Molecular potential perturbational method

Bash, P.A., Field, M.J.,Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase A dynamical approach baaed on a combined quantum and molecular dynamics potential. J. Am. Chem. Soc. 109 (1987) 8092-8094. 

The problems that occur when one tries to estimate affinity in terms of component terms do not arise when perturbation methods are used with simulations in order to compute potentials of mean force or free energies for molecular transformations simulations use a simple physical force field and thereby implicitly include all component terms discussed earlier. We have used the molecular transformation approach to compute binding affinities from these first principles [14]. The basic approach had been introduced in early work, in which we studied the affinity of xenon for myoglobin [11]. The procedure was to gradually decrease the interactions between xenon atom and protein, and compute the free energy change by standard perturbation methods, cf. (10). An (issential component is to impose a restraint on the... 

Choose the region (single or multiple molecules) of interest for an ab initio calculation from the total molecular system. HyperChem performs the ab initio calculation for the selected region using the perturbation of an electrostatic potential arising from the net charges on the atoms of the un selected part. (For further details of this electrostatic potential perturbation implemented in HyperChem, please see the second part of this book. Theory and Methods). 

Kofke, D.A., Cummings, P.T., Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation, Fluid Phase... 

In spite of these potential concerns, the MEHMC method is expected to be a useful tool for many applications. One task for which it might be particularly well suited is to generate a canonical ensemble of representative configurations of a bio-molecular system quickly. Such an ensemble is needed, for example, to represent the initial conditions for the ensemble of trajectories used in fast-growth free energy perturbation methods such as the one suggested by Jarzynski s identity [104] (see also Chap. 5). 

Bash, P.A., Field M.J. and Karplus M., Free Energy Perturbation Method for Chemical Reactions in the Condensed Phase A Dynamical Approach Based on a Combined Quantum and Molecular Mechanics Potential. J. Am. Chem.Soc. (1987) 109 8092-8094. 

Anisotropy of the repulsion core can also be treated by perturbation methods and gives similar deviations as a function of molecular radius as those seen by varying R in y,(R ) for a spherical potential. Note that in all cases, at a given temperature, 1/Ti still follows a y,(/ ) [or 0Hs( e)] law, as exemplified by the behavior of compressed CO2 gas and liquid. ... 

Thus Eq. (4.7) for the optical activity tensors of the molecule are again employed, but now the summation is over all occupied LMOs and the vectors Ri define the positions of the orbital centroids. Once the wavefunctions are known, the polarizability of the ith LMO and the position of its centroid R( can be determined. The derivatives of a, and Rj with respect to the normal coordinates are calculated using the electric field perturbation approach recently shown to be very effective for the calculation of conventional infrared and Raman intensities61) the required derivatives of R= and a. are determined from the first and second derivatives, respectively, of the gradient of the molecular potential energy with respect to a small applied electric field. One important aspect of this method is that both infrared CD and ROA can be determined from the same conceptual and calculational method, which will enhance the study of the relationship between these two forms of vibrational optical activity. So far, only one ROA calculation using LMO methods has been reported59), and since that was for the model compound NHDT there has been no comparison with experimental data. 

They utilize X-ray diffraction. X-ray diffraction allows direct qualitative and quantitative phase characterization — even in multiphase regions — and no potentially perturbing additives or molecular labels are needed. Although the high photon flux of synchrotron radiation is potentially damaging to the sample [15], particular parts need only be exposed to the beam for a short period of time and as a result, radiation damage is not a problem with this method. 

The method used here for considering conformal solution models for fluids with molecular anisotropies is based on the method used by Smith (4) for treating isotropic one-fluid conformal solution methods as a class of perturbation methods. The objective of the method is to closely approximate the properties of a mixture by calculating the properties of a hypothetical pure reference fluid. The characterization parameters (in this case, intermolecular potential parameters) of the reference fluid are chosen to be functions of composition (i.e., mole fractions) and the characterization parameters for the various possible molecular pair interactions (like-like and unlike-unlike). In principle, all molecular anisotropies (dipole-dipole, quadrupole-quadrupole, dipole-quadrupole, and higher multipole interactions, as well as overlap and dispersion interactions ) can be included in the method. Here, the various molecular anisotropies are lumped into a single term, so that the intermolecular potential energy uy(ri2, on, a>2) between Molecules 1 and 2 of Species i and / can be written in the form... 

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