Semiempirical Molecular Orbital Program Research Articles

EMPIRE: a highly parallel semiempirical molecular orbital program: 3: Born-Oppenheimer molecular dynamics

Direct NDDO-based Born-Oppenheimer molecular dynamics (MD) have been implemented in the semiempirical molecular orbital program EMPIRE. Fully quantum mechanical MD simulations on unprecedented time and length scales are possible, since the calculation of self-consistent wavefunctions and gradients is performed in a massively parallel manner. MD simulations can be performed in the NVE and NVT ensembles, using either deterministic (Berendsen) or stochastic (Langevin) thermostats. Furthermore, dynamics for condensed-phase systems can be performed under periodic boundary conditions. We show three exemplary applications: the dynamics of molecular reorganization upon ionization, long timescale dynamics of an endohedral fullerene, and calculation of the vibrational spectrum of a nanoparticle consisting of more than eight hundred atoms.Graphical A snapshot from an MNDO-H simulation of NH4+@C60 at 4000 K shortly before a proton crosses the fullerene wall to give NH3@C60H+.

EMPIRE: a highly parallel semiempirical molecular orbital program: 1: self-consistent field calculations.

EMPIRE is a massively parallel semiempirical (NDDO) molecular-orbital program designed to scale well both on single multi-core nodes (using open MP) and on large clusters (using a hybrid open MP/MPI model). The program design and performance are discussed for single self-consistent-field calculations on up to 55,000 (the adamantane crystal shown in the graphic) atoms and on both single- and multi-node machines using either Windows 7 or Linux. EMPIRE currently carries out the full SCF calculation with no local approximations or other linear-scaling techniques. The single-node version is available free of charge to bona fide academic groups.

Study of Spectral and Thermodynamics properties for Hydrogen Sulfide (H2S)

In this research theoretical semi – empirical calculations using PM3 method to study the molecular structure for H2S in Infra-red regin by using MOPAC, it is semi-empirical molecular orbital program ,Mopac using semi-empirical quantum mechanic for Hamiltonen through PM3 method, then study and calculated some of spectroscopy and thermodynamics properties for this molecule and determine the minimum total energy at equilibrium structure for molecule, this study and calculation yielded the equilibrium geometry distance, energetic value, for H2S total energy was (-217.03eV) at equilibrium distance(1.3Å) Through unharmonic potential of energy curve we founded the spectroscopic dissociation energy for this molecule is(8.81eV). The main purpose from this research calculate study the fundamental vibrational frequencies, absorption spectrum of molecule was between (1192.72 ,1808.53, 1812.91) cm-1 and intensity a absorption band was (7.58, 12.63 , 15.197) respectively. And using Hyper-chem program including occupied molecular orbital and unoccupied molecular orbital with highest energy value ( HOMA) and lawest energy value (LUMO), Were for H2S (EHOMO = -9.63eV) (ELUMO= 0.552eV) and calculate energy gab between EHOMO, ELUMO was ( Eg = 10.128eV) . From final matrix we get on the Thermodynamics properties at many degree of heating such as heat of formation (∆Hf) for H2S was (- 0.897 kcal/mal ) enthalpy ( 2397.6599 cal/mol), heat capacity ( 8.214 cal/ mal.K), entropy( 54.904 cal/mal .K ). And Gibbs free energy ( -14.0737 kcal/ mol).These properties taken at standard heating degree (298K) and agreement with experimental result.

Preferred Conformations of Cyclophosphamide

The important anti-cancer agent cyclophosphamide and its derivatives have been subjected to 22 crystal structure determinations, 19 of which are unique, revealing 24 independent molecules. These crystal structures show a general preference for chair conformations of the six-membered ring but unexpected occurrence of boat and half-chair forms, placement of the exocyclic oxygen atom that is more often axial than equatorial, flattening at the nitrogen atom of the oxazaphosphorinane ring, and a preference for antiperiplanar NCCC1 torsion angles in the N-chloroethyl groups. Calculations are reported here that demonstrate the suitability of semi-empirical molecular orbital methods for these systems and evaluate the energy and geometry of the molecules after optimization. Optimization of geometry with the semi-empirical molecular orbital program, MOPAC, yielded torsion angles and ring puckering generally closer to the crystal structure and the result of ab-initio optimization when the PM3 Hamiltonian was employed rather than AMI. However, AMI generally predicted an axial disposition of the exocyclic P = O bond, as found in the majority of crystal structures, while PM3 did not. The chair conformation of the ring is preferred, but boat and half-chair forms are only 1–3 kcal mol−1 higher in energy, as are alternative arrangements of the exocyclic P = O bond. Dipole moments usually increase when this bond is made equatorial; thus interaction with a polar solvent could mitigate the energy disadvantage of this conformation.

Modified genetic algorithms to model cluster structures in medium-sized silicon clusters:Si18−Si60

This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of medium-size silicon clusters. This is the third report in which a GA coupled with the MSINDO semiempirical molecular orbital program is used to find stable atomic cluster structures. The structures selected by the GA-MSINDO method were further optimized using the density functional theory (DFT). This combination of GA-MSINDO global optimization followed by DFT local optimization proves to be very effective for searching the structures of medium-size Si clusters. For most of the clusters studied here we report different structures with significant lower energy than those previously found using limited search approaches on common structural motifs. This demonstrates the need for global optimization schemes when searching for stable structures of medium-size silicon clusters.

Molecular Orbital Study of the Interaction between MgATP and the Myosin Motor Domain: The Highest Occupied Molecular Orbitals Indicate the Reaction Site of ATP Hydrolysis

We constructed a model structure of Mg−adenosine triphosphate (MgATP) and the surrounding portion of myosin by using the X-ray crystal structure of the myosin motor domain bound to the stable MgATP analogue, MgADP−BeFx, and by adding hydrogen atoms and replacing beryllium with phosphorus and fluorine with oxygen. The positions of the hydrogen atoms were determined by optimization using the semiempirical molecular orbital program MOPAC 97. Analysis of the electronic states of the model structure revealed that the highest occupied molecular orbitals (HOMO) indicate that the reaction site of the ATP hydrolysis is the nonbridging γ-phosphoryl oxygen atoms and confirmed that H2O(1181) is the hydrolytic water. Thus, hypothetical mechanisms of the initial phase of the hydrolysis are proposed.

Molecular orbital theory examination into improved gate oxide integrity through the incorporation of nitrogen and fluorine

Molecular orbital theory was used to examine the improved gate oxide integrity of MOS (metal-oxide-semiconductor) devices against hot-hole injection; this improvement is associated with the incorporation of a nitrogen atom and subsequent incorporation of a fluorine atom. The bond dissociation energies of eight cluster models containing representative chemical bond environments in a modified oxide film – –Si–O–Si–, N(–Si–O–)– 3, Si–N(–Si)–O–Si, Si–N(–O–Si) 2, Si–N(–Si)–H, Si–F, Si–O–F, Si–N(–Si)–F – were extensively evaluated for both the neutral state and the hole-trapped state since the bond dissociation energy change is thought to be a relevant measure of bond durability against hot holes. A semiempirical molecular orbital program package, MOPAC, was used because of its short computational time. The applicability of MOPAC to the hole-trapped state was confirmed by comparing the MOPAC results with those obtained by first-principle calculations. The calculated changes in bond dissociation energy upon hole trapping imply that the improvement stems from the chemical bond formation of a silicon–nitride-like structure, N(–Si–O–)– 3, in oxide bulk, and a Si–F structure in the Si/SiO 2 interfacial region. The synergetic effect of nitrogen and fluorine incorporation is most likely brought about by the formation of a Si 2N–F structure in both the oxide and the interfacial region.

Semiempirical molecular orbital calculations with linear system size scaling

Details are provided for the implementation of a density matrix divide-and-conquer approximation into the framework of molecular orbital theory on nonperiodic systems. Originally developed for density functional theory, the divide-and-conquer procedure is one of the most promising in a growing list of techniques that exhibit linear scaling with respect to the number of basis functions in the system. The key to linear scaling is the division of the electronic structure calculation into a series of calculations over a set of small, overlapping subsystems. A semiempirical molecular orbital program designed around the divide-and-conquer approach has been written and a number of tests are carried out on polyglycine structures in order to evaluate its performance. For the systems examined, linear scaling is indeed observed, and the accuracy of the calculations can be controlled quite readily by the manner in which the system is divided into its component subsystems. For very large structures, the expense associated with the computation of two-center interactions will ultimately dominate the calculation, and quadratic scaling will become apparent. Techniques to linearize this aspect of the calculation are investigated and discussed.

Functional sites of cytochrome c and other electron carrier proteins: Semi-empirical molecular orbital program PM3 applied to the conformational analysis of Cys-X1-X2-Cys peptides

The semi empirical molecular orbital progrram, MOPAC version 6.0, PM3 was applied to estimate the distance between two sulfur atoms of two Cys side chains in optimized conformers of Cys-X1-X2-Cys sequences, as well as the total energy of that conformer relative to the most stable one. Some Cys-X1-X2-Cys tetrapeptides found in cytochrome c were optimized to conformers whose sulfur-sulfur distances were just suitable for binding to heme, whereas some tetrapeptides not found in cytochrome c were unable to be optimized to heme-binding conformers. Similarly, Cys-X1-X2-Cys tetrapeptides found in [4Fe4S]ferredoxin were optimized to [4Fe4S]-binding conformers, etc. The tetrapeptides found in the redox site of thioredoxin were optimized to conformers in which the two sulfur atoms were in van der Waals contact, so that a disulfide bond may be formed during the function. The conclusion has been drawn that the combination of X1 and X2 in a Cys-X1-X2-Cys sequence may be determining for that sequence to te a functional redox site in an electron carrier protein.

Relationship between gas chromatographic retention indexes and computer-calculated physical properties of four compound classes

The Austin Model (AM1) hamiltonian in MOPAC, a semi-empirical molecular orbital program, was used to calculate molecular polarizabilites, ionization potentials, and dipole moments for polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polychlorinated dibenzo-p-dioxins, and dibenzofurans. The relationship between these three physical properties and gas chromatographic retention behavior was inverstigated. Linear predictive equations were developped for four classes of compounds, using the physical properties as independent variables and GC retention indexes as dependent variables.

The symmetry group of labile intramolecularly hydrogen-bonded naphthazarin

After discussing the changes in the geometry of the molecule naphthazarin ( I) caused by the labile hydrogen atoms of the two planar intramolecularly bonded hydroxyl groups, the molecular symmetry group of the molecule is deduced as C s( M); this allows the interpretation of the IR and Raman spectra of the compound. The potential opposing the concomitant interchange of two hydrogen atoms is calculated by means of the MINDO/3 semiempirical molecular orbital program. The resulting energy values are fitted to a Morse potential and the energy levels are calculated. There is a possibility of quantum mechanical tunnelling.

A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties

With the aid of molecular modeling, both adenosine and adenosine A1 receptor antagonists belonging to various chemical classes were compared with respect to their minimum-energy conformations and molecular electrostatic potentials, as computed by the semiempirical molecular orbital program MOPAC. Distinct steric and electrostatic similarities between adenosine and the prototypic adenosine antagonist theophylline are evident when both compounds are superimposed, with theophylline in a so-called flipped orientation. Similar patterns were found for all other A1 antagonists investigated in this study. A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties contributing to potency, is proposed.

Semiempirical molecular orbital techniques applied to silicon dioxide: MINDO/3

We present a discussion of MINDO/3, a semiempirical molecular orbital program, which we have applied to clusters of atoms used to represent silicon dioxide. We have obtained MINDO/3 parameters for the Si-O interaction and have calculated a variety of observables for both molecules and solid-state clusters, for both open- and closed-shell systems. With some exceptions, we find very good agreement with other calculations and with experiment. In particular, our results for both E′ 1 and E′ 4 defects support existing models which feature asymmetric atomic relaxations.

Theory of the peroxy-radical defect ina-SiO2

We have investigated the peroxy-radical defect in glassy Si${\mathrm{O}}_{2}$ by means of MOPN, a semiempirical molecular-orbital program, applied to a cluster of atoms chosen to simulate the defect. Our calculations are consistent with important features of Griscom's model of the defect as a perturbed ${\mathrm{O}}_{2}^{\ensuremath{-}}$ ion substituted for a single-bridging ${\mathrm{O}}^{2\ensuremath{-}}$ ion in Si${\mathrm{O}}_{2}$ and attached to a single silicon, and they place geometrical constraints on the defect structure for this model to be valid. We predict the existence of a related defect (the small peroxy radical, or SPR) wherein the peroxy radical is strongly bonded to two silicons. We have also investigated the formation of the peroxy radical. Griscom and co-workers envision peroxy linkages substituting for single-bridging oxygens during the growth process. They suggest that upon annealing these linkages readily give up an electron to form the observed radical. Our calculations lead us to argue against this process; rather, capture of a free hole seems more likely. We suggest that the SPR could form via a process in which neutral oxygen molecules diffuse through the solid and combine with ${E}_{1}^{\ensuremath{'}}$ centers to form peroxy radicals.