Semi-empirical Quantum Mechanical Calculations Research Articles

Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations

We have implemented a parallel divide-and-conquer method for semiempirical quantum mechanical calculations. The standard message passing library, the message passing interface (MPI), was used. In this parallel version, the memory needed to store the Fock and density matrix elements is distributed among the processors. This memory distribution solves the problem of demanding requirement of memory for very large molecules. While the parallel calculation for construction of matrix elements is straightforward, the parallel calculation of Fock matrix diagonalization is achieved via the divide-and-conquer method. Geometry optimization is also implemented with parallel gradient calculations. The code has been tested on a Cray T3E parallel computer, and impressive speedup of calculations has been achieved. Our results indicate that the divide-and-conquer method is efficient for parallel implementation. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1101–1109, 1998

Exciton Interactions and Femtosecond Relaxation in Chlorophyll a−Water and Chlorophyll a−Dioxane Aggregates

Chlorophyll a (Chl a) in hydrocarbon solution with a small amount of dioxane or water shows red-shifted absorption bands at 686 nm and at 700 nm (dioxane) and at 745 nm (water), indicative of self-organized aggregate structures in solution. To study the relationship between the structure and spectral properties of the aggregates, several one-dimensional model structures of Chl a−dioxane and Chl a−water aggregates were computed by the molecular mechanics method. Three overall structures ranging from stick to a ring shape were energetically favored for the dioxane system. All these structures contain structural heterogeneity that consists of repeating dimers that further form tetramer substructures. For the Chl a−water system a one-dimensional homogenous helical structure was obtained. By using the model structures, the transition energies and fluorescence excitation polarizations were computed. Exciton theory with dipole−dipole interaction approximation and semiempirical quantum mechanical CI calculations ...

Excited-state intramolecular proton transfer in 2-(2′-aminophenyl) benzimidazole

An excited-state intramolecular proton transfer process has been studied in 2-(2′-aminophenyl)benzimidazole (2-APBI) in different solvents using steady state and time resolved fluorescence spectroscopy. Semi-empirical quantum mechanical calculations (AM1 and CNDO/S-CI) have also been carried out. Dual fluorescence (normal and tautomer fluorescence) is observed in non-polar solvents. Based on the fluorescence excitation spectra recorded at different wavelengths, it is concluded that the normal fluorescence originates from rotamer II or IV and tautomer fluorescence from rotamer V. The tautomer fluorescence intensity decreases with increase in the polarity and hydrogen bonding capacity of the solvents. Different fluorescence lifetimes of the normal and tautomer bands indicate that rotamer I and II are not in equilibrium in the excited state. Semi-empirical quantum mechanical calculations have shown that the rotamer II is slightly more stable than the rotamer I in the ground state whereas in polar solvents, the stability of rotamer II increases due to extra solvation. For isolated molecule the activation energy for the interconversion of rotamers is 2.71 kJ mol −1 in the ground state, whereas it is 36 kJ mol −1 in the first excited singlet state.

Vibrational spectra and thin solid films of a bi(propylperylenediimide)

The synthesis, the fabrication of thin solid films and the optical spectra of a member of a new series of bis-perylene materials—the bi(propylperylenediimide),N′,N′″-dipropyl-N,N″-bi[perylene-3,4:9,10-bis(dicarboximide)] (Pr2)—are reported. The objective of the present research effort is to provide the fundamental spectroscopic characterization of the ground electronic state and the methods for the fabrication of submicron thin solid films of these new materials which are being tested for performing elementary electrical functions of electronic devices. Pr2 is a high molecular weight perylene dye and the molecular organization formed in vacuum evaporated nanometric films is one of the key elements determining the electrical and optical properties of thin solid films. The spectroscopic techniques used in the study of fundamental vibrational modes were transmission and reflection–absorption infrared spectroscopy (RAIRS). The inelastic scattering was investigated using out-of-resonance excitation (FT-Raman), resonance Raman scattering (RRS) and surface-enhanced resonance Raman scattering (SERRS) on silver island films. The vibrational assignment of characteristic wavenumbers was assisted with semi-empirical quantum mechanical calculations.

Rotation about the N2–N3 bond in 3,3-dimethyl-1-(isoxazol-3-yl)triazenes

The rotational barrier around the N2–N3 bond of a series of 3,3-dimethyl-1-(isoxazol-3-yl)triazenes was evaluated by means of NMR line shape analysis. The results obtained were compared to 15N chemical shift measurements and semi-empirical quantum mechanical calculations. An increase of N2–N3 bond order, possibly due to an electron withdrawing effect of the isoxazole ring, was noted in our compounds.

Ground and excited state prototropic reactions in 2-(2′-methoxyphenyl)-3H -imidazo[4,5-b]pyridine †

The absorption, fluorescence and fluorescence excitation spectra of 2-(2′-methoxyphenyl)-3H-imidazo[4,5-b]pyridine (2-MPIP) have been studied in five different solvents and at different acid–base concentrations. Semi-empirical quantum mechanical calculations have been carried out to supplement the experimental results. Spectral characteristics of 2-MPIP in different solvents and semi-empirical quantum mechanical calculations suggest the presence of both a-1 and b-1 isomers. The observation of a single exponential decay and one lifetime suggests an equilibrium between the isomers. Out of five monocations two kinds of monocations (MC’s) are possible, one from protonation of N1 (MC1) and the second from protonation of N4 (MC2) atoms. Spectral characteristics and semi-empirical calculations carried out on MC’s neglect the presence of isomer b-1. Only one kind of dication and one kind of monoanion are formed by protonating both the nitrogen atoms (N1 and N4) and deprotonating the >NH atom respectively. pKa and pKa* values for the various prototropic reactions are determined and discussed.

Solvatochromic effects in the absorption and fluorescence spectra of indazole and its amino derivatives

Absorption and fluorescence spectra of Indazole (In) in five solvents and those of 5-amino, 6-amino, and 7-aminoindazoles (5-AI 6-AI, 7-Al) in thirteen solvents have been studied. Using the multiparametric approach of Taft et al., spectral characteristics of these molecules have been analysed on the basis of electrostatic effects, hydrogen bond donor ability and hydrogen bond accepting ability of the solvents. In the excited singlet state, all three effects are nearly equally prominent, whereas in the ground state 5-AI acts as a better hydrogen bond acceptor than the other amines. Stokes shifts and the difference between the radiative decay constants determined experimentally and using Strickler and Berg's equation indicate different geometries of the amines in the S 0 and S 1 states. A decrease in the non-radiative decay constants of 5-AI and 6-AI with an increase in the polarity of the solvents predict better planar geometry in the S 1 state in comparison to that in the S 0 state. Semi-empirical quantum mechanical calculations have been used to find the nature of transitions, total atomic charges at the basic centres and dipole moments of all the aromatic amines in the S 0 and S 1 states. Results so obtained are compared and discussed.

Electronic properties of poly(1,4-phenylene methylidynenitrilo-1,4-phenylene nitrilomethylidyne) (PPI)

Poly(1,4-phenylene methylidynenitrilo-1,4-phenylene nitrilomethylidyne) (PPI) was prepared and investigated using UV spectroscopy and tunneling current measurements at metal/PPI interfaces. The difference between the LUMO and HOMO level energies of PPI is determined as well as its electron affinity. The measured shift of the LUMO level of PPI relative to unsubstituted poly( p-phenylene vinylene) (PPV) agrees with semi-empirical quantum mechanical calculations performed on the dimer using the CNDO/S method which predicts a stabilization of both LUMO and HOMO levels with respect to unsubstituted PPV.

AM1 Study of the Ground and Excited State Potential Energy Surfaces of Symmetric Carbocyanines

Ground (S0) and first excited singlet state (S1) potential energy surfaces were calculated for a series of six symmetric carbocyanines as a function of the twisting angle (θ), around a carbon−carbon bond of the polymethine chain. The surfaces were computed using AM1 semiempirical quantum mechanical calculations. Rotations around different bonds were considered in order to determine the relevant rotation for isomerization, that is, the rotation with the lowest activation energy for the isolated molecule (E0). For that rotation, the computed values of E0 are in good agreement with values extrapolated from experiments in solutions of n-primary alcohols. The same holds for the computed transition energies between both surfaces for the thermodynamically stable N isomer (θ = 0°) and the P photoisomer (θ = 180°). The effects of chain length and pattern substitution of the indoline moiety on E0 were also analyzed for both surfaces. The shape of the potential surfaces referred as the Rullière's model holds in all cases for at least one rotational coordinate. The electrical dipole moment with respect to the center of electrical charges was calculated as a function of θ. The calculations show that the dipole moment remains almost constant except in the vicinity of θ = 90°, where a sudden increase with a sharp peak was obtained in both surfaces. This gives a simple explanation for the well-known experimental observation that the activation energy on the excited state surface is independent of solvent polarity, as the angle of the transition state is smaller than 90°. On the other hand, the transition state is at θ = 90° on the ground state, and a polarity influence is predicted. An improvement in the description of the experimental isomerization rate constants in S0 is obtained for the two smallest carbocyanines considered when polarity contributions are included.

Regiospecificity of Peroxyl Radical Addition to (E)-Retinoic Acid

The regiochemistry of peroxyl radical addition to (E)-retinoic acid (RA) was investigated. Peroxyl radicals, generated by reaction of 13-hydroperoxy-(9Z,11E)-octadecadienoic acid with hydroxo(porphyrinato)iron(III) in Tween 20 micelles, were reacted with RA. The major, and virtually exclusive, RA oxidation product was 5,6-epoxy-RA which was identified on the basis of cochromatography with the synthetic synthetic oxirane (in a reverse phase HPLC system), electronic absorption spectroscopy, high-field 1H-NMR, and EI mass spectrometry. These results suggest that peroxyl radicals react with RA by regioselective addition to either C5 or C6 yielding an endocyclic tertiary allylic or tertiary carbon-centered radical adduct, respectively. Subsequent beta-elimination of an alkoxyl radical yields the oxirane. Computational studies were carried out in order to gain mechanistic insights into the observed regiospecificity of the peroxyl radical-dependent epoxidation reaction; molecular mechanics and semiempirical quantum mechanical calculations were carried out using Tripos force field parameters and AM1, respectively. The results suggest that the regiospecific epoxidation may be influenced by the 5,6-olefinic function behaving as a partially-isolated double bond as well as inherent allylic A1,2 strain in the substituted cyclohexene ring as a consequence of substitutions at C1 and C6. In addition, calculated heats of formation indicated preferential peroxyl radical addition to C5 versus C6; this may reflect differences in the geometries of sp2-orbitals containing the radical densities rather than resonance contributions by the highly conjugated polyene system.

EFFECT OF CHALCOGEN SUBSTITUENTS (X=Se, S, O) ON MOLECULAR PROPERTIES OF 5-p-CHLOROBENZYLIDENE-3-METHYL-2-X-HYDANTOIN: X-RAY, PM-3 AND DATABASE STUDY

The X-ray structure analysis of a single crystal of 5-p-chlorobenzylidene-3-metyl-2-Se-hydantoin was carried out. It revealed that the molecule is a 2 isomer with approximately planar conformation, the angle between the hydantoin and p-chlorophenyl planes being 4.2(1)°. The molecules form dimers linked by weak hydrogen bonds N-H···, Se and C-H··· Se about an inversion center. Semiempirical quantum mechanics calculations (PM-3) were performed for the three molecules of 5-p-chlorobenzylidene-3-methyl-2-X-hydantoin, where X=Se, S, O. Their results suggest that the planar conformation of these molecules is less energetically favourable than that with the planar molecular fragments significantly tilted to each other. Thus, the planar conformation which was found for many benzylidene derivatives in the crystalline state using Cambridge Structural Database System may be stabilized by intermolecular interactions. The net atomic charges and the bond lengths in the hydantoin ring are strongly affected by the X substituents. The electronegativity of X and the charge distribution in the hydantoin ring seem to be the most important factors in determining the anticonvulsant activity in the three compounds.

Calculations of Spectroscopic Properties of the LH2 Bacteriochlorophyll−Protein Antenna Complex from Rhodopseudomonas acidophila

Absorption and CD spectra of a photosynthetic bacterial antenna complex are calculated on the basis of the crystal structure of the LH2 (B800-850) complex from Rhodopseudomonas acidophila. This complex contains a ring of 18 tightly coupled bacteriochlorophylls (B850) and a ring of 9 more weakly coupled bacteriochlorophylls (B800). Molecular orbitals for bacteriochlorophylls with the three different geometries seen in the crystal structure are obtained by semiempirical quantum mechanical calculations (QCFF/PI). Exciton and charge-transfer interactions are introduced at the level of configuration interactions. Particular attention is paid to the dependence of these interactions on the interatomic distances and on dielectric screening. Absorption band shapes are treated with the aid of vibronic parameters and homogeneous line widths that have been measured by hole burning (Reddy, N. R. S., et al., Photochem. Photobiol. 1993, 57, 35−39). Inhomogeneous broadening due to diagonal disorder in the monomeric and charge-transfer transition energies is included by a Monte Carlo method. The calculations successfully reproduce the main features of measured absorption and CD spectra of the complex. The results support the view that the excited states of the B850 bacteriochlorophylls are extensively delocalized over the ring of pigments while the excited states of the B800 bacteriochlorophylls are much more localized.

Interest of cluster significance analysis in structure-affinity relationships for non-xanthine heterocyclic antagonists of adenosine

In order to define some predictive rules for the discrimination of adenosine antagonists by their A 1 -receptor affinity, we performed a systematic QSAR analysis. As no significant descriptors of affinity were found, we then proposed to introduce a calculated enthalpy or entropy change for the interaction as a first approximation of the affinity descriptors. Since the structural details of the common receptor binding site remain to be determined, we utilized an indirect strategy involving the simulation of amino acid residues that are thought to interact with the ligand. Estimating enthalpic and entropic components by means of a semi-empirical quantum mechanical AM1 force calculation, we found a significant clustering of enthalpy change values. This method provides a good descriptor of interaction and also a simple tool for testing hypotheses on the nature of putative binding sites.

Photophysical properties of stilbenes with imide groups

Imide model compounds synthesized from 2,5-dimethoxy-4′-aminostilbene and different anhydrides, such as hexafluoroisopropylidene-2,2′-bis(phthalic anhydride), pyromellitic anhydride, 3,3′,4,4′-benzophenone tetracarboxylic dianhydride and phthalic anhydride, were photochemically characterized by UV absorption spectroscopy and stationary and time-resolved fluorescence spectroscopy. The fluorescence measurements in solution showed the dominance of non-radiative processes at room temperature. The fluorescence decay curves were multiexponential, their course depending on the temperature and viscosity of the surroundings. Steady state fluorescence experiments were performed in various polymer matrices. The spectra obtained showed differences in the number of bands. The molecular structure and the alignment of the polymer influenced the emission behaviour of the imide model compounds. Furthermore, semiempirical quantum mechanical calculations indicated the dominance of a charge transfer for the HOMO-LUMO configuration from the stilbone skeleton to the imide subunit. Irradiation experiments in solution indicated the high photostability of all the compounds investigated.

Crysteine Proteases such as papain are not inhibited by substrate analogue peptidyl boronic acids

Peptidyl boronic acids that are close structural analogues of good substrates have been prepared and evaluated as potential transition state analogue inhibitors of the representative cysteine protease, papain. However, no inhibition could be detected at concentrations up to 10 mM. The reasons for the lack of inhibition were sought from molecular modeling. Molecular mechanics and semi-empirical quantum mechanics calculations indicated that the absence of inhibition was due to boronic acid—cysteine protease tetrahedral complexes being 0.79 kcal mol −1 less stable than their preceding noncovalent EI-complexes. In contrast, an analogous boronic acid-serine protease tetrahedral complex was calculated to be 2.74 kcal mol −1 more stable than its precursor Michaelis EI-complex. It thus appears that boronic acids are ineffective inhibitors of cysteine proteases due to the thermodynamic favoring of a weak EI-complex preceding tetrahedral intermediate formation, and that any oxyanion hole stabilization of the subsequent tetrahedral intermediate cannot overcome this energy handicap.

Structural investigation of four-centre photopolymerisation of bis-phthalamic bis-chalcone derivative in the crystalline state

By combining the results obtained from an electron diffraction tilting series with solid state NMR and powder X-ray diffraction, it was possible to determine the unit cell parameters and space group of BPABC crystals grown from DMAA solution both before and after irradiation. Subsequently semi-empirical quantum mechanical and packing energy calculations led to a model structure which agreed well with all the electron diffraction data and thus provided insight into the cross-linking mechanism. © 1997 John Wiley & Sons Ltd.

Structural and theoretical analysis of some mesogenic azines containing strong electron donor–acceptor groups

A structural and theoretical analysis of some mesogenic bis(phenylene)azines containing a methyl group on the azine system and strong electron donor–acceptor groups on the phenylene rings is reported. Starting from the X-ray molecular structures and with the support of semiempirical quantum mechanical calculations, the structural and conformational properties of the azines are analysed and compared with recent literature data on similar acetophenone azines. Some geometrical and electronic data of the molecules are also calculated and discussed in the paper, which may be useful for a better understanding of the mesophasic behaviour of the compounds.

Electrochemical reduction and oxidation of some photochromic compounds

The electrochemical oxidation and reduction of 11 spiro compounds have been investigated in ACN and DMF. The reversible voltammograms were obtained only for nitro and Cl substituted spiro compounds for reduction and oxidation, respectively. Oxidation potentials are more sensitive to the structural differences and the type of substituent than reduction potentials. The reduction potentials were in the range of − 1.22 to − 1.28 V vs sce, which is in the range of reduction potentials expected for substituted nitro-benzenes. Semi-empirical quantum mechanical calculations carried out on MeO- and NO 2-substituted chloro spirobenzopyrans focus on the determination of the enthalpies of the samples and comparison with the oxidation potentials of the same samples.

Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

A method is developed to include solvation effects in linear-scaling semiempirical quantum calculations. Favorable scaling of computational effort for large molecules is achieved using a preconditioned conjugate gradient technique in conjunction with a linear-scaling recursive bisection method for evaluation of electrostatic interactions. The method requires approximately 30% computational overhead relative to gas-phase calculations. Effective atomic radii for biological macromolecules are derived from fitting to experimental and theoretical solvation energies for small molecules homologous to amino- and nucleic acid residues.

Effect of Internal Hydrogen Bonding onBase-Catalyzed NH Proton-Exchange Reactionsof Isomeric Enamines

Proton NMR spectra of the E and Z isomers of enamines 2–4, R′CH2NHC(CO2R) CHCO2R [2, R′ = C6H5, R = C(CH3)3; 3, R′ = 2-furyl, R = CH3; 4, R′ = 2-furyl, R = C(CH3)3], were obtained in neutral and basic solutions at 25°C. Base-catalyzed exchange of the E isomer was found to be faster than that for the Z isomer. These differences in exchange rate are discussed in terms of steric, electronic and hydrogen bonding effects. The results of AM1 semiempirical quantum-mechanical calculations on various geometries of 3 show that the NH proton is involved in simultaneous three-center hydrogen bonds.