1
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Sharma M, Banik S, Roy TK. Performance of Effective Harmonic Oscillator Approach for the Calculations of Vibrational Transition Energies of Large Molecules. J Phys Chem A 2024; 128:5762-5776. [PMID: 38979981 DOI: 10.1021/acs.jpca.4c01583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The accuracy and performance of the effective harmonic oscillator approximation for the description of anharmonic vibrational structure calculations are tested for large molecular systems and compared with experimental values along with vibrational self-consistent field and second-order perturbation theories. The effective harmonic oscillator approach is an effective single-particle approximation where the variational parameters are the centroids and widths of the multidimensional Gaussian product functions posited as the vibrational wave functions. A comprehensive calculation for 849 transitions that include the fundamentals, two and three quanta overtone transitions, and several combination bands of three polyaromatic hydrocarbons and one DNA nucleobase with a total of 231 normal modes are assessed. A comparison of EHO results with the experimental values is done for the polyaromatic hydrocarbons, and a close agreement is found between the two results. It also offers anharmonic eigenstates and eigenfunctions that are nearly identical with vibrational self-consistent field theory. An extensive analysis on the resultant wave functions of the excited states is performed. The overall root-mean-square deviation (RMSD) between these two methods for 849 transitions understudy is only about 8.3 cm-1, suggesting the effective harmonic oscillator as a viable alternative for the reliable calculations of transition energies of large molecular systems.
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Affiliation(s)
- Mokshi Sharma
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
| | - Subrata Banik
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
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2
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Carvalho JR, Vidal LN. Calculation of absolute Raman scattering cross-sections using vibrational self-consistent field/vibrational configuration interaction wave functions. J Comput Chem 2022; 43:1484-1494. [PMID: 35731622 DOI: 10.1002/jcc.26951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/21/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022]
Abstract
In the present study, the differential scattering cross-sections, depolarization ratios and Raman shifts of small molecular systems are obtained from configuration iteration wave functions of vibrational self-consistent field (VSCF) states. The transition polarizabilities were modeled using the Placzek approximation, neglecting those contributions not arising from the electric dipole mechanism. This theoretical approach is considered a good approximation for samples that absorb in the UV range if the excitation radiation falls in the visible region, as is the case of the molecules selected for the present study, namely: water, methane, and acetylene. Potential energy and electronic polarizability surfaces are calculated by the CCSD(T) and CC3 methods with aug-cc-p(C)V(T,Q,5)Z basis sets. The vibrational Hamiltonian includes the vibrational angular momentum contribution of the Watson kinetic energy operator. As expected, due to the variational nature of the VSCF and vibrational configuration interaction (VCI) methods, the Raman transition wavenumbers are substantially improved over the harmonic predictions. Surprisingly, the scattering cross-sections obtained using the harmonic approximation or the VSCF method better agrees with the experimental values than those cross-sections predicted using VCI wave functions. The more significant deviations of the VCI results from the experimental reference may be related to the significant uncertainties of the measured cross-sections. Still, it may also indicate that the VCI Raman transition moments may require a more accurate description of the electronic polarizability surface. Finally, the depolarization ratios calculated for H2 O and C2 D2 using harmonic and VCI wave functions have similar accuracy, whereas, for C2 H2 and C2 HD, the VCI results are more accurate.
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Affiliation(s)
- Jhonatas R Carvalho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Luciano N Vidal
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Curitiba, Paraná, Brazil
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3
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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4
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Brehm M, Thomas M. Computing Bulk Phase Resonance Raman Spectra from ab Initio Molecular Dynamics and Real-Time TDDFT. J Chem Theory Comput 2019; 15:3901-3905. [PMID: 31246025 DOI: 10.1021/acs.jctc.9b00512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase systems from ab initio molecular dynamics, including solvent influence and some anharmonic effects. Based on real-time time-dependent density functional theory, we obtain the RR spectra for all laser wavelengths in one pass. We compute the RR spectrum of uracil in aqueous solution, which is in good agreement with experiment. This is the first simulation of a bulk phase RR spectrum.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie , Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4 , 06120 Halle (Saale) , Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie , Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4 , 06120 Halle (Saale) , Germany
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5
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Keiderling TA, Bouř P. Theory of Molecular Vibrational Zeeman Effects as Measured with Circular Dichroism. PHYSICAL REVIEW LETTERS 2018; 121:073201. [PMID: 30169061 DOI: 10.1103/physrevlett.121.073201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 06/08/2023]
Abstract
We present a general theory that enables the first nonempirical computation of molecular vibrational Zeeman effects as are detectable with magnetic vibrational circular dichroism spectroscopy (MVCD). In this method, the second derivatives of the molecular magnetic moment appear to be essential to determine the observable MVCD intensities. Using a quasiharmonic approximation, computations based on our method allowed a band-to-band comparison of simulated to measured spectra. Given this new possibility of its reliable interpretation, MVCD spectroscopy may develop as a useful tool to yield detailed information on molecular vibrational states and structure, including achiral systems.
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Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, USA
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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6
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Proppe J, Husch T, Simm GN, Reiher M. Uncertainty quantification for quantum chemical models of complex reaction networks. Faraday Discuss 2018; 195:497-520. [PMID: 27730243 DOI: 10.1039/c6fd00144k] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.
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Affiliation(s)
- Jonny Proppe
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Tamara Husch
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Gregor N Simm
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
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7
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Jungwirth J, Šebestík J, Šafařík M, Kapitán J, Bouř P. Quantitative Determination of Ala-Ala Conformer Ratios in Solution by Decomposition of Raman Optical Activity Spectra. J Phys Chem B 2017; 121:8956-8964. [DOI: 10.1021/acs.jpcb.7b07154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jakub Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, 12116 Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
| | - Martin Šafařík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department
of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
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8
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Brehm M, Thomas M. Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations. J Phys Chem Lett 2017; 8:3409-3414. [PMID: 28685571 DOI: 10.1021/acs.jpclett.7b01616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present our novel methodology for computing Raman optical activity (ROA) spectra of liquid systems from ab initio molecular dynamics (AIMD) simulations. The method is built upon the recent developments to obtain magnetic dipole moments from AIMD and to integrate molecular properties by using radical Voronoi tessellation. These techniques are used to calculate optical activity tensors for large and complex periodic bulk phase systems. Only AIMD simulations are required as input, and no time-consuming perturbation theory is involved. The approach relies only on the total electron density in each time step and can readily be combined with a wide range of electronic structure methods. To the best of our knowledge, these are the first computed ROA spectra for a periodic bulk phase system. As an example, the experimental ROA spectrum of liquid (R)-propylene oxide is reproduced very well.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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9
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Fagan P, Kocourková L, Tatarkovič M, Králík F, Kuchař M, Setnička V, Bouř P. Cocaine Hydrochloride Structure in Solution Revealed by Three Chiroptical Methods. Chemphyschem 2017; 18:2258-2265. [DOI: 10.1002/cphc.201700452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/31/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Patrik Fagan
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Lucie Kocourková
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Michal Tatarkovič
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - František Králík
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Martin Kuchař
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Vladimír Setnička
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Flemingovo náměstí 2 16610 Prague Czech Republic
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
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10
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Iwata T, Nozaki D, Yamamoto A, Koyama T, Nishina Y, Shiga K, Tokutomi S, Unno M, Kandori H. Hydrogen Bonding Environment of the N3-H Group of Flavin Mononucleotide in the Light Oxygen Voltage Domains of Phototropins. Biochemistry 2017; 56:3099-3108. [PMID: 28530801 DOI: 10.1021/acs.biochem.7b00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The light oxygen voltage (LOV) domain is a flavin-binding blue-light receptor domain, originally found in a plant photoreceptor phototropin (phot). Recently, LOV domains have been used in optogenetics as the photosensory domain of fusion proteins. Therefore, it is important to understand how LOV domains exhibit light-induced structural changes for the kinase domain regulation, which enables the design of LOV-containing optogenetics tools with higher photoactivation efficiency. In this study, the hydrogen bonding environment of the N3-H group of flavin mononucleotide (FMN) of the LOV2 domain from Adiantum neochrome (neo) 1 was investigated by low-temperature Fourier transform infrared spectroscopy. Using specifically 15N-labeled FMN, [1,3-15N2]FMN, the N3-H stretch was identified at 2831 cm-1 for the unphotolyzed state at 150 K, indicating that the N3-H group forms a fairly strong hydrogen bond. The N3-H stretch showed temperature dependence, with a shift to lower frequencies at ≤200 K and to higher frequencies at ≥250 K from the unphotolyzed to the intermediate states. Similar trends were observed in the LOV2 domains from Arabidopsis phot1 and phot2. By contrast, the N3-H stretch of the Q1029L mutant of neo1-LOV2 and neo1-LOV1 was not temperature dependent in the intermediate state. These results seemed correlated with our previous finding that the LOV2 domains show the structural changes in the β-sheet region and/or the adjacent Jα helix of LOV2 domain, but that such structural changes do not take place in the Q1029L mutant or neo1-LOV1 domain. The environment around the N3-H group was also investigated.
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Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Dai Nozaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Atsushi Yamamoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Takayuki Koyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Yasuzo Nishina
- Department of Molecular Physiology, Graduate School of Medical Sciences, Kumamoto University , Honjo, Kumamoto 860-8556, Japan
| | - Kiyoshi Shiga
- Department of Physiology, School of Health Sciences, Kumamoto University , Kuhonji, Kumamoto 862-0976, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University , Sakai, Osaka 599-8531, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University , Saga 840-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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11
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Luber S. Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics. J Chem Theory Comput 2017; 13:1254-1262. [DOI: 10.1021/acs.jctc.6b00820] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Luber
- Department of Chemistry C, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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12
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Abstract
Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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13
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Roy TK, Sharma R, Gerber RB. First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments. Phys Chem Chem Phys 2016; 18:1607-14. [DOI: 10.1039/c5cp05979h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data.
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Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- Central University of Rajasthan
| | - Rahul Sharma
- Department of Chemistry
- Indian Institute of Technology
- Roorkee
- India
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- University of California
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14
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Andrushchenko V, Benda L, Páv O, Dračínský M, Bouř P. Vibrational Properties of the Phosphate Group Investigated by Molecular Dynamics and Density Functional Theory. J Phys Chem B 2015; 119:10682-92. [PMID: 26193890 DOI: 10.1021/acs.jpcb.5b05124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phosphate group (PO2(-)) is an important building block occurring in many components of living matter including nucleic acids. It provides distinct features in vibrational spectra and is useful as a local probe of NA conformation and interactions with the environment. For this purpose, it is desirable to explore in detail various factors influencing spectral shapes of characteristic phosphate vibrations. In the present study, effects of the solvent and conformational averaging are analyzed for simple model molecules, dimethylphosphate, ethylmethylphosphate, and ethylmethylthiophosphate. Infrared absorption (IR) and Raman spectra were measured and calculated using a combination of molecular dynamics (MD) and density functional theory (DFT). To fully understand the link between the structure and the spectra, the solvent has to be explicitly included in the computational modeling. The results indicate that vibrational properties of the phosphate moiety are very sensitive to its conformation and interactions with the aqueous environment indeed. Polarizable continuum solvent models without explicit water molecules provided significantly worse agreement with the experiment. The combined MD/DFT approach captures well spectral characteristics for the model systems and constitutes the most reliable basis for exploration of phosphate vibrational properties in biomolecular structural studies.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
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15
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Mutter ST, Zielinski F, Popelier PLA, Blanch EW. Calculation of Raman optical activity spectra for vibrational analysis. Analyst 2015; 140:2944-56. [DOI: 10.1039/c4an02357a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review provides the necessary knowledge to accurately model ROA spectra of solvated systems and interpret their vibrational characteristics.
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Affiliation(s)
- Shaun T. Mutter
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
| | - François Zielinski
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Ewan W. Blanch
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
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16
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Refat MS, Al-Azab FM, Al-Maydama HMA, Amin RR, Jamil YMS. Synthesis and in vitro microbial evaluation of La(III), Ce(III), Sm(III) and Y(III) metal complexes of vitamin B6 drug. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:196-215. [PMID: 24632173 DOI: 10.1016/j.saa.2014.02.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 01/30/2014] [Accepted: 02/09/2014] [Indexed: 06/03/2023]
Abstract
Metal complexes of pyridoxine mono hydrochloride (vitamin B6) are prepared using La(III), Ce(III), Sm(III) and Y(III). The resulting complexes are investigated. Some physical properties, conductivity, analytical data and the composition of the four pyridoxine complexes are discussed. The elemental analysis shows that the formed complexes of La(III), Ce(III), Sm(III) and Y(III) with pyridoxine are of 1:2 (metal:PN) molar ratio. All the synthesized complexes are brown in color and possess high melting points. These complexes are partially soluble in hot methanol, dimethylsulfoxide and dimethylformamide and insoluble in water and some other organic solvents. Elemental analysis data, spectroscopic (IR, UV-vis. and florescence), effective magnetic moment in Bohr magnetons and the proton NMR suggest the structures. However, definite particle size is determined by invoking the X-ray powder diffraction and scanning electron microscopy data. The results obtained suggested that pyridoxine reacted with metal ions as a bidentate ligand through its phenolate oxygen and the oxygen of the adjacent group at the 4'-position. The molar conductance measurements proved that the pyridoxine complexes are electrolytic in nature. The kinetic and thermodynamic parameters such as: Ea, ΔH(*), ΔS(*) and ΔG(*) were estimated from the DTG curves. The antibacterial evaluation of the pyridoxine and their complexes were also performed against some gram positive, negative bacteria as well as fungi.
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Affiliation(s)
- Moamen S Refat
- Department of Chemistry, Faculty of Science, Taif University, Al-Hawiah, P.O. Box 888, Taif 21974, Saudi Arabia; Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt.
| | - Fathi M Al-Azab
- Department of Chemistry, Faculty of Science, Sana'a University, Yemen
| | | | | | - Yasmin M S Jamil
- Department of Chemistry, Faculty of Science, Sana'a University, Yemen
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17
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Hudecová J, Profant V, Novotná P, Baumruk V, Urbanová M, Bouř P. CH Stretching Region: Computational Modeling of Vibrational Optical Activity. J Chem Theory Comput 2013; 9:3096-108. [PMID: 26583989 DOI: 10.1021/ct400285n] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most organic compounds provide vibrational spectra within the CH stretching region, yet the signal is difficult to interpret because of multiple difficulties in experiment and modeling. To better understand various factors involved, the ability of several harmonic and anharmonic computational approaches to describe these vibrations was explored for α-pinene, fenchone, and camphor as test compounds. Raman, Raman optical activity (ROA), infrared absorption (IR), and vibrational circular dichroism (VCD) spectra were measured and compared to quantum chemical computations. Surprisingly, the harmonic vibrational approach reasonably well reproduced the measured spectral patterns, including the vibrational optical activity (VOA). The CH stretching, however, appeared to be more sensitive to the basis set and solvent variations than lower-frequency vibrations. For a higher accuracy in frequencies and spectral shapes, anharmonic corrections were necessary. Accurate harmonic and anharmonic force fields were obtained with the mPW2PLYP double-hybrid functional. A limited vibrational configuration interaction (LVCI) where the CH stretching motion was decoupled from other vibrations provided the best simulated spectra. A balanced harmonic oscillator basis set had to be used, containing also states indirectly interacting with fundamental vibrations. A simpler second-order perturbational approach (PT2) appeared less useful. The modeling provided unprecedented agreement with experimental vibrational frequencies; spectral shapes were reproduced less faithfully. The possibility of ab initio interpretation of the CH spectral region for relatively large molecules further broadens the application span of vibrational spectroscopy.
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Affiliation(s)
- Jana Hudecová
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Václav Profant
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Pavlína Novotná
- Department of Physics and Measurements and Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Vladimír Baumruk
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements and Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
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18
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Dračínský M, Bouř P. Vibrational averaging of the chemical shift in crystalline α-glycine. J Comput Chem 2012; 33:1080-9. [PMID: 22410968 DOI: 10.1002/jcc.22940] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/04/2012] [Accepted: 01/04/2012] [Indexed: 11/06/2022]
Abstract
Averaging of the chemical shift over the molecular motion improves the simulated data and provides additional information about the temperature dependence and system dynamics. However, crystal modeling is difficult due to the limited precision of the plane-wave density functional theory (DFT) methods and approximate vibrational schemes. On the glycine example, we investigate how the averaging can be achieved within the periodic boundary conditions at the DFT level. The nuclear motion is modeled with the vibrational configuration interaction, with other simplified quantum anharmonic schemes, and the classical Born-Oppenheimer molecular dynamics (BOMD). The results confirm a large vibrational contribution to the isotropic shielding values. Both the first and second derivatives of the shielding were found important for the quantum averaging. The first derivatives influence the shielding mostly due to the anharmonic character of the CH and NH stretching modes, whereas second derivatives produce most vibrational corrections associated with the lower-frequency vibrational modes. Temperature excitations of the lowest-frequency vibrational states and the expansion of the crystal cell both determine the temperature dependence of nuclear magnetic resonance parameters. The vibrational quantum approach as well as classical BOMD schemes provided temperature dependencies of the chemical shifts that are consistent with the previous experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 166 10, Czech Republic.
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19
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Yamamoto S, Kaminský J, Bouř P. Structure and Vibrational Motion of Insulin from Raman Optical Activity Spectra. Anal Chem 2012; 84:2440-51. [DOI: 10.1021/ac2032436] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shigeki Yamamoto
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
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20
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Hudecová J, Hopmann KH, Bouř P. Correction of Vibrational Broadening in Molecular Dynamics Clusters with the Normal Mode Optimization Method. J Phys Chem B 2011; 116:336-42. [DOI: 10.1021/jp208785a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague 2, Czech Republic
| | - Kathrin H. Hopmann
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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21
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Profant V, Baumruk V, Li X, Šafařík M, Bouř P. Tracking of the Polyproline Folding by Density Functional Computations and Raman Optical Activity Spectra. J Phys Chem B 2011; 115:15079-89. [DOI: 10.1021/jp207706p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Václav Profant
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Vladimír Baumruk
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Xiaojun Li
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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22
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Ganesan A, Wang F, Brunger M, Prince K. Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:733-742. [PMID: 21862853 DOI: 10.1107/s0909049511029499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/21/2011] [Indexed: 05/31/2023]
Abstract
Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP < 290 eV (where IP is the ionization potential). The two glycyl parent spectral peaks of the amide 291.0 eV [C((2))] and carboxylic 293.5 eV [C((1))] C atoms are shifted in the aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.
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Affiliation(s)
- Aravindhan Ganesan
- Faculty of Life and Social Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
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23
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Yamamoto S, Bouř P. On the limited precision of transfer of molecular optical activity tensors. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Transfer of molecular property tensors (force field, dipole derivatives, polarizabilities, etc.) from smaller fragments to bigger molecules is powerful tool to calculate molecular vibrational spectra. However, we found serious accuracy limits for valinomycin (Phys. Chem. Chem. Phys. 2010, 12, 11021), where the transfer of the Raman optical activity tensors (ROA) had to be avoided. Therefore, in this study, the individual polarizable group model is analyzed for a model water dimer, and the corrections stemming from mutual group polarizations neglected in the transfer are estimated ab initio. The electric dipole polarizability was found more local and less sensitive to the interaction of distant molecular parts than the optical activity tensors (G′, A), which can partially explain the error observed during the transfer. In the second part of the study, tensor derivatives are transferred from smaller fragments to model valinomycin and insulin molecules, and the resultant tensor derivatives and ROA spectra compared to benchmark computations. The results confirmed that the error is caused by mutual polarization of molecular parts, more significant in insulin than in valinomycin, and could only partially be improved by increased size of the fragments.
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24
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Hopmann KH, Ruud K, Pecul M, Kudelski A, Dračínský M, Bouř P. Explicit versus Implicit Solvent Modeling of Raman Optical Activity Spectra. J Phys Chem B 2011; 115:4128-37. [DOI: 10.1021/jp110662w] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kathrin H. Hopmann
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Magdalena Pecul
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kudelski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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25
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Yamamoto S, Watarai H, Bouř P. Monitoring the Backbone Conformation of Valinomycin by Raman Optical Activity. Chemphyschem 2011; 12:1509-18. [DOI: 10.1002/cphc.201000917] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/18/2011] [Indexed: 11/11/2022]
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26
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Li XJ, Zhong ZJ, Wu HZ. DFT and MP2 investigations of L-proline and its hydrated complexes. J Mol Model 2011; 17:2623-30. [PMID: 21264484 DOI: 10.1007/s00894-011-0957-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 01/03/2011] [Indexed: 11/25/2022]
Abstract
A theoretical study of L-proline-nH(2)O (n = 1-3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet-triplet excitation energies tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13. As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O-H stretching or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior and provide reference data for further studies of biological systems.
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Affiliation(s)
- Xiao-Jun Li
- Department of Chemistry and Chemical Engineering, Weinan Teachers University, Weinan, Shaanxi 714000, People's Republic of China.
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27
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Parchaňský V, Bouř P. Transferability of anharmonic force fields in simulations of molecular vibrations. J Chem Phys 2010; 133:044117. [DOI: 10.1063/1.3464759] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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28
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Hudecová J, Kapitán J, Baumruk V, Hammer RP, Keiderling TA, Bouř P. Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide. J Phys Chem A 2010; 114:7642-51. [DOI: 10.1021/jp104744a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
| | - Robert P. Hammer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
| | - Timothy A. Keiderling
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, Prague 6, 16610, Czech Republic, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607-7061
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29
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Ivani I, Baumruk V, Bouř P. A Fourier Transform Method for Generation of Anharmonic Vibrational Molecular Spectra. J Chem Theory Comput 2010; 6:2095-102. [DOI: 10.1021/ct100150f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivan Ivani
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague, Czech Republic
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30
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Sulaiman A, Zen FP, Alatas H, Handoko LT. Anharmonic oscillation effect on the Davydov-Scott monomer in a thermal bath. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061907. [PMID: 20866440 DOI: 10.1103/physreve.81.061907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 04/27/2010] [Indexed: 05/29/2023]
Abstract
The dynamics of Davydov-Scott monomer in a thermal bath with higher order amide-site's displacement leads to anharmonic oscillation effect is investigated using full-quantum approach and the Lindblad formulation of master equation. The specific heat is calculated based on the thermodynamic partition function using the path integral method. The temperature dependence of the specific heat is studied. In the model the specific heat anomaly as pointed out in recent works by Ingold [Phys. Rev. E 79, 061105 (2009)] is also observed. However, it is found that the anomaly occurs at high-temperature region, and the anharmonic oscillation restores the positivity of specific heat.
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Affiliation(s)
- A Sulaiman
- Theoretical Physics Laboratory, THEPI, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40135, Indonesia.
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31
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Kapitán J, Johannessen C, Bour P, Hecht L, Barron LD. Vibrational Raman optical activity of 1-phenylethanol and 1-phenylethylamine: revisiting old friends. Chirality 2010; 21 Suppl 1:E4-12. [PMID: 19544353 DOI: 10.1002/chir.20747] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The samples used for the first observations of vibrational Raman optical activity (ROA) in 1972, namely both enantiomers of 1-phenylethanol and 1-phenylethylamine, have been revisited using a modern commercial ROA instrument together with state-of-the-art ab initio calculations. The simulated ROA spectra reveal for the first time the vibrational origins of the first reported ROA signals, which comprised similar couplets in the alcohol and amine in the spectral range approximately 280-400 cm(-1). The results demonstrate how easy and routine ROA measurements have become, and how current ab initio quantum-chemical calculations are capable of simulating experimental ROA spectra quite closely provided sufficient averaging over accessible conformations is included. Assignment of absolute configuration is, inter alia, completely secure from results of this quality. Anharmonic corrections provided small improvements in the simulated Raman and ROA spectra. The importance of conformational averaging emphasized by this and previous related work provides the underlying theoretical background to ROA studies of dynamic aspects of chiral molecular and biomolecular structure and behavior.
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Affiliation(s)
- Josef Kapitán
- WestChem, Department of Chemistry, University of Glasgow, Glasgow, UK
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32
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Paulson LO, Kaminský J, Anderson DT, Bouř P, Kubelka J. Theoretical Study of Vibrationally Averaged Dipole Moments for the Ground and Excited C═O Stretching States of trans-Formic Acid. J Chem Theory Comput 2010; 6:817-27. [PMID: 26613309 DOI: 10.1021/ct900608t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent experimental studies of trans-formic acid (FA) in solid para-hydrogen (pH2) highlighted the importance of vibrationally averaged dipole moments for the interpretation of the high-resolution infrared (IR) spectra, in particular for the C═O stretch (ν3) mode. In this report, dipole moments for the ν3 ground (v = 0) and excited (v = 1, 2, 3, and 4) anharmonic vibrational states in trans-FA are investigated using two different approaches: a single mode approximation, where the vibrational states are obtained from the solution of the one-dimensional Schrödinger equation for the harmonic normal coordinate, and a limited vibrational configuration interaction (VCI) approximation. Density functional theory (B3LYP, BPW91) and correlated ab initio (MP2 and CCSD(T)) electronic methods were employed with a number of double- and triple-ζ and correlation consistent basis sets. Both single mode and VCI approaches show comparable agreement with experimental data, which is more dependent on the level of theory used. In particular, the BPW91/cc-pVDZ level appears to perform remarkably well. Effects of solvation of FA in solid state Ar and pH2 matrices were simulated at the BPW91/cc-pVDZ level using a conductor-like polarized continuum model (CPCM). The Ar and pH2 solid-state matrices cause quite a substantial increase in the FA dipole moments. Compared to gas-phase calculations, the CPCM model for pH2 better reproduces the experimental FA spectral shifts caused by interaction with traces of ortho-hydrogen (oH2) species in solid pH2. The validity of the single mode approach is tested against the multidimensional VCI results, suggesting that the isolated (noninteracting) mode approximation is valid up to the third vibrationally excited state (v = 3). Finally, the contribution of the ground anharmonic vibrational states of the remaining modes to the resulting ν3 single mode dipole moments is examined and discussed.
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Affiliation(s)
- Leif O Paulson
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, and Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Jakub Kaminský
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, and Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - David T Anderson
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, and Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, and Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, and Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague, Czech Republic
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33
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Yamamoto S, Straka M, Watarai H, Bouř P. Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy. Phys Chem Chem Phys 2010; 12:11021-32. [DOI: 10.1039/c003277h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Bouř P. Cross-Polarization Detection Enables Fast Measurement of Vibrational Circular Dichroism. Chemphyschem 2009; 10:1983-5. [DOI: 10.1002/cphc.200900383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Andrushchenko V, Matějka P, Anderson DT, Kaminský J, Horníček J, Paulson LO, Bouř P. Solvent Dependence of the N-Methylacetamide Structure and Force Field. J Phys Chem A 2009; 113:9727-36. [DOI: 10.1021/jp9045512] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Pavel Matějka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - David T. Anderson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jan Horníček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Leif O. Paulson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
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36
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Miani A, Helfand MS, Raugei S. Ab Initio Raman Spectra of β-Lactamase Inhibitor Intermediates Bound to E166A SHV β-Lactamase. J Chem Theory Comput 2009; 5:2158-72. [DOI: 10.1021/ct900131q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Andrea Miani
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Marion Skalweit Helfand
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Simone Raugei
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
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37
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Šebek J, Kapitán J, Šebestík J, Baumruk V, Bouř P. l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra. J Phys Chem A 2009; 113:7760-8. [DOI: 10.1021/jp902739r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Šebek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
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Tkachev SN, Pravica M, Kim E, Weck PF. Raman spectroscopic study of cyclopentane at high pressure. J Chem Phys 2009; 130:204505. [DOI: 10.1063/1.3137075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Dracínský M, Kaminský J, Bour P. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging. J Chem Phys 2009; 130:094106. [PMID: 19275395 DOI: 10.1063/1.3081317] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in future quantum chemistry packages is desirable.
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Affiliation(s)
- Martin Dracínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic.
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Kaminský J, ŠEbek J, Bouř P. Molecular dynamics with restrictions derived from optical spectra. J Comput Chem 2009; 30:983-91. [DOI: 10.1002/jcc.21123] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kaminský J, Kapitán J, Baumruk V, Bednárová L, Bouř P. Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion. J Phys Chem A 2009; 113:3594-601. [DOI: 10.1021/jp809210n] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
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Bednárová L, Bouř P, Maloň P. Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation. Chirality 2009; 22:514-26. [DOI: 10.1002/chir.20772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Buděšínský M, Daněček P, Bednárová L, Kapitán J, Baumruk V, Bouř P. Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides. J Phys Chem A 2008; 112:8633-40. [DOI: 10.1021/jp806181q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Petr Daněček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
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Kapitán J, Hecht L, Bouř P. Raman spectral evidence of methyl rotation in liquid toluene. Phys Chem Chem Phys 2008; 10:1003-8. [DOI: 10.1039/b713965a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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