Dynamical calculations

There is, of course, a mass of rather direct evidence on orientation at the liquid-vapor interface, much of which is at least implicit in this chapter and in Chapter IV. The methods of statistical mechanics are applicable to the calculation of surface orientation of assymmetric molecules, usually by introducing an angular dependence to the inter-molecular potential function (see Refs. 67, 68, 77 as examples). Widom has applied a mean-held approximation to a lattice model to predict the tendency of AB molecules to adsorb and orient perpendicular to the interface between phases of AA and BB [78]. In the case of water, a molecular dynamics calculation concluded that the surface dipole density corresponded to a tendency for surface-OH groups to point toward the vapor phase [79]. 

The theoretical treatments of Section III-2B have been used to calculate interfacial tensions of solutions using suitable interaction potential functions. Thus Gubbins and co-workers [88] report a molecular dynamics calculation of the surface tension of a solution of A and B molecules obeying Eq. III-46 with o,bb/ o,aa = 0.4 and... 

It was noted in connection with Eq. III-56 that molecular dynamics calculations can be made for a liquid mixture of rare gas-like atoms to obtain surface tension versus composition. The same calculation also gives the variation of density for each species across the interface [88], as illustrated in Fig. Ill-13b. The density profiles allow a calculation, of course, of the surface excess quantities. 

Molecular dynamics calculations have been made on atomic crystals using a Lennard-Jones potential. These have to be done near the melting point in order for the iterations not to be too lengthy and have yielded density functioi). as one passes through the solid-vapor interface (see Ref. 45). The calculations showed considerable mobility in the surface region, amounting to the presence of a... 

The alternative simulation approaches are based on molecular dynamics calculations. This is conceptually simpler that the Monte Carlo method the equations of motion are solved for a system of A molecules, and periodic boundary conditions are again imposed. This method pennits both the equilibrium and transport properties of the system to be evaluated, essentially by numerically solvmg the equations of motion... 

Truhlar D G (ed) 1981 Potential Energy Surfaces and Dynamics Calculations (New York Plenum)... 

Detailed analyses of the above experiments suggest that the apparent steps in k E) may not arise from quantized transition state energy levels [110.111]. Transition state models used to interpret the ketene and acetaldehyde dissociation experiments are not consistent with the results of high-level ab initio calculations [110.111]. The steps observed for NO2 dissociation may originate from the opening of electronically excited dissociation chaimels [107.108]. It is also of interest that RRKM-like steps in k E) are not found from detailed quantum dynamical calculations of unimolecular dissociation [91.101.102.112]. More studies are needed of unimolecular reactions near tln-eshold to detennine whether tiiere are actual quantized transition states and steps in k E) and, if not, what is the origin of the apparent steps in the above measurements of k E). 

The summation of pair-wise potentials is a good approximation for molecular dynamics calculations for simple classical many-body problems [27], It has been widely used to simulate hyperthennal energy (>1 eV) atom-surface scattering ... 

Allen M P, Warren M A, Wilson M R, Sauron A and Wiliam S 1996 Molecular dynamics calculation of elastic constants in Gay-Berne nematic liquid crystals J. Chem. Phys. 105 2850-8... 

Andersen H C 1983 RATTLE a velocity version of the SHAKE algorithm for molecular dynamics calculations J. Comput. Phys. 52 24-34... 

Herman M F and Kluk E 1984 A semiclassical justification for the use of non-spreading wavepackets in dynamics calculations Chem. Phys. 91 27... 

Baldridge K K, Gordon M S, Steckler R and Truhlar D G 1989 Ab initio reaction paths and direct dynamics calculations J. Phys. Chem. 93 5107... 

To demonstrate the basic ideas of molecular dynamics calculations, we shall first examine its application to adiabatic systems. The theory of vibronic coupling and non-adiabatic effects will then be discussed to define the sorts of processes in which we are interested. The complications added to dynamics calculations by these effects will then be considered. Some details of the mathematical formalism are included in appendices. Finally, examples will be given of direct dynamics studies that show how well the systems of interest can at present be treated. 

The Helgaker-Chen algorithm results in very large steps being possible, and despite the extra cost of the required second derivatives, this is the method of choice for direct dynamics calculations. A number of systems have been treated, and a review of the method as applied to chemical reactions is given in [2]. 

Importantly for direct dynamics calculations, analytic gradients for MCSCF methods [124-126] are available in many standard quantum chemistiy packages. This is a big advantage as numerical gradients require many evaluations of the wave function. The evaluation of the non-Hellmann-Feynman forces is the major effort, and requires the solution of what are termed the coupled-perturbed MCSCF (CP-MCSCF) equations. The large memory requirements of these equations can be bypassed if a direct method is used [233]. Modem computer architectures and codes then make the evaluation of first and second derivatives relatively straightforward in this theoretical framework. 

Being able to ntn direct dynamics calculations will add an extra, important, tool to help chemists understand photochemical systems. This chapter has outlined the present standpoint of the theory and practice of such calculations showing that, although much work remains to be done, they are already bringing new insight to mechanistic studies of photochemistry. 

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

H. C. Andersen. Rattle A velocity version of the Shake algorithm for molecular dynamics calculations. J. Comp. Phys., 52 24-34, 1983. 

Prepare a molecii le for a molecii lar dynamics sim illation. If the forces on atoms are too large, th e in legralion algorithm may-fail during a molecular dynamics calculation. ... 

HyperChem uses th e ril 31 water m odel for solvation. You can place th e solute in a box of T1P3P water m oleeules an d impose periodic boun dary eon dition s. You may then turn off the boundary conditions for specific geometry optimi/.aiion or molecular dynamics calculations. However, th is produces undesirable edge effects at the solvent-vacuum interface. 

In a molecular dynamics calculation, you can add a term to adjust the velocities, keeping the molecular system near a desired temperature. During a constant temperature simulation, velocities are scaled at each time step. This couples the system to a simulated heat bath at Tq, with a temperature relaxation time of "r. The velocities arc scaled bv a factor X. where... 

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Molecular dynamics calculations can automatically average and save these values ... 

Toxvaerd S 1990. Molecular Dynamics Calculation of the Equation of State of Alkanes. Journal of Chemical Physics 93 4290-4295. 

There are many algorithms for integrating the equations of motion using finite difference methods, several of which are commonly used in molecular dynamics calculations. All algorithms assume that the positions and dynamic properties (velocities, accelerations, etc.) can be approximated as Taylor series expansions ... 

One of the main advantages of the stochastic dynamics methods is that dramatic tirn savings can he achieved, which enables much longer stimulations to he performed. Fc example, Widmalm and Pastor performed 1 ns molecular dynamics and stochastic dynamic simulations of an ethylene glycol molecule in aqueous solution of the solute and 259 vvatc jnolecules [Widmalm and Pastor 1992]. The molecular dynamics simulation require 300 hours whereas the stochastic dynamics simulation of the solute alone required ju 24 minutes. The dramatic reduction in time for the stochastic dynamics calculation is du not only to the very much smaller number of molecules present hut also to the fact the longer time steps can often he used in stochastic dynamics simulations. 

---