MMFF

Force fields like MM3, MM4, CFF, or MMFF therefore use cubic and/or quartic or even higher contributions, up to the sixth power. Special attention has to be paid in the case of reference angles approaching 180°, e.g., for molecules with linear firag-ments such as acetylene compounds. In this circumstance, replacing Eq. (23) by a... 

This model (e.g., implemented in MMFF) allows the charges on each atom i to be modified by the electronegativity of the bonded atoms j. The additional charge q is normally zero, but it ensures that the correct total charge of a molecule or fragment is maintained. 

Inadequate availability of experimental data can considerably inhibit the development of improved energy functions for more accurate simulations of energetic, structural, and spectroscopic properties. This has led to the development of class II force fields such as CFF and the Merck Molecular Force Field (MMFF), which are both based primarily on quantum mechanical calculations of the energy surface. The purpose of MMFF, which has been developed by Thomas Halgren at Merck and Co., is to be able to handle all functional groups of interest in pharmaceutical design. 

The Merck molecular force field (MMFF) is one of the more recently published force fields in the literature. It is a general-purpose method, particularly popular for organic molecules. MMFF94 was originally intended for molecular dynamics simulations, but has also seen much use for geometry optimization. It uses five valence terms, one of which is an electrostatic term, and one cross tenn. 

The MM2, MM3, and Merck (MMFF) force fields perform best for a wide range of organic molecules. 

The force fields available are MM2, MM3, AMBER, OPLSA, AMBER94, and MMFF. The asterisk ( ) indicates force fields that use a modification of the original description in the literature. There is support for user-defined metal atoms, but not many metals are predefined. MM2 has atom types for describing transition structures. The user can designate a substructure for energy computation. 

Halgren TA. MMFF VI. MMFF94s option for energy minimization studies. 

Current efforts toward oPE foldamers have focused on developing a computational model that will allow useful predictions of structure. This model was validated by comparing computational results to previously published experimental results [101]. For both crystal structure data and methyl- and hydrogen-series mPEs [25,57], the MMFF molecular mechanics system [102,103]... 

Table 5 Helix stabilization energies (kcal mol for substituted oPE hexamers calculated with MMFF... 

This part of the case study was broken into two sections, the original descriptor set (2,125,127) (Hansch descriptors) and a new set of descriptors calculated in MOE (6) (MOE descriptors). The MOE Descriptors were calculated for molecules assigned Gasteiger (70) partial charges in the MMFF (46-52). The new descriptor set is constructed of three properties. The water accessible surface area (ASA) calculated using a radius of 1.4 A for a water molecule and the... 

Using SOMFA2 (11), QSAR models were constructed based on shape and electrostatic potential [Gasteiger (70) and MMFF (46-52) partial charges] for... 

These settings proved to be adequate for the models constructed based on the molecular shape and original bioactivities (it R2 0.77, Q1 0.58, + R2 0.80). The models show that by increasing the bulk of the molecules at the rnela substituent and reducing the bulk at the para would create molecules with better bioactivities. The original bioactivities and partial charge-based models of MMFF... 

Halgren, T. A. (1999) MMFF VI. MMFF94s option for energy minimization studies. J. Comput. Chem. 20, 720-729. 

This chapter describes the basis of molecular mechanics models and introduces the SYBYL and MMFF force fields. It also compares and contrasts molecular mechanics and quantum chemical models. 

Molecular mechanics models differ both in the number and specific nature of the terms which they incorporate, as well as in the details of their parameterization. Taken together, functional form and parameterization, constitute what is termed a force field. Very simple force fields such as SYBYL, developed by Tripos, Inc., may easily be extended to diverse systems but would not be expected to yield quantitatively accurate results. On the other hand, a more complex force field such as MMFF94 (or more simply MMFF), developed at Merck Pharmaceuticals, while limited in scope to common organic systems and biopolymers, is better able to provide quantitative accounts of molecular geometry and conformation. Both SYBYL and MMFF are incorporated into Spartan. 

T. A. Halgren, J. Computational Chem., 17,490 (1996), and following papers in this issue. Two different variations of MMFF have been published. The default choice in Spartan is the one in which nitrogen attached to an unsaturated carbon, e.g., the nitrogen in aniline, is allowed to pucker. The other variation assumes that the nitrogen attached to unsaturated carbon is planar. 

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