Dynamic trajectory calculation

Traditionally, trajectory calculations were only performed on previously calculated (or empirically estimated) potential energy surfaces. With the increased computational speed of modern computers, it has also become possible to employ direct dynamics trajectory calculations [34, 35]. In this method, a global potential energy surface is not needed. Instead, from some... 

Direct dynamics trajectory calculations at the MP2/6-31-FG level of theory were then used to explore the reaction dynamics of this system [63]. Sixty-four trajectories were started from the central barrier shown at A in Fig. 11, with initial conditions sampled from a 300 K Boltzmann distribution. Of the 31 trajectories that moved in the direction of products, four trajectories followed the MEP and became trapped in the hydrogen-bonded [CH3OH ... 

A very simple implementation of a molecular dynamics trajectory calculation is achieved by using a velocity Verlet algorithm to calculate the... 

Ab initio direct dynamics trajectory calculations were performed at the B3LYP/6-311+G(d,p) level of theory.39 The trajectories were initiated at the separated reactants, TS (HOOCH3- F ), and the CII 2( 011)0 H- F region on IRC, with quasiclassical sampling including ZPE. The trajectories from the reactants were started at 15 A separation of the two species with small attractive potentials of -0.21 or -0.13 kcalmol-1. The collision impact parameter was chosen randomly between zero and maximum. The initial CH3OOH vibrational and rotational degrees of freedom were selected from their 300 K Boltzmann distributions. 

Ab inito direct dynamics trajectory calculations that include ab initio structure calculations on the Sn2 reaction in the gas phase have been carried out. A particularly interesting application is described in Scheme 1.10, in which hydroxide ion displaces fluoride ion in an Sn2 reaction... 

More recently, Arenas and co-workers studied the diazirine system at the complete active space, self-consistent field (CASSCF) level of theory using the cc-pVDZ basis set to map the potential energy surfaces with the critical points recalculated at the CASPT2/cc-pVDZ level.The active space used for these calculations was 12 electrons in 10 orbitals. Additionally, they performed limited direct dynamic trajectory calculations on the S, and Sj surfaces. The key features of the potential energy surfaces are depicted in Figure 92.2. 

They compared the PME method with equivalent simulations based on a 9 A residue-based cutoflF and found that for PME the averaged RMS deviations of the nonhydrogen atoms from the X-ray structure were considerably smaller than in the non-PME case. Also, the atomic fluctuations calculated from the PME dynamics simulation were in close agreement with those derived from the crystallographic temperature factors. In the case of DNA, which is highly charged, the application of PME electrostatics leads to more stable dynamics trajectories with geometries closer to experimental data [30]. A theoretical and numerical comparison of various particle mesh routines has been published by Desemo and Holm [31]. 

A sequence of successive con figurations from a Mon te Carlo simulation constitutes a trajectory in phase space with IlypcrC hem. this trajectory in ay be saved and played back in the same way as a dynamics trajectory. With appropriate choices of setup parameters, the Mon te Carlo m ethod m ay ach leve ec nilibration more rapidly than molecular dynamics. Tor some systems, then. Monte C arlo provides a more direct route to equilibrium sinictural and thermodynamic properties. However, these calculations can be quite long, depentiing upon the system studied. 

Quantum mechanical calculation of molecular dynamics trajectories can sim ulate bon d breakin g and frtrm ation.. Although you dt) n ot see th e appearance or disappearan ce ofhonds, you can plot the distan ce between two bonded atom s.. A distan ce excccdi n g a theoretical bond length suggests bond breaking. 

Finite difference techniques are used to generate molecular dynamics trajectories with continuous potential models, which we will assume to be pairwise additive. The essential idea is that the integration is broken down into many small stages, each separated in time by a fixed time 6t. The total force on each particle in the configuration at a time t is calculated as the vector sum of its interactions with other particles. From the force we can determine the accelerations of the particles, which are then combined with the positions and velocities at a time t to calculate the positions and velocities at a time t + 6t. The force is assumed to be constant during the time step. The forces on the particles in their new positions are then determined, leading to new positions and velocities at time t - - 2St, and so on. 

Both molecular dynamics studies and femtosecond laser spectroscopy results show that molecules with a sufficient amount of energy to react often vibrate until the nuclei follow a path that leads to the reaction coordinate. Dynamical calculations, called trajectory calculations, are an application of the molecular dynamics method that can be performed at semiempirical or ah initio levels of theory. See Chapter 19 for further details. 

Ah initio trajectory calculations have now been performed. However, these calculations require such an enormous amount of computer time that they have only been done on the simplest systems. At the present time, these calculations are too expensive to be used for computing rate constants, which require many trajectories to be computed. Semiempirical methods have been designed specifically for dynamics calculations, which have given insight into vibrational motion, but they have not been the methods of choice for computing rate constants since they are generally inferior to analytic potential energy surfaces fitted from ah initio results. 

Quasiclassical trajectory calculations are the method of choice for determining the dynamics of intramolecular vibrational energy redistribution leading to a chemical reaction. If this information is desired, an accurate reaction rate can be obtained at little extra expense. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

Once HyperChem calculates potential energy, it can obtain all of the forces on the nuclei at negligible additional expense. This allows for rapid optimization of equilibrium and transition-state geometries and the possibility of computing force constants, vibrational modes, and molecular dynamics trajectories. 

Figure 3 Calculated X-ray diffuse scattering patterns from (a) a full molecular dynamics trajectory of orthorhombic hen egg white lysozyme and (b) a trajectory obtained by fitting to the full trajectory rigid-body side chains and segments of the backbone. A full description is given in Ref. 13.

Another principal difficulty is that the precise effect of local dynamics on the NOE intensity cannot be determined from the data. The dynamic correction factor [85] describes the ratio of the effects of distance and angular fluctuations. Theoretical studies based on NOE intensities extracted from molecular dynamics trajectories [86,87] are helpful to understand the detailed relationship between NMR parameters and local dynamics and may lead to structure-dependent corrections. In an implicit way, an estimate of the dynamic correction factor has been used in an ensemble relaxation matrix refinement by including order parameters for proton-proton vectors derived from molecular dynamics calculations [72]. One remaining challenge is to incorporate data describing the local dynamics of the molecule directly into the refinement, in such a way that an order parameter calculated from the calculated ensemble is similar to the measured order parameter. 

Figure 2. Temperature dependence of mean square atomic fluctuations of the Z-DNA hexamer. (a) Mean square atomic fluctuations were calculated directly from the molecular dynamics trajectories.

The second channel, producing CO, was first observed by Seakins and Leone [64], who estimated 40% branching to this channel. Later measurements by Lockenberg et al. [65] and Preses et al. [66] concluded the branching to CO is 18%. Note that decomposition of formaldehyde formed in reaction (26a) is not a possible source of CO due to the large barrier for formaldehyde decomposition. Marcy et al. [67] recently combined time-resolved Lourier spectroscopy experiments with direct dynamics classical trajectory calculations to examine the mechanism of the CO product channel. They observed two pathways for CO formation, neither of which involve crossing a TS. 

For both statistical and dynamical pathway branching, trajectory calculations are an indispensable tool, providing qualitative insight into the mechanisms and quantitative predictions of the branching ratios. For systems beyond four or five atoms, direct dynamics calculations will continue to play the leading theoretical role. In any case, predictions of reaction mechanisms based on examinations of the potential energy surface and/or statistical calculations based on stationary point properties should be viewed with caution. 

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