Molecular systems complexes

Wang H, Sun X and Miller W H 1998 Semiclassical approximations for the calculation of thermal rate constants for chemical reactions in complex molecular systems J. Chem. Phys. 108 9726... 

Procacci P, Darden T A, Paci E and Marchi M 1997 ORAC a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J. Comput. Chem. 18 1848-62... 

Singh, U.C., Kollman, P.A. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems Applications to the CH3CI 4- Cl exchange reaction and gas phase protonation of polyethers. J. Comput. Chem. 7 (1986) 718-730. 

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

Singh U C and P A Kollman 1986. A Combined Ab Initio Quantum Mechanical and Molecule Mechanical Method for Carrying out Simulations on Complex Molecular Systems Applicatior to the CHsQ + Cr Exchange Reaction and Gas Phase Protonation of Polyethers. Journal Computational Chemistry 7 718-730. 

How can the continuous transition pathway l(r) be represented by a computer for a complex molecular system l(r) can be approximately represented as a set of configurations of the system rj,. ... 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

The applicability of the Born-Oppenheimer approximation for complex molecular systems is basic to all classical simulation methods. It enables the formulation of an effective potential field for nuclei on the basis of the SchrdJdinger equation. In practice this is not simple, since the number of electrons is usually large and the extent of configuration space is too vast to allow accurate initio determination of the effective fields. One has to resort to simplifications and semi-empirical or empirical adjustments of potential fields, thus introducing interdependence of parameters that tend to obscure the pure significance of each term. This applies in... 

An analogous role has been played by other scientists in strengthening the ties between quantum chemistry of type I (and type II) with the area corresponding to biochemistry (or complex molecular systems in general), a task made more difficult by the explosive growth of structural and functional information about biomolecular systems. It is worth to remark here that such a fruitful use of quantum chemical concepts in biology has requested the extension of the methods to approaches different from quantum molecular theory in the strict sense introduced before. We shall comeA back to this remark later. 

In recent years, dynamic calculations of both the electronic and the molecular structure of complex molecular systems have started to become feasible. " These methods are based on the general idea that the electronic structure of the system is to be calculated on the fly as the nuclei move, while the nuclei respond to the forces determined from the dynamically calculated electronic structure. This assumes that the system moves on the lowest electronic state, and transitions between states are either ignored (because they are well separated in energy) or treated semiclassi-cally. 

In any complex molecular system, there will always be extremely minor but almost inaccessible basins. 

In more complex molecular systems, increased coupling between the translational motion and both rotational and vibrational modes occurs. It is difficult to separate these effects completely. Nevertheless, the velocity autocorrelation functions of the Lennard—Jones spheres [519] (Fig. 52) and the numerical simulation of the carbon tetrachloride (Fig. 39) are quite similar [452a]. 

In summary, fs DFWM spectroscopy proofs here its strength and importance for the rotationally-resolved spectroscopic investigation of complex molecular systems without dipole moment. 

Quantum-dynamical modeling of ultrafast processes in complex molecular systems multiconfigurational system-bath dynamics using Gaussian wavepackets... 

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