Geometry optimization, intermolecular

For (HF)j full geometry optimizations in all internal coordinates have been carried out with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. With the aug-cc-pVQZ set just the F-F distance was optimized by fitting 5 points to polynomials in (R-RJ. In these calculations, the two intermolecular angles were held fixed at their optimized aug-cc-pVTZ values, and the two HF bond lengths were held fixed at... 

Other potential functions differ in the way the potential is partitioned into various contributions representing intra and intermolecular interactions. Cornell and collaborators 300 proposed an approach to determine the force field parameters based as much as possible on ab initio calculations. In this work each biomolecular system is divided into small residua, for which geometry optimization can be performed by an ab initio method. Ab initio calculations give partial atomic charges on atoms and the equilibrium geometry, i.e. the equilibrium values for the bond lengths, and planar and dihedral angles. 

Although many satisfactory VCD studies based on the gas phase simulations have been reported, it may be necessary to account for solvent effects in order to achieve conclusive AC assignments. Currently, there are two approaches to take solvent effects into account. One of them is the implicit solvent model, which treats a solvent as a continuum dielectric environment and does not consider the explicit intermolecular interactions between chiral solute and solvent molecules. The two most used computational methods for the implicit solvent model are the polarizable continuum model (PCM) [93-95] and the conductor-like screening model (COSMO) [96, 97]. In this treatment, geometry optimizations and harmonic frequency calculations are repeated with the inclusion of PCM or COSMO for all the conformers found. Changes in the conformational structures, the relative energies of conformers, and the harmonic frequencies, as well as in the VA and VCD intensities have been reported with the inclusion of the implicit solvent model. The second approach is called the explicit solvent model, which takes the explicit intermolecular interactions into account. The applications of these two approaches, in particular the latter one will be further discussed in Sect. 4.2. 

Gate and coworkers37 have made an X-ray crystallographic study of 1-methylamino-2-nitroethene (Scheme 3) and found the intermolecularly hydrogen-bonded EZ form (.E for C1==C2, Z for C1—N) to be stable in the crystal, while STO-3G calculations predicted the ZE form to be more stable than the EZ and EE forms by 2.4 and 2.6 kcal mol-1. The predicted energy of the ZZ form, 178 kcal mol"1, is exorbitantly high, but no geometry optimization had been performed. 

Synthetic fibers are generally made from polymers whose chemical composition and geometry enhance intermolecular attractive forces and crystallization. A certain degree of moisture affinity is also desirable for wearer comfort in textile applications. The same chemical species can be used as a plastic, without fiber-like axial orientation. Thus most fiber forming polymers can also be used as plastics, with adjustment of molecular size if necessary to optimize properties for particular fabrication conditions and end u.ses. Not all plastics can form practical fibers, however, because the intermolecular forces or... 

Whereas optimization of the geometry of a single molecule is relatively straightforward, the same procedure can encounter difficulties for a molecular complex, particularly if weakly bound. The first problem here is that the force constants for motions of one molecule relative to the other are quite a bit smaller than those for stretches or bends wholly within one molecule. One tactic to circumvent this difference is to perform a geometry optimization using frozen subunits. That is, the internal geometry of each partner can be taken as fixed, and the optimization carried out over the intermolecular parameters. The final result is thus not fully optimized but the earlier restraint can then be released and the geometry now optimized over all parameters, intramolecular as well as intermolecular. 

The major differences in the two methods used are that the empirical method does not contain terms with explicit electron overlap dependence such as a charge transfer term but does include total intermolecular geometry optimization. 

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