Computer programs MOPAC

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 computer program package MOPAC contains - MINDO/3, MNDO, AMI and PM3 [J.J.P. Stewart, MOPAC - 7.0 A semi-empirical Molecular Orbital Program, Program No 455, Quantum Chemistry Program Exchange (QCPE), Indiana University, Bloomington, IN 47405 USA],... 

Old attitudes also lingered. Richard Counts has described an instance of a researcher who carried out a series of MOPAC (a computer program for semi-empirical quantum chemistry) calculations, producing a fairly comprehensive explanation of an observed phenomenon. The student s research director, however, insisted that the molecules in question be synthesized and their behavior analyzed using an established analytical technique. This was done, and the computational results were shown to be correct. For this research director, clearly, computational studies did not count as research. 

In Sections 11.2 and 11.3, highly sensitive detection mechanisms involving bromate formation and chemiluminescence were quantitatively analyzed using computational chemical methods. In the case of bromate, the MOPAC/ZINDO in CAChe programs were used to calculate spectra, while in the case of chemiluminescence, a MOPAC/PM5 program was used to calculate ape values as indicators of electron localization. 

The descriptors were calculated here, for each complex, using the computer programs MOPAC/PM6, PRoperty Evaluation by CLAss Variables (PRECLAV) (Tarko 2005), and DESCRIPT (Tarko 2008a). The LogP descriptor was calculated using the KowWin algorithm of EPISuite software (EPISuite Meylan and Howard 1995). The type of chemical bonds was defined according to Table 4.1. 

Table 3 lists chemists who have been most cited in chapters of prior volumes of our book series. Not surprisingly, all those listed are computational chemists, and many have written a chapter for Reviews in Computational Chemistry. It is interesting to notice how frequently the listed individuals are associated with developing a computer program that is well known in the lexicon of computational chemistry AMBER, CHARMM, Gaussian, UHBD, GROMOS, MM2/MM3, ECEPP, BOSS, DGEOM, MOPAC, DOCK, and so forth. 

The classical trajectory simulations were carried out with VENUS interfaced with the semiempirical electronic structure theory computer program MOPAC. To simulate experimental conditions for (gly-H) -I-diamond collisions, the center of a beam of (gly-H)+ ion projectiles is aimed at the center of the surface, with fixed incident angle 0, and fixed initial translational energy, E,. The radius of the beam was chosen so that the beam overlapped a unit area on the surface. For each trajectory, the projectile was randomly placed in the cross section of this beam and then randomly rotated about its center of mass so that it had an initial random orientation with respect to the surface. The azimuthal angle, %, between the beam and a fixed plane perpendicular to the surface, was sampled randomly between 0 and 2n. Such a random sampling of X simulates collisions with different domains of growth on the diamond surface. 

Stewart, J.J.P. MOPAC A Sem iem pirical Molecular Orbital Program../. Computer-Aided Molecular Design 4 1-105, 1990. 

MOPAC runs in batch mode using an ASCII input hie. The input hie format is easy to use. It consists of a molecular structure dehned either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. Version 6 and older have limits on the size of molecule that can be computed due to the use of hxed array sizes, which can be changed by recompiling the source code. This input format allows MOPAC to be run in conjunction with a batch job-queueing system. 

A semiempirical crystal band structure program, called BZ, is bundled with MOPAC 2000. There is also a utility, referred to as MAKPOL, for generating the input for band structure calculations with BZ. With the use of MAKPOL, the input for band-structure computations is only slightly more complicated than that for molecular calculations. 

Stewart, J. J. P. MOPAC A Semiempirical Molecular Orbital Program J. Computer-Aided... 

Semi-empirical methods, such as AMI, MINDO/3 and PM3, implemented in programs like MOPAC, AMPAC, HyperChem, and Gaussian, use parameters derived from experimental data to simplify the computation. They solve an approximate form of the Schrodinger equation that depends on having appropriate parameters available for the type of chemical system under investigation. Different semi-emipirical methods are largely characterized by their differing parameter sets. 

Stewart HP. MOPAC A semiempirical molecular orbital program. J Computer-Aided Mol Des 1990 4 1-105. 

With respect to calculations of the electronic structure of molecular clusters and their complexes with oxygen, the PM 3 program of the computer-driven system called MOPAC was used. 

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