Home About us Contact
|
Home About us Contact | ||
|
|
||
Force Constants (force + constant)
Selected AbstractsAb initio calculations of intramolecular parameters for a class of arylamide polymersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2006Satyavani Vemparala Abstract Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 693,700, 2006 [source] Influence of pressure on the lengths of chemical bondsACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2003I. David Brown An expression to describe the force that a chemical bond exerts on its terminal atoms is proposed, and is used to derive expressions for the bond force constant and bond compressibility. The unknown parameter in this model, the effective charge on the atoms that form the bond, is determined by comparing the derived force constants with those obtained spectroscopically. The resultant bond compressibilities are shown to generally agree well with those determined from high-pressure structure determinations and from the bulk moduli of high-symmetry structures. Bond valences can be corrected for pressure by recognizing that the bond-valence parameter, R0, changes with pressure according to the equation [source] Disproving a Silicon Analog of an Alkyne with the Aid of Topological Analyses of the Electronic Structure and Ab Initio Molecular Dynamics CalculationsCHEMPHYSCHEM, Issue 9 2005Carlo A. Pignedoli Dr. Abstract A silicon compound has recently been synthesized that was claimed to exhibit the first realization of a silicon,silicon triple bond. We debate this classification on the basis of a thorough investigation of the nature of the chemical bond, using the rigorous topological analysis of the electron density as developed in Bader's atoms-in-molecules theory, that of the electron localization function and the related orbital-independent definitions of the bond order. Our results refer both to the ground-state geometry and to nonequilibrium configurations, which are accessed by the system in a room-temperature ab initio molecular dynamics simulation. We also use the reciprocal compliance force constant as an independent chemical descriptor. All the above procedures are in agreement and do not support the classification of the silicon,silicon central bond as triple. The characterization which consistently emerges from the present study is one in which two electron pairs participate in the bonding and the other pair belongs mainly to nonbonding regions. [source] Optimization of strong and weak coordinatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2006Marcel Swart Abstract We present a new scheme for the geometry optimization of equilibrium and transition state structures that can be used for both strong and weak coordinates. We use a screening function that depends on atom-pair distances to differentiate strong coordinates from weak coordinates. This differentiation significantly accelerates the optimization of these coordinates, and thus of the overall geometry. An adapted version of the delocalized coordinates setup is used to generate automatically a set of internal coordinates that is shown to perform well for the geometry optimization of systems with weak and strong coordinates. For the Baker test set of 30 molecules, we need only 173 geometry cycles with PW91/TZ2P calculations, which compares well with the best previous attempts reported in literature. For the localization of transition state structures, we generate the initial Hessian matrix, using appropriate force constants from a database. In this way, one avoids the explicit computation of the Hessian matrix. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] Vibrational spectroscopic and force field studies of copper(II) chloride and bromide compounds, and crystal structure of KCuBr3JOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2008Liubov V. Stepakova Abstract Vibrational spectroscopic and force field studies have been performed of 15 related copper(II) chloride and copper(II) bromide compounds, including hydrated salts crystallizing in ternary aqueous systems with alkali and ammonium halides. For halocuprates with distorted octahedral coordination characteristic stretching Raman wavenumbers, corresponding to symmetric stretching CuIIX modes in the equatorial plane, were found in the ranges 247,288 cm,1 for X = Cl, and 173,189 cm,1 for X = Br, while the low-wavenumber stretching modes for the weaker axial CuX interactions varied considerably. The tetrahedral coordination for Cs2CuCl4 and Cs2CuBr4 leads to somewhat lower CuX symmetric stretching wavenumbers, 295 and 173 cm,1, respectively. The assignments of the copper,ligand stretching vibrations were performed with the aid of normal coordinate calculations. Correlations between force constants, averaged CuX stretching wavenumbers and bond distances have been evaluated considering the following aspects: (1) Jahn,Teller tetragonal distortion (axial elongation) of the octahedral copper(II) coordination environment, (2) differences between terminal and bridging halide ligands (3) effects of coordinated water and the influence of outer-sphere cations. Force constant ratios for terminal and bridging metal,halide bonds reveal characteristic differences between planar and tetrahedrally coordinated M2X6 species. In the hydrated copper(II) halide complexes, the halide ligands are more strongly bound than coordinated water molecules. The crystal structure of KCuBr3 (K2Cu2Br6), which was determined to provide structural information for the force field analyses, contains stacks of planar dimeric [Cu2Br6]2, complexes held together by weak axial CuBr interactions. Copyright © 2007 John Wiley & Sons, Ltd. [source] Lattice dynamics of tetragonal Nd2BaZnO5JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2007H. C. Gupta Abstract A short-range force constant model (SRFCM) has been applied to investigate the Raman and the infrared wavenumbers in Nd2BaZnO5 in its tetragonal phase of space group I4/mcm. Calculations of zone-center phonons are made with five stretching and five bending force constants. All the Raman and infrared values are then assigned to their corresponding modes. Two Raman modes are reassigned on the basis of group theoretical calculations. The calculated Raman wavenumbers exhibit good agreement with the observed values. Copyright © 2007 John Wiley & Sons, Ltd. [source] Vibrational spectra and quantum chemical calculations of uracilyl,pyridinium mesomeric betaineJOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2007A. Schmidt Abstract Modified nucleobases (MNs) are promising molecules with potential application in non-linear optic (NLO) and drug design against a wide number of diseases. In the present paper we report studies on a cross-conjugated mesomeric betaine, which can act as a MN, formed by the covalent union of a 4-dimethylamino pyridinium and a uracilyl groups. The molecule thus formed must be presented by a dipolar canonical formulae in which positive and negative charges are delocalized within separated moieties. Quantum chemistry density functional theory (DFT) calculations, at the B3PW91/6-31G** level, and Fourier transform (FT) infrared and Raman spectra of this molecule and its N -deuterated derivative were performed. The calculated structural properties over the ground state optimized structure evidenced a strong separation between the two conjugated systems. Comparison with previous results obtained for the cationic species indicated that N -protonation clearly affects the degree of conjugation. Assignments of the FT-IR and FT-Raman spectra were supported by the DFT wavenumbers, intensities and normal modes, which also evidenced the separation of the two conjugated systems. Significant deviations were found for the stretching force constants of the inter-ring and the uracilyl skeletal bonds when comparing this molecule with its N -protonated species. Copyright © 2007 John Wiley & Sons, Ltd. [source] Lattice dynamic investigation of the Raman and infrared wavenumbers of orthorhombic R2BaNiO5 (R = Y, Gd) oxides in Immm structureJOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2007H. C. Gupta Abstract A short-range force constant model has been applied to investigate the Raman and the infrared wavenumbers in R2BaNiO5 (R = Y, Gd) in their orthorhombic phase of space group Immm. Calculations of zone-center phonons are made with seven stretching and four bending force constants. The force constants are evaluated by fitting nine Raman and two infrared modes. Two Raman modes are reassigned on the basis of group theoretical calculations. The calculated Raman and infrared modes show good agreement with the observed values. The infrared values are assigned for the first time in these oxides. Copyright © 2006 John Wiley & Sons, Ltd. [source] Lattice dynamic investigation of the Raman and infrared wavenumbers of orthorhombic R2BaCuO5 (R = Y, Ho, Gd) oxidesJOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2005H. C. Gupta Abstract A short-range force constant model was applied for the first time to investigate the Raman and infrared wavenumbers in R2BaCuO5 (R = Y, Ho, Gd) oxides in their orthorhombic phase of space group Pnma. Calculations of zone center phonons were made with 17 stretching and four bending force constants. The force constants were evaluated using the electronegativities and the atomic distances. The calculated values of Raman wavenumbers are in reasonable agreement with the available observed values. The infrared wavenumbers were assigned for the first time. Copyright © 2004 John Wiley & Sons, Ltd. [source] Fourier transform Raman and Fourier transform infrared spectra of cross-linked polyurethaneurea films synthesized from solutionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2002Valentina Romanova Cross-linked polyurethaneurea films based on polyoxytetramethylene glycol and polyoxypropylene glycol with toluene diisocyanate and 3,3,-dichloro-4,4,-diaminodiphenylmethane were synthesized in a solution where the solvent evaporates during the polymerization. FT-Raman and FTIR spectra were analysed and intermolecular force constants of hydrogen bonds were calculated. On the basis of the intensity of the Raman and IR spectral lines, which reflects hydrogen bond formation, the optimum structure of hydrogen bonds and the conformations of macromolecules of polyurethaneurea were observed for the solvent ethyl acetate. Copyright © 2002 John Wiley & Sons, Ltd. [source] Force constant calculation from Raman and IR spectra in the three non-cubic phases of BaCeO3JOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2001H. C. Gupta Raman spectroscopic data for BaCeO3 were modeled with the use of a small set of force constants in its three phases (Pnma, Imma and R3c) using experimental IR and Raman data. An IR reflectance spectrum of BaCeO3 in its Pnma phase is provided for the first time. Raman band symmetry assignments in the Pnma phase were re-examined and the assignments of Genet et al. were confirmed. The distribution of the Raman bands of the Pnma phase between the zone center and X point in Imma is provided and band assignments were extended to the Imma and R3c phases. Calculated values for both Raman- and IR-active modes are provided in the three phases. The variations in force constants throughout the phase transitions are briefly discussed. Copyright © 2001 John Wiley & Sons, Ltd. [source] Symmetry-based analysis of the electron,phonon interaction in graphenePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 11-12 2009I. Milo Abstract Symmetry-based analysis of the electron,phonon interaction in graphene is performed. Some nontrivial physical properties of graphene are shown to be direct consequence of symmetry, independent on the applied dynamical model. Namely, it is found that there are vibronically uncoupled non symmetric modes which thus might be responsible for the stability of the honeycomb lattice. Symmetry also predicts vanishing of the electron,phonon interaction for quite a number of the normal displacements. Consequently, lattice dynamics along these degrees of freedom is governed by the ion repulsion which leads to the anharmonic terms, being linear in absolute elongation. In particular, this effect is attributed to the K and , points of the Brillouin zone, giving insight into origin of the Kohn anomaly. The results are further numerically confirmed within full and tight-binding density functional calculations and force constants model. [source] Pressure evolution of the phonon modes and force constants of Tb3Al5O12 and Lu3Al5O12PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2003K. Papagelis Abstract The pressure evolution of the Raman modes of Tb3Al5O12 and Lu3Al5O12 has been measured at room temperature and analyzed theoretically with the rigid ion model. Satisfactory agreement between experiment and theory has been found. The extracted pressure variation of the bond bending and bond stretching force constants shows that the compressibility of the various polyhedra types increases with increasing cation coordination, indicating that the dodecahedra play an important role in the compressibility of the garnet structure. Finally, an estimation of the pressure coefficients for the transverse optical infrared active mode frequencies is given. [source] Phonons and Raman spectra of lithiated titanate Li0.5TiO2PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2004R. Baddour-Hadjean Abstract Raman spectra of the electrochemically lithiated TiO2 anatase evidence that Li intercalation induces complex spectral features in the high wavenumber range. These modes can be assigned to the stretching vibrations of Li-O valence bonds. Two theoretical approaches are used to describe the vibrations of Li atoms within the TiO2 lattice. First, the quantum-mechanical calculations of molecular clusters imitating the Li...TiO2 system, which showed formation of covalent Li-O bonds and allowed an estimation of their force constants. Second, the lattice dynamics simulation which enabled to predict the whole spectrum of Li-phonons and their interaction with TiO2 lattice vibrations. Complex structure of the observed Raman spectra is explained by multiplicity of the Li positions. This results in multiple Raman bands originated from the Li atom vibrations covering a wide frequency range from 450 up to 950 cm,1. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Giant reflectance anisotropy of polar cubic semiconductors in the far infraredPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 8 2003Yu. A. Kosevich Abstract We present our measurements and model for the reflectancre anisotropy of the (001) surface of polar cubic zinc-blende semiconductor in the far infrared. We observe that the relative reflectance difference of GaAs(001) in the far infrared can reach the value of twenty percents which is two orders of magnitude higher than the reflectance difference of the GaAs(001) in the near-ultraviolet - visible range. The most strong reflectance anisotropy was observed in the optical phonon Reststrahlbande and its vicinity. We relate the observed reflectance anisotropy with the anisotropy of the optical-phonon and plasma damping constants. Such anisotropy can be caused by anisotropic inhomogeneous broadening of the frequencies of the optical-phonon and plasma oscillations polarized respectively along the [110] and directions. This effect can be understood in terms of the lattice-deformation-induced changes of the optical-phonon force constants and electron-effective-mass tensor components. Anisotropic inhomogeneous strain of the lattice can in turn be induced by anisotropic microscopic short-range ordering of point defects (dopants) and dislocations in near-surface regions of noncentrosymmentric zinc-blende semiconductors. The observed giant reflectance anisotropy can be used as a sensitive tool for the far infrared characterization of zinc-blende semiconductors. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Influence of pressure on the lengths of chemical bondsACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2003I. David Brown An expression to describe the force that a chemical bond exerts on its terminal atoms is proposed, and is used to derive expressions for the bond force constant and bond compressibility. The unknown parameter in this model, the effective charge on the atoms that form the bond, is determined by comparing the derived force constants with those obtained spectroscopically. The resultant bond compressibilities are shown to generally agree well with those determined from high-pressure structure determinations and from the bulk moduli of high-symmetry structures. Bond valences can be corrected for pressure by recognizing that the bond-valence parameter, R0, changes with pressure according to the equation [source] | |||||||||||||