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Usnic acid is a secondary metabolitefound in several species oflichens, organisms resulting from the symbiosis between fungi andalgae. This compound has been extensively studied because of its pharmacologicalproperties. Despite its potential medicinal importance, it exhibitsa high degree of toxicity. The confinement of the usnic acid withinliposomes has been investigated as a possibility to reduce its toxicity.In this work, we characterize the interaction of usnic acid in itsneutral and anionic states (usniate) with DPPC and DOPC by means ofmolecular dynamics simulations. A lamellar to nonlamellar transitionis observed for both membranes upon contact with usniate within 100ns time scale. The transition suggests the formation of a liposome-likestructure encapsulating the metabolyte. Furthermore, such processoccurs at a significantly shorter time frame for DOPC. [ABSTRACT FROM AUTHOR]

Principal component analysis was used in the selection of the B3PW91/6-311+G(3df) method for calculations of As2O3 molecular species. This multivariate analysis compared experimental properties (structure and ionization energy) of As4O6 molecule with several computational methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, and density functional theory) and basis sets. At the selected level of theory, we were able to calculate nine structures of As2O3 with three of them being stable ones (no negative force constants) in the following stability order: D3H (0.0), DIAMOND OUT (32.77 kJ mol−1), and GAUCHE (43.81 kJ mol−1). Several intramolecular conversions were studied with the GAUCHE → DIAMOND OUT transformation being barrierless, whereas the DIAMOND OUT structure is converted into the D3H isomer through a Gibbs free-energy barrier of 40.83 kJ mol−1. Starting from the GAUCHE structure of As2O3 and its enantiomeric form, it was possible to obtain directly (barrierless) the As4O6 species in a spontaneous process (Δr G = −399.92 kJ mol−1 at 298 K and 1 atm) in gas phase. Thus, the As4O6 species is probably the precursor of arsenic hydroxide through hydrolysis reactions. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The chemical compound hydantoin is commonly used in the synthesis of broad-spectrum medicaments with multiple pharmacological activities. There are several papers in literature describing hydantoin derivates, yet few are related to the isolated molecule. In this work, we have performed B3LYP and MP2 calculations with the 6-31++G(d,p) basis set in order to obtain the geometric, energetic, and electronic parameters of the isolated hydantoin and its dimers. We have performed a complete energetic analysis of these complexes considering corrections from the basis set superposition error ( BSSE) and zero-point energy (ZPE) approaches. On the basis of these results, we have proposed and tested an additive model which has successfully predicted the complexation energies of larges hydantoin complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Abstract: MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C2H2F2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C2H2F···HF are 8.7 and 9.0kJmol−1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C2H2F2···HF. In this latter, Δμ(cyclic) is −3.07D, whereas Δμ(non-cyclic) is +1.92D using B3LYP calculations. Their corresponding MP2 values are +0.44D and −1.89D, respectively. As expected, the complexation produces an Hing frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C2H2F2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule. [Copyright &y& Elsevier]

Abstract: MP2/6-31++G(d,p) ab initio molecular orbital calculations have been employed to investigate the effect of the F–H⋯N hydrogen bond between aromatic azines and hydrogen fluoride on the degree of aromaticity of these azines in considering the CH stretching region of its IR spectrum. Our results have revealed a lowering of the aromatic character of the azine ring. This corresponds to larger vibrational frequencies and smaller CH stretching intensities after complexation. An analysis based on a charge–charge flux-overlap model for infrared intensities indicates that this decrease on the intensity values is mainly due to the CH charge flux term. It becomes less negative upon the H-bond formation, whereas the hydrogen charge is only slightly increased. [Copyright &y& Elsevier]

MP2/6-31++G(d,p) ab initio molecular orbital calculations have been employed to characterize hydrogen-bonded complexes between hydrogen fluoride as proton donor and aromatic azines (pyridine, pyrimidine, pyridazine, pyrazine, 1,3,5-triazine, and 1,2,4-triazine). Our calculations have shown that the H-bond strength in these complexes depends on both the number of nitrogen atoms as well as the position of these atoms in aromatic ring. The binding energies of azines-HF with or without BSSE and ZPE corrections decrease with the increasing number of nitrogen atoms in the ring. For example, its ΔEBSSE,ZPE value is 40.9 kJ · mol-1 in pyridine-HF, whereas its corresponding values in pyrazine-HF and 1,3,5-triazine-HF are 34.0 kJ · mol-1 and 26.6 kJ · mol-1, respectively. With respect to position of the nitrogen atom in the aromatic ring, the more pronounced effect is verified when it is at meta-position relative to the pyridine ring. There is a high linear correlation between the H-bond strength in these complexes and the intermolecular charge transfer using corrected Mulliken charges obtained from the charge-charge flux-overlap (CCFO) modified model for infrared intensities. Finally, our MP2/6-31++G(d,p) calculations have revealed that stronger hydrogen bonds are associated with smaller H-bond length values, larger intermolecular charge transfers and greater H&bond;F downward stretching frequency displacements. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [ABSTRACT FROM AUTHOR]

The molecular electrostatic potential (MEP) of the indole molecule was calculated in a three-dimensional grid in which the molecule was centered at the origin. To evaluate the dependence of MEP on the type of calculation, semiempirical, ab initio, and density functional theory methods with different basis sets were employed. The data matrix generated by these calculations was analyzed by principal component analysis (PCA). The appearance of outliers and the effect of wavefunction modifications such as the introduction of electron correlations and diffuse functions were highlighted by the use of PCA. The spatial localization of such effects around the molecule was possible from the loadings values associated with the graphical analysis of the grid points. [ABSTRACT FROM AUTHOR]

The stabilities of N-ethyl,N-methylformamide and N-ethyl,N-methylacetamide in their syn and anti forms have been calculated using HF/6-311++G**, MP2(FC)/6-311++G**//HF/6-311++G** and B3LYP/6-311++G**//HF/6-311++G** methods. The calculated NMR chemical shifts were evaluated using the last method. The relative position of the methyl part of the N-ethyl group has been found to be almost perpendicular to the plane of the heavy atoms in disagreement with the previous report. The conformational preference is discussed in terms of both steric and hyperconjugative/anomeric effects. The consequences of these effects on the geometry and NMR spectra have been analyzed. [Copyright &y& Elsevier]

RHF and MP2 ab initio molecular orbital calculations using the 4-31G** and 6-311G** basis sets have been employed to obtain Green''s function matrix elements (GD,A) and intermolecular charge transfers (ΔQcorr) of the CnNH…CnNH and CnNH…NCnH (n=1 and 3) hydrogen bonded complexes. Our calculations reveal that these two parameters are linearly correlated. Their values increase by effect of the addition of a C2 group to the proton donor and/or acceptor and when the hydrogen bonding is formed by the NH…C skeleton in comparison to the NH…N one. Our calculations have also revealed that the corresponding increments in GD,A and ΔQcorr due to change from NCH…NCH to CNH…NCH or from NCH…CNH to CNH…CNH are very similar. Finally, both GD,A and ΔQcorr show the same behavior when the hydrogen bonding distance is progressively increased from the equilibrium position until 4.5 A˚, forming two exponential curves practically superposed. Correlations between ΔE and ΔQcorr as well as ΔE and GD,A are also discussed. [Copyright &y& Elsevier]

Abstract: Configurational and conformational analysis were performed using ab initio and semi-empirical molecular orbital methods in order to obtain structural, electronic and energetic information about three previously synthesized imidazolidine derivatives, namely: 3-benzyl-5-benzylidene-imidazolidine-2,4-dione (5), 3-benzyl-5-benzylidene-2-thioxo-imidazolidine-4-one (6), 5-benzylidene-3-(2-oxo-2-phenyl-ethyl)-2-thioxo-imidazolidine-4-one (7) and other two new proposed imidazolidine derivatives: 3-benzyl-5-benzylidene-4-thioxo-imidazolidine-2-one (8) and 3-benzyl-5-benzylidene-imidazolidine-2,4-dithione (9). Important aspects related to structure activity relationship are highlighted. [Copyright &y& Elsevier]

A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20-4800 cm(-1)) and systems: XH(3) (D(3h) ) with X = B, Al, Ga, N, P, As, O, S, and Se, YH(4) (D(4h) ) with Y = C, Si, and Ge, conformers of RDX, S(N) 2 and E2 reactions, [W(dppe)(2)(NNC(5)H(10))] complex, carbon nanotubes, and hydrogen-bonded complexes including guanine-cytosine pair., (Copyright © 2012 Wiley Periodicals, Inc.)

The multivariate chemometric techniques two level factorial design (TLFD) and principal component analysis (PCA) were used to investigate the TIP4P model potential behavior with respect to perturbations on all intermolecular interaction parameters. The effects of these perturbations were calculated for the enthalpy of vaporization, the density, the first maximum of the radial distribution functions of the O-H and O-O pairs, and the second maximum of the radial distribution function of the O-H pair obtained from Monte Carlo simulations of liquid water at 25 degrees C. The principal effects were quantified and rationalized in terms of the pair-wise interaction potential of the TIP4P model. They also corroborate previously published sensitivity analysis results using molecular dynamics and other model potentials. In addition, significant interaction effects between some parameters of the TIP4P model potential were observed and quantified, which hardly could be obtained without such a statistic approach. These interaction effects are very regular and systematic, and their behavior has not been encountered in other chemometric studies and cannot be rationalized in terms of the functional form of the pair-wise potential., (Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 973-981, 2003)

Theoretical studies involving minimization of model 3-propanoylaminopicolinic acids (10d-trans, 10d-cis), methyl ester (10a), and corresponding -N-oxide derivatives (10b, 10c-trans, 10c-cis) using AM1 gave conformations contrary to both sound chemical intuition and experimental data. RHF ab initio calculations using the 6-31G and 6-31G basis sets on the other hand corroborated spectroscopic data. 3-Amidopicolinic acid derivatives (7a-9a, 7b-9b, 7c-9c, 9d) were prepared and studied by NMR and IR spectroscopy. The results show that a strong intramolecular hydrogen bond between amide-H and the 2-carboxyl substituent results in a planar molecular conformation. This is particularly profound in the 3-acylaminopicolinic acid N-oxides (c-series). When the 2-substituent is a methyl ester on the other hand, repulsion between N-oxide and ester functions induces twisting of the carbomethoxy group out of the plane of the aromatic ring. The type of method used in molecular modeling can have profound impact on the final theoretical result in the case of the above-mentioned class of compounds. Our results indicate, that it is advisable to employ ab initio methods for modeling these types of compounds, and further, that the choice of basis set used for such calculations should depend on the type of information required. Thus, for most purposes pertaining to molecular conformation the 6-31G basis set provides sufficiently sound data in relatively short CPU time. For data related to electronic properties such as involvement of the N-oxide function or spectroscopic information such as IR frequencies or (1)H or (15)N NMR chemical shifts, the use of polarization functions as contained in the 6-31G basis set seems to be a must.