Modified corrections for London forces in solid-state density functional theory calculations of structure and lattice dynamics of molecular crystals

Dispersion forces are critical for defining the crystal structures and vibrational potentials of molecular crystals. It is, therefore, important to include corrections for these forces in periodic density functional theory (DFT) calculations of lattice vibrational frequencies. In this study, DFT was augmented with a correction term for London-type dispersion forces in the simulations of the structures and terahertz (THz) vibrational spectra of the dispersion-bound solids naphthalene and durene. The parameters of the correction term were modified to best reproduce the experimental crystal structures and THz spectra. It was found that the accurate reproduction of the lattice dimensions by adjusting the magnitude of the applied dispersion forces resulted in the highest-quality fit of the calculated vibrational modes with the observed THz absorptions. The method presented for the modification of the dispersion corrections provides a practical approach to accurately simulating the THz spectra of molecular crystals, accounting for inherent systematic errors imposed by computational and experimental factors.     

DCMB that combines divide‐and‐conquer and mixed‐basis set methods for accurate geometry optimizations,total energies,and vibrational frequencies of large molecules

We present a method, named DCMB, for the calculations of large molecules. It is a combination of a parallel divide‐and‐conquer (DC) method and a mixed‐basis (MB) set scheme. In this approach, atomic forces, total energy and vibrational frequencies are obtained from a series of MB calculations, which are derived from the target system utilizing the DC concept. Unlike the fragmentation based methods, all DCMB calculations are performed over the whole target system and no artificial caps are introduced so that it is particularly useful for charged and/or delocalized systems. By comparing the DCMB results with those from the conventional method, we demonstrate that DCMB is capable of providing accurate prediction of molecular geometries, total energies, and vibrational frequencies of molecules of general interest. We also demonstrate that the high efficiency of the parallel DCMB code holds the promise for a routine geometry optimization of large complex systems. © 2012 Wiley Periodicals, Inc.     

Molecular equilibrium geometries and vibrational frequencies by maximum overlap symmetry molecular orbital method

It is demonstrated that the maximum overlap symmetry molecular orbital method can be used for optimization of molecular geometries and calculation of vibrational frequencies by adding a two-body repulsive energy term and a modification of the Wolfsberg–Helmholz formula. The obtained equilibrium geometries and vibrational frequencies are on the whole in good accordance with experimental data, which shows that the basic idea using the method to optimize molecular geometries and to calculate vibrational frequencies is reasonable.     

Ab initio studies on the vibrational spectra and conformational isomerism of 2,4-dimethyl-1,3-pentadiene

Ab initio was used to study the structure of various conformational isomers and their vibrational spectra of 2,4-dimethyl-1,3-pentadiene (2,4-PD) in detail. Two stable conformations, s-trans and s-cis, were found in which s-trans is more stable. The geometry of stable conformations and charge distributions were studied, and the effect of different basis sets on geometry optimization is discussed. The results of complete optimization indicate that molecular skeleton is nearly in a plane, its largest deviation is only 0.3 degrees. Therefore, it is reasonable and available to hypothesis that the molecule has Cs symmetry. The thermal dynamics conformations were calculated and compared with experimental values. DeltaH(o) between two conformations of 2,4-PD measured from experiment is 4.36 kJ/mol, deltaS(o) is 2.56 J/mol K., calculated results are slightly different from experimental ones. Vibrational frequencies of 2,4-PD conformers have been studied by ab initio molecular orbital calculations using different basis set. The calculated vibrational frequencies are analyzed and compared with the experimental spectra.     

Solid state vibrational spectroscopy of disordered crystals. A study of dimethylsulphoxide at 213 K

The vibrational spectrum of crystalline dimethylsulphoxide at 213 K has been studied by i.r. and Raman spectroscopy. Such an experiment is proposed as an example to show how much the dipole-dipole interaction forces can affect the molecular disorder often observed in molecular crystals of compounds containing sulphur atoms.     

Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.     

The anisotropic forces acting on the bonds of benzene in liquid crystals

The HH and CH dipolar couplings of benzene measured in five different liquid crystal solvents are subjected to an analysis which allows for the correlation between the molecular reorientational and vibrational motions. The number of adjustable parameters is reduced by treating the CH bonds or both the CH and CC bonds as effectively cylindrically symmetric entities. In this way detailed information on the anisotropic forces acting on the bonds of benzene dissolved in liquid crystals is obtained. The behaviour of the CC bonds, but not that of the CH bonds, may be explained by anisotropic dispersion forces. There is an approximately linear relation between the torques acting on the CH bonds of benzene and methane in the same liquid crystal environment. This suggests that these forces stem from a common interaction mechanism, possibly the van der Waals interaction between the atoms of the solute molecule and the liquid crystal surroundings or the interaction between the molecular quadrupole moment and the electric field gradient due to the surrounding medium. A bond additivity model for the molecular quadrupole moment tensor is developed and discussed.     

Theoretical studies of solute vibrational energy relaxation at liquid interfaces

Recent advances in the theoretical understanding of solute vibrational energy relaxation at liquid interfaces and surfaces are described. Non-equilibrium molecular dynamics simulations of the relaxation of an initially excited solute molecule are combined with equilibrium force autocorrelation calculations to gain insight into the factors that influence the vibrational relaxation rate. Diatomic and triatomic nonpolar, polar, and ionic solute molecules adsorbed at the liquid/vapor interface of several liquids as well as at the water/CCl(4) liquid/liquid interface are considered. In general, the vibrational relaxation rate is significantly slower (a factor of 3 to 4) at the liquid/vapor and liquid/liquid interface than in the bulk due to the reduced density, which gives rise to a reduced contribution of the repulsive solvent-solute forces on the vibrational mode. The surface effects on the ionic solutes are much smaller (50% or less slower relaxation relative to the bulk). This is due to the fact that ionic solutes at the interface are able to keep part of their solvation shell to a degree that depends on their size. Thus, a significant portion of the repulsive forces is maintained. A high degree of correlation is found between the peak height of the solvent-solute radial distribution function and the vibrational relaxation rate. The relaxation rate at the liquid/liquid interface strongly depends on the location of the solute across the interface and correlates with the change in the density and polarity profile of the interface.     

A modified landau-teller model for vibrational relaxation of small molecular ions

We report a new interpretation of vibrational relaxation of molecular ions based on a modified Landau-Teller model. Distorted wave calculations show the relaxation to be dominated by repulsive forces. The ion-induced-dipole forces alter the steepness of the repulsive force and increase the effective collision energy. Incorporating these modifications into the Landau-Teller model correctly predicts the observed dependence of the cross sections on collision energy.     

Spectroscopic and theoretical studies on nickel(II) complex of maleonitriledithiolate and 2,2'-bipyridine

The complete IR spectra of the title complex Ni(mnt)(bpy) (mnt=maleonitriledithiolate, bpy=2,2'-bipyridine) and a new method to analyze vibrational spectra for such a complicated metal complex are reported in this paper. The molecular geometry, binding, electronic structure and spectroscopic property of it have been studied in detail by theoretical calculations. The geometry optimization from PM3 calculations give that this molecule is of a planar structure with the symmetry point group C(2v) and its ground state is the spin triplet state. The vibrational and electronic spectra were calculated by PM3 and ZINDO/S methods, respectively. The scientific method of analyzing vibrational spectra is established herein by giving main fixed points and pivotal vibrational units. Besides the regular symbols, the new defined symbols eta and M play an important role in describing the vibration modes accurately and vividly.     

Laser Raman scattering studies of vibrational relaxation and noncoincidence effect in liquid cyclohexanone

The vibrational relaxation and noncoincidence effect in liquid cyclohexanone have been studied and explained in terms of molecular attraction parameters and van der Waals interactions. The line broadening of the isotropic component of the CO stretching mode of cyclohexanone in different solvents is explained on the basis of dispersion forces. The parameter involving viscosity, density and refractive index has been correlated with the vibrational relaxation rate.     

The anisotropic forces acting on the bonds of benzene in liquid crystals

Abstract

The HH and CH dipolar couplings of benzene measured in five different liquid crystal solvents are subjected to an analysis which allows for the correlation between the molecular reorientational and vibrational motions. The number of adjustable parameters is reduced by treating the CH bonds or both the CH and CC bonds as effectively cylindrically symmetric entities. In this way detailed information on the anisotropic forces acting on the bonds of benzene dissolved in liquid crystals is obtained. The behaviour of the CC bonds, but not that of the CH bonds, may be explained by anisotropic dispersion forces. There is an approximately linear relation between the torques acting on the CH bonds of benzene and methane in the same liquid crystal environment. This suggests that these forces stem from a common interaction mechanism, possibly the van der Waals interaction between the atoms of the solute molecule and the liquid crystal surroundings or the interaction between the molecular quadrupole moment and the electric field gradient due to the surrounding medium. A bond additivity model for the molecular quadrupole moment tensor is developed and discussed.     

Selective excitation of molecular modes in a mixture by optimal control of electronically nonresonant femtosecond four-wave mixing spectroscopy

Femtosecond time-resolved coherent anti-Stokes Raman scattering (fs-CARS) gives access to ultrafast molecular dynamics. Due to the spectrally broad laser pulses, usually poorly resolved spectra result from this spectroscopy. However, it can be demonstrated that by shaping the femtosecond pulses a selective excitation of specific vibrational modes is possible. We demonstrate that using a feedback-controlled optimization technique, molecule-specific CARS spectra can be obtained from a mixture of different substances. A careful analysis of the experimental results points to a nontrivial control of the vibrational mode dynamics in the electronic ground state of the molecules as underlying mechanism.     

First principles calculation of the thermodynamic properties of silicon clusters

The thermodynamic properties of Si clusters are calculated using first principles quantum methods combined with molecular dynamics for simulating the trajectories of clusters. A plane wave basis is used with ab initio pseudo potentials and the local density approximation for determining the electronic energies and forces. Langevin molecular dynamics simulates thermal contact with a constant temperature reservoir. Vibrational spectra, moments of inertia, anharmonic corrections, and free energies are predicted for Si₂ through Si₅. The translational contribution is based on the ideal gas limit. The rotation contribution is approximated using a classical rigid rotator. Vibrational modes are determined from the dynamical matrix in the harmonic approximation. Corrections due to anharmonicity and coupling between rotational and vibrational modes are fit from the molecular dynamics simulations. Received: 17 September 1997 / Accepted: 14 October 1997     

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.     

原子团簇Ge11同分异体的密度泛函研究

用分子图形软件设计出多种Ge_11原子团簇模型,使用B3LYP密度泛函方法进行几何构型优化和振动频率计算,比较了14种同分异构体的总能量,得到了新的基态构型。锗原子团簇的大部分原子以三、四、五和六配位成键。在Ge11原子团簇中,双角反四棱柱衍生出来的构型能量较低,它是设计大分子锗原子团簇初始模型的重要结构单元。由三棱柱演变的构型能量居中。带心结构和共边构型带有高配位原子,其总能量较高,是不稳定的结构。     

1-异丙基环己硅烷类液晶化合物的量子化学研究--取代联苯基乙烷系列

我们曾用半经验的分子轨道方法对标题化合物的某些系列进行过计算[1 ,2 ] 。本文选择 7种 1 异丙基环己硅烷 取代联苯基乙烷系列化合物 ,以ＳＣＦ—ＭＯ—ＡＭ1 [3] 和ＰＭ3[4] 两种方法 ,优化出它们稳定的几何构型 (分子的总能量最低、核—核排斥能最小 )并对其作了振动分析 ;同时计算了标题物在该稳定构型下的电子结构和若干基本性质。1　计算图 1示出了 7种标题化合物的结构及原子编号。用ＭＯＰＡＣ7.0程序中的ＡＭ1 和ＰＭ3方法 ,分子的初始构型参数采用Ｐｏｐｌｅ’ｓ标准构型数据[5] 。对每个分子实行能量梯度全优化和ＳＣＦ计算。…     

分子团簇的量子化学研究

采用Hartree-Fock方法、密度泛函(DFT)方法(BLYP、B3LYP)和MP2方法对Se4分子团簇的各种可能构型进行了结构优化和频率分析, 结果表明有5种构型是势能面上的稳定驻点, 同时对上述4种量子化学方法计算结果的差异进行了分析。并对这5种构型的结构稳定性、几何构型、前线分子轨道、Mulliken布局分析和偶极矩进行了分析, 根据分析结果对Se4分子的某些物理和化学性质进行了预测。     

On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.