Showing papers in "Journal of Molecular Structure-theochem in 2003"

QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

Abstract: We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP25047) which has sought to develop a flexible QM/MM scheme and to apply it to a range of industrial problems. A number of QM/MM approaches were implemented within the computational chemistry scripting system, ChemShell, which provides the framework for deploying a variety of independent program packages. This software was applied in several large-scale QM/MM studies which addressed the catalytic decomposition of N 2 O by Cu-containing zeolites, the methanol synthesis reaction catalysed by Cu clusters supported on ZnO surfaces, and the modelling of enzyme structure and reactivity.

Pitfalls in QSAR

Abstract: There are no formal guidelines for the development of quantitative structure–activity relationships (QSARs) However, there are a number of practices that should be avoided This paper describes the pitfalls in QSAR, and problems that can arise if they occur The emphasis of this paper is particularly for the development of QSARs for toxicity for environmental endpoints and drugs, but is equally applicable to pharmacological endpoints Problems may arise from all three areas of the QSAR, namely the biological activity, physico-chemical and/or structural descriptors, and the use of a statistical technique Biological data for use in a QSAR should be of a known (and preferably high) quality Physico-chemical descriptors and statistical processes should be appropriate for the endpoint being modelled They should allow for the development of a clear, transparent and mechanistically interpretable QSAR To have any practical utility, QSARs should be validated by means of an external testing set

Performance of the Vienna ab initio simulation package (VASP) in chemical applications

Abstract: Five different density functionals in combination with ultra-soft pseudopotentials and plane wave basis sets were used to optimize the geometries of common chemical systems using solid state program Vienna ab initio simulation package (VASP). These systems included diatomics, N2, O2, F2 and CO, and carbon based organic systems, ethane, ethylene, acetylene, 1,3-butadiene, 1,3,5-hexatriene, benzene, biphenyl, naphtalene graphene, polyethylene and all-trans-polyacetylene. The four functionals based on the generalized gradient approximation gave very good agreement on bond lengths and angles as compared with each other, with localized Gaussian basis set calculations and with experimental values. Reasonable results were also obtained for vibrational frequencies of selected normal modes of benzene and for torsional potentials of 1,3-butadiene and biphenyl. On the other hand, local density approximation tends to underestimate bond lengths. The performance of VASP for these properties is very similar to Gaussian type implementations of density functional theory explaining its successes in molecular, solid state, surface and polymer applications.

Quantitative structure–activity relationships (QSARs) in toxicology: a historical perspective

Abstract: The history of the use of quantitative structure–activity relationships (QSARs) in toxicology, both for environmental, and human health effects is described. A particular emphasis is made on the science in response to the United States Toxic Substance Control Act of 1976. Specifically, the basic concepts and objectives of QSARs for toxicity are reviewed. QSARs for environmental and human health effects are discussed separately. Environmental, and more specifically, ecotoxicity, QSARs have focused historically on modeling congeneric series and non-specific effects in aquatic organisms through the use of the logarithm of the 1-octanol/water partition coefficient to describe hydrophobicity, and hence uptake. Compounds that do not fit these QSARs (namely the outliers) have been explained by differences in mechanism of acute toxicity, especially as a result of electro(nucleo)philic interactions. In light of this, mechanisms of acute toxicity are discussed. QSAR approaches to receptor-mediated effects, such as those exhibited by environmental estrogens, and competitive binding to the estrogen receptor, are different from those typically applied to model acute toxic endpoints. Several of these approaches, including three-dimensional QSAR techniques, are reviewed. Human health effects include both local and systemic effects. Local effects (e.g. corrosivity and skin sensitization) are often modeled by multivariate QSAR methods such as linear regression and discriminant analysis. The prediction of systemic effects such as mutagenesis and carcinogenesis requires consideration of the endpoint and a more mechanistic basis for modeling. Approaches to predict these endpoints include the use of expert systems.

Structure and vibrational spectra of p-methylaniline: Hartree-Fock, MP2 and density functional theory studies

Abstract: The FT-IR and FT-Raman spectra of p-methylaniline (pMA) have been recorded. Optimized molecular structures and normal vibrations of pMA have been obtained from the HF, MP2 and DFT-B3LYP methods implementing the 6-31G* and 6-31G** basis sets. Scale factors, which bring computational frequencies in closer agreement with the experimental data, have been calculated for predominant vibrational motions of the normal modes at each level considered. All observed harmonic IR and Raman bands of pMA have been assigned in the frameworks of the calculations. The assignments have been compared each other and with the 30 benzene-like modes. The effects of the methyl and amino substituents on vibrational frequencies have been investigated. The applicability limits of HF, MP2 and DFT-B3LYP methods have been discussed. The DFT-B3LYP method has been found very promising for vibrational spectral analyses.

Artificial neural networks and genetic algorithms in QSAR

Abstract: Artificial neural networks are presented from the perspective of their potential use as modeling tools in quantitative structure–activity relationships (QSAR) research. First, general merits and drawbacks of the neural network modeling approach are discussed, and the relationship between neural networks, statistics and expert systems is clarified. A separate section is devoted exclusively to the subject of validating neural networks models. Next, the review focuses on presenting the most commonly used artificial neural networks in QSAR: backpropagation neural networks, probabilistic neural networks, Bayesian regularized neural networks, and Kohonen SOM. For each of them, both merits and shortcomings are revealed, and references are made to publications presenting their QSAR applications. Another section is devoted to genetic algorithms, their merits and shortcomings, and their potential use for model variables dimensionality reduction in QSAR studies. The last section is devoted to software resources.

An approximate DFT method for QM/MM simulations of biological structures and processes

Abstract: In the last years, we have developed a computationally efficient approximation to density functional theory, the so called self-consistent charge density functional tight-binding scheme (SCC-DFTB). To extend its applicability to biomolecular structures, this method has been implemented into quantum mechanical/molecular mechanics (QM/MM) and linear scaling schemes and augmented with an empirical treatment of the dispersion forces. We review here applications of the SCC-DFTB QM/MM method to proton transfer (PT) reactions in enzymes like liver alcohol dehydrogenase and triosephosphate isomerase. The computational speed of SCC-DFTB allows not only to compute minimum energy pathways for the PT but also the potential of mean force. Further applications concern the dynamics of polypeptides in solution and of ligands in their biological environment. The developments reviewed allowed for the first time realistic QM simulations of polypeptides, a protein and a DNA dodecamer in the nanosecond time scale.

α-Amylases of medical and industrial importance

Abstract: α-Amylases (α-1,4-glucan-4-glucanohydrolases; EC 3.2.1.1) are classical calcium-containing enzymes, which constitute a family of endo -amylases catalysing the cleavage of α- d -(1-4) glycosidic bonds in starch and related carbohydrates with retention of the α-anomeric configuration in the products. They can be found in microorganisms, plants and higher organisms where they play a dominant role in carbohydrate metabolism. This study characterizes the substrate binding sites of Bacillus licheniformis α-amylase (BLA), human salivary α-amylase (HSA) and its Y151M mutant. It describes the first subsite maps, namely, number of subsites, position of cleavage sites and apparent subsite energies. The product pattern and cleavage frequencies were determined by HPLC, utilising a homologous series of chromophore-substituted maltooligosaccharides of degree of polymerisation (DP) 3–10 as model substrates. 2-Chloro-4-nitrophenyl (CNP) and 4,6- O -benzylidene-modified 4-nitrophenyl (Bnl-NP) β-maltooligosaccharides (DP 4–8) were synthesised from cyclodextrins using a chemical procedure. For the preparation of CNP-maltooligosides of longer chain length a new chemoenzymatic procedure was developed using rabbit skeletal muscle glycogen phosphorylase b. Our results confirmed the presence of eight binding sites in BLA, five glycone sites (−5,−4,−3,−2,−1), three aglycone sites (+1,+2,+3) and the catalytic site is located between subsites (−1 and +1). In addition, the subsite map revealed a barrier site at the reducing end of active site which repulses the glucose residue. The binding region of HSA is composed of four glycone and three aglycone-binding sites, while that of Tyr151Met mutant is composed of four glycone and two aglycone-binding sites. The subsite maps show that Y151M has strikingly decreased binding energy at subsite (+2), where the mutation has occurred (−2.6 kJ/mol), compared to the binding energy at subsite (+2) of HSA (−12.0 kJ/mol).

Theoretical and experimental studies of the vibrational spectra of m-methylaniline

Abstract: The FT-IR and FT-Raman spectra of m-methylaniline (mMA) have been recorded. Optimized molecular structures and normal vibrations of mMA have been obtained from the ab initio-HF and the DFT-B3LYP levels. The 6-31G* basis set has been used for each level of calculations. Correction factors, which bring computational frequencies in closer agreement with the experimental data, have been calculated for predominant vibrational motions of the normal modes at each level of theory. All IR and Raman bands of mMA have been assigned in the frameworks of the calculations. The assignments have been compared each other and with the 30 benzene-like modes. The DFT-B3LYP/6-31G* calculations have been found more reliable than the ab initio-MP2/6-31G* calculations for the vibrational study of mMA.

Nonlinear optical (NLO) properties of novel organometallic complexes: high accuracy density functional theory (DFT) calculations

Abstract: Density Functional Theory (DFT) calculations are performed to determine the accurate first static hyperpolarizability ( β ) of nitrogen bound low valent (M 0 ) group six metal carbonyls representing the class of chromophores displaying weak coupling between donor and acceptor. The nonlinear optical (NLO) response of this class of second-order NLO metal complexes is dominated by metal-to-ligand charge transfer excitations involving low lying, filled metal-carbonyl based orbitals and empty π ∗ orbitals of nitrogen bound ligand. We report novel organometallic systems with high β values. The full geometry optimizations of chromium and tungsten carbonyls were performed using DFT method at B3LYP/LanL2DZ level of theory using gaussian 98W. The calculations of the first hyperpolarizability ( β ) of these complexes were performed at the same level of theory. The calculated values of β were compared with available data in the literature. To understand the variation of β in these complexes, we examined the molecular HOMO and molecular LUMO generated via gaussian 98W. The present study concludes that these organometallic systems may contribute to the development of NLO materials.

QSPR models of boiling point, octanol–water partition coefficient and retention time index of polycyclic aromatic hydrocarbons

Abstract: A Quantitative Structure–Property Relationship (QSPR) analysis and study of polycyclic aromatic hydrocarbons (PAHs) is presented. Three physicochemical properties related to their environmental impact are studied: boiling point (bp), octanol–water partition coefficient ( log K ow ) and retention time index (RI) for reversed-phase liquid chromatography analysis. The geometry of all PAHs were optimized by the semi-empirical method AM1 and used to calculate thermodynamic, electronic, steric and topological descriptors: HOMO and LUMO energies and the GAP between them, molecular hardness, polarizability, atomic charges, connectivity index, volume and surface area among others. After variable selection, principal component regression (PCR) and partial least squares (PLS) with leave-one-out crossvalidation were used for building the regression models. The regression coefficients obtained for the models were 0.995 (PCR and PLS) for bp, 0.975 (PCR) and 0.976 (PLS) for log K ow , and 0.898 (PCR and PLS) for RI. Finally, the models were used to predict these properties for those compounds for which experimental measurements are still unknown.

Correlation between the molecular structure and the corrosion inhibition efficiency of chestnut tannin in acidic solutions

Abstract: The frontier orbital theory and the inhibitor adsorption theory were applied to the results of the quantum calculations and corrosion rate measurements, respectively, in order to elucidate the chestnut tannin inhibitory action on low-carbon steel corrosion in 2 M HCl. Nine major constituents of chestnut tannin—vescalagin, castalagin, vescalin, castalin, gallic acid, ellagic acid, mono-, di- and trigalloylglucose—were modeled by molecular mechanics, molecular dynamics and semiempirical quantum NDDO method with PM3 parametrization. The geometrical structure, the energy of the highest occupied (HOMO) and lowest unoccupied molecular orbital (LUMO), the HOMO–LUMO energy gap, the distribution of the HOMO electron density and the magnitude and direction of the dipole moment were calculated for each molecule. Molecular reactivity that is related to its adsorbability by the HSAB principle, was studied by calculating the absolute electronegativity, absolute hardness and the electron donating ability. The quantum calculations results, coupled with those derived from the adsorption theory, gave a consistent picture of the investigated corrosion system.

The present status of QSAR in toxicology

Abstract: The current status of the use of Quantitative Structure–Activity Relationships (QSARs) in toxicology, both environmental (i.e. ecotoxicology) and human health effects, are described with a particular emphasis on the science since 1995. Discussions of ecotoxicity QSARs focus on recent information that relates to separation of effects based on modes of toxic action. Particular attention is given to the response-surface approach to modeling toxic potency of baseline and non-specific soft electrophiles (i.e. the majority of industrial organic chemicals) and the development of rules-based expert systems to aid in the selection of the most appropriate QSAR. In addition the more recent application self-organizing dynamical algorithms such as artificial neural networks to ecotoxicity data is described. Recent QSAR modeling of estrogenicity, an example of receptor-mediated effects, are described with particular emphasis on 2D structural alerts as screening tools and QSARs developed with data for the recombinant yeast assay. In addition the current status of modeling human health effects include mutagenesis and carcinogenesis, developmental toxicity, skin sensitization, and skin and eye irritation is described.

The use of discriminant analysis, logistic regression and classification tree analysis in the development of classification models for human health effects

Abstract: This paper describes the statistical techniques of discriminant analysis, logistic regression and classification tree (CT) analysis, which can be used to develop classification models (CMs) for predicting the membership of chemicals into two or more pre-defined groups, such as toxicological categories. One difference between the three methods is that discriminant analysis and logistic regression make a number of assumptions about the underlying data, whereas CT analysis is a non-parametric technique. Another difference is that discriminant analysis and logistic regression can be used to derive probabilities of group membership for individual chemicals, whereas CT analysis only produces average probabilities for the different groups. The application of the three techniques is illustrated by comparing the CMs obtained by applying them to an eye irritation data set.

The sequential Monte Carlo-quantum mechanics methodology. Application to the solvent effects in the Stokes shift of acetone in water

Abstract: The sequential Monte Carlo quantum mechanics methodology is used to obtain the solvent effects on the Stokes shift of acetone in water. One of the great advantages of this methodology is that all the important statistical information is known before running into the costly quantum mechanical calculations. This advantage is discussed not only with respect to the statistical correlation between the different structures generated by the simulation but also in the proper identification of hydrogen bonds in liquids. To obtain the solvent effects in the Stokes shift of the n–π ∗ absorption transition of acetone in water, quantum-mechanical calculations are performed in super-molecular structures generated by NVT Monte Carlo simulation. The statistical correlation between configurations is analyzed using the auto-correlation function of the energy. The largest calculations include one acetone and 170 water molecules. One-hundred INDO/CIS super-molecular calculations are performed for each solvation shell to obtain the statistical average value. The calculated solvatochromic shift of the n–π ∗ absorption transition of acetone in water, compared to gas phase, is ∼1310 cm −1 in good agreement with the experimental blue shift of 1500±200 cm −1 . For the emission of the relaxed excited state, the calculated shift is ∼1850 cm −1 . The total calculated solvent effect on the Stokes shift of acetone in aqueous solution is thus 540 cm −1 . A detailed analysis of the sampling of the configurations obtained in the Monte Carlo simulation is made and it is shown that all results represent statistically converged values.

Quantum chemical studies on the inhibition efficiencies of some piperazine derivatives for the corrosion of steel in acidic medium

Abstract: Computational calculations on some piperazine derivatives those behave as corrosion inhibitor for steel in presence of KI in sulphuric acid of different normality in gas and aqueous phases using semi-empirical methods (i.e. MINDO/3, MNDO, PM3 and AM1) were carried out to search possible correlation between corrosion rates and geometric structures, charges on nitrogen atoms, highest occupied molecular energy level ( E HOMO ), lowest unoccupied molecular energy level ( E LUMO ), the differences between highest occupied molecular orbital energies and lowest unoccupied molecular orbital energies ( E HOMO − E LUMO ) were carried out. The obtained correlations were satisfactory.

The functional benefits of protein disorder

Abstract: Intrinsically unstructured proteins, which exist and function without a well-defined folded structure, constitute a newly recognized class of the protein world. Such proteins are common in living organisms and occupy a unique niche in which function is intimately linked with structural disorder. In this paper it is shown that these proteins assume no compact structural state in vivo, despite a significant macromolecular crowding effect that could force them fold under cellular conditions. Further, it is argued that they are not fully unstructured, but contain functionally indispensable residual structure. Their recently suggested functional classification is delineated and extended through novel examples. Finally, the functional benefits of structural disorder encompassing some newly recognized features, such as direct proteasomal degradation and chaperone activity, will be thoroughly discussed. Through all these details, the message is conveyed that our understanding of protein function will not be complete as long as the functional benefits of protein disorder are not fully appreciated.

Electric multipole moment, dipole and quadrupole (hyper)polarizability derivatives for HF (X1Σ+)

Abstract: We report accurate values for the electric properties and property derivatives of hydrogen fluoride. Our approach is based on finite-field Moller–Plesset perturbation theory and coupled cluster calculations performed with large, carefully optimised basis sets of gaussian-type functions. All basis sets used in this study are of well-evidenced near-Hartree–Fock quality for all properties of interest. Our best values are obtained from CCSD(T) calculations (all electrons correlated) with a (16s11p8d4f/10s6p3d2f) basis set at the experimental bond length Re=1.7328a0: dipole, μ=0.7043ea0, quadrupole, Θ=1.71ea02, octopole, Ω=2.50ea 0 3 , and hexadecapole, Φ=4.83ea03, moment, mean α =5.60 and anisotropy, Δα=1.14e2a02Eh−1 of the dipole polarizability, mean first, β =−7.4e 3 a 0 3 E h −2 and second, γ =512e 4 a 0 4 E h −3 hyperpolarizability, mean quadrupole, C =10.61e 2 a 0 4 E h −1 polarizability. The R-dependence around Re is obtained for all properties. At the CCSD(T)/[9s6p5d4f/6s4p3d1f] level of theory (all electrons correlated) α and Δα vary around Re as α (R)/e 2 a 0 2 E h −1 =5.66+2.92(R−R e )+1.10(R−R e ) 2 +0.24(R−R e ) 3 −0.01(R−R e ) 4 Δ α(R)/e 2 a 0 2 E h −1 =1.12+4.30(R−R e )+2.97(R−R e ) 2 +0.78(R−R e ) 3 +0.07(R−R e ) 4 For the mean higher polarizabilities we report CCSD(T)/[9s6p5d4f/6s4p3d1f] (all electrons correlated) first derivatives, d β d R e =12.4e 3 a 0 2 E h −2 , d γ d R e =437e 4 a 0 3 E h −3 and d C d R e =8.02e 2 a 0 3 E h −1 . At the MP2/[9s6p5d4f/6s4p3d1f] level of theory, the dipole–quadrupole (Aα,βγ) polarizability varies around Re as: A z,zz (R)/e 2 a 0 3 E h −1 =4.33+10.83(R−R e )+8.69(R−R e ) 2 +2.99(R−R e ) 3 +0.19(R−R e ) 4 A x,zx (R)/e 2 a 0 3 E h −1 =1.32+2.27(R−R e )+1.30(R−R e ) 2 +0.27(R−R e ) 3 +0.07(R−R e ) 4

Ab initio calculations of pKa values of some organic acids in aqueous solution

Abstract: The acidity of different classes of organic compounds in aqueous solution has been calculated. The calculations are carried out at the SCF level with inclusion of entropic and thermochemical correction to yield free energies of dissociations. The polarized continuum model is used to describe the solvent. The model furnishes pKa values in relatively good agreement with experimental data. Scaling different parts of solvation energies provides a significant improvement in results and signifies the importance of balance of individual contributions from electrostatic, cavity, dispersion and repulsion interactions. q 2002 Elsevier Science B.V. All rights reserved.

Density functional calculations of the heats of formation for various aromatic nitro compounds

Abstract: Isodesmic reactions of 18 aromatic nitro compounds were selected in order to study their heats of formation at 298 K. Calculations were carried out by various density functional theories, together with different basis sets. The calculated heats of formation of 2-nitrotoluene, 3-nitrtoluene, 4-nitrotoluene, 2,4-dinitrotoluene, 2,5-dinitrotoluene, 2,6-dinitrotoluene, 2,4,6-trinitrotoluene, 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 2,4-dinitrophenol, 2,6-dinitrophenol, 2,4,6-trinitrophenol, 2-nitroaniline, 3-nitroaniline, 4-nitroaniline, 2,4-dinitroaniline, and 2,6-dinitroaniline were averaged to be 8.61, 5.26, 4.89, 5.58, 5.84, 10.52, 10.32, −29.77, −24.67, −25.98, −29.16, −21.73, −18.32, 15.12, 18.17, 15.85, 14.04, and 14.60 kcal/mol, respectively. These values are very close to the experimental or multivariable linear regression results.

Analysis of weakly bound structures: Hydrogen bond and the electron density in a water dimer

Abstract: The formation of the hydrogen bond is investigated in terms of the charge density. The water dimer is chosen as an example, and the redistribution of the electrons due to the H-bond is discussed. The density difference between interacting and non-interacting monomers is partitioned using localized orbitals and localized partial densities. Although the change in the electronic density is not completely described by the deformation of the two localized orbitals, OH bond and the appropriate lone pair orbital, the binding region is already well characterized with these local densities.

Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding

Abstract: The extremely localized molecular orbitals (ELMOs) are a set of molecular orbitals strictly localized only on a few atoms of a molecule They are obtained in an a priori fashion through the direct application of the variation principle Even if the theoretical aspects of their determination have been discussed already in the literature, stable and fast algorithms to obtain ELMOs are still not trivial and a comparison between different methods is reported We furthermore investigate the applicability of ELMOs to quantum mechanics/molecular mechanics (QM/MM) methods which employ frozen localized orbitals to represent covalent bonds across the QM and the MM region In addition it is shown that ELMOs can be used to describe species with intramolecular hydrogen bonds, where a correct elimination of the intramolecular basis set superposition error can be essential to perform accurate conformational studies

Ground and excited state dipole moments of exalite 404 and exalite 417 UV laser dyes determined from solvatochromic shifts of absorption and fluorescence spectra

Abstract: The ground state ( μ g ) and the excited state ( μ e ) dipole moments of two exalite dyes were studied at room temperature in various solvents. The dipole moments ( μ g and μ e ) were estimated from solvatochromic shifts of absorption and fluorescence spectra as function of the dielectric constant ( e ) and refractive index ( n ). The results show that excited state dipole moments of exalite 404 and exalite 417 dyes (radii a =4.968 and 5.902 A) are 2.419 and 3.977 D, respectively; and the change in the dipole moments were found to be 1.243 and 2.106 D. It was observed that the dipole moments of excited state were higher than those of ground state for both the dyes.

DFT and AIM studies on two-ring resonance assisted hydrogen bonds

Abstract: DFT calculations on molecules with intramolecular hydrogen bonds have been performed at B3LYP/6-311++G(d,p) level of theory. The investigated 2,4-dihydroxybut-2-ene-4-dial molecule and its derivatives contain two intramolecular H-bonded rings. Each ring is the resonance-assisted system. The results of calculations show that two rings within the same molecule do not cause an increase of the resonance effect. It is shown that the topological parameters such as features of bond critical points and ring critical points may be treated as measures of H-bond strength.

Global modeling of narcotic chemicals: ciliate and fish toxicity

Abstract: This work explores the possibilities of generalizing a variety of narcotic global quantitative structure–activity relationships used in aquatic toxicological studies. The models developed herein are based on the static ciliate ( Tetrahymena pyriformis ) population growth impairment (IGC 50 −1 ) data. Results are compared with models previously developed with the flow-through fish ( Pimephales promelas ) mortality (LC 50 −1 ) data. The modeling approach is an extension of a recently developed expert system coupled with the response-surface concept. The expert system characterizes the molecular domain of non-specifically acting chemicals, both for neutral and amine narcotics. Toxicity surface(s) are defined using hydrophobicity quantified by the log 1-octanol/water partition coefficient (log K ow ) and orbital electrophilicity quantified by the energy of the lowest unoccupied molecular orbital ( E LUMO ) as global molecular descriptors. The ciliate response surface models: log(IGC 50 −1 )=1.50+0.68 log K ow −0.13 E LUMO ; n =411, R 2 =0.890 and log(IGC 50 −1 )=1.80+0.68 log K ow ; n =51, R 2 =0.854 for neutral and amine narcotics, respectively, compares favorably with the fish model. The fish and ciliates response-surfaces appear to be parallel as they significantly deviate only by their intercepts.

DFT study of electronic structure and geometry of neutral and anionic silver clusters

Abstract: A comparative analysis of bond lengths (re), vertical detachment energies (VDE), excitation energies of neutral clusters with geometry of anions (Te) and vertical ionization potentials of neutral clusters (IPv) calculated within density functional theory (DFT) using different functionals with both effective core potential (ECP) and all-electron basis sets for silver clusters Agn, n≤6, have been carried out. DFT methods provide a good agreement between calculated and experimental data of some characteristics. The accurate prediction of all characteristics simultaneously can be achieved with all-electron DZVP basis set only. A new functional has been developed. It provides results close to experimental data using the moderate basis set. For anionic clusters Ag2–10−, the difference between calculations with this functional and experimental values of VDE and Te for the most stable isomers does not exceed 0.1 eV. Based on both total energy calculations and comparison of experimental and calculated photoelectron spectra, the structural assignment of clusters Ag7−, Ag9− and Ag10− has been made. The electronic structure and geometrical characteristics of the low-lying isomers has been studied.

Flavin reduction potential tuning by substitution and bending

Abstract: Computations on a series of flavin derivatives with the B3LYP hybrid density functional and 6-311G(2d,2p) basis set indicate that the ionization potentials (IPs) of the anionic semiquinone and hydroquinone states serve as accurate predictors of the flavin one- and two-electron reduction potentials. The relation between the semiquinone IPs and the two-electron reduction potentials, Em, is ΔIPsq−/ΔEm=3.69±0.18 meV/mV, with a very similar relation obtained for the flavin derivatives' Kohn–Sham highest occupied molecular orbital (KS-HOMO) energies, EKS-HOMO vs. Em. Interestingly, these good correlations between vertical IPs and Ems are observed even though the second reduction step, Flsq⇌Flred− involves significant conformational changes for a number of the derivatives. In fact, the flavin derivatives can be divided roughly into two categories. Those derivatives with high Ems are either planar in the anionic reduced state, or else a negligible amount of energy ( kT), and tend to have larger butterfly bends. The flavin parent compound, lumiflavin, represents the dividing point between these two categories, a result with possibly interesting biological implications for the conformational control of flavin redox potentials by enzymes. B3LYP/6-311G(2d,2p) calculations on lumiflavin constrained to various butterfly bend angles show that the oxidized and semiquinone states (both anionic and protonated at N5) resist bending, with the oxidized state being by far the stiffest. On the other hand, the optimum geometry of the fully reduced state is bent by 15.9° in the anionic state and 24.4° in the neutral state. Full MP2 geometry optimizations confirm the reduced flavin butterfly bend, however the bend angles are larger than the DFT results: 28.7° and 32.6° for the anionic and neutral states, respectively. The relation of the N5 and N10 pyramidalization to the flavin butterfly bend is discussed. The results indicate that a protein-enforced flavin conformation should have significant and differing effect on each of the one electron reduction steps.

AM1 treatment of endohedrally hydrogen doped fullerene, nH2@C60

Abstract: Endohedrally hydrogen doped C60 systems, nH2@C60 (n: 9,12,15,19,21,24) have been theoretically investigated at the level of AM1 (RHF) type quantum chemical treatment. It has been found that n:24 is the maximum number of hydrogen molecules which should result a stable composite system. The calculations indicate that all these structures are stable but highly endothermic. Also some geometrical and physicochemical properties of these structures are reported.

Application of ab initio theory for the prediction of acidity constants of some 1-hydroxy-9,10-anthraquinone derivatives using genetic neural network

Abstract: A genetic algorithm based neural network model (GA-NN) has been applied for the prediction of the acidity constants of some recently synthesized 1-hydroxy-9,10-anthraquinone derivatives using quantum chemical descriptors. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. A three-layered feed forward neural network with back-propagation of error learning algorithm was employed to model the nonlinear and complex relationships between the acidity constant of anthraquinones and their quantum chemical descriptors. The subset of descriptors, which resulted in the low prediction error, was selected by genetic algorithm. A proper model with low prediction error and high correlation coefficient was obtained. This model was applied for the prediction of the pKa of some anthraquinone derivatives, which were not used in the modeling procedure. The relative errors of prediction lower than 2% were obtained.

Some theoretical observations on the 1:1 glycine zwitterion-water complex

Abstract: The structural transformation of three minima on the HF/6-31G∗ glycine zwitterion–water complex potential energy surface have been investigated at the Hartree-Fock (HF), second order Moller–Plesset perturbation theory (MP2)and the density functional theory using the B3LYP hybrid exchange-correlation functional employing several Pople's standard basis sets. Contrary to the previous computational results, our results clearly confirm that the zwitterionic structure of glycine does not exist in the 1:1 complex with a water molecule in the gas phase. Several above mentioned computational methods were examined. HF calculations performed at various levels (up to 6-311++G(3df,3pd)) demonstrated the difficulty of obtaining reliable results. Generally, the agreement between B3LYP and MP2 calculations was good. With accurate basis sets, they got the proper results. At the same time, the results at different levels from CP-corrected gradient optimization and CP-uncorrected were also compared.