Frozen approximation

Sterile 1.5-ml microcentrifuge tubes (for aliquots of competent cells if these are to be frozen)—Approximately 80 of these will be required. 

As methods based on dynamic programming cannot account for pairwise-interaction potentials the so-called frozen approximation approach [189] has been proposed. This method performs several iterations of profile environments. In the first iteration, the chemical environment is defined via the contact partners of the template. In subsequent rounds the aligned residues from the previous iteration replace the residues of the template. The idea is that target and template structure are similar enough such that the iterative process converges towards the optimal assignment. 

Skolnick, J., Kihara, D. Defrosting the frozen approximation PROSPECTOR—A new approach to threading. Proteins Struct., Funct., Genet. 2001,42,319-31. 

Berdichevsky, D., Reisdorf, W. Systematic study of the heavy-ion fusion barrier in the frozen approximation. Z. Phys. A327, 217-224 (1987)... 

Heller E J 1981 Frozen Gaussians a very simple semiclassical approximation J. Chem. Phys. 75 2923... 

The Hemian-Kluk method has been developed further [153-155], and used in a number of applications [156-159]. Despite the formal accuracy of the approach, it has difficulties, especially if chaotic regions of phase space are present. It also needs many trajectories to converge, and the initial integration is time consuming for large systems. Despite these problems, the frozen Gaussian approximation is the basis of the spawning method that has been applied to... 

While it is not essential to the method, frozen Gaussians have been used in all applications to date, that is, the width is kept fixed in the equation for the phase evolution. The widths of the Gaussian functions are then a further parameter to be chosen, although it appears that the method is relatively insensitive to the choice. One possibility is to use the width taken from the harmonic approximation to the ground-state potential surface [221]. 

As usual there is the question of the initial conditions. In general, more than one frozen Gaussian function will be required in the initial set. In keeping with the frozen Gaussian approximation, these basis functions can be chosen by selecting the Gaussian momenta and positions from a Wigner, or other appropriate phase space, distribution. The initial expansion coefficients are then defined by the equation... 

To obtain the Hamiltonian at zeroth-order of approximation, it is necessary not only to exclude the kinetic energy of the nuclei, but also to assume that the nuclear internal coordinates are frozen at R = Ro, where Ro is a certain reference nucleai configuration, for example, the absolute minimum or the conical intersection. Thus, as an initial basis, the states t / (r,s) = t / (r,s Ro) are the eigenfunctions of the Hamiltonian s, R ). Accordingly, instead of Eq. (3), one has... 

HyperChem supports MP2 (second order Mdllcr-l Icsset) correlation energy calcu latiou s u sin g any available basis set. lu order to save main memory and disk space, the HyperChem MP2 electron correlation calculation normally uses a so called frozen-core approximation, i.e. th e in n er sh el I (core) orbitals are omitted. A sett in g in CHHM.IX I allows excitation s from th e core orbitals to be include if necessary (melted core). Only the single poin t calcula-tion is available for this option. 

A Hbasis functions provides K molecular orbitals, but lUJiW of these will not be occupied by smy electrons they are the virtual spin orbitals. If u c were to add an electron to one of these virtual orbitals then this should provide a means of calculating the electron affinity of the system. Electron affinities predicted by Konpman s theorem are always positive when Hartree-Fock calculations are used, because fhe irtucil orbitals always have a positive energy. However, it is observed experimentally that many neutral molecules will accept an electron to form a stable anion and so have negative electron affinities. This can be understood if one realises that electron correlation uDiild be expected to add to the error due to the frozen orbital approximation, rather ihan to counteract it as for ionisation potentials. 

There are several variations of this method. The PRDDO/M method is parameterized to reproduce electrostatic potentials. The PRDDO/M/FCP method uses frozen core potentials. PRDDO/M/NQ uses an approximation called not quite orthogonal orbitals in order to give efficient calculations on very large molecules. The results of these methods are fairly good overall, although bond lengths involving alkali metals tend to be somewhat in error. 

Physically the cutting-corner trajectory implies that the particle crosses the barrier suddenly on the time scale of the slow -vibration period. In the literature this approximation is usually called sudden , frozen bath and fast flip approximation, or large curvature case. In the opposite case of small curvature (also called adiabatic and slow flip approximation), coj/coo < sin tp, which is relevant for transfer of fairly heavy masses, the MEP may be taken to a good accuracy to be the reaction path. 

The dielectric constant of unsymmetrical molecules containing dipoles (polar molecules) will be dependent on the internal viscosity of the dielectric. If very hard frozen ethyl alcohol is used as the dielectric the dielectric constant is approximately 3 at the melting point, when the molecules are free to orient themselves, the dielectric constant is about 55. Further heating reduces the ratio by increasing the energy of molecular motions which tend to disorient the molecules but at room temperature the dielectric constant is still as high as 35. 

Most of the scale factors in this table are from the recent paper of Wong. The HF/6-31G(d) and MP2(Full) scale factors are the traditional ones computed by Pople and coworkers and cited by Wong. Note that the MP2 scale factor used in this book is the one for MP2(Full) even though our jobs are run using the (defriultj frozen core approximation. Scott and Radom computed the MP2(FC) and HF/3-21G entries in the table, but this work came to our attention only just as this book was going to press. 

It is usual to make the frozen core approximation in calculations of this type. This means that the seven inner shells are left frozen and not included in the Cl calculation. 

The HF-LCAO calculation follows the usual lines (Figure 11.10) and the frozen core approximation is invoked by default for the CISD calculation. CISD is iterative, and eventually we arrive at the improved ground-state energy and normalization coefficient (as given by equation 11.7) — Figure 11.11. 

The MP2 and CCSD(T) values in Tables 11.2 and 11.3 are for correlation of the valence electrons only, i.e. the frozen core approximation. In order to asses the effect of core-electron correlation, the basis set needs to be augmented with tight polarization functions. The corresponding MP2 results are shown in Table 11.4, where the A values refer to the change relative to the valence only MP2 with the same basis set. Essentially identical changes are found at the CCSD(T) level. 

In the frozen MO approximation the last terms are zero and the Fukui functions are given directly by the contributions from the HOMO and LUMO. The preferred site of attack is therefore at the atom(s) with the largest MO coefficients in the HOMO/LUMO, in exact agreement with FMO theory. The Fukui function(s) may be considered as the equivalent (or generalization) of FMO methods within Density Functional Theory (Chapter 6). 

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