Atom types, in force field

An MM force field assigns each atom in a molecule to one of a number of possible atom types, depending on the atom s atomic number and molecular environment. For example, some commonly used atom types in force fields for organic compounds are sp (saturated) carbon, sp (doubly bonded) carbon, sp (triply bonded) carbon, carbonyl carbon, aromatic carbon, and so on, H bonded to C, H bonded to O, H bonded to N, and so on. Different force fields contain somewhat different numbers and kinds of atom types, based on the decisions made by their constructors. A force field for organic compounds typically contains 50 to 75 atom types. 

Antarafacial, Woodward-Hoffmann rules, 357 Antisyimnetrizing operator, 59 Atom types, in force field, 7, 8 Atomic basin, 223 Atomic units, 54, 415 Atomic Natural Orbitals (ANO), 161 Atomic orbital (AO), 65, 150 Atomic Polar Tensor (APT), use for atomic charges, 226... 

Eor some atom types, thermodynamic data may be lacking to assign a reference heat of formation. When a molecule contains one or more of these atom types, the force field cannot compute a molecular heat of formation, and energetic comparisons are necessarily limited to conformers, or other isomers that can be formed without any change in atom types. 

Hccausc of Ihc restricted availability of corn ptilation al resources, sorn e force fields use Un itcd. torn types, fli is type of force field represeri ts implicitly all hydrogens associated with a methyl, rn elli yieti e, or rn etii in e group. Th e van der Waals param eters for united atom carbons reflect the increased si/.e because of the implicit (included) hydrogens. 

Atoms are assigned types , much as in force field methods, i.e. the parameters depend on the nuclear charge and the bonding situation. The a a and /3ab parameters for atom types A and B are related to the corresponding parameters for sp -hybridized carbon by means of dimensionless constants /ia and /cab-... 

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

The last term in the formula (1-196) describes electrostatic and Van der Waals interactions between atoms. In the Amber force field the Van der Waals interactions are approximated by the Lennard-Jones potential with appropriate Atj and force field parameters parametrized for monoatomic systems, i.e. i = j. Mixing rules are applied to obtain parameters for pairs of different atom types. Cornell et al.300 determined the parameters of various Lenard-Jones potentials by extensive Monte Carlo simulations for a number of simple liquids containing all necessary atom types in order to reproduce densities and enthalpies of vaporization of these liquids. Finally, the energy of electrostatic interactions between non-bonded atoms is calculated using a simple classical Coulomb potential with the partial atomic charges qt and q, obtained, e.g. by fitting them to reproduce the electrostatic potential around the molecule. 

A central issue is the number of different atom types that are used in a particular force field. There is always a compromise between increasing the number to allow for the inclusion of more environmental effects (i.e., local electronic interactions) vs. the increase in the number of parameters to be determined to adequately represent a new atom type. In general, the more subtypes of atoms (how many different kinds of nitrogen, for example), the less likely that the parameters for a particular application will be available in the force field. The extreme, of course, would be a special atom type for each kind of atomic environment in which the parameters were chosen, so that the calculated properties of each molecule would simply reproduce the experimental observations. One major assumption, therefore, is that the force constants (parameters) and equilibrium values of the equations are functions of a limited number of atom types and can be transferred from one molecular environment to another. This assumption holds reasonably well where one may be primarily interested in geometric issues, but is not so valid in molecular spectroscopy. This had led to the introduction of additional equations, the so-called "cross-terms" which allow additional parameters to account for correlations between bond lengths and bond angles... 

The basic unit of a force field is fhe atom type. In general, there is at least one atom type for each element, more if several chemical environments are to be considered. For example, all force fields differentiate between sp and sp hybridized carbons, assigning a distinct atom type to each. For organometallic modeling, it is frequently necessary to add new metal atom types to existing force fields. Even when fhe mefal atom types exist in the force field, fhere is seldom any differentiation based on, for example, oxidation state.f Atom types are used to classify other interactions. Any unique pair of connected atom types identifies a bond type an angle type is labeled by a unique set of three connected atoms, etc. Each unique interaction type needs its own set of parameters. Many atom-... 

Build the bispidine complex using Momec and refine the corresponding cobalt(III) and cobalt(II) complexes (note that the force fields are not optimized for tetrahedral chromophores, but our aim here is just to compute relative metal—ligand distances). Note that all these structural optimizations need to be performed with 1,3-non-bonded interactions alone for the angular geometry around the metal ions (i.e., deactivate the multiple harmonic functions for both metal atom types in the force field) compare your results with those in Table 17.16. 

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