined. The theoretical calculations are in excellent agreement with the observed frequencies and intensities of the transitions in this spectral region. The calculations also serve as a valuable aid for assigning many of the transitions. This work validates the ab initio generated potential energy surface for HNO3 by comparing vibrational perturbation theory calculations to experimental spectra focused on combination band and overtone absorptions.
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Affiliation(s)
- Karl J Feierabend
- Department of Chemistry and Biochemistry and CIRES, University of Colorado, Boulder, Colorado 80309, USA.
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Ramazan KA, Wingen LM, Miller Y, Chaban GM, Gerber RB, Xantheas SS, Finlayson-Pitts BJ. New Experimental and Theoretical Approach to the Heterogeneous Hydrolysis of NO2: Key Role of Molecular Nitric Acid and Its Complexes. J Phys Chem A 2006; 110:6886-97. [PMID: 16722704 DOI: 10.1021/jp056426n] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although heterogeneous chemistry on surfaces in the troposphere is known to be important, there are currently only a few techniques available for studying the nature of surface-adsorbed species as well as their chemistry and photochemistry under atmospheric conditions of 1 atm pressure and in the presence of water vapor. We report here a new laboratory approach using a combination of long path Fourier transform infrared spectroscopy (FTIR) and attenuated total reflectance (ATR) FTIR that allows the simultaneous observation and measurement of gases and surface species. Theory is used to identify the surface-adsorbed intermediates and products, and to estimate their relative concentrations. At intermediate relative humidities typical of the tropospheric boundary layer, the nitric acid formed during NO2 heterogeneous hydrolysis is shown to exist both as nitrate ions from the dissociation of nitric acid formed on the surface and as molecular nitric acid. In both cases, the ions and HNO3 are complexed to water molecules. Upon pumping, water is selectively removed, shifting the NO(3-)-HNO3(H2O)y equilibria toward more dehydrated forms of HNO3 and ultimately to nitric acid dimers. Irradiation of the nitric acid-water film using 300-400 nm radiation generates gaseous NO, while irradiation at 254 nm generates both NO and HONO, resulting in conversion of surface-adsorbed nitrogen oxides into photochemically active NO(x). These studies suggest that the assumption that deposition or formation of nitric acid provides a permanent removal mechanism from the atmosphere may not be correct. Furthermore, a potential role of surface-adsorbed nitric acid and other species formed during the heterogeneous hydrolysis of NO2 in the oxidation of organics on surfaces, and in the generation of gas-phase HONO on local to global scales, should be considered.
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Affiliation(s)
- K A Ramazan
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Kowal AT. First-principles calculation of geometry and anharmonic vibrational spectra of thioformamide and thioformamide-d2. J Chem Phys 2006; 124:14304. [PMID: 16409033 DOI: 10.1063/1.2139995] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The equilibrium geometry of thioformamide HCSNH2 has been determined at the MP2 and CCSD(T) electron correlation levels under C(s) symmetry constraints using triple-zeta basis sets up to cc-pVTZ. All optimized planar structures are true minima on the potential-energy surface and are characterized by the C-N bond length within 1.353-1.343 A, C-S distances of 1.656-1.628 A, and NCS angle between 125.7 degrees and 125.9 degrees . The wave number of the NH2 out-of-plane wagging mode computed in the harmonic approximation shows stronger dependence on the basis set rather than the electron correlation level and varies from 85.9 cm(-1) at CCSD(T)cc-pVDZ level to 335 cm(-1) at MP2/aug-cc-pVTZ level. Anharmonic vibrational spectra of HCSNH2 and HCSND2 have been determined directly from the potential-energy surfaces computed at MP2 level in triple-zeta valence (TZV)(2df,2p) and TZV+(2df,2p) basis sets using vibrational self-consistent-field (VSCF) and correlation-corrected VSCF (CC-VSCF) methods. CC-VSCF wave numbers of fundamental, first overtone, and most intense combination transitions are reported for thioformamide and those of fundamentals for thioformamide-d2. The NH2 wagging (nu12) mode is strongly anharmonic and its fundamentals have been computed at 406.9 cm(-1) [TZV(2df,2p)] and 399.5 cm(-1) [TZV+(2df,2p)], which is remarkably close to the experimental energy of 393 cm(-1). Anharmonically computed fundamentals of this mode in thioformamide-d2, 299.7 cm(-1) [TZV(2df,2p)] and 299.6 cm(-1) [TZV+(2df,2p)], are only approximately 7 cm(-1) higher than the transition energy (293 cm(-1)) observed in the gas phase spectrum of HCSND2. The first overtone of the NH2 wagging mode of thioformamide (nu12 (02)) has been calculated by CC-VSCF procedure at 830.8 cm(-1) [TZV(2df,2p)] and 880.0 cm(-1) [TZV+(2df,2p)], which implies "negative" (nu12 (02)>2*nu12 (01)) anharmonicity of this mode.
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Affiliation(s)
- Andrzej T Kowal
- Department of Chemistry, Wrocław University of Technology, Wyb. St. Wyspiańskiego 27, 50-370 Wrocław, Poland.
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A comparative study of the vibrational corrections for the dynamic electric properties of the LiF molecule using numerical and perturbation methods. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.06.084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Miller Y, Chaban GM, Gerber RB. Ab Initio Vibrational Calculations for H2SO4 and H2SO4·H2O: Spectroscopy and the Nature of the Anharmonic Couplings. J Phys Chem A 2005; 109:6565-74. [PMID: 16834003 DOI: 10.1021/jp058110l] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H2SO4) and of sulfuric acid monohydrate cluster (H2SO4 x H2O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H2SO4 and H2SO4 x H2O.
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Affiliation(s)
- Y Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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