Home About us Contact
|
Home About us Contact | ||
|
|
||
Vibrational Frequencies (vibrational + frequency)
Kinds of Vibrational Frequencies Selected AbstractsOn the performance of eleven DFT functionals in the description of the vibrational properties of aluminosilicatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2010Raffaella Demichelis Abstract The performance of eleven DFT functionals in describing the equilibrium structure and the vibrational spectra at the , point of pyrope (Mg3Al2Si3O12), forsterite (,-Mg2SiO4), ,-quartz (,-SiO2) and corundum (,-Al2O3) is discussed. The four systems, for which accurate experimental data are available, are here used as a representative sample of the large aluminosilicates family. Calculations were performed with the periodic ab initio CRYSTAL code by using all-electron Gaussian-type basis sets. All the functionals here considered provide reasonable structural predictions, the hybrid PBE0 giving the least deviation from the experimental unit cell volumes (from ,0.3% to +0.6%). At the other extreme, SVWN and SPWLSD (,,3%) and PBE and PW91 (, +3%) provide the largest volume under- and over-estimation, respectively. Vibrational frequencies are more accurate when computed with hybrid functionals, with the best performance provided by B3LYP and WC1LYP (mean absolute differences with respect to experiments evaluated on a set of 134 vibrational frequencies, ||t , 5.5 cm,1). The three recently proposed GGA functionals, PBEsol, SOGGA-PBE and WC-PBE, provide a good description of the vibrational spectra, of the same quality as the one provided by PBE0 and B1WC (||t , 10 cm,1), whereas poorer results are obtained with PBE (||t , 17 cm,1). © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Structures and energies of D -galactose and galabiose conformers as calculated by ab initio and semiempirical methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Majda Rahal-Sekkal Abstract Optimized geometries and total energies of some conformers of ,- and ,- D -galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of ,- and ,- D -galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units , 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles , and , of the glycosidic linkage are considered. In each calculation, at each increment of , and ,, using a step of 30° from 0 to 330°, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 806,818, 2003 [source] Synthesis and characterization of potassium magnesium sulphate hexahydrate crystalsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 4 2006M. Dhandapani Abstract Potassium magnesium sulphate hexahydrate (picromerite) was synthesized and single crystals were obtained from saturated aqueous solution by slow evaporation method at room temperature. The crystals were bright, colourless and transparent having well defined external faces. The grown crystals were characterized through Fourier Transform Infrared (FTIR) spectral studies and thermal analysis. The FTIR data were used to assign the characteristic vibrational frequencies of the various chemical bonds in the compound. The compound crystallizes in monoclinic lattice with the space group P21/c. The thermogravimetry (TG) indicates the removal of only two water molecules around 100 °C. A suitable decomposition pattern was formulated based on the percentage weight losses observed in TG of the compound. The results of differential thermal analysis (DTA) conform to the results of TGA. Differential scanning calorimetry (DSC) analysis carried out at high temperature suggests that the occurrence of two phase transitions in the crystal between 140 and 180 °C. When the crystal was cooled below the room temperature up to ,170 °C, no thermal anomaly was observed. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Synthesis, structural and thermal studies of tetrathioureacopper(I) chloride crystalsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 8 2005M. Dhandapani Abstract Tetrathioureacopper(I) chloride, hereafter abbreviated as TCC, was synthesised and single crystals were obtained from saturated aqueous solution by slow evaporation (solution growth) method at room temperature. The crystals obtained are bright, colourless and transparent having well defined external faces. The grown crystals were characterized through elemental analysis, single crystal X-ray diffraction study, thermal analysis, electron spin resonance spectroscopy and Fourier Transform infrared spectroscopy. The elemental analysis confirms the stoichiometry of the compound. The single crystal diffraction studies indicate that TCC crystallises in the tetragonal lattice and the unit cell parameters are a = b = 13.4082 Å, c = 13.8074 Å, V = 2482.29 Å3, , = , = , = 90°. Space group and the number of molecules per unit cell (Z) are found to be P41212 and 8 respectively. The TG curve of the sample shows a prolonged decomposition from 210 to 628.3 °C, from which the decomposition pattern has been formulated. The endothermic peaks in the DTA curve indicate melting and decomposition of the compound at 165.2 and 633.8 °C respectively. An exothermic peak in high temperature DSC indicates a phase transition in the compound at 274.8 °C. Thermal anomalies observed in the low temperature DSC at ,163.3, ,152.0, ,141.5, ,108.3, 1.0 and 12.1 °C in the heating run and ,157.1 and ,153.9 °C in the cooling run reveal first order phase transitions in the crystal. The peaks observed at ,146.2 °C in both the heating and cooling runs suggest occurrence of a second order phase transition in this compound. The IR spectroscopic data were used to assign the characteristic vibrational frequencies of various groups present in the compound. The ESR study confirms that the copper is in the +1 oxidation state in the complex. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A Combined Gas-Phase Electron Diffraction/Mass Spectrometric Study of the Sublimation Processes of TeBr4 and TeI4: The Molecular Structure of Tellurium Dibromide and Tellurium DiiodideEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 33 2008Sergey A. Shlykov Abstract The sublimation processes of TeBr4 at 471(5) K and TeI4 at 373(5) K were studied with a combined gas-phase electron diffraction and mass spectrometric technique (GED/MS). The mass spectra and the analysis of the GED intensities showed that a contribution of 40(3) mol-% TeBr2, 59(3) mol-% Br2, and 1 mol-% TeBr4 was formed in the vapor over TeBr4(s). Solid tellurium tetraiodide decomposes to form I2(g) and Te(s). A very small contribution of 3.3,±,2.1 mol-% of gaseous TeI2 was also determined by both GED and MS. The "metallic" Te accumulated in the solid phase vaporizes at above ca. 670 K as the predominately Te2 molcular species. Refinement of the GED intensities resulted in rg(Te,Br) = 2.480(5) Å and ,gBr,Te,Br = 99.0(6)° for TeBr2 and rg(Te,I) = 2.693(9) Å and ,g(I,Te,I) = 103.1(22)° for TeI2. The small contribution of TeBr4 observed in the mass spectra of the vapor over TeBr4 could not be observed in the GED data. Geometric parameters and vibrational frequencies for the tellurium dihalides TeX2 with X = F, Cl, Br, and I were calculated with B3LYP, MP2, CCSD, and CCSD(T) methods by using aug-cc-pVTZ basis sets and various core potentials for the tellurium atom. Bonding properties in tellurium dihalides are discussed on the basis of natural bond orbital analyses. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Evaluation of data for atmospheric models: Master Equation/RRKM calculations on the combination reaction ClO + NO2 , ClONO2, a recurring issueINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 9 2009David M. Golden Experimental data for the title reaction have been modeled using Master Equation/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA and IUPAC data evaluation panels, which represent the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies and a value of the bond dissociation energy of ClONO2, DH298(ClONO2) = 26.5 kcal mol,1, corresponding to ,H00 = 25.35 kcal mol,1 at 0 K) and use of RRKM/Master Equation methods, fitting calculations to the reported data was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca 4 at, or close to, the low-pressure limit. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 573,581, 2009 [source] Theoretical studies on the mechanism and kinetics of the reaction of F atom with NCO radicalINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2003Zheng-Yu Zhou The reaction of a F atom with an NCO radical was studied at 6-311+g* level, using DFT methods. All geometries, vibrational frequencies, and energies of different stationary points were calculated by HF, UMP2, and DFT methods, and the results agreed with the experimental values. The vibrational frequencies and vibrational modes of the reactant, intermediates, transition states, and products were calculated and the changes of these frequencies and modes were analyzed. Simultaneously, the vibrational modes of various species were assigned. The relationship and the change among these confirmed the mechanism of the reaction and the process of electron transfer. The major channel for the reaction was found to be the cis-channel. At the same time the rate constant was estimated. A new method of analyzing reaction mechanism is also presented. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 52,60, 2003 [source] Reaction of H + ketene to formyl methyl and acetyl radicals and reverse dissociationsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2003Jongwoo Lee Thermochemical properties for reactants, intermediates, products, and transition states important in the ketene (CH2CO) + H reaction system and unimolecular reactions of the stabilized formyl methyl (C·H2CHO) and the acetyl radicals (CH3C·O) were analyzed with density functional and ab initio calculations. Enthalpies of formation (,Hf°298) were determined using isodesmic reaction analysis at the CBS-QCI/APNO and the CBSQ levels. Entropies (S°298) and heat capacities (Cp°(T)) were determined using geometric parameters and vibrational frequencies obtained at the HF/6-311G(d,p) level of theory. Internal rotor contributions were included in the S and Cp(T) values. A hydrogen atom can add to the CH2 -group of the ketene to form the acetyl radical, CH3C·O (Ea = 2.49 in CBS-QCI/APNO, units: kcal/mol). The acetyl radical can undergo ,-scission back to reactants, CH2CO + H (Ea = 45.97), isomerize via hydrogen shift (Ea = 46.35) to form the slight higher energy, formyl methyl radical, C·H2CHO, or decompose to CH3 + CO (Ea = 17.33). The hydrogen atom also can add to the carbonyl group to form C·H2CHO (Ea = 6.72). This formyl methyl radical can undergo , scission back to reactants, CH2CO + H (Ea = 43.85), or isomerize via hydrogen shift (Ea = 40.00) to form the acetyl radical isomer, CH3C·O, which can decompose to CH3 + CO. Rate constants are estimated as function of pressure and temperature, using quantum Rice,Ramsperger,Kassel analysis for k(E) and the master equation for falloff. Important reaction products are CH3 + CO via decomposition at both high and low temperatures. A transition state for direct abstraction of hydrogen atom on CH2CO by H to form, ketenyl radical plus H2 is identified with a barrier of 12.27, at the CBS-QCI/APNO level. ,Hf°298 values are estimated for the following compounds at the CBS-QCI/APNO level: CH3C·O (,3.27), C·H2CHO (3.08), CH2CO (,11.89), HC·CO (41.98) (kcal/mol). © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 20,44, 2003 [source] Kinetics and mechanism for the H-for-X exchange process in the H + C6H5X reactions: A computational studyINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2001I. V. Tokmakov The addition of H atoms to benzene and toluene and subsequent transformations were investigated using high level ab initio and density functional theory methods. Molecular structures and vibrational frequencies calculated at the B3LYP/6-311++G(d,p) level of theory were used in combination with adjusted G2M energetic parameters for RRKM rate constant calculations. Standard heats of formation for cyclohexadienyl and cyclohexadienyl, 6-methyl radicals calculated through isodesmic reactions amounted to 49.5 ± 2 and 42.9 ± 3 kcal/mol, respectively. Rate constants for various elementary reactions involved in the H-for-X exchange (X = D, CH3) were calculated and closely correlated with the available experimental kinetic data. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 633,653, 2001 [source] Hydrogen bond of radicals: Interaction of HNO with HCO, HNO, and HOOINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2010Yong Yang Abstract Ab initio quantum mechanics methods are employed to investigate hydrogen bonding interactions between HNO and HCO, HOO radicals, and closed-shell HNO. The systems were calculated at MP2/6-311++G (2d, 2p) level and G2MP2 level. The topological and NBO analysis were investigated the origin of hydrogen bonds red- or blue-shifts. In addition, the comparisons were performed between HNO-opened-shell radical (HCO, HOO) complexes and HNO-corresponding closed-shell molecule (H2CO, HOOH) complexes. It is found that the stabilities of complexes increase from HNO-HCO to HNO-HOO. There are blue-shifts of NH, CH stretching vibrational frequencies and a red-shift of OH stretching vibrational frequency in the complexes. Rehybridization and electron density redistribution contribute to the blue-shifts of CH and NH stretching vibrational frequencies. Compared with the closed-shell H2CO, HCO is weaker proton donor and weaker proton acceptor. For the HOO, it is stronger proton donor and weaker proton acceptor than the HOOH is. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] On the performance of eleven DFT functionals in the description of the vibrational properties of aluminosilicatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2010Raffaella Demichelis Abstract The performance of eleven DFT functionals in describing the equilibrium structure and the vibrational spectra at the , point of pyrope (Mg3Al2Si3O12), forsterite (,-Mg2SiO4), ,-quartz (,-SiO2) and corundum (,-Al2O3) is discussed. The four systems, for which accurate experimental data are available, are here used as a representative sample of the large aluminosilicates family. Calculations were performed with the periodic ab initio CRYSTAL code by using all-electron Gaussian-type basis sets. All the functionals here considered provide reasonable structural predictions, the hybrid PBE0 giving the least deviation from the experimental unit cell volumes (from ,0.3% to +0.6%). At the other extreme, SVWN and SPWLSD (,,3%) and PBE and PW91 (, +3%) provide the largest volume under- and over-estimation, respectively. Vibrational frequencies are more accurate when computed with hybrid functionals, with the best performance provided by B3LYP and WC1LYP (mean absolute differences with respect to experiments evaluated on a set of 134 vibrational frequencies, ||t , 5.5 cm,1). The three recently proposed GGA functionals, PBEsol, SOGGA-PBE and WC-PBE, provide a good description of the vibrational spectra, of the same quality as the one provided by PBE0 and B1WC (||t , 10 cm,1), whereas poorer results are obtained with PBE (||t , 17 cm,1). © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Infrared spectra of water molecule encapsulated inside fullerene studied by instantaneous vibrational analysis,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2009Kiyoshi Yagi Abstract Instantaneous vibrational analysis (IVA) is proposed for computing the infrared spectrum of dynamically fluctuating system, and applied to a water molecule encapsulated into fullerene (H2O@C60). A molecular dynamics simulation is first carried out to generate an ensemble of configurations averaging the rotational and translational motion of H2O inside fullerene. At each configuration, instantaneous vibrational frequencies of the water molecule are computed by the vibrational configuration interaction method, which are then employed to construct the line-shape of the spectrum. The vibrational spectrum in the OH stretching region is computed at a temperature of 10 and 100 K based on a direct potential energy surface incorporating the electronic structure theory. It is found that the vibrational frequency of the symmetric stretching mode is blue-shifted compared to that of isolated water, whereas that of the asymmetric stretching mode exhibits no shift in average. The relation between IVA and instantaneous normal mode analysis is presented, and their performances are compared. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Mechanisms and kinetics for preparing carbohydrazide by reacting dimethyl carbonate with hydrazine: A theoretical studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2008Jianguo Zhang Abstract The mechanism and kinetic modeling for preparing carbohydrazide from dimethyl carbonate and hydrazine has been declared. The geometries of all the stationary points (reactants, intermediates, transition states, and products) are optimized by using the B3LYP method with the cc-pVDZ basis set, and the harmonic vibrational frequencies as well as infrared intensities are predicted with the same method. The minimum-energy paths are obtained by using the intrinsic reaction coordinate (IRC) theory at the B3LYP/cc-pVDZ level of theory with the step length 0.02 (amu)1/2·bohr. The rate constants are evaluated by using the TST, TST/Eckart, and RRKM (T)/Eckart methods. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Improvement of scale factors for harmonic vibrational frequency calculations using new polarization functionsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2008Anibal Sierraalta Abstract Density functional calculations were carried to improve the calculated CO vibrational frequencies for transition metal carbonyls. Two types of density functionals were studied, hybrid and generalized-gradient methods. Using the simplex optimization method, new polarization functions for C and O atoms were obtained. With these new optimized functions, new scaling factors were obtained. The results reveal that, with the new polarization functions, the agreement between the calculated and the experimental values improves considerably. In general, the new scaling factors are very close to unit, with standard uncertainties close to ±0.006 cm,1. The use of the new polarization functions allows more precise calculations of the transition metal carbonyl CO vibrational frequencies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Geometries, vibrational frequencies, and electron affinities of X2Cl (X=C,Si,Ge) clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007Feng-You Hao Abstract Ab initio quantum chemical calculations have been performed on X2Cl, and X2Cl (X = C, Si, Ge) clusters. The geometrical structures, vibrational frequencies, electronic properties and dissociation energies are investigated at the Hartree,Fock (HF), Møller,Plesset second- and fourth-order (MP2, MP4), CCSD(T) level with the 6-311+G(d) basis set. The X2Cl (X = C, Si, Ge) and X2Cl, (X = Si, Ge) take a bent shape obtained at the ground state, while C2Cl, has a linear structure. The impact on internal electron transfer between the X2Cl and the corresponding anional clusters is studied. The three different types of electron affinities (EAs) at the CCSD(T) are reported. The most reliable adiabatic electronic affinities, obtained at the CCSD(T)/cc-pvqz level of theory, are predicted to be 3.30, 2.62, and 1.98 eV for C2Cl, Si2Cl, and Ge2Cl, respectively. The calculated EAs of C2Cl and Ge2Cl are in good agreement with theoretical results reported. The correlation effects and basis sets effects on the geometrical structures and dissociation energies are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Density functional and ab initio studies on structures and energies of the ground state of CrCOINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007Joonghan Kim Abstract CrCO was studied using density functional theory (DFT) and ab initio methods. We obtained the two-dimensional potential energy surface (PES), geometry, and vibrational frequencies for CrCO in a septet state. Two minimum structures were found in the CCSD(T) calculation, including a local minimum that is a weak van der Waals (vdW) complex. All DFT methods yield only one minimum structure. We demonstrate that the bond dissociation energy (0.50 kcal/mol) and vibrational frequency (1981.1 cm,1) of CrCO calculated using CCSD(T) are in better agreement with experimental values (<1.5 kcal/mol and 1977 cm,1) than any of the reported theoretical studies. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Blue-shifted and red-shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2006Yong Yang Abstract The blue-shifted and red-shifted H-bonds have been studied in complexes CH3CHO,HNO. At the MP2/6-31G(d), MP2/6-31+G(d,p) MP2/6-311++G(d,p), B3LYP/6-31G(d), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH3CHO,HNO are calculated by both standard and CP-corrected methods, respectively. Complex A exhibits simultaneously red-shifted CH,O and blue-shifted NH,O H-bonds. Complex B possesses simultaneously two blue-shifted H-bonds: CH,O and NH,O. From NBO analysis, it becomes evident that the red-shifted CH,O H-bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue-shifted CH,O H-bond is a result of conjunct CH bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue-shifted NH,O H-bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the NH stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Model density approach to the Kohn,Sham problem: Efficient extension of the density fitting techniqueINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Uwe Birkenheuer Abstract We present a novel procedure for treating the exchange-correlation contributions in the Kohn,Sham procedure. The approach proposed is fully variational and closely related to the so-called "fitting functions" method for the Coulomb Hartree problem; in fact, the method consistently uses this auxiliary representation of the electron density to determine the exchange-correlation contributions. The exchange-correlation potential and its matrix elements in a basis set of localized (atomic) orbitals can be evaluated by reusing the three-center Coulomb integrals involving fitting functions, while the computational cost of the remaining numerical integration is significantly reduced and scales only linearly with the size of the auxiliary basis. We tested the approach extensively for a large set of atoms and small molecules as well as for transition-metal carbonyls and clusters, by comparing total energies, atomization energies, structure parameters, and vibrational frequencies at the local density approximation and generalized gradient approximation levels of theory. The method requires a sufficiently flexible auxiliary basis set. We propose a minimal extension of the conventional auxiliary basis set, which yields essentially the same accuracy for the quantities just mentioned as the standard approach. The new method allows one to achieve substantial savings compared with a fully numerical integration of the exchange-correlation contributions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Benzonitriles: Survey of their importance and scaling of their vibrational frequenciesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2003M. Alcolea Palafox Abstract This work provides a short survey of the studies carried out on benzonitrile and its derivatives, with special attention on a spectroscopic point of view. The importance and main applications of these molecules are also briefly indicated. For an accurate assignment of their vibrational spectra, the scaling procedures for the wave numbers are described. For this purpose, the performance of semiempirical, ab initio, and density functional methods, with different basis sets, is determined. A "resume" of the main scaling factors to be used in the calculated wave numbers is shown. The results obtained for several benzene derivatives, and in particular for four benzonitriles, are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 189,204, 2003 [source] Explicitly correlated SCF study of anharmonic vibrations in (H2O)2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002Donald D. Shillady Abstract Modeling solvation in high-pressure liquid chromatography (HPLC) requires calculation of anharmonic vibrational frequencies of solvent clusters for a statistical partition function. An efficient computational method that includes electron correlation is highly desirable for large clusters. A modified version of the "soft Coulomb hole" method of Chakravorty and Clementi has recently been implemented in a Gaussian-lobe-orbital (GLO) program (PCLOBE) to include explicit electron,electron correlation in molecules. The soft Coulomb hole is based on a modified form of Coulomb's law: An algorithm has been developed to obtain the parameter "w" from a polynomial in the effective scaling of each primitive Gaussian orbital relative to the best single Gaussian of the H1s orbital. This method yields over 90% of the correlation energy for molecules of low symmetry for which the original formula of Chakravorty and Clementi does not apply. In this work, all the vibrations of the water dimer are treated anharmonically. A quartic perturbation of the harmonic vibrational modes is constrained to be equal to the exact Morse potential eigenvalue based on a three-point fit. This work evaluates the usefulness of fitting a Morse potential to a hydrogen bond vibrational mode and finds it to be slightly better than using MP2 vibrational analysis for this important dimer. A three-point estimate of the depth, De, of a Morse potential leads to a correction formula for anharmonicity in terms of the perturbed harmonic frequency: When scaled by 0.9141, the harmonic Morse method leads to essentially the same results as scaling the BPW91 local density method by 0.9827. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Structures and properties of the hydrides of light elementsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002Garry T. Smith Abstract Basic geometric and other properties for a number of neutral holovalent hydrides of light elements (M = Li , F)(MHn) are discussed. Their molecular geometries, energies, and vibrational frequencies have been determined from ab initio calculations of benchmark quality. We calculated harmonic vibrational frequencies, zero point vibrational energies, and atomization energies for the deuterides, tritiides, and combinations of them for these light elements. These isotopomers are of great interest for thermonuclear applications because they are often used as thermonuclear fuels or components of such fuels. In fact, only for these substances thermonuclear energy gain exceeds (at some densities and temperatures) the bremsstrahlung loss and other high-temperature losses, i.e., thermonuclear burn-up is possible. The vibrational frequencies are useful in determining the composition of mixed samples by means of spectroscopy. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] A phase-space method for arbitrary bimolecular gas-phase reactions: Theoretical descriptionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2001A. Gross Abstract A theoretical model for the calculation of rate constants for arbitrary bimolecular gas-phase reactions was developed. The method is based on the phase-space statistical method developed by Light and co-workers 1,6. In the present article this method is extended to arbitrary molecular systems. The new method requires knowledge of the molecular properties in the reaction and products channels of the chemical system. The properties are the vibrational frequencies, moments of inertia, and potential energy for the interacting species in their ground state equilibrium configuration. Furthermore, we have to calculate either the energy barrier or the long-range potential for the chemical system (if the reaction channel does not have an energy barrier). The usefulness of the method is that it can be applied to all bimolecular reactions, trimolecular reactions, and even reactions of higher orders. Therefore, it can be applied to cases where rate constants of complex chemical reactions are required, but reliable laboratory measurements or other means to estimate rate parameters are not yet possible. Even if spectroscopic data are not available for the reactants and products, it is possible to use electronic structure theory to calculate the required data. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Theoretical study of CnCl, CnCl+, CnCl, (n=1,7) clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001Antonio Largo Abstract A theoretical study of CnCl, CnCl+, and CnCl, (n=1,7) clusters has been carried out. Predictions for their electronic structures, dipole moments, and vibrational frequencies have been made at the B3LYP/6-311G(d) level. According to our calculations the lowest-lying geometry of all these species (with the only exception of neutral C3Cl) is predicted to be either a linear or quasi-linear structure with chlorine located at the end of the carbon chain. CnCl clusters all have doublet ground states, whereas the anionic clusters, with the only exception of CCl,, all have singlet ground states. For CnCl+ species, n -even clusters have triplet ground states whereas n -odd ones have singlet ground states. An even,odd parity effect (n -even clusters more stable than n -odd ones) is found for both the neutral and anionic species, whereas in the case of the cations the alternation in stability is reversed. The ionization potential (IP) and electron affinity (EA) also exhibit regular variations with the size of the cluster, with n -even clusters having both higher IP and EA than n -odd ones. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 127,135, 2001 [source] 27 ps DFT molecular dynamics simulation of ,-maltose: A reduced basis set study,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Udo Schnupf Abstract DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as ,-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in ,-maltose. In previous studies, the gg,-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in ,20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1,···H4 distance of 2.28 Å confirms that the syn form is the primary glycosidic conformation, while the average C1,O1,C4 bond angle was 118.8°, in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolasesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Nikolaj Otte Abstract CHARMM force-field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6-31G*) interaction energies of complexes between water and the model compound 1,1-dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6-311+G*//B3LYP/6-31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6-31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008Chen Levi Abstract Ab initio and density functional theory (DFT) calculations were performed for obtaining fundamental vibrational frequencies of methylamine, CH3NH2, and its deuterated variants CH3ND2, CD3NH2, and CD3ND2. The calculations were carried out using the CCSD(T) coupled cluster approximation with cc-pVTZ and cc-pVQZ basis sets, and by the DFT method with the semiempirical hybrid functional B97-1 with polarization consistent pc-2 and pc-3 basis sets. Reasonable performance of the DFT harmonic and ab initio harmonic calculations was found, which improved considerably upon combination of the harmonic fundamental frequencies with anharmonic corrections from the smaller, pc-2, basis. The computed anharmonic fundamental frequencies of methylamine isotopologues agree very well with the experimental values and represent a useful tool for assignment and analysis of the dominant resonances. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2007N. R. Jena Abstract Reactions of peroxynitrite with guanine were investigated using density functional theory (B3LYP) employing 6-31G** and AUG-cc-pVDZ basis sets. Single point energy calculations were performed at the MP2/AUG-cc-pVDZ level. Genuineness of the calculated transition states (TS) was tested by visually examining the vibrational modes corresponding to the imaginary vibrational frequencies and applying the criterion that the TS properly connected the reactant and product complexes (PC). Genuineness of all the calculated TS was further ensured by intrinsic reaction coordinate (IRC) calculations. Effects of aqueous media were investigated by solvating all the species involved in the reactions using the polarizable continuum model (PCM). The calculations reveal that the most stable nitro-product complex involving the anion of 8-nitroguanine and a water molecule i.e. 8NO2G, + H2O can be formed according to one reaction mechanism while there are two possible reaction mechanisms for the formation of the oxo-product complex involving 8-oxoguanine and anion of the NO2 group i.e. 8OG + NO2,. The calculated relative stabilities of the PC, barrier energies of the reactions and the corresponding enthalpy changes suggest that formation of the complex 8OG + NO2, would be somewhat preferred over that of the complex 8NO2G, + H2O. The possible biological implications of this result are discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2007Z. J. Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 703,714, 2007 [source] Electronic structures of 3d -metal mononitridesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Zhijian Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 267,276, 2006 [source] A molecular mechanics force field for biologically important sterolsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Zoe Cournia Abstract A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point charges to quantum-chemically calculated electrostatic potentials. To model the dynamics of the hydroxyl groups of the sterols correctly, the parameter set was refined to reproduce the energy barrier for the rotation of the hydroxyl group around the carbon connected to the hydroxyl of each sterol. The frequency-matching plots show good agreement between the CHARMM and quantum chemical normal modes. The parameters are tested in a molecular dynamics simulation of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol, and campesterol, and a variety of steroids. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1383,1399, 2005 [source] | ||||||||||||||||||||||||||||