Bond stretch

One can note some interesting features from these trajectories. For example, the Mulliken population on the participating atoms in Figure 1 show that the departing deuterium canies a full electron. Also, the deuterium transferred to the NHj undergoes an initial substantial bond stretch with the up spin and down spin populations separating so that the system temporarily looks like a biradical before it settles into a normal closed-shell behavior. 

Figure 1, Coordinates used for describing the dynamics of a) H -I- H2 (6) NOCl, (c) butatriene, (a), (b) Are Jacobi coordinates, where and are the dissociative and vibrational coordinates, respectively, (c) Shows the two most important normal mode coordinates, Qs and Q a, which are the torsional and central C—C bond stretch, respectively.

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

For example, the SHAKE algorithm [17] freezes out particular motions, such as bond stretching, using holonomic constraints. One of the differences between SHAKE and the present approach is that in SHAKE we have to know in advance the identity of the fast modes. No such restriction is imposed in the present investigation. Another related algorithm is the Backward Euler approach [18], in which a Langevin equation is solved and the slow modes are constantly cooled down. However, the Backward Euler scheme employs an initial value solver of the differential equation and therefore the increase in step size is limited. 

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

In this article we describe an extension of SISM to a system of molecules for which it can be assumed that both bond stretching and angle bending describe satisfactorily all vibrational motions of the molecule. The SISM presented here allows the use of an integration time step up to an order of magnitude larger than possible with other methods of the same order and complexity. 

SISM Treatment of Bond Stretching and Angle Bending Terms... 

For the model Hamiltonian used in this study it was assumed that the bond stretching and angle i)ending satisfactorily describe all vibrational motions... 

SISM Treatment of only Bond Stretching Term... 

SISM for an Isolated Linear Molecule An efficient symplectic algorithm of second order for an isolated molecule was studied in details in ref. [6]. Assuming that bond stretching satisfactorily describes all vibrational motions for linear molecule, the partitioned parts of the Hamiltonian are... 

For each pair of interacting atoms (/r is their reduced mass), three parameters are needed D, (depth of the potential energy minimum, k (force constant of the par-tictilar bond), and l(, (reference bond length). The Morse ftinction will correctly allow the bond to dissociate, but has the disadvantage that it is computationally very expensive. Moreover, force fields arc normally not parameterized to handle bond dissociation. To circumvent these disadvantages, the Morse function is replaced by a simple harmonic potential, which describes bond stretching by Hooke s law (Eq. (20)). 

As for bond stretching, the simplest description of the energy necessary for a bond angle to deviate firom the reference value is a harmonic potential following Hooke s law, as shown in Eq. (22). 

Intensive use of cross-terms is important in force fields designed to predict vibrational spectra, whereas for the calculation of molecular structure only a limited set of cross-terms was found to be necessary. For the above-mentioned example, the coupling of bond-stretching (f and / and angle-bending (B) within a water molecule (see Figure 7-1.3, top left) can be calculated according to Eq. (30). 

Figure 7-13. Cross-terms combining internal vibrational modes such as bond stretch, angle bend, and bond torsion within a molecule.

Directly bonded (a 1-2 bond stretch relationship) Geniinal to each other (a 1-3 angle bending relationship)... 

In addition to these basic term s. force fieldsoften h ave cross term s that combine the above interactions. For example there may be a term which causes ati angle bend to interact with a bond stretch term (opening a bond angle may tend to lengthen the bonds in volved). 

In stead, the electrostatic con tribn tion conies from definin g a set of bond dipole moments associated woth polar bonds. These bond moments are defined in the m m psir.LxL(dbf) file along with the bond stretching parameters and are given in units of Debyes. The cen ter of th e dipole Is defined to be th e m Idpoint of the bond an d two dipoles p. and pj. separated by Rjj. as shown beltnv ... 

Bond Stretch and Angle Bending Cross Term... 

Th c fun ction al form for bon d stretch in g in HlOa, as in CHARMM, is quadratic only and is identical to that shown in equation (1 1) on page I 75. Th e bond stretch in g force con stan ts are in units of... 

The default parameters for bond stretching are an ec iiilibriiim bond length an d a stretch in g force eon starit. fb e fun etion al form isjiist that of the. M.M+ force field including a correction for cubic stretches. The default force constant depends only on the bond... 

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