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Chem Phys (chem + phy)
Kinds of Chem Phys Selected AbstractsRate constants for H + CH4, CH3 + H2, and CH4 dissociation at high temperatureINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2001J. W. Sutherland The Laser Photolysis-Shock Tube technique coupled with H-atom atomic resonance absorption spectrometry has been used to study the reaction, H + CH4 , CH3 + H2, over the temperature range, 928,1697 K. Shock-tube studies on the reverse of this reaction, CH3 + H2 , H + CH4, using CH3I dissociation in the presence of H2 yielded H-atom formation rates and rate constants for the reverse process over the temperature range, 1269,1806 K. These results were transformed (using well-established equilibrium constants) to the forward direction. The combined results for H + CH4 can be represented by an experimental three parameter expression, k = 6.78 × 10,21 T3.156 exp(,4406 K/T) cm3 molecule,1 s,1 (348,1950 K) that was evaluated from the present work and seven previous studies. Using this evaluation, disagreements between previously reported values for the dissociation of CH4 could be reconciled. The thermal decomposition of CH4 was then studied in Kr bath gas. The dissociation results agreed with the earlier studies and were theoretically modeled with the Troe formalism. The energy transfer parameter necessary to explain both the present results and those of Kiefer and Kumaran (J Phys Chem 1993, 97, 414) is, ,,,E,all/cm,1 = 0.3323 T0.7. The low temperature data on the reverse reaction, H + CH3 (in He) from Brouard et al. (J Phys Chem 1989, 93, 4047) were also modeled with the Troe formalism. Lastly, the rate constant for H + CH4 was theoretically calculated using conventional transition state theory with Eckart tunneling corrections. The potential energy surface used was from Kraka et al. (J Chem Phys 1993, 99, 5306) and the derived T-dependence with this method agreed almost perfectly with the experimental evaluation. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 669,684, 2001 [source] Nonrelativistic CI calculations for B+, B, and B, ground statesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010César X. Almora-Díaz Abstract State of the art configuration interaction (CI) techniques are used to obtain the best possible nonrelativistic CI results for B+, B, and B, ground states using energy-optimized basis sets of 252, 294, and 294 radial Slater-type functions, respectively. For positive boron, E(B+) = ,24.348861 + ,Ebie = ,24.348883(1) a.u.(B) with a basis set incompleteness error ,Ebie = ,0.000022(1), in good agreement with the latest exponentially correlated Gaussian (ECG) result of ,24.348883 a.u.(B) of Komasa et al. (Phys Rev A, 2002, 65, 042507). For neutral B, E(B) = ,24.653837 ,0.000024(2) = ,24.653861(2), which is the most accurate ab initio estimate and lies slightly below a recent (not fully optimized) ECG result of ,24.653840 a.u.(B) of Bubin et al (J Chem Phys, 2009, 131, 044128). For negative boron, E(B,) = ,24.664014 ,0.000024(2) to which an energy error of ,0.000001 must be added to give ,24.664039(2), which is the first fully correlated ab initio result. Comparison with experimental values of ionization energy and electron affinity must await the results of corresponding relativistic calculations, in progress. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Convergence radii of the polarization expansion of intermolecular potentialsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009William H. Adams Abstract A new method is presented to evaluate convergence radii of the polarization expansion of interaction energies for pairs of atoms or molecules. The method is based on an analysis of the variation of the perturbed state vector as a function of the coupling constant , and does not require a calculation of perturbation corrections to high order. The convergence radii at infinite interatomic/intermolecular distances R, as well as a remarkably accurate representation of the R dependence of the convergence radii are obtained from simple calculations involving only monomer wave functions. For the interaction of the lithium and hydrogen atoms, the obtained convergence radii agree well with those obtained previously from the large-order calculations of Patkowski et al. (Patkowski et al., J Chem Phys, 2002, 117, 5124), but are expected to be considerably more accurate. Rigorous upper bounds and reasonable approximations to the convergence radii at R = , are obtained for the pairs of lithium, beryllium, boron, neon, and sodium atoms, as well as for the dimer consisting of two LiH molecules. For all the systems studied, the convergence radii are significantly smaller than the unity and rapidly decrease with the increase of the nuclear charge. It is hoped that the results of this investigation will help to analyze and eventually to compute the convergence radii of the symmetry-adapted perturbation theories which utilize the same partitioning of the Hamiltonian as the polarization expansion. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] A rigorous approach to the formulation of extended Born-Oppenheimer equation for a three-state systemINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2009Biplab Sarkar Abstract If a coupled three-state electronic manifold forms a sub-Hilbert space, it is possible to express the non-adiabatic coupling (NAC) elements in terms of adiabatic,diabatic transformation (ADT) angles. Consequently, we demonstrate: (a) Those explicit forms of the NAC terms satisfy the Curl conditions with non-zero Divergences; (b) The formulation of extended Born-Oppenheimer (EBO) equation for any three-state BO system is possible only when there exists coordinate independent ratio of the gradients for each pair of ADT angles leading to zero Curls at and around the conical intersection(s). With these analytic advancements, we formulate a rigorous EBO equation and explore its validity as well as necessity with respect to the approximate one (Sarkar and Adhikari, J Chem Phys 2006, 124, 074101) by performing numerical calculations on two different models constructed with different chosen forms of the NAC elements. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] An accurate total energy density functionalINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2007Baojing Zhou Abstract We propose a new density functional for the evaluation of the total electronic energy by subtracting the Roothaan energy, i.e. the Hartree energy of the density residual, from the Hohenberg,Kohn,Sham (HKS) functional, which is normally used in self-consistent Kohn,Sham (KS) density functional theory (DFT) calculations. Because of the positive semi-definite nature of the Roothaan energy, the resulting Wang,Zhou (WZ) functional always produces a total energy lower than that from the HKS functional and usually converges to the exact total energy from below. Following the same spirit of the Zhou,Wang-, (ZW,) functional in the recently proposed orbital-corrected orbital-free (OO) DFT method (Zhou and Wang, J Chem Phys 2006, 124, 081107), we linearly mix the WZ functional with the HKS functional to allow further systematic error cancellations. The resulting Wang,Zhou-, (WZ,) functional is compared with the ZW, functional in OO-DFT calculations for systems within different chemical environment. We find that the optimal value of , for the WZ, functional is more stable than that of , for the ZW, functional. This is because the WZ functional remedies the oscillatory convergence behavior of the Harris functional and renders the direct evaluation of , for the WZ, functional more plausible in the application of the linear-scaling OO-DFT method for large systems. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Relativistic effects in the optical response of HgSe by time-dependent density functionals theoryINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001P. L. de Boeij Abstract We treat the dominant relativistic effects in the optical response properties of mercury selenide using time-dependent density functional theory (TDDFT). The scalar relativistic effects have been included within the zeroth-order regular approximation (ZORA) in both the ground-state DFT calculations and in the time-dependent response calculations. Within this approximation the HgSe crystal is found to be a semimetal. In a previous study [J Chem Phys 2001, 114, 1860] we have shown that TDDFT/ZORA can be applied successfully to narrow-gap semiconductors, such as indium antimonide, that become semimetallic within the local density approximation when scalar relativistic effects are included. Results are given for the band structure, the static dielectric constant ,,, and the dielectric function ,(,) of HgSe, and these results are compared with the similar ones for InSb. We find considerably improved results for the dielectric function of HgSe when relativistic effects are included. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] High-level ab initio calculations on HGeCl and the equilibrium geometry of the Ã1A, state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeClJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2010Daniel K. W. Mok Abstract CCSD(T) and/or CASSCF/MRCI calculations have been carried out on the X,1A, and Ã1A, states of HGeCl. The fully relativistic effective core potential, ECP10MDF, and associated standard valence basis sets of up to the aug-cc-pV5Z quality were employed for Ge. Contributions from core correlation and extrapolation to the complete basis set limit were included in determining the computed equilibrium geometrical parameters and relative electronic energy of these two states of HGeCl. Based on the currently, most systematic CCSD(T) calculations performed in this study, the best theoretical geometrical parameters of the X,1A, state are re(HGe) = 1.580 ± 0.001 Å, ,e = 93.88 ± 0.01° and re(GeCl) = 2.170 ± 0.001 Å. In addition, Franck-Condon factors including allowance for anharmonicity and Duschinsky rotation between these two states of HGeCl and DGeCl were calculated employing CCSD(T) and CASSCF/MRCI potential energy functions, and were used to simulate Ã1A, , X,1A, SVL emission spectra of HGeCl and DGeCl. The iterative Franck-Condon analysis (IFCA) procedure was carried out to determine the equilibrium geometrical parameters of the Ã1A, state of HGeCl by matching the simulated, and available experimental SVL emission spectra of HGeCl and DGeCl of Tackett et al., J Chem Phys 2006, 124, 124320, using the available, estimated experimental equilibrium (r) structure for the X,1A, state, while varying the equilibrium geometrical parameters of the Ã1A, state systematically. Employing the derived IFCA geometry of re(HGe) = 1.590 Å, re(GeCl) = 2.155 Å and ,e(HGeCl) = 112.7° for the Ã1A, state of HGeCl in the spectral simulation, the simulated absorption and SVL emission spectra of HGeCl and DGeCl agree very well with the available experimental LIF and SVL emission spectra, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] A dual-level state-specific time-dependent density-functional theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008Seiken Tokura Abstract A highly efficient new algorithm for time-dependent density-functional theory (TDDFT) calculations is presented. In this algorithm, a dual-level approach to speed up DFT calculations (Nakajima and Hirao, J Chem Phys 2006, 124, 184108) is combined with a state-specific (SS) algorithm for TDDFT (Chiba et al., Chem Phys Lett 2006, 420, 391). The dual-level SS-TDDFT algorithm was applied to excitation energy calculations of typical small molecules, the Q bands of the chlorophyll A molecule, the charge-transfer energy of the zincbacteriochlorin,bacteriochlorin model system, and the lowest-lying excitation of the circumcoronene molecule. As a result, it was found that the dual-level SS-TDDFT gave correct excitation energies with errors of 0.2,0.3 eV from the standard TDDFT approach, with much lower CPU times for various types of excitation energies of large-scale molecules. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Globally convergent computation of chemical equilibrium compositionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2008Sunil Patil Abstract We report the Newton,Raphson based globally convergent computational method for determination of chemical equilibrium composition. In the computation of chemical equilibrium composition, an appearance of nonpositive value of number of moles of any component leads to discrepancy. The process of conditional backtracking and adaptive set of refining factors for Newton,Raphson steps are employed to resolve the problem. The mathematical formulation proposed by Heuze et al. (J Chem Phys 1985, 83, 4734) has been solved using proposed computational method, instead of empirical iterative formulation, as proposed by them. Results for the same numerical example, used by Heuze et al. (J Chem Phys 1985, 83, 4734) and White et al. (J Chem Phys 1958, 28, 751) are presented in addition to decomposition of Cyclotrimethylenetrinitramine for fixed temperature and pressure. It is observed that the proposed method is efficient and globally convergent. An even noteworthy finding is that the set of refining factors can be chosen from the range 0.1 to ,, where , may be greater than one depending on how smoothly system of nonlinear equations is dependant on corresponding variable. Related analysis and results are discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Molecular dynamics simulation in the grand canonical ensembleJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2007Hossein Eslami Abstract An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard,Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard,Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard,Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averagesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2006Arnaldo RapalloArticle first published online: 17 JAN 200 Abstract In this article an algorithm is proposed to efficiently perform the uniform sampling of an iso-energy surface corresponding to a fixed potential energy U of a molecular system, and for calculating averages of certain quantities over microstates having this energy (microcanonical averages). The developed sampling technique is based upon the combination of a recently proposed method for performing constant potential energy molecular dynamics simulations [Rapallo, A. J Chem Phys 2004, 121, 4033] with well-established thermostatting techniques used in the framework of standard molecular dynamics simulations, such as the Andersen thermostat, and the Nose,Hoover chain thermostat. The proposed strategy leads to very accurate and drift-free potential energy conservation during the whole sampling process, and, very important, specially when dealing with high-dimensional or complicated potential functions, it does not require the calculation of the potential energy function hessian. The technique proved to be very reliable for sampling both low- and high-dimensional surfaces. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 414,425, 2006 [source] Improved third-order Møller,Plesset perturbation theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2003Stefan Grimme Abstract Based on a partitioning of the total correlation energy into contributions from parallel- and antiparallel-spin pairs of electrons, a modified third-order Møller,Plesset (MP) perturbation theory is developed. The method, termed SCS,MP3 (SCS for spin-component-scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third-order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C20 isomers, transition states) demonstrate that the SCS,MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529,1537, 2003 [source] New analytic approximation to the standard molecular volume definition and its application to generalized Born calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Michael S. Lee Abstract In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee,Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1348,1356, 2003 [source] Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiencyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003Wataru Shinoda Abstract We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 920,930, 2003 [source] Inverse Monte Carlo procedure for conformation determination of macromoleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Mark Bathe Abstract A novel numerical method for determining the conformational structure of macromolecules is applied to idealized biomacromolecules in solution. The method computes effective inter-residue interaction potentials solely from the corresponding radial distribution functions, such as would be obtained from experimental data. The interaction potentials generate conformational ensembles that reproduce thermodynamic properties of the macromolecule (mean energy and heat capacity) in addition to the target radial distribution functions. As an evaluation of its utility in structure determination, we apply the method to a homopolymer and a heteropolymer model of a three-helix bundle protein [Zhou, Y.; Karplus, M. Proc Natl Acad Sci USA 1997, 94, 14429; Zhou, Y. et al. J Chem Phys 1997, 107, 10691] at various thermodynamic state points, including the ordered globule, disordered globule, and random coil states. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 876,890, 2003 [source] Highly efficient square wave distant dipolar field and its application for in vivo MRIMAGNETIC RESONANCE IN MEDICINE, Issue 4 2010Congbo Cai Abstract Intermolecular multiple quantum coherences generated by distant dipolar field (DDF) have some attractive properties, but the intrinsic weak signal intensity prevents their widespread applications. Recently, Branca et al. (J Chem Phys 2008;129:054502) suggested that square wave DDF was more efficient than conventional sinusoidal DDF because it could simultaneously produce intermolecular multiple quantum coherences signal with various major orders. In this article, instead of a series of adiabatic inversion pulses proposed previously, a more efficient composite adiabatic inversion pulse was applied to create square wave DDF. The square wave DDF was applied to in vivo MRI for the first time, and the corresponding simulations were performed. Both experimental and simulated results show that square wave DDF with composite adiabatic inversion pulse improves over the original Z-modulation enhanced to binary for self-refocused acquisition implementation and can enhance the signal intensity to about 2-fold of that from conventional correlation spectroscopy (COSY) revamped with asymmetric Z-gradient echo detection sequence for in vivo MRI, close to the theoretical prediction. Magn Reson Med, 2010. © 2010 Wiley-Liss, Inc. [source] Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands?,BIOPOLYMERS, Issue 11 2010Daria A. Beshnova Abstract Conventional methods, such as Scatchard or McGhee-von Hippel analyses, used to treat ligand-biopolymer interactions, indirectly make the assumption that the microscopic binding constant is independent of the number of ligands, i, already bound to the biopolymer. Recent results on the aggregation of aromatic molecules (Beshnova et al., J Chem Phys 2009, 130, 165105) indicated that the equilibrium constant of self-association depends intrinsically on the number of molecules in an aggregate due to loss of translational and rotational degrees of freedom on formation of the complex. The influence of these factors on the equilibrium binding constant for ligand-biopolymer complexation was analyzed in this work. It was shown that under the conditions of binding of "small" molecules, these factors can effectively be ignored and, hence, do not provide any hidden systematic error in such widely-used approaches, such as the Scatchard or McGhee-von Hippel methods for analyzing ligand-biopolymer complexation. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 932,935, 2010. [source] Terahertz time-domain spectroscopy of poly- L -lysineBIOPOLYMERS, Issue 8 2010Ohki Kambara Abstract Poly- L -lysine is known to have three different secondary structures depending on solvent conditions because of its flexible nature. In previous work (Kambara et al., Phys Chem Chem Phys 2008, 10, 5042-5044), we observed two different types of structural changes in poly- L -lysine. In the present study, we investigated the low-frequency spectrum of poly- L -lysine with a ,-sheet structure in the solid state by terahertz time-domain spectroscopy. On the basis of this spectroscopic analysis, we found that the low-frequency dynamics differed from those of other polypeptides. Furthermore, we performed powder X-ray diffraction measurement on poly- L -lysine, which was found to be highly amorphous compared with other polypeptides. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 735,739, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||