MOPAC Software Research Articles

Calculations of the enthalpies of formation of oxygen-containing adamantane derivatives by quantum-chemical methods

The enthalpies of formation of oxygen-containing adamantane derivatives were calculated using the semiempirical quantum-chemical PM3, MINDO, AM1, and MNDO methods implemented in the MOPAC package. The calculated and experimental values were compared. The best correlation was obtained for AM1 calculations. This method was therefore used to calculate the enthalpies of formation of 20 oxygen-containing adamantane derivatives.

Spectral and electro-chemical characterization of transition metal complexes of a modified [N6] macrocycle. A mimic to cyclic hexapeptide

The 16-membered modified [N6] macrocylic ligand (L), a mimic to cyclic, hexapeptide is reacted with MCl2 and MCl3 resulting in complexes with stoichiometrices [MLCl2] (M = Cr, Mn, Co, Ni, Cu), [MLCl3] (M = Pt, Pd) and [MLCl2]Cl (M = Fe, Ru). Its reactions with the precursors [M(Ph3P)2Cl2] (M = Co, Ni, Pt, Pd) follow a ligand displacement path affording the final products which do not contain coordinated Ph3P. Complexes have been characterized from results of elemental analyses, conductometric, magnetic susceptibility, i.r. and u.v.–vis (ligand field) spectral studies. Magnetic susceptibility and ligand field spectral data are consistent with a hexacoordinate geometry for Cr2+, Mn2+, Fe3+, Co2+, Ni2+ and Cu2+ and four coordinate square-planar geometry for Pt2+ and Pd2+. Molecular orbital computations using CSChem ultra MOPAC software for an optimized minimum energy plot of the structure shows that the ligand binds metal ions as a tetradentate (N,N,N,N) chelating agent. Cyclic voltammetric studies indicate formation of stable reversible or quasi-reversible redox couples in solutions, which corroborates a kinetic stability of these complexes in their variable oxidation states.

Mixed implicit/explicit solvation models in quantum mechanical calculations of binding enthalpy for protein–ligand complexes

AbstractAn approach to quantum mechanical investigation of interactions in protein–ligand complexes has been developed that treats the solvation effect in a mixed scheme combining implicit and explicit solvent models. In this approach, the first solvation shell of the solvent around the solute is modeled with a limited number of hydrogen bonded explicit solvent molecules. The influence of the remaining bulk solvent is treated as a surrounding continuum in the conductor‐like screening model (COSMO). The enthalpy term of the binding free energy for the protein–ligand complexes was calculated using the semiempirical PM3 method implemented in the MOPAC package, applied to a trimmed model of the protein–ligand complex constructed with special rules. The dependence of the accuracy of binding enthalpy calculations on size of the trimmed model and number of optimized parameters was evaluated. Testing of the approach was performed for 12 complexes of different ligands with trypsin, thrombin, and ribonuclease with experimentally known binding enthalpies. The root‐mean‐square deviation (RMSD) of the calculated binding enthalpies from experimental data was found as ∼1 kcal/mol over a large range. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Syntheses, Spectroscopy and Calculated Second-Order Nonlinear Optical Properties of a New Series of Square-Pyramidal Substituted Phenylthiourea Zinc(II) Complexes

A new series of square-pyramidal coordination compounds L·Zn(acac)2 (acac = acetylacetonate; L is a variety of substituted phenylthioureas: p-N,N ′-dimethylaminophenylthiourea 1, p-methoxy-phenylthiourea 2, p-nitrophenylthiourea 3, p-acetylphenylthiourea 4) have been synthesized and characterized by 1H NMR and IR spectra and elemental analysis. Most of these compounds exhibit wide transparent ranges in the visible region. Their electronic spectra have been studied experimentally, and theoretically by ZINDO/S calculation. The MOPAC software package has been used to evaluate their first-order molecular hyperpolarizabilities (β). All β values of the four coordination compounds are greater than or equal to those of p-nitroaniline, and are larger than β values of their corresponding substituted phenthylthiourea ligands.

A new approach to suppress nonlinearity-transparency trade-off through coordination chemistry: syntheses and spectroscopic study on second-order nonlinear optical properties of a series of square-pyramidal zinc(II) complexes

Five new square-pyramidal coordination compounds L · Zn(acac) 2 ( 1– 5) (acac=acetylacetonate; L is a variety of thiosemicarbazones: p-dimethylaminobenzaldehyde thiosemicarbazone ( 1), p-hydroxy- o-methoxybenzaldehyde thiosemicarbazone ( 2), p-methoxybenzaldehyde thiosemicarbazone ( 3), p-hydroxybenzaldehyde thiosemicarbazone ( 4), o-hydroxybenzaldehyde thiosemicarbazone ( 5)) have been synthesized and characterized by 1H NMR, IR, and elemental analysis. All of these compounds exhibit pretty wide transparent ranges in the visible region. Their electronic absorption spectra have been studied experimentally, and theoretically by ZINDO/S calculation. The latter has also been utilized to estimate the extent of intramolecular charge transfer. The MOPAC software package has been used to evaluate their first-order molecular hyperpolarizabilities ( β). All β values of the five coordination compounds are larger than those of the corresponding thiosemicarbazones. And complex 1 shows the largest β 0 (39.1×10 −30 esu) in the series.

Synthesis, Crystal Structure, Spectroscopy and Calculated First-Order Molecular Hyperpolarizability of a New Square-pyramidal Complex Zn(DMABT)(acac) 2

A new square-pyramidal complex, Zn(DMABT)(acac) 2 (DMABT = p -dimethylaminobenzaldehyde thiosemicarbazone; acac = acetylacetonate), has been synthesized and characterized by IR, 1 H NMR, elemental analysis and X-ray crystal structure analysis. Crystal data: crystal system Monoclinic, space group P 2 1 / n , with M r = 485.89 (C 20 H 28 N 4 O 4 SZn), a = 8.208(3) Å, b = 10.982(5) Å, c = 26.647(9) Å, f = 90°, g = 93.67(3)°, n = 90°, V = 2396.8(15) Å 3 , Z = 4, D c = 1.347 g/cm 3 , F (000) = 1016, w = 1.143 mm m 1 , R 1 = 0.0444, wR 2 = 0.1182. Reflections collected are 4733, while unique reflections are 4636 with I S 2 σ ( I ). The complex structure contains a square-pyramid formed by four oxygen atoms and one sulfur atom around a zinc atom. The molecular shape is like a screw, in which two acetylacetonate groups form the head and the DMABT group forms the tail. The first-order molecular hyperpolarizabilities ( g ) of the complex and DMABT were calculated utilizing PM3 method through MOPAC software package in Chem 3D, the result of which shows that the g 0 value of the complex (30.6 2 10 m 30 esu) is higher than that of DMABT (21.5 2 10 m 30 esu). Electronic absorption spectroscopy was compared with ZINDO/S calculated result.

A QUANTUM CHEMISTRY GIAO MOLECULAR SITE APPROACH OF NMR CHEMICAL SHIFTS GENERALIZED TO THE WHOLE PERIODIC TABLE

An accurate and rapid quantum chemistry approach to predicting chemical shifts is applied to 15 N natural abundance NMR spectra of benzothiazoles. This method is of interest in the study of toxic contaminants of biological media. A GIAO approach is used to calculate the nuclear shielding tensor in a perturbational scheme. Similar methods had previously been used for both ab initio and semi-empirical calculations programmed in Gaussian and MOPAC respectively but atomic orbitals specific to molecular sites are shown to improve accuracy in the present work. Some molecular sites are defined in order to polarize the molecular orbitals in the presence of the solvent interactions. For convenience, the extensions are carried out in an independent NMR module designed to work with the MOPAC package and the present application is generalized to the third row elements for the first time. This new theoretical work is described. The application to 15 N chemical shifts for benzothiazoles led to results within 0.5 ppm of values measured in this work. Structural investigations were carried out using the Gaussian98 suite of programs at the DFT B3LYP level of calculation over an extended basis set. These studies show the single chemical shift for benzothiazoles could be the result of rapid tautomeric equilibria. Further investigations show that solvent interactions involving hydrogen bonds should also be taken into account.

Spectroscopy of a Eu(III)-imidazolate complex

We have performed semi-empirical calculations on a Eu(III)-imidazole complex. We use a Scaled Quantum Mechanical Force field approach from the MOPAC software. We obtain molecular force constants used in the normal mode calculation to modelize experimental Raman frequencies. Furthermore, we discuss the structure and the electronic properties of this complex by means of spectroscopic techniques such as photoluminescence and X-Ray Absorption Near-edge Spectroscopy (XANES).

13C]Dynamic NMR and Molecular Modeling of 2,4-Bis(N-Pyrrolidinyl)-6-chloro-s-triazine

The room temperature [13C]NMR spectrum of 2,4-bis(N-pyrrolidinyl)-6-chloro-s-triazine shows doubled signals for the pyrrolidine rings, which suggests restricted rotation about the Ar-C—N bond. The rotational barrier around this bond was determined by [13C]dynamic NMR (DNMR) spectra run at different increasing temperatures and also by the PM3 Hamiltonian contained in the MOPAC package. The values thus obtained, 16.6 and 13.6 kcal mol−1, respectively, are in good agreement.

Polarizability and hyperpolarizability of push–pull quinoid molecules Simulation of donor–acceptor pairs

AM1 calculations are performed to study the non-linear optical (NLO) properties of push–pull quinones. The variations of molecular structure, linear (α) and NLO polarizabilities (β, γ) for a set of push–pull quinones are discussed in terms of quinoid–benzenoid character (QBC), and the strength of donor–acceptor pairs (δDA). The parameter δDA, already used for the polyenebridge, is still valid in rationalizing the donor–acceptor strength for quinoid derivatives. In addition, we examined how an external electric field created by ‘Sparkles’ in the MOPAC package drives a quinoid molecule from the quinoid limit to the benzenoid limit, and how it affects the NLO properties. The results show that the effect produced by Sparkles is qualitatively similar to that of donor–acceptor pairs.

Future ESR and optical dating of outer planet ICY materials

The possibility of future TL and ESR dating of icy materials in the outer planet world in our solar system is discussed. considering radiation effects by solar wind protons and cosmic rays as well as the long lifetime of radical species at extremely low ambient temperatures. A lightweight portable ESR and a gas combustion heating type TL using a photodetector are described for the in-situ observation, i.e. for the use on a landing craft with a -further suggestion to develop remote TL and OSL using laser beams. Both TL and ESR studies of ice (solid H 2O doped with H 2SO 3 were made to estimate the lifetimes of SO 3 − at the ambient temperature for comets from the Arrhenius plot of lifetimes. Molecular orbital calculation and g-factors of SO 3 − were made with MOPAC software. It is suggested that both ESR and optical dating of icy materials are useful for future dating in planetary science.

Cluster modeling of the neutral oxygen vacancy in pure silicon dioxide

The main results of the computer simulation of the oxygen vacancy in pure silicon dioxide are presented. The semi-empirical method, MNDO from the MOPAC package, is used. Silicon dioxide is simulated by molecular clusters of different sizes and structures. Calculated positions of the absorption and luminescence bands of the neutral oxygen vacancy are in satisfactory agreement with those of the oxygen-deficient center observed in pure silicon dioxide. The absorption and luminescence bands of the vacancy correspond to the dipole allowed one-electron transitions between two localized states with the levels in the energy gap of SiO 2. The lower level is doubly occupied; the upper one is empty, resulting from the bonding and antibonding combination of sp orbitals of two silicon atoms adjacent to the vacant site, respectively.

Physicochemical properties of dimethyl sulfoxide–methanol liquid mixtures. Experimental and semiempirical quantum chemical studies

The 1H NMR spectra of liquid binary mixtures of dimethyl sulfoxide (DMSO) and methanol (MeOH), were recorded at 298 K over almost the whole range of the mixed solvent compositions. From these data were found the values of the spectral parameter, Δδ(DMSO–MeOH). The densities (d12) and viscosities (η12) of the mixed solvent were measured at 298.15 K, as well as the relative permittivities (ε12) at 293.15, 298.15, 303.15 and 308.15 K. From all these data, the molar volumes (V12) and their deviations from ideality were calculated. Additionally, the temperature coefficients of relative permittivity, α12, were found. These structural parameters of functions of concentration suggest the formation of stable DMSO–MeOH and DMSO–2 MeOH type complexes. The semiempirical quantum chemical (MOPAC package) method was applied to optimize the geometry, energy and hydrogen-bond lengths of dimers and trimers formed by molecules of dimethyl sulfoxide and methanol, and these conclusions wholly support the conclusions drawn from the physicochemical studies.

Semi-empirical calculations of the nonlinear optical properties of polycyclic aromatic compounds

A systematic study of factors influencing nonlinear optical properties, in particular the second hyperpolarizability 〈γ〉, is conducted for a series of polycyclic aromatic hydrocarbons (PAHs). The HOMO-LUMO gap, polarizability 〈α〉, first hyperpolarizability 〈β〉, and second hyperpolarizability 〈γ〉 of polycyclic aromatic compounds are computed by using semi-empirical MNDO-FF calculation implemented in the MOPAC package. For linear polyacenes, the linear and nonlinear properties and total resonance energy are found to increase while the HOMO-LUMO gap and resonance energy per electron decrease as the number of six-membered rings increases. For nonlinear PAHs, the chain topology should be taken into account. An empirical formula is given to relate the computed 〈γ〉 and 〈α〉.

Asymmetric Synthesis of a Homochiral D2-Isoxazoline Amino Acid Derivative

(2R)-4-Methylene-2-phenyl-3-propionyloxazolidin-5-one underwent 1,3-dipolar cycloaddition with 2,6-dichlorobenzonitrile oxide to give (5S,7R)-3-(2,6-diphenyl)-7-phenyl-6-propionyl-2,6-diaza-1,8-dioxaspiro [4.4] non-2-en-9-one, a protected isoxazoline amino acid. The reaction proceeded regiospecifically and with high stereoselectivity. The anti addition product predominated. The regiochemistry of addition was determined by nmr and the stereochemistry of addition was determined by X-ray analysis. The transition state energies for syn and anti addition were calculated using the semi-empirical AM1 method in the MOPAC package

Semiempirical calculations of molecular polarizabilities and hyperpolarizabilities of polycyclic aromatic compounds

AbstractThe correlation of 2D conjugation and the nonlinear properties of a series of polycyclic aromatic compounds were studied by performing semiempirical calculations using the MOPAC package. For linear polyacenes, both linear and nonlinear properties are found to be increased as the number of six‐membered rings increases. In general, the polarizabilities, 〈α〉, and second hyperpolarizabilities, 〈γ〉, are found to correlate very well with total resonance energies. In the case of first hyperpolarizabilities, 〈β〉, symmetry is the dominating factor. © 1992 John Wiley & Sons, Inc.