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Monday, 4 July 2011

Force field (chemistry)

Force field (chemistry)


A force field is used to minimize the bond stretching energy of this ethane molecule.
In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles (typically molecules and atoms). Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical calculations. "All-atom" force fields provide parameters for every type of atom in a system, including hydrogen, while "united-atom" force fields treat the hydrogen and carbon atoms in methyl and methylene groups as a single interaction center. "Coarse-grained" force fields, which are frequently used in long-time simulations of proteins, provide even more crude representations for increased computational efficiency.
The usage of the term "force field" in chemistry and computational biology differs from the standard usage in physics. In chemistry it is a system of potential energy functions rather than the gradient of a scalar potential, as defined in physics.

Functional form

Functional form

Molecular mechanics potential energy function with continuum solvent.
The basic functional form of a force field encapsulates both bonded terms relating to atoms that are linked by covalent bonds, and nonbonded (also called "noncovalent") terms describing the long-range electrostatic and van der Waals forces. The specific decomposition of the terms depends on the force field, but a general form for the total energy in an additive force field can be written as \ E_{total} = E_{bonded} + E_{nonbonded} where the components of the covalent and noncovalent contributions are given by the following summations:
\ E_{bonded} = E_{bond} + E_{angle} + E_{dihedral}
\ E_{nonbonded} = E_{electrostatic} + E_{van der Waals}
The bond and angle terms are usually modeled as harmonic oscillators in force fields that do not allow bond breaking. A more realistic description of a covalent bond at higher stretching is provided by the more expensive Morse potential. The functional form for the rest of the bonded terms is highly variable. Proper dihedral potentials are usually included. Additionally, "improper torsional" terms may be added to enforce the planarity of aromatic rings and other conjugated systems, and "cross-terms" that describe coupling of different internal variables, such as angles and bond lengths. Some force fields also include explicit terms for hydrogen bonds.
The nonbonded terms are most computationally intensive because they include many more interactions per atom. A popular choice is to limit interactions to pairwise energies. The van der Waals term is usually computed with a Lennard-Jones potential and the electrostatic term with Coulomb's law, although both can be buffered or scaled by a constant factor to account for electronic polarizability and produce better agreement with experimental observations.

Parameterization

Parameterization

In addition to the functional form of the potentials, a force field defines a set of parameters for each type of atom. For example, a force field would include distinct parameters for an oxygen atom in a carbonyl functional group and in a hydroxyl group. The typical parameter set includes values for atomic mass, van der Waals radius, and partial charge for individual atoms, and equilibrium values of bond lengths, bond angles, and dihedral angles for pairs, triplets, and quadruplets of bonded atoms, and values corresponding to the effective spring constant for each potential. Most current force fields use a "fixed-charge" model by which each atom is assigned a single value for the atomic charge that is not affected by the local electrostatic environment; proposed developments in next-generation force fields incorporate models for polarizability, in which a particle's charge is influenced by electrostatic interactions with its neighbors. For example, polarizability can be approximated by the introduction of induced dipoles; it can also be represented by Drude particles, or massless, charge-carrying virtual sites attached by a springlike harmonic potential to each polarizable atom. The introduction of polarizability into force fields in common use has been inhibited by the high computational expense associated with calculating the local electrostatic field.
Although many molecular simulations involve biological macromolecules such as proteins, DNA, and RNA, the parameters for given atom types are generally derived from observations on small organic molecules that are more tractable for experimental studies and quantum calculations. Different force fields can be derived from dissimilar types of experimental data, such as enthalpy of vaporization (OPLS), enthalpy of sublimation (CFF), dipole moments, or various spectroscopic parameters (CFF).
Parameter sets and functional forms are defined by force field developers to be self-consistent. Because the functional forms of the potential terms vary extensively between even closely related force fields (or successive versions of the same force field), the parameters from one force field should never be used in conjunction with the potential from another.

Deficiencies

Deficiencies

All force fields are based on numerous approximations and derived from different types of experimental data. Therefore they are called empirical. Some existing force fields do not account for electronic polarization of the environment, an effect that can significantly reduce electrostatic interactions of partial atomic charges. This problem was addressed by developing “polarizable force fields” or using macroscopic dielectric constant. However, application of a single value of dielectric constant is questionable in the highly heterogeneous environments of proteins or biological membranes, and the nature of the dielectric depends on the model used [3].
All types of van der Waals forces are also strongly environment-dependent, because these forces originate from interactions of induced and “instantaneous” dipoles (see Intermolecular force). The original Fritz London theory of these forces can only be applied in vacuum. A more general theory of van der Waals forces in condensed media was developed by A. D. McLachlan in 1963 (this theory includes the original London’s approach as a special case) [4]. The McLachlan theory predicts that van der Waals attractions in media are weaker than in vacuum and follow the "like dissolves like" rule, which means that different types of atoms interact more weakly than identical types of atoms.[5]. This is in contrast to “combinatorial rules” or Slater-Kirkwood equation applied for development of the classical force fields. The “combinatorial rules” state that interaction energy of two dissimilar atoms (e.g. C…N) is an average of the interaction energies of corresponding identical atom pairs (i.e. C…C and N…N). According to McLachlan theory, the interactions of particles in a media can even be completely repulsive, as observed for liquid helium [4]. The conclusions of McLachlan theory are supported by direct measurements of attraction forces between different materials (Hamaker constant), as explained by Jacob Israelachvili in his book "Intermolecular and surface forces". It was concluded that "the interaction between hydrocarbons across water is about 10% of that across vacuum" [4]. Such effects are unaccounted in the standard molecular mechanics.

Future Perspectives

Future Perspectives

Molecular mechanics or force field was first introduced apparently independently by Hill and by Westheimer in 1949, primarily applied to organic chemistry to estimate properties such as strain energies among others. The functional form of the force field, focused in this article applied to biological systems, was established by Lifson in the 1960s. For over a half century, force fields have served us well, providing useful insights into and interpretation of biomolecular structure and function. Undoubtedly, it will continue to be widely used, thanks to its computational efficiency, while its reliability will continue to be improved. Yet, there are many well-known deficiencies as noted above. In addition, the number of energy terms used in a given force field cannot be uniquely determined and a highly redundant number of degrees of freedom are typically used. Consequently, the "parameters" in different force fields can be vastly different. Of course, the emphasis to incorporate polarization into the standard pair-wise potentials can be very useful; however, there is no unique way of treating polarization in molecular mechanics because it is of quantum mechanical origin Furthermore, often we are more interested in the properties derived from the dynamic dependence of the force field itself on molecular fluctuations.
One possibility is that the future development of force field ought to move beyond the current molecular mechanics approach, by using quantum mechanics explicitly to construct the force field. A number of the "polarizable force fields" listed below, such as density fitting and bond-polarization, already included some of the key ingredients towards this goal. The explicit polarization (X-Pol) method appears to have established the fundamental theoretical framework for a quantal force field; the next step is to develop the necessary parameters to achieve more accurate results than classical mechanics can offe

Popular force fieldsPopular force fields

Popular force fields

Different force fields are designed for different purposes.
MM2 was developed by Norman Allinger primarily for conformational analysis of hydrocarbons and other small organic molecules. It is designed to reproduce the equilibrium covalent geometry of molecules as precisely as possible. It iPopular force fieldsPopular force fieldsmplements a large set of parameters that is continuously refined and updated for many different classes of organic compounds (MM3 and MM4).
CFF was developed by Warshel, Lifson and coworkers as a general method for unifying studies of energies, structures and vibration of general molecules and molecular crystals. The CFF program, developed by Levitt and Warshel, is based on the Cartesian representation of all the atoms, and it served as the basis for many subsequent simulation programs.
ECEPP was developed specifically for modeling of peptides and proteins. It uses fixed geometries of amino acid residues to simplify the potential energy surface. Thus, the energy minimization is conducted in the space of protein torsion angles. Both MM2 and ECEPP include potentials for H-bonds and torsion potentials for describing rotations around single bonds. ECEPP/3 was implemented (with some modifications) in Internal Coordinate Mechanics and FANTOM [33].
AMBER, CHARMM and GROMOS have been developed primarily for molecular dynamics of macromolecules, although they are also commonly applied for energy minimization. Therefore, the coordinates of all atoms are considered as free variables.