MOPAC, molecular modelling

Structures of various dioxacarbenium and oxiranium intermediates were modeled using CAChe MOPAC molecular orbital software along with a Macintosh Ilci workstation. The conformations and energies of the structures were first computationally minimized and then the heats of formation were calculated. 

Tel. 703-658-4854, fax 703-658-4887, e-mail syazdi presto.ig.com Desktop molecular modeling. NEMESIS SAMPLER for simple modeling. PRO-EXPLORE for sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and BOSS via a graphical interface. PRO-QUANTUM for semiempirical (MOPAC, extended Hiickel) and ab initio (CADPAC) calculations via a graphical interface. FDCALC and ESCALC for electrostatics calculations. N-DEE for analysis of NMR data. PC-PROT-I- (sequence analysis), PC-TAMMO-I- (protein—lipid modeling), and MASCA (statistics). Macintosh, PCs, and UNIX workstations. 

The role of CI2 and monochloroacetic acid in the selective chlorination is a difficult problem to understand from the experimental studies. There are several possible orientations for the reactant, product and promoter molecules inside the complex structure of zeolite-L. In this context, it is pertinent to note that molecular modelling techniques are contributing in considerable amount to understand the reaction mechanisms. Molecular modelling includes force field based calculations [3] such as energy minimisation, Monte Carlo, and molecular dynamics calculations and quantum chemical calculations [4 ] such as EHMO, CNDO/INDO, MOPAC, Hartree-Fock and density functional theory calculations. In this study, we have attempted to apply the combination of molecular graphics, force field calculations and quantum chemical calculations to understand the mechanism of selective chlorination of DCB to TCB over zeolite K-L promoted by monochloroacetic acid. 

The structure of each compound is stored as a connection table. A molecular models is generated for each stored structure using molecular mechanics model building such as MM2, the semiempirical method MOPAC 6.0, or specialized methods such as a recently developed extended Hiickel method. Three-dimensional structures can also be generated directly from their connection tables by structure generators (see Three-dimensional Structure Generation Automation) such as concord or CORINA. Some approaches to QSPR use only descriptors derived from the topological representation of the molecular structures, and in this case the development of three-dimensional molecular models is not necessary. 

Semi-empirical methods, such as those implemented in the MOPAC [9] program, simplify the equations considerably by neglecting many terms, but then compensate for this by parameterising some of them so that the calculations reproduce experimental information on, for example, the heat of formation. Once the various approximations are made, the molecular properties to which the parameters are fitted, and the molecules used in the fitting, define a model Hamiltonian, of which the most commonly used are the AMI and the PM3 Hamiltonians found in MOPAC. A major advantage of semi-empirical methods is... 

A specialized MOPAC computer software package and, in particular, its PM3 quantum-chemical program has been successfully applied in calculations. The results of calculations have shown that both oxygen atoms form bonds with two more active carbon atoms of CP molecular cluster (so-called bridge model of adsorption). The total energy of system after a chemical adsorption at such active atoms is minimal. 

The opening window of Chem3D consists of the workspace (display window where 3D structures are displayed with rotation bar, slider knob, and action buttons), the menu bar (File, Edit, View, Tools, Object, Analyze, MM2, Gaussian, MOPAC, and Window menus), tool pallette (action icons for the cursor), and replacement text box (element, label, or structure name typed in this box is converted to chemical structure). Structure hie in. mol,. pdb, or. sml can be opened and saved from the File menu. Note PDB hies saved from Chem3D do not contain residue IDs.) The accompanying program, ChemDraw, draws 2D structures (.cdx) that are converted into 3D models (.c3d) by Chem3D. The molecular sketches from ISIS Draw (. skc) have to be converted to. cdx with ChemDraw for the 3D conversion. 

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