Torsional interaction

The chemistry of molecules consists of three major modules molecular architecture (structure) molecular dynamics (conformational analysis) and molecular transformation (chemical reactions). The molecular architecture consists of the basic principles of molecular structure and it deals with the atomic structure, orbitals, hybridization and bonding. Molecular dynamics deals with the molecular motion involving rotation around chemical bonds, steric interactions, torsional strain and properties associated with the conformational changes. Molecular transformation accounts for bond formation and bond breaking within the molecule or between molecules, which is generally called the chemical reaction, and consists of two major aspects, reaction mechanism and kinetics. The third module is one of the major areas of chemistry. This aims to understand the reaction mechanism and its manipulation to reduce the reaction barrier, improve stereoselectivity, increase product yield, or suppress undesirable side reactions. 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

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. 

Isolated Linear Molecule Figure 6 shows the error in total energy for an isolated linear molecule H-(-C=C-)5-H. It is obvious that for the same level of accuracy, the time step in the SISM can be ten times or more larger as in the LFV. Furthermore, the LFV method is stable for only very short time steps, up to 5 fs, while the SISM is stable even for a time step up to 200 fs. However, such large time steps no longer represent physical reality and arc a particular property identified with linear molecules without bending or torsional intramolecular interactions. 

For acyclic fragments and molecules, the principle of longest pathways has been implemented in CORINA (sec Figure 2-95) i.e., since no ch configuration is specified, all torsions arc set to anti in order to minimize steric interactions. 

The PEF is a sum of many individual contributions, Tt can be divided into bonded (bonds, angles, and torsions) and non-bonded (electrostatic and van der Waals) contributions V, responsible for intramolecular and, in tlic case of more than one molecule, also intermoleculai interactions. Figure 7-8 shows schematically these types of interactions between atoms, which arc included in almost all force field implementations. 

The origin of a torsional barrier can be studied best in simple cases like ethane. Here, rotation about the central carbon-carbon bond results in three staggered and three eclipsed stationary points on the potential energy surface, at least when symmetry considerations are not taken into account. Quantum mechanically, the barrier of rotation is explained by anti-bonding interactions between the hydrogens attached to different carbon atoms. These interactions are small when the conformation of ethane is staggered, and reach a maximum value when the molecule approaches an eclipsed geometry. 

It is noteworthy that it is not obligatory to use a torsional potential within a PEF. Depending on the parameterization, it is also possible to represent the torsional barrier by non-bonding interactions between the atoms separated by three bonds. In fact, torsional potentials and non-bonding 1,4-interactions are in a close relationship. This is one reason why force fields like AMBER downscale the 1,4-non-bonded Coulomb and van der Waals interactions. 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

Th e dih edral an gle or torsional energy interaction in MM-t- is of th e general form ofec naiion (12) on page 175 but explicitly includes... 

A restrain t (not to be confused with a Model Builder constraint) is a nser-specified one-atom tether, two-atom stretch, three-atom bend, or four-atom torsional interaction to add to the list ol molec-11 lar mechanics m teraction s computed for a molecule. These added iiueraciious are treated no differently IVoin any other stretch, bend, or torsion, except that they employ a quadratic functional form. They replace no in teraction, on ly add to the computed in teraction s. 

A typical force field model for propane contains ten bond-stretching terms, eighteen angle-bending terms, eighteen torsional terms and 27 non-bonded interactions. 

Fhe van der Waals and electrostatic interactions between atoms separated by three bonds (i.c. the 1,4 atoms) are often treated differently from other non-bonded interactions. The interaction between such atoms contributes to the rotational barrier about the central bond, in conjunction with the torsional potential. These 1,4 non-bonded interactions are often scaled down by an empirical factor for example, a factor of 2.0 is suggested for both the electrostatic and van der Waals terms in the 1984 AMBER force field (a scale factor of 1/1.2 is used for the electrostatic terms in the 1995 AMBER force field). There are several reasons why one would wish to scale the 1,4 interactions. The error associated wilh the use of an repulsion term (which is too steep compared with the more correct exponential term) would be most significant for 1,4 atoms. In addition, when two 1,4... 

The computational effort is significantly increased if three-body terms are included in the model. Even with a simple pairwise model, the non-bonded interactions usually require by far the greatest amount of computational effort. The number of bond, angle and torsional terms increases approximately with the number of atoms (N) in the system, but the number of non-bonded interactions increases with N. There are N(N —l)/2 distinct pairs of... 

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