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Wang LF, You CX. Application of periodic density functional theory calculations for exploring copper(II) coordination effects on the mesophase behavior of p-n-alkoxybenzoic acids. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Copper(II) benzoates ([Formula: see text]OBA-Cu) with various terminal alkoxy carbon numbers, [Formula: see text]–12, were prepared from [Formula: see text]-[Formula: see text]-alkoxy benzoic acids (nOBAs). Fourier transform infrared (IR) experiments suggested that dimerization through copper(II) chelating bidentate coordination created [Formula: see text]OBA-Cu with a linear rod-like structure, similar to the hydrogen-bonded structure of its parent [Formula: see text]OBA. However, the coordination structure of [Formula: see text]OBA-Cu changed during heating. Periodic density functional theory calculations provided valuable insight into the possible arrangement of the parent and copper(II)-coordinated [Formula: see text]OBAs. The formation of binuclear complexes between two adjacent [Formula: see text]OBA-Cu dimers forced [Formula: see text]OBA-Cu to arrange itself in a layer and exhibit smectic A mesophase. Accordingly, four types of IR stretching absorption of benzoyl carbonyl were observed in binuclear [Formula: see text]OBA-Cu complexes, replacing the original symmetric and asymmetric vibrations of benzoyl carboxylate in chelating bidentate coordination. The lateral association by [Formula: see text]–[Formula: see text] interactions between adjacent parent [Formula: see text]OBA dimers preferred a progressive smectic C arrangement. The origin of the odd–even effect was understood from the consideration of the molecular structure.
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Affiliation(s)
- Li-Fen Wang
- Department of Applied Chemistry and Material Science, Fooyin University, Kaohsiung 83102, Taiwan, R. O. C
| | - Cheng-Xian You
- Department of Applied Chemistry and Material Science, Fooyin University, Kaohsiung 83102, Taiwan, R. O. C
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Firdaus-Raih M, Hamdani HY, Nadzirin N, Ramlan EI, Willett P, Artymiuk PJ. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. Nucleic Acids Res 2014; 42:W382-8. [PMID: 24831543 PMCID: PMC4086061 DOI: 10.1093/nar/gku438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac.
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Affiliation(s)
- Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Hazrina Yusof Hamdani
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Nurul Nadzirin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Effirul Ikhwan Ramlan
- Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Peter Willett
- Information School, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Peter J Artymiuk
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Abstract
The present paper reports a conformational study of solid-state anhydrous guanine, using vibrational spectroscopy techniques—infrared, Raman, and inelastic neutron scattering—coupled to quantum mechanical methods at the DFT level, both for the isolated molecule and the condensed state. In both cases, the 7H-keto-amino tautomer was found to be the prevalent form, contrary to aqueous solutions and hydrated polycrystalline guanine, where the 9H-keto-amino tautomer is the most favoured species. This paper is a significant contribution for the existing spectroscopic characterization of this purine base, by unambiguously assigning its vibrational spectra.
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Johnson M, Trommsdorff H. Vibrational spectra of crystalline formic and acetic acid isotopologues by inelastic neutron scattering and numerical simulations. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Fontaine-Vive F, Merzel F, Johnson M, Kearley G. Collagen and component polypeptides: Low frequency and amide vibrations. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Hafner J. Ab-initiosimulations of materials using VASP: Density-functional theory and beyond. J Comput Chem 2008; 29:2044-78. [DOI: 10.1002/jcc.21057] [Citation(s) in RCA: 1810] [Impact Index Per Article: 113.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sládkovičová M, Smrčok Ľ, Mach P, Tunega D, Ramirez-Cuesta AJ. Inelastic neutron scattering and DFT study of 1,6-anhydro-β-d-glucopyranose (levoglucosan). J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.03.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ortmann F, Hannewald K, Bechstedt F. Guanine Crystals: A First Principles Study. J Phys Chem B 2008; 112:1540-8. [DOI: 10.1021/jp076455t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Ortmann
- European Theoretical Spectroscopy Facility (ETSF), Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität, Max-Wien-Platz 1, 07743 Jena, Germany
| | - K. Hannewald
- European Theoretical Spectroscopy Facility (ETSF), Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität, Max-Wien-Platz 1, 07743 Jena, Germany
| | - F. Bechstedt
- European Theoretical Spectroscopy Facility (ETSF), Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität, Max-Wien-Platz 1, 07743 Jena, Germany
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Fontaine-Vive F, Johnson MR, Kearley GJ, Cowan JA, Howard JAK, Parker SF. Phonon driven proton transfer in crystals with short strong hydrogen bonds. J Chem Phys 2007; 124:234503. [PMID: 16821925 DOI: 10.1063/1.2206774] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.
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Affiliation(s)
- F Fontaine-Vive
- Institut Laue Langevin, BP 156, 38042 Grenoble Cedex 9, France
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Takahashi M, Kawazoe Y, Ishikawa Y, Ito H. Low-frequency vibrations of crystalline α,α-trehalose dihydrate. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ciezak JA, Trevino SF. Inelastic Neutron Scattering Spectrum of Cyclotrimethylenetrinitramine: A Comparison with Solid-State Electronic Structure Calculations. J Phys Chem A 2006; 110:5149-55. [PMID: 16610838 DOI: 10.1021/jp057098u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.
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Affiliation(s)
- Jennifer A Ciezak
- U.S. Army Research Laboratory, Weapons and Materials Research Directorate, Aberdeen Proving Ground, Maryland 21005, USA.
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Fontaine-Vive F, Johnson MR, Kearley GJ, Howard JAK, Parker SF. How Phonons Govern the Behavior of Short, Strong Hydrogen Bonds in Urea−Phosphoric Acid. J Am Chem Soc 2006; 128:2963-9. [PMID: 16506776 DOI: 10.1021/ja0569712] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent neutron diffraction data have shown that the hydrogen atom involved in the short, strong hydrogen bond in urea-phosphoric acid migrates toward the midpoint of the hydrogen bond as the temperature increases. With the help of solid state ab initio calculations and inelastic neutron scattering, we have investigated the temperature dependence of the structural and vibrational properties of the system. The potential energy surface of the proton in the short, strong hydrogen bond and the thermal population of the energy levels therein cannot account for the observed proton migration. Ab initio molecular dynamics simulations clearly reveal the migration of the proton. This molecular dynamics result was reported recently by other authors, but they only offered a tentative explanation in terms of a resonance between high-frequency vibrations, which is not supported by the calculations presented here. We explain the proton migration in terms of phonon-driven structural fluctuations and their impact on the temperature-dependent evolution of the potential energy surface of the short hydrogen-bond proton.
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Biomolecular Spectroscopy Using Pulsed-Source Instruments. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/3-540-29111-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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16
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Whitten AE, McKinnon JJ, Spackman MA. Electric field-derived point charges to mimic the electrostatics in molecular crystals. J Comput Chem 2006; 27:1063-70. [PMID: 16685714 DOI: 10.1002/jcc.20419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.
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Affiliation(s)
- Andrew E Whitten
- Chemistry, University of New England, Armidale NSW 2351, Australia
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Theoretical and experimental study of the inelastic neutron scattering spectra of β-5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Plazanet M, Fontaine-Vive F, Gardner KH, Forsyth VT, Ivanov A, Ramirez-Cuesta AJ, Johnson MR. Neutron Vibrational Spectroscopy Gives New Insights into the Structure of Poly(p-phenylene terephthalamide). J Am Chem Soc 2005; 127:6672-8. [PMID: 15869288 DOI: 10.1021/ja0437205] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The vibrational spectra of benzanilide and poly(p-phenylene terephthalamide) have been measured using inelastic neutron scattering. These compounds have similar hydrogen-bond networks, which, for poly(p-phenylene terephthalamide), lead to two-dimensional hydrogen-bonded sheets in the crystal. Experimental spectra are compared with solid-state, quantum chemical calculations based on density functional theory (DFT). Such "parameter-free" calculations allow the structure-dynamics relation in this type of compound to be quantified, which is demonstrated here for benzanilide. In the case of poly(p-phenylene terephthalamide), vibrational spectroscopy and DFT calculations help resolve long-standing questions about the packing of hydrogen-bonded sheets in the solid state.
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Affiliation(s)
- M Plazanet
- Institut Laue Langevin, BP156, 38042 Grenoble Cedex 9, France
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Eckert J, Sewell TD, Kress JD, Kober EM, Lily L.Wang, and, Olah G. Vibrational Analysis of the Inelastic Neutron Scattering Spectrum of Tetramethylammonium Borohydride by Molecular Dynamics Simulations and Electronic Structure Calculations. J Phys Chem A 2004. [DOI: 10.1021/jp048479v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juergen Eckert
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Thomas D. Sewell
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Joel D. Kress
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Edward M. Kober
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Lily L.Wang, and
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Glenn Olah
- LANSCE, T and MST Divisions, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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Jezierska A, Panek J, Ryng S. DFT study of a novel lead structure in the isoxazole heterocyclic system. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00482-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Johnson M, Parlinski K, Natkaniec I, Hudson B. Ab initio calculations and INS measurements of phonons and molecular vibrations in a model peptide compound – urea. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00178-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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