Computational protocol

By systematically applying a series of corrections to approximate solutions of the Schroedinger equation the Pople group has anived at a family of computational protocols that include an early method Gl, more recent methods, G2 and G3, and their variants by which one can anive at themiochemical energies and enthalpies of formation, Af and that rival exper imental accuracy. The important thing... 

In many cases, it is also helpful to have the path repel itself so that the transition pathway is self-avoiding. An acmal dynamic trajectory may oscillate about a minimum energy configuration prior to an activated transition. In the computed restrained, selfavoiding path, there will be no clusters of intermediates isolated in potential energy minima and no loops or redundant segments. The self-avoidance restraint reduces the wasted effort in the search for a characteristic reaction pathway. The constraints and restraints are essential components of the computational protocol. 

Eollowing the computational protocol of Czerminski and Elber [39,40] a number of restraints and constraints are added to (1) encourage the mean-square distances between adjacent structures to be approximately constant. 

In this paper a method [11], which allows for an a priori BSSE removal at the SCF level, is for the first time applied to interaction densities studies. This computational protocol which has been called SCF-MI (Self-Consistent Field for Molecular Interactions) to highlight its relationship to the standard Roothaan equations and its special usefulness in the evaluation of molecular interactions, has recently been successfully used [11-13] for evaluating Eint in a number of intermolecular complexes. Comparison of standard SCF interaction densities with those obtained from the SCF-MI approach should shed light on the effects of BSSE removal. Such effects may then be compared with those deriving from the introduction of Coulomb correlation corrections. To this aim, we adopt a variational perturbative valence bond (VB) approach that uses orbitals derived from the SCF-MI step and thus maintains a BSSE-free picture. Finally, no bias should be introduced in our study by the particular approach chosen to analyze the observed charge density rearrangements. Therefore, not a model but a theory which is firmly rooted in Quantum Mechanics, applied directly to the electron density p and giving quantitative answers, is to be adopted. Bader s Quantum Theory of Atoms in Molecules (QTAM) [14, 15] meets nicely all these requirements. Such a theory has also been recently applied to molecular crystals as a valid tool to rationalize and quantitatively detect crystal field effects on the molecular densities [16-18]. 

The overall trend described in this section in going from a more complex and time-consuming computational protocol, such as PSAhydrogen-bonding counts, while still capturing the same information content is a general one that will be an overall theme in this chapter The simpler, the better but do not fumble the ball . 

Note, however, that this one-dimensional representation can be somewhat misleading if it is taken to be a computational protocol. The trouble is that the one-dimensional slice of... 

Ab initio calculations by Durandurdu and Drabold [273] also support the existence of amorphous-amorphous transition in Ge. They found that LDA Ge was abruptly transformed to an HDA form at 12.75 GPa by using the same computational protocol as that used in their LDA-VHDA transition study of Si [266]. The density of the resultant HDA form is about 20% higher than that of LDA Ge, and its Nc is calculated as 8. This HDA form therefore strongly resembles the VHDA form of Si, rather than the HDA form of Si. This simulation in passing shows that the transition is irreversible, which is consistent with the experiment by Principi et al. [272],... 

The computational protocol utilized here is similar to the one employed in case of LAP.54-58 The total binding energy was taken from a pairwise analysis of the interactions between the PAL active site residues and particular inhibitor molecules (model A). With the goal of deriving some justified approximations in mind, the decrese of correlation with experimental data was monitored that resulted in a... 

After this brief discussion of the physical significance of the OR parameter, the role of TDDFT in the description of chiroptical effects becomes clear. Chiroptical effects, on a molecular level, are related to perturbations of the electric or magnetic dipole moment by time-dependent magnetic and electric fields, respectively. Since equations (1) establish that the perturbations are linear in the applied field amplitudes, the computational protocol will typically first involve a (static, no external fields) DFT computation of the molecule s ground state, followed by a linear response computation to determine />(oj) from the elements of the tensor computed for a specific EM field frequency co. These tensor elements are computed from the first-order perturbations of the dipole moments due to the presence of EM fields of a specified frequency. 

Due to recurring problems with the treatment of methyl rotations in calculations of vibrational averages of optical rotations, Mort and Autschbach [149] have proposed a computational protocol for a separate treatment of hindered rotations. In a nutshell, in this approach a quasi-free rotation of a functional group is treated separately from the vibrational average, with numerically calculated hindered-rotor wavefunctions. With regards to optical activity, the authors studied their protocol on three molecules (R)-methyloxirane, (lS)-norbomanone, and... 

The merits of NIGS, obtained by an upgraded computational protocol, as a measure of the aromaticity, nonaromaticity, or antiaromaticity of, inter alia, planar five-membered heterocycles (including furan) have been discussed. The subtypes NICS(0),izz and NICS(l)zz appear to perform most reliably in providing a linear relationship with aromatic stabilization energies (ASEs) <20060L863>. 

The same model and computational protocol was used in another MD study of the distal side effects [74]. Three distal side mutants were studied. The His64Gln mutation resulted in a conformation similar to that of the wild-type 64N5H tautomer, the His64Leu mutant showed little interaction with the ligand, while... 

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