MMX force field

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

Vinylindoles have been studied extensively and used in the synthesis of carbazoles, alkaloids and other classes of pharmacologically active compounds. MMX force field calculations have shown that coplanar s-cis and. s-trans conformations of 3-vinylindole (84, Figure 2.11) are the most stable conformers they exhibit only slight differences in their thermodynamic stabilities [86]. 

Global-MMX (GMMX) is a steric energy minimization program that uses the MMX force field and operates in batch mode. Its main purpose is to search conformational space and to fist the lowest-energy unique conformations found. It is available in desktop PC running Windows, Macintosh OS, and Unix-based workstation versions. 

The systematic conformational search for herbarumin I (40) using the MMX force field as implemented in the PCMODEL program revealed the presence of the minimum energy conformation depicted in Fig. 11 (Tmmx = 9.51 kcal/mol), which is related to the chair-chair-chair conformation found in cyclodecane.In this conformation, the value of... 

Note (a) The relative energy difference AG° = (energy of structure A) - (energy of structure B). The energies of structures 6A-12A, and 6B-12B were calculated using the MMX force-field in PCMODEL. 

Semiempirical and molecular mechanics calculations have been widely used. Thus, conformation of indolo benzazepine 423 (Figure 8) with its conjugated benzo and indole rings has been studied by molecular mechanics (MMX force field). Its planarity was estimated from a calculation of dihedral angle Ti 2 3 4 the value of ca. 22° is due to strain as contributed by azepine ring. This characteristic was further compared to that of the open-chain and six-membered... 

For CH3SC50 four local conformational minima are obtained by molecular mechanics calculations using the MMX force field (Figure 6.4) [7]. Thereby, as shown in Figure 6.4, the asymmetric conformation for this radical is preferred. 

The molecular mechanics method is extremely parameter dependent. A force field equation that has been empirically parameterized for calculating peptides must be used for peptides it cannot be applied to nucleic acids without being re-parameterized for that particular class of molecules. Thankfully, most small organic molecules, with molecular weights less than 800, share similar properties. Therefore, a force field that has been parameterized for one class of drug molecules can usually be transferred to another class of drug molecules. In medicinal chemistry and quantum pharmacology, a number of force fields currently enjoy widespread use. The MM2/MM3/MMX force fields are currently widely used for small molecules, while AMBER and CHARMM are used for macromolecules such as peptides and nucleic acids. 

DeKock et al. have studied the bonding in [ti -C5H5)2M( jl-X)]2 compounds where M = Zr (X = I, PH2, and NH) and M = Ti (X = Cl). PCMODEL software and MMX force field were used to determine the importance of steric effects on the geometry of these molecules. No details are given about the potential energy terms or the origin of the parameters. The authors concluded that Zr—Zr distance is controlled by an interplay of sterics and electronics. 

Studies by Ciarkowski et al. (1994) of the mechanism of AP by molecular mechanics with the MMX force field (Gajewski et al., 1990) and by semiempirical quantum mechanics methods AMI (Dewar et al, 1985) and PM3 ( Stewart, 1989) are hardly useful since energies are not reported for the first study while the model for a quantum mechanical study (constructed of two malonic acid molecules and water molecules that bridge the malonates) bears little resemblance to the X-ray structures of the active site of AP and includes effects that are not expected in the interaction of the peptide with the active site (Oldziej and Ciarkowski, 1994). 

Force field calculations were done with PCMODEL 4.0 (Serena Software, Bloomington, IN, USA) using the MMX-force field... 

The MMX force field embodies many years of work by J. J. Gajewski and K. Gilbert, University of Indiana, Bloomington, IN. The MMX program is available from Serena Software through Professor K. Steliou, University of Montreal, Quebec, Canada. 

The lack of correlation between cyclization stereoselectivity and the steric energy of the products (calculated by the MMX force field)... 

Using the MMX force field these authors first determine the distribution of conformational states accessible to the analytes and then evaluated the preferred conformations of L-ZGP in the neutral and ionic forms. Then the authors brought these components together to form the various diastereomeric complexes. Their... 

There are a variety of PC-based programs that perform molecular mechanics calculations. They include PCMODEL, " which uses the MMX force field that is very similar to the MM2 force field but includes parameters for transition metals, MOBY,2 which has its own force field but directed toward... 

Indeed, MMX force-field calculations place the product roughly 5.5 kcal/mol higher in enthalpy than the starting diene. ... 

MMX force-field calculations " suggest that the reaction is exothermic by 25 kcal/mol, so there must be a very negative reaction entropy associated with the cyclization which is not unreasonable. 

MMX force-field calculations are also given in italics in Scheme 13.21. ... 

A summary of all the reactions reported in the (CH)i2 series is given in Scheme 13.22 along with the RHF/6-31G calculations and MMX force-field calculations of the heat of formation relative to two benzene molecules. The experimental activation free energies are given over the arrows. 

The aim of our work is to develop an MM2-type force field capable of handling a wide range of oligomeric organosilanes. The MMX force field was chosen as a suitable environment for the implementation of new parameters [11]. 

PCMODEL contains sixty atom types and generalized parameters, as well as functions and parameters for transition metals, and thus the built-in MMX force field minimizations provide some of the most complete molecular modeling available. Unrestricted Hartree-Fock tt calculations for conjugated systems provide unparalleled accuracy for molecular mechanics calculations of open-shell species. Standard RHF n calculations can be used to model closed-shell species containing carbon, nitrogen, and oxygen. Also, specific aromatic carbon types provide excellent aromatic geometries without n calculations. 

Below is an example of one of the force potentials, and parameters one may find in a force field. This example is from Allingeds MM2 force field [(a)"Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing VI and V2 Torsional Terms", Allinger, N. L., J. Am. Chem. Soc. 1977, 99, 8127. (b) Burket, U. Allinger, N. L. Molecular Mechanics American Chemical Society Washington, DC, 1982.] and the MMX force field of PCMODEL ["PCMODEL", Gilbert, K., Serena Software Bloomington, IN, 1993]. 

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