Geometry, molecular optimization

LIndh R, Bernhardsson A, Karlstrdm G and Malmqvist P-A 1995 On the use of a Hessian model function In molecular geometry optimizations Chem. Phys. Lett. 241 423... 

YETI is a force held designed for the accurate representation of nonbonded interactions. It is most often used for modeling interactions between biomolecules and small substrate molecules. It is not designed for molecular geometry optimization so researchers often optimize the molecular geometry with some other force held, such as AMBER, then use YETI to model the docking process. Recent additions to YETI are support for metals and solvent effects. 

With rigid molecular geometry as well as molecular geometry optimization, the calculated minima of potential energy increase in the following order of anions Br , SbBr , Sb2Br (see Fig. 8). 

Methods of Quantum Pharmacology for Molecular Geometry Optimization Quantum Mechanics, Molecular Mechanics, QM/MM Calculations... 

The reaction of BF3+HF has been looked at from a different viewpoint by Silla et a/.105 SCF calculations using both minimal and 4-31G basis sets were carried out and the molecular geometry optimized. For BF4 the results were similar for the MBS case to those found earlier by Fitzpatrick.108 The geometry of the adduct HBF4- was determined. The 4-31G basis set results gave longer bond lengths. Differences in the... 

This numerical problem of integration can be avoided using the ADMA technique. Within the ADMA method, the integration in Eq. (361) can be performed using the analytical expressions of macromolecular density matrices and AOs. As an option of the ADMA algorithm, the calculated ADMA Hellmann-Feynman forces can be used for macro-molecular geometry optimization and macromolecular conformational analysis. 

At the time the CLAP force field was proposed, many of the existing ionic liquid models used to borrow parameters from different, not always compatible, sources. For instance, it was common to see parameterizations of the cation and of the anion using information from different force fields [10,11,13], In the development of the CLAP force-field, in order to respect internal consistency, ab initio calculations were used extensively to provide essential data for the development of an internally consistent force field. This included molecular geometry optimization and the description of electron density using extended basis sets, leading to the evaluation of force field parameters such as torsion energy profiles and electrostatic charges on the interaction centers. 

J. D. Head and M. C. Zerner, Chem. Phys. Lett., 131,359 (1986). An Approximate Hessian for Molecular Geometry Optimization. (Introduced is an approximate analytical Hessian that decreases the amount of work required by a factor of N in ZDO methods, where N is the size of the basis.)... 

The best way to illustrate the important role of basis set quality in these calculations is by example. For purposes of comparison and to focus on basis set effects alone, we performed TDHF calculations on the HCN molecule with many of the basis sets discussed above and a few others. All calculations were performed with the free ab initio program GAMESS at the same molecular geometry, optimized with the cc-pVDZ basis = 1.1342 A,... 

The CEO computation of electronic structure starts with molecular geometry, optimized using standard quantum chemical methods, or obtained from experimental X-ray diffraction or NMR data. For excited-state calculations, we usually use the INDO/S semiempirical Hamiltonian model (Section IIA) generated by the ZINDO code " however, other model Hamiltonians may be employed as well. The next step is to calculate the Hartree— Fock (HE) ground state density matrix. This density matrix and the Hamiltonian are the Input Into the CEO calculation. Solving the TDHE equation of motion (Appendix A) Involves the diagonalization of the Liouville operator (Section IIB) which is efficiently performed using Kiylov-space techniques e.g., IDSMA (Appendix C), Lanczos (Appendix D), or... 

Although simple, this molecule presents some interesting conformational properties and is a good example to illustrate both (i) ab initio molecular geometry optimization of minima and transition structures (which may be located by symmetry analysis), and (ii) ab initio calculations of vibrational frequencies. 

Parameters of the molecular geometry, electronic structure and thermodynamic properties of the benzoyl peroxide (BPO) molecule and its symmetrical derivatives were calculated by the GAUSSIAN09 [9]. The molecular geometry optimization of all objects was carried out at the first stage of the work. The calculation of harmonic frequencies of vibrations and thermodynamic parameters were performed after that. The stationary points obtained after the molecular geometry optimization were identified as minima, as there were no negative values of analytic harmonic vibration frequencies for them. The reaction center of the peroxide compounds is a peroxide bond -0-0-. Therefore, selection criterion for the quantum chemical calculation method was the best reproduction of the peroxide moiety molecular geometry. 

Lindh, R., Bernhardsson, A., Karlstrom, G., Malmquist, P.-A. (1995). On the use of a Hessian model function in molecular geometry optimizations. Chemical Physics Letters, 241, 423. 

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