Calculation of molecular vibrations: Selective scaling factors for semiempirical force constants

The complete force constant matrices of a set of 50 aliphatic and aromatic hydrocarbons are calculated at the density functional theory B3LYP/6–31+G(d, p) and semiempirical PM3 levels of theory. After transformation from Cartesian to nonredundant internal coordinates, the errors in the semiempirical force constants are systematically analyzed. The force constants of the C(SINGLE BOND)C stretching coordinates can be easily corrected by a second-order fit. Thus, only two parameters are needed to reduce the mean error from 21.2 to 1.23%. The errors of other internal coordinates, particulary those including torsional modes, exhibit a larger diversity. The performance of the correction scheme in predicting vibrational spectra is shown for several examples including buckminsterfullerene (C₆₀). © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2050–2059, 1997     

The determination of force constants from isotopic frequencies using parameter representation

The problem of fixing the molecular force field using isotopic frequencies is approached from a new angle with the help of the parameter technique. A parameter space is defined with the parameters for the molecule and its isotopic substituent as the coordinates. Making use of the constraint that the F elements are invariant under isotopic substitution in the ideal case, it is shown that unique points must exist in the parameter space enabling the determination of the force field. The method is applied to harmonic vibrations of molecules with 2 × 2 secular equations. The displays in the parameter space indicate that two such points exist for all molecules. Thus there can be two sets of force fields capable of reproducing the observed frequencies for the molecule and its isotopic substituents. Checks with mean amplitudes of vibration favour only one set. The calculated values of the force constants compare well with the values from the literature.     

On the representation of force fields for chemically reacting systems

“Relaxed” force constants are uniquely defined for systems involving redundant coordinates, in contradistinction to the usual “rigid” force constants, and thus their use allows meaningful correlations to be made between force fields calculated for reactants, transition state, and product of a chemical reaction, for example formaldehyde hydration.     

Chiral force constants: Recommendations for the presentation of internal coordinate force constants

Some force constants associated with the internal coordinates that sense handedness or chirality can have opposite signs in the enantiomers of chiral molecules. Examples of such force constants include interaction force constants between a torsional and stretching or bending internal coordinates. The sign reversal for these force constants in the enantiomers of chiral molecules or in opposite-handed molecular segments is best recognized by labeling them as chiral force constants. Recognition of chiral force constants suggests that certain guidelines are to be followed in the presentation of internal coordinate force constants. © 1993 by John Wiley & Sons, Inc. © John Wiley & Sons, Inc.     

Water-silica force field for simulating nanodevices

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.     

Constrained force constants for octahedral molecules

A set of constrained force constants has been derived from experimental vibrational frequency data for eighty three octahedral molecules. Superimposing the condition that the larger value for f_d—f_dd′ be used when f_dα—f_dα″ is a maximum on the six equations relating vibrational frequencies to force constants generates a seventh. This provides a uniform set of results for all 83 molecules. The values of the force constants have a simple rationale in terms of chemical bonding theory. Some preliminary calculations for SF₆ show that these force constants are suitable for use in generating reliable molecular dynamical trajectory data.     

An intermolecular force field for chlorinated benzene crystals

Intermolecular potential parameters corresponding to atom—atom interactions of the Buckingham form are refined on the basis of static and dynamic properties of some chlorinated benzene crystals. The model reproduces well the observed properties, including k ≠ 0 vibrations.     

Method of calculation of force constants self consistent with isotopic shifts for large molecular systems

A method of force constant calculation for large molecular system is proposed. The force constants of GVFF self consistent with small isotopic shifts are obtained with the help of kinematically defined proper vectors in parametric representation. The procedure of general rotations in the space of vibrational coordinates is applied to obtain agreement with experimental data.     

A spectroscopically effective molecular mechanics model for the intermolecular interactions of the hydrogen-bonded N-methylacetamide dimer

An MP2/6-31+G¹ calculation of the N-methylacetamide dimer shows that it has two minimum energy structures, both hydrogen bonded with peptide planes roughly perpendicular to each other. A complete molecular mechanics optimization of the dimer has been done, using a model for the intermolecular interactions consisting of charges, atomic dipoles, and van der Waals interactions and the methodology of our spectroscopically determined force field for the intramolecular interactions. The two structures are satisfactorily reproduced, as are their interaction energies, their dipole moments, and, from the point of view of our goal of a spectroscopically accurate force field, their six intermolecular normal mode frequencies.     

Calculation of anharmonic force constants

Non-linear transformations from internal to cartesian displacements are considered for anharmonic calculation of vibrational frequencies. Force constants in normal coordinates, up to quartic terms, are related to Christoffel symbols. The latter are tabulated for valence angles or, for torsion and wagging out of plane, evaluated through expressions which avoid differentiation of explicit functional forms for each type of internal coordinate. The same symbols are used for cartesian tensors and redundancy coefficients up to the third order.     

Calculation of macromolecular force constants

Force constant refinement may be carried under a system of constraints imposed on well characterized modes as the refinement proceeds. Resulting stability permits the accurate calculation of many independent macromolecular force constants. A useful formalism for this technique is developed. Prediction of initially poorly characterized modes can emerge from this stability. A brief discussion of currently used refinement schemes has been included. We show that the standard least-squares procedure is a special case of our present more general method, the former being useful when the molecule is not too large.     

A new force field for simulating phosphatidylcholine bilayers

A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid‐crystalline, fluid phase at zero surface tension is presented. The structure of the bilayer with the area per lipid (0.629 nm²; experiment 0.629–0.64 nm²), the volume per lipid (1.226 nm³; experiment 1.229–1.232 nm³), and the ordering of the palmitoyl chains (order parameters) are all in very good agreement with experiment. Experimental electron density profiles are well reproduced in particular with regard to the penetration of water into the bilayer. The force field was further validated by simulating the spontaneous assembly of DPPC into a bilayer in water. Notably, the timescale on which membrane sealing was observed using this model appears closer to the timescales for membrane resealing suggested by electroporation experiments than previous simulations using existing models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A BSSE-free SCF algorithm for intermolecular interactions. II. Sample calculations on hydrogen-bonded complexes

The usefulness and reliability of the recent BSSE -free SCF algorithm based on the “chemical Hamiltonian approach” (CHA /F ) is demonstrated by calculating potential curves for several hydrogen-bonded complexes with 4-31G , 6-31G , and 6-31G ** basis sets. It is concluded that the CHA /F scheme gives results that are numerically close to those of the Boys–Bernardi a posteriori correction scheme but are free from the “overcompensation” characteristic of the latter at smaller distances and given basis sets. © 1992 John Wiley & Sons, Inc.     

Constrained variations for diatomic forces and force constants

The results of earlier studies of diatomic forces and force constants are used to formulate force constraints. It is proposed that such constrained variations should improve force constant calculations.

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Zusammenfassung Mittels früherer Ergebnisse für Bindungskräfte bei zweiatomigen Molekülen werden Neben-bedingungen für die Wellenfunktion formuliert. Es ist anzunehmen, da\ dies zu einer Verbesserung der Berechnung für die entsprechenden Kraftkonstanten führt.

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Résumé Les résultats d'études antérieures des forces et des constantes de force diatomiques sont utilisés pour formuler des contraintes de force. De telles variations contraintes devraient améliorer les calculs de constante de force.

     

静电势方法研究分子间的电子转移 II: 在光电转移模拟体系中的应用

用从头算和静电势方法研究了光电转换模拟体系C~6H~7N+C~6H~8N^+中的分子间电荷转移。通过计算分子间的静电势分布, 确定了电子在分子间运动所需穿透势垒的特性, 对电子穿透几率及穿透弛时间等参数作了理论预测并研究了外接基团的影响。在分子间距d=0.35nm时, 穿透几率P=2.94x10^-^4, 穿透弛豫时间τ=3.4x10^-^1^0s, 在此情况下, 由模型分子组成的截面积为10x1mm^2的多层分子膜, 在光照条件下可能产生的理论光电流为0.28A。     

Properties of strong hydrogen-bonded systems: The formation of hydrogen-bonded ion pair in amine·HCL systems

The hydrogen-bonded complexes between CH₃NH₂ and (CH₃)₂NH with HCl have been studied by the ab initio molecular orbital method using the 4–31G basis set. Calculations show that the proton potential curve has a single minimum near to the nitrogen atom in both complexes. This means that the proton has been transferred from HCl to the amine. ΔE and the dipole moment of the complexes studied are as follows: ?18.2 kcal mol^?1, 10.3 D for methylamine ·HCl, and ?21.7 kcal mol^?1 11.1 D for the corresponding dimethylamine complex. Other properties of the hydrogen-bonded ion pairs are discussed.     

Optical constants of monoclinic anisotropic crystals: Orthoclase

The optical constants of the monoclinic crystal orthoclase [ideal composition 4(KAlSi₃O₈)] have been derived in the i.r. region of the spectrum by the use of dispersion theory. Values for the E||b orientation and for the a—c plane have been used, together with a theory of the emittance of particulate materials, to simulate the spectrum of orthoclase powder.