1
|
Jayachandran P, Angamuthu A, Gopalan P. Redox potentials of puckered 1,4-benzoquinone. J CHEM SCI 2022. [DOI: 10.1007/s12039-021-02005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
2
|
Schwörer M, Wichmann C, Tavan P. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water. J Chem Phys 2016; 144:114504. [PMID: 27004884 DOI: 10.1063/1.4943972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.
Collapse
Affiliation(s)
- Magnus Schwörer
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Christoph Wichmann
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| |
Collapse
|
3
|
VandeVondele J, Tröster P, Tavan P, Mathias G. Vibrational Spectra of Phosphate Ions in Aqueous Solution Probed by First-Principles Molecular Dynamics. J Phys Chem A 2012; 116:2466-74. [DOI: 10.1021/jp211783z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Philipp Tröster
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| | - Paul Tavan
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| | - Gerald Mathias
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| |
Collapse
|
4
|
Rieff B, Bauer S, Mathias G, Tavan P. DFT/MM description of flavin IR spectra in BLUF domains. J Phys Chem B 2011; 115:11239-53. [PMID: 21888341 DOI: 10.1021/jp2043637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A class of photoreceptors occurring in various organisms consists of domains that are blue light sensing using flavin (BLUF). The vibrational spectra of the flavin chromophore are spectroscopically well characterized for the dark-adapted resting states and for the light-adapted signaling states of BLUF domains in solution. Here we present a theoretical analysis of such spectra by applying density functional theory (DFT) to the flavin embedded in molecular mechanics (MM) models of its protein and solvent environment. By DFT/MM we calculate flavin spectra for seven different X-ray and NMR structures of BLUF domains occurring in the transcriptional antirepressor AppA and in the blue light receptor B (BlrB) of the purple bacterium Rb. Sphaeroides as well as in the phototaxis photoreceptor Slr1694 of the cyanobacterium Synechocystis. By considering the dynamical stabilities of associated all-atom simulation models and by comparing calculated with observed vibrational spectra, we show that two of the considered structures (both AppA) are obviously erroneous and that specific features of two further crystal structures (BlrB and Slr1694) cannot represent the states of the respective BLUF domains in solution. Thereby, the conformational transitions elicited by solvation are identified. In this context we demonstrate how hydrogen bonds of varying strengths can tune in BLUF domains the C═O stretching frequencies of the flavin chromophore. Furthermore we show that the DFT/MM spectra of the flavin calculated for two different AppA BLUF conformations, which are called Trp(in) and Met(in), fit very well to the spectroscopic data observed for the dark and light states, respectively, if (i) polarized MM force fields, which are calculated by an iterative DFT/MM procedure, are employed for the flavin binding pockets and (ii) the calculated frequencies are properly scaled. Although the associated analysis indicates that the Trp(in) conformation belongs to the dark state, no clear light vs dark distinction emerges for the Met(in) conformation. In this connection, a number of methodological issues relevant for such complex computations are thoroughly discussed showing, in particular, why our current descriptions could not decide the light vs dark question for Met(in).
Collapse
Affiliation(s)
- Benjamin Rieff
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | | | | | | |
Collapse
|
5
|
Rieff B, Mathias G, Bauer S, Tavan P. Density Functional Theory Combined with Molecular Mechanics: The Infrared Spectra of Flavin in Solution†. Photochem Photobiol 2010; 87:511-23. [DOI: 10.1111/j.1751-1097.2010.00866.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Kartal Z. FT-IR spectroscopic study on some Hofmann-type clathrates: M(p-Benzoquinone)Ni(CN)4·2G (M=Mn, Co, Ni or Hg; G=Aniline). J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Babitzki G, Denschlag R, Tavan P. Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study. J Phys Chem B 2009; 113:10483-95. [DOI: 10.1021/jp902428x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. Babitzki
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - R. Denschlag
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - P. Tavan
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| |
Collapse
|
8
|
Schultheis V, Reichold R, Schropp B, Tavan P. A polarizable force field for computing the infrared spectra of the polypeptide backbone. J Phys Chem B 2008; 112:12217-30. [PMID: 18781720 DOI: 10.1021/jp8013767] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The shapes of the amide bands in the infrared (IR) spectra of proteins and peptides are caused by electrostatically coupled vibrations within the polypeptide backbone and code the structures of these biopolymers. A structural decoding of the amide bands has to resort to simplified models because the huge size of these macromolecules prevents the application of accurate quantum mechanical methods such as density functional theory (DFT). Previous models employed transition-dipole coupling methods that are of limited accuracy. Here we propose a concept for the computation of protein IR spectra, which describes the molecular mechanics (MM) of polypeptide backbones by a polarizable force field of "type II". By extending the concepts of conventional polarizable MM force fields, such a PMM/II approach employs field-dependent parameters not only for the electrostatic signatures of the molecular components but also for the local potentials modeling the stiffness of chemical bonds with respect to elongations, angle deformations, and torsions. Using a PMM/II force field, the IR spectra of the polypeptide backbone can be efficiently calculated from the time dependence of the backbone's dipole moment during a short (e.g., 100 ps) MD simulation by Fourier transformation. PMM/II parameters are derived for harmonic bonding potentials of amide groups in polypeptides from a series of DFT calculations on the model molecule N-methylacetamide (NMA) exposed to homogeneous external electric fields. The amide force constants are shown to vary by as much as 20% for relevant field strengths. As a proof of principle, it is shown that the large solvatochromic effects observed in the IR spectra of NMA upon transfer from the gas phase into aqueous solution are not only excellently reproduced by DFT/MM simulations but are also nicely modeled by the PMM/II approach. The tasks remaining for a proof of practice are specified.
Collapse
Affiliation(s)
- Verena Schultheis
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, Munich, Germany
| | | | | | | |
Collapse
|
9
|
Klähn M, Mathias G, Kötting C, Nonella M, Schlitter J, Gerwert K, Tavan P. IR Spectra of Phosphate Ions in Aqueous Solution: Predictions of a DFT/MM Approach Compared with Observations. J Phys Chem A 2004. [DOI: 10.1021/jp048617g] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Xiang-Yuan L, Chun-Xiu H, Meng-Long L, Zhi-Gang L. A study on photoinduced electronic transition in complex of vitamin E and benzoquinone. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0166-1280(03)00460-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Nonella M, Mathias G, Tavan P. Infrared Spectrum of p-Benzoquinone in Water Obtained from a QM/MM Hybrid Molecular Dynamics Simulation. J Phys Chem A 2003. [DOI: 10.1021/jp027747r] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Nonella
- Theoretische Biophysik, Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Gerald Mathias
- Theoretische Biophysik, Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Paul Tavan
- Theoretische Biophysik, Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| |
Collapse
|
12
|
Vogel R, Siebert F, Mathias G, Tavan P, Fan G, Sheves M. Deactivation of rhodopsin in the transition from the signaling state meta II to meta III involves a thermal isomerization of the retinal chromophore C[double bond]D. Biochemistry 2003; 42:9863-74. [PMID: 12924935 DOI: 10.1021/bi034684+] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-induced isomerization of rhodopsin's retinal chromophore to the activating all-trans geometry initializes the formation of the active receptor state, Meta II. In the absence of peripheral regulatory proteins, the activity of Meta II is switched off spontaneously by two independent pathways: either by hydrolysis of the retinal Schiff base and dissociation of the light receptor into apoprotein opsin plus free retinal or by formation of Meta III, an inactive species with intact retinal protonated Schiff base absorbing at 470 nm. By FTIR spectroscopy on rhodopsin reconstituted with isotopically labeled chromophores in combination with quantum mechanical DFT calculations, we show that the deactivating step during formation of Meta III involves a thermal isomerization of the chromophore C[double bond]N, such that the chromophore in Meta III is all-trans-15-syn. This isomerization step is catalyzed by the protein environment and proceeds via Meta I, as suggested by its dependence on pH and on properties of the lipid/detergent environment of the protein. In the long term, Meta III decays likewise to opsin and free retinal by slow hydrolysis of the Schiff base.
Collapse
Affiliation(s)
- Reiner Vogel
- Biophysics Group, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, D-79104 Freiburg, Germany.
| | | | | | | | | | | |
Collapse
|
13
|
Celebre G, De Luca G. Short-Range Molecular Interactions Governing the Orientational Ordering of Apolar Molecules Dissolved in Nematic Solvents. J Phys Chem B 2003. [DOI: 10.1021/jp026923t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Giorgio Celebre
- Dipartimento di Chimica, Università della Calabria, I-87036 Rende (CS), Italy
| | - Giuseppina De Luca
- Dipartimento di Chimica, Università della Calabria, I-87036 Rende (CS), Italy
| |
Collapse
|
14
|
Nonella M, Mathias G, Eichinger M, Tavan P. Structures and Vibrational Frequencies of the Quinones inRb.sphaeroidesDerived by a Combined Density Functional/Molecular Mechanics Approach. J Phys Chem B 2003. [DOI: 10.1021/jp026810+] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Mohapatra H, Umapathy S. Time-Resolved Resonance Raman Spectroscopic Studies on the Radical Anions of Methyl-1,4-benzoquinone and 2,6-Dimethyl-1,4-benzoquinone. J Phys Chem A 2002. [DOI: 10.1021/jp013750j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Himansu Mohapatra
- Department of Inorganic & Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| | - Siva Umapathy
- Department of Inorganic & Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
16
|
Schmitz M, Tavan P, Nonella M. Vibrational analysis of carbonyl modes in different stages of light-induced cyclopyrimidine dimer repair reactions. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01221-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
17
|
Pawlukojć A, Natkaniec I, Majerz I, Sobczyk L, Grech E. Inelastic neutron scattering (INS) studies on low frequency vibrations of 1,4-benzoquinone. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00948-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Balakrishnan G, Mohandas P, Umapathy S. Time Resolved Resonance Raman, Ab Initio Hartree−Fock, and Density Functional Theoretical Studies on the Transients States of Perfluoro-p-Benzoquinone. J Phys Chem A 2001. [DOI: 10.1021/jp003933q] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Balakrishnan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| | - P. Mohandas
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| | - S. Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
19
|
|
20
|
Wheeler RA. Quinones and quinoidal radicals in photosynthesis. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1380-7323(01)80016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
21
|
Biswas N, Umapathy S. Structures, Vibrational Frequencies, and Normal Modes of Substituted Azo Dyes: Infrared, Raman, and Density Functional Calculations. J Phys Chem A 2000. [DOI: 10.1021/jp9929263] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nandita Biswas
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
22
|
Affiliation(s)
- Marco Nonella
- Biochemisches Institut der Universität, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
23
|
Nonella M, Boullais C, Mioskowski C, Nabedryk E, Breton J. Vibrational Spectrum and Torsional Potential of 2-Methoxy-3-methyl-1,4-benzoquinone. J Phys Chem B 1999. [DOI: 10.1021/jp984800w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Nonella
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | | | | | | |
Collapse
|
24
|
Eichinger M, Tavan P, Hutter J, Parrinello M. A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields. J Chem Phys 1999. [DOI: 10.1063/1.479049] [Citation(s) in RCA: 272] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
25
|
Pou-Amérigo R, Merchán M, Ortı́ E. Theoretical study of the electronic spectrum of p-benzoquinone. J Chem Phys 1999. [DOI: 10.1063/1.478918] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Suter HU, Nonella M. A Quantum Chemical Investigation of the C−O Bond Length and Stretching Mode of the Phenolate Anion. J Phys Chem A 1998. [DOI: 10.1021/jp982205o] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hans Ulrich Suter
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Marco Nonella
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
27
|
Nonella M. A Density Functional Investigation of Model Molecules for Ubisemiquinone Radical Anions. J Phys Chem B 1998. [DOI: 10.1021/jp980138s] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Nonella
- Biochemisches Institut der Universität, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
28
|
Zhan CG, Iwata S. Ab initio MO and density functional studies on the vibrational spectra of 1,4-benzoquinone, and its anion and dianion. Chem Phys 1998. [DOI: 10.1016/s0301-0104(98)00007-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Effect of benzannelation on the conformational flexibility of the rings in oxo, imino, and methylene derivatives of cyclohexa-1,4-diene. Russ Chem Bull 1998. [DOI: 10.1007/bf02495637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
30
|
Nonella M. A reinvestigation of the ν2 and ν3 modes of 1,4-benzoquinone on the basis of a quantum mechanical harmonic force field. Chem Phys Lett 1997. [DOI: 10.1016/s0009-2614(97)01066-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
31
|
Burie JR, Boullais C, Nonella M, Mioskowski C, Nabedryk E, Breton J. Importance of the Conformation of Methoxy Groups on the Vibrational and Electrochemical Properties of Ubiquinones. J Phys Chem B 1997. [DOI: 10.1021/jp970640x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
32
|
Biswas N, Umapathy S. Density Functional Calculations of Structures, Vibrational Frequencies, and Normal Modes of trans- and cis-Azobenzene. J Phys Chem A 1997. [DOI: 10.1021/jp970312x] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nandita Biswas
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
33
|
Mohandas P, Umapathy S. Density-Functional Studies on the Structure and Vibrational Spectra of Transient Intermediates of p-Benzoquinone. J Phys Chem A 1997. [DOI: 10.1021/jp9701597] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pothukattil Mohandas
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
34
|
Nonella M. Structures and Vibrational Spectra of p-Benzoquinone in Different Oxidation and Protonation States: A Density Functional Study. J Phys Chem B 1997. [DOI: 10.1021/jp9626071] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Nonella
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
35
|
Ultraviolet resonance Raman spectra and ab initio vibrational analyses of 1,4-benzoquinone: reassignments of the ν2 and ν3 bands. Chem Phys Lett 1996. [DOI: 10.1016/s0009-2614(96)01121-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
36
|
El-Azhary AA, Suter HU. Comparison between Optimized Geometries and Vibrational Frequencies Calculated by the DFT Methods. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp960618o] [Citation(s) in RCA: 165] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. A. El-Azhary
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - H. U. Suter
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
| |
Collapse
|
37
|
Nonella M, Brändli C. Density Functional Investigation of Methoxy-Substituted p-Benzoquinones: Conformational Analysis and Harmonic Force Fields of 2-Methoxy- and 2,3-Dimethoxy-1,4-benzoquinone. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9609747] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Nonella
- Physikalisch-Chemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Christof Brändli
- Physikalisch-Chemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
38
|
Nonella M. Structures and harmonic force fields of 1,4-naphthoquinone and naphthalene: A density functional study. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0166-1280(95)04390-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|