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PubMed2003

Molecular complexes of some anthraquinone anti-cancer drugs: experimental and computational study.

It is known that anti-cancer drugs target DNA in the cell. The mechanism of interaction of anti-cancer drugs with DNA is not fully understood. It is thought that the forces of interaction have some contribution from charge-transfer (CT) binding. The ability of some anthraquinones (AQs) anti-cancer drugs to form CT complexes with well-known electron donor molecules was investigated by NMR. The NMR spectroscopy has indicated the formation of CT complexes between 1,4-bis[[2-(dimethylamino) ethyl]amino]-5,8-dihydroxyanthracene-9,10-dione, (AQ4), and its des-hydroxylated equivalent 1,4-bis[[2-(dimethylamino) ethyl]amino]anthracene-9,10-dione, (AQ4H), as electron acceptors and pyrene (PY) and hexamethylbenzene (HMB) as electron donors. Association constants of the formed CT complexes were determined from the NMR data. AQ4 showed weaker electron accepting power than AQ4H, which could be easily explained on the basis of the electron donating nature of the two-hydroxyl groups. AQ4 and AQ4H have higher stability constant with PY than with HMB. This reflects the weaker interaction of the AQs with the latter, which is a direct effect of the six bulky methyl groups. Electronic absorption spectroscopy of the studied system was performed in chloroform and showed the absence of new absorption bands. The extent of interaction between AQs and donors has been computed using molecular mechanics and quantum mechanics. The computed values were compared with the experimental results of association constants.

Anthraquinones↗

PubMed2006

Wave function analysis of MHC-peptide interactions.

We have carried out an analysis of the wave function data for three MHC-peptide complexes: HLA-DRbeta1*0101-HA, HLA-DRbeta1*0401-HA and HLA-DRbeta1*0401-Col. We used quantum chemistry computer programs to generate wave function coefficients for these complexes, from which we obtained both molecular and atomic orbital data for both pocket and peptide amino acids within each pocket region. From these discriminated data, interaction molecular orbitals (IMOs) were identified as those with large and similar atomic orbital coefficient contributions from both pocket and peptide amino acids. The present results correlate well with our previous research where only electrostatic moments were used to explore molecular component interactions. Furthermore, we show a quantum chemical methodology to produce more fine-grained results concerning amino acid behavior in the MHC-peptide interaction.

Amino Acids↗

PubMed2000

Modeling of the inhibition of retroviral integrases by styrylquinoline derivatives.

Styrylquinoline derivatives, known to be potent inhibitors of HIV-1 integrase, have been experimentally tested for their inhibitory effect on the disintegration reaction catalyzed by catalytic cores of HIV-1 and Rous sarcoma virus (RSV) integrases. A modified docking protocol, consisting of coupling a grid search method with full energy minimization, has been specially designed to study the interaction between the inhibitors and the integrases. The inhibitors consist of two moieties that have hydroxyl and/or carboxyl substituents: the first moiety is either benzene, phenol, catechol, resorcinol, or salicycilic acid; the hydroxyl substituents on the second (quinoline) moiety may be in the keto or in the enol forms. Several tautomeric forms of the drugs have been docked to the crystallographic structure of the RSV catalytic core. The computed binding energy of the keto forms correlates best with the measured inhibitory effect. The docking procedure shows that the inhibitors bind closely to the crystallographic catalytic Mg(2+) dication. Additional quantum chemistry computations show that there is no direct correlation between the binding energy of the drugs with the Mg(2+) dication and their in vitro inhibitory effect. The designed method is a leading way for identification of potent integrase inhibitors using in silico experiments.

Algorithms↗

PubMed2006

Evidence of variable H-bond network for nitroxide radicals in protic solvents.

This letter presents the results of a thorough computational investigation of two prototypical nitroxide spin probes in two different protic solvents, namely water and methanol, based on the combined use of Car-Parrinello molecular dynamic simulations and static cluster/continuum quantum chemical computations. Remarkable changes in solvation networks were found on going from aqueous to methanolic solutions. Moreover, despite their structural similarity, the two nitroxide probes display quite different behaviors in water. This provides a rationalization of indirect experimentally available indications. Eventually, the combination of static and dynamical ab initio methods exploited in the present study allows to dissect many subtle features of the nitroxide-solvent interaction, and also allows for an analysis of solvent effects on magnetic parameters (hyperfine coupling constants and g-tensor shift).

Letter↗

PubMed2006

Theoretical studies on farnesyl cation cyclization: pathways to pentalenene.

In this article, we describe studies, using quantum chemical computations, on possible polycyclization pathways of the farnesyl cation leading to the complex sesquiterpene pentalenene. Two distinct pathways to pentalenene with similar activation barriers are described, each differing from previous mechanistic proposals, and each involving unusual and unexpected intermediates. Direct deprotonation of intermediates on these pathways leads to sesquiterpene byproducts, such as humulene, protoilludene, and asteriscadiene, supporting the notion that a key function of pentalenene synthase, the enzyme that produces pentalenene in Nature, is to regulate the timing and location of proton removal. The implications of the computational results for experimental studies on pentalenene synthase are discussed.

Cations↗

PubMed2005

Computational studies of Cu(II)/Met and Cu(I)/Met binding motifs relevant for the chemistry of Alzheimer's disease.

A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namely, N-formylmethioninamide 1, has been carried out by quantum chemical computations. Geometries of the coordination modes obtained at the B3LYP/6-31G(d) level of theory are discussed in the context of copper coordination by the peptide backbone and the S atom of a methionine residue in peptides with special emphasis on Met35 of the amyloid-beta peptide (Abeta) of Alzheimer's disease. The relative binding free energies in the gas phase, DeltaG(g), are calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level of theory, and the solvation affects are included by means of the COSMO model to obtain the relative binding energies in solution, DeltaG(aq). A free energy of binding, DeltaG(aq) = -19.4 kJ mol(-1), relative to aqueous Cu(II) and the free peptide is found for the most stable Cu(II)/Met complex, 12. The most stable Cu(I)/Met complex, 23, is bound by -15.6 kJ mol(-1) relative to the separated species. The reduction potential relative to the standard hydrogen electrode is estimated to be E degrees (12/23) = 0.41 V. On the basis of these results, the participation of Met35 as a low affinity binding site of Cu(II) in Abeta, and its role in the redox chemistry underlying Alzheimer's disease is discussed.

Alzheimer Disease↗

PubMed2005

Simple empirical method for prediction of impact sensitivity of selected class of explosives.

A new approach is described in this work to predict impact sensitivity of a variety of polynitroaliphatics, polynitroaromatics and the explosives containing N-NO2. This paper introduces some simple correlations for prediction of impact sensitivity of C(a)H(b)N(c)O(d) explosives using a, b, c, d, molecular weight and structure information of the explosive. The new correlations are applied to test different polynitroaromatics, benzofuroxans and nitramines. The results are compared with experimental data and some models of complex quantum mechanics computation. Predicted impact sensitivities for 46 explosives have a root mean square (rms) of deviation from experiment of 24 cm, which show good agreement with respect to measured values as compared to five different quantum mechanical models. Impact sensitivities for 58 polynitroaliphatics and related explosives are also calculated, and have a rms deviation from experiment of 40 cm.

Empirical Research↗

PubMed2006

Hybrid density functional theory for pi-stacking interactions: application to benzenes, pyridines, and DNA bases.

The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel pi-stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel-displaced benzene dimer in good agreement with the best available high-level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel-displaced benzene dimer. This method was further critically compared to high-level calculations recently reported in the literature for a range of pi-stacked complexes, including monosubstituted benzene-benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within +/-2 kJ mol(-1). We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large pi-stacked systems such as DNA.

Algorithms↗

PubMed2005

Systematic size study of an insect antifreeze protein and its interaction with ice.

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations.

Animals↗

PubMed1989

The effect of a distribution of separations upon intramolecular distances in biopolymers, as determined by radiationless energy transfer.

In a fluorescent donor group and a nonfluorescent acceptor group are incorporated into a biopolymer, so that radiationless energy transfer occurs between the two groups, the apparent separation of the groups, as determined by energy transfer, will be influenced by the existence of a distribution of separations. This might arise from the presence of significant localized flexibility at the sites of attachment of the two groups, or from internal flexibility involving the biopolymer itself. If a Gaussian form is assumed for the distribution of separations of the donor and acceptor groups, the efficiency of transfer is dependent upon the width of the distribution, as well as the average distance between the groups. Significant differences may thereby arise between the true average separation and the separation computed from transfer efficiencies by the usual procedures. The deviations are different for transfer efficiencies computed from quantum yields and from decay times. They become more important with increasing width of the distribution of separations and increasing efficiency of transfer. In general, if a distribution of separations is present, the average separation is most reliably computed by procedures which take into account the effects of this distribution.

Biopolymers↗

PubMed2006

Order parameters of alpha,omega-diphenylpolyenes in a nematic liquid crystal from an integrated computational and 13C NMR spectroscopic approach.

The orientational order parameters and conformational behavior of five relatively large rodlike molecules, biphenyl, trans-stilbene, 1,3-diphenyl-butadiene, 1,3,5-diphenyl-hexatriene, and 1,3,5,7-diphenyl-octatetraene, dissolved in the thermotropic liquid crystal ZLI-1167, have been studied using an integrated approach combining (13)C NMR measurements and quantum mechanical computations of carbon chemical shift tensors. Besides biphenyl, the phenyl moiety of all structures has been found to have a high rotational mobility in the temperature range of the present experiments. The rank-two order parameter in the nematic phase is found to increase steadily from the shortest to the longest term of the series at any temperature within the nematic range. The molecular biaxiality order parameter is found to be small and essentially constant with temperature, giving further support to the common assumption of effective uniaxiality for these probes.

Journal Article↗

PubMed2005

Assessment of a mechanism for reactive inhibition of carboxypeptidase A with QM/MM methods.

The mechanism for inhibition of carboxypeptidase A (CPA) by the two enantiomers of a reactive inhibitor, N-(2-chloroethyl)-N-methylphenylalanine, has been investigated using computational methods. Quantum mechanical and molecular mechanical (QM/MM) methods have been employed to find likely enzyme binding conformations by comparison with the observed rates of inactivation of the enzyme. The study has shown that the enzyme active site appears to be flexible enough to allow the nucleophilic deactivation reactions of both the (R) and (S) forms of a model of the inhibitor to be catalysed by the Zn(II) cofactor of CPA.

Binding Sites↗

PubMedDate not supplied

Computer-modeling-based QSARs for analyzing experimental data on biotransformation and toxicity.

Over the past decades the description of quantitative structure-activity relationships (QSARs) has been undertaken in order to find predictive models and/or mechanistic explanations for chemical as well as biological activities. This includes QSAR studies in toxicology. In an approach beyond the classical QSAR approaches, attempts have been made to define parameters for the QSAR studies on the basis of quantum mechanical computer calculations. The conversion of relatively small xenobiotics within the active sites of biotransformation enzymes can be expected to follow the general rules of chemistry. This makes the description of QSARs on the basis of only one parameter, chosen on the basis of insight in the mechanism, feasible. In contrast, toxicological endpoints can very often be the result of more than one physico-chemical interaction of the compound with the model system of interest. Therefore the description of quantitative structure-toxicity relationships often does not follow a one-descriptor mechanistic approach but starts from the other end, describing QSARs by multi-parameter approaches. The present paper focuses on the possibilities and restrictions of using computer-based QSAR modeling for analyzing experimental toxicological data, with emphasis on examples from the field of biotransformation and toxicity.

Animal Testing Alternatives↗

PubMed2007

Structures of the hexafluorocyclopropane, octafluorocyclobutane, and decafluorocyclopentane radical anions probed by experimental and computational studies of anisotropic electron spin resonance (ESR) spectra.

Anisotropic electron spin resonance (ESR) spectra are reported for the radical anions of hexafluorocyclopropane (c-C(3)F(6)(-)), octafluorocyclobutane (c-C(4)F(8)(-)), and decafluorocyclopentane (c-C(5)F(10)(-)) generated via gamma-irradiation in plastically crystalline tetramethylsilane (TMS) and rigid 2-methyltetrahydrofuran (MTHF) matrices. By combining the analysis of these experimental ESR spectra involving anisotropic hyperfine (hf) couplings with a series of quantum chemical computations, the geometrical and electronic structure of these unusual perfluorocycloalkane radical anions have been characterized more fully than in previous studies that considered only the isotropic couplings. Unrestricted Hartree-Fock (UHF) computations with the 6-311+G(d,p) basis set predict planar ring structures for all three radical anions, the ground electronic states being (2)A(2)(") for c-C(3)F(6)(-) (D(3h) symmetry), (2)A(2u) for c-C(4)F(8)(-) (D(4h)), and (2)A(2)(") for c-C(5)F(10)(-) (D(5h)), in which the respective six, eight, and ten 19F-atoms are equivalent by symmetry. A successful test of the theoretical computation is indicated by the fact that the isotropic 19F hf couplings computed by the B3LYP method with the 6-311+G(2df,p) basis set for the optimized geometries are in almost perfect agreement with the experimental values: viz., 19.8 mT (exp) vs 19.78 mT (calc) for c-C(3)F(6)(-); 14.85 mT (exp) vs 14.84 mT (calc) for c-C(4)F(8)(-); 11.6 mT (exp) vs 11.65 mT (calc) for c-C(5)F(10)(-). Consequently, the same computation method has been applied to calculate the almost axially symmetric anisotropic 19F hf couplings for the magnetically equivalent 19F atoms: (-4.90 mT, -4.84 mT, 9.75 mT) for c-C(3)F(6), (-3.54 mT, -3.48 mT, 7.02 mT) for c-C(4)F(8)(-), and (-2.62 mT, -2.56 mT, 5.18 mT) for c-C(5)F(10)(-). ESR spectral simulations performed using the computed principal values of the hf couplings and the spatial orientations of the 19F nuclei as input parameters reveal an excellent fit to the experimental anisotropic ESR spectra of c-C(3)F(6)(-), c-C(4)F(8)(-), and c-C(5)F(10)(-), thereby providing a convincing proof of the highly symmetric D(nh) structures that are predicted for these negative ions. Furthermore, using the computed 19F principal values and their orientations, the effective 19F anisotropic hf couplings along the molecular symmetry axes were evaluated for c-C(3)F(6)(-) and c-C(4)F(8)(-) and successfully correlated with the positions of the characteristic outermost features in both the experimental and calculated anisotropic spectra. In addition, the electronic excitation energies and oscillator strengths for the c-C(3)F(6)(-) , c-C(4)F(8)(-), and c-C(5)F(10)(-) radical anions were computed for the first time using time-dependent density functional theory (TD-DFT) methods.

Journal Article↗

PubMed2005

Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives.

A large number of conformations and chemically modified variants of the protein crambin were used to extensively test the field-adapted adjustable density matrix assembler (FA-ADMA) method developed for ab initio quality quantum chemistry computations of proteins and other macromolecules, introduced in an earlier publication. In this method, the fuzzy density matrix fragmentation scheme of the original adjustable density matrix assembler (ADMA) method has been made more efficient by combining it with an approach of using point charges to approximate the effects of additional, distant parts of a given macromolecule in the quantum chemical calculation of each fragment. In this way, smaller parent molecules can be used for fragment generation, while achieving accuracy that can be obtained only with large parent molecules in the original ADMA method. Whereas in both methods the error relative to the Hartree-Fock result can be reduced below any threshold by choosing large enough parent molecules, this can be done more efficiently with the new method. In order to obtain reliable test results for the accuracy obtainable by the new method when compared to conventional Hartree-Fock calculations, we performed a large number of energy calculations for the protein crambin using various conformations available in the Protein Data Bank, various protonation states, and side chain mutations. Additionally, in order to test the performance of the method for protein-solvent interaction studies, the energy changes due to the formation of complexes with ethanol and single and multiple water molecules were investigated.

Chemical Phenomena↗

PubMed2004

Reconstruction of thermally symmetrized quantum autocorrelation functions from imaginary-time data.

In this paper, I propose a technique for recovering quantum dynamical information from imaginary-time data via the resolution of a one-dimensional Hamburger moment problem. It is shown that the quantum autocorrelation functions are uniquely determined by and can be reconstructed from their sequence of derivatives at origin. A general class of reconstruction algorithms is then identified, according to Theorem 3. The technique is advocated as especially effective for a certain class of quantum problems in continuum space, for which only a few moments are necessary. For such problems, it is argued that the derivatives at origin can be evaluated by Monte Carlo simulations via estimators of finite variances in the limit of an infinite number of path variables. Finally, a maximum entropy inversion algorithm for the Hamburger moment problem is utilized to compute the quantum rate of reaction for a one-dimensional symmetric Eckart barrier.

Journal Article↗

PubMedDate not supplied

Use of statistical and neural net approaches in predicting toxicity of chemicals.

Hierarchical quantitative structure-activity relationships (H-QSAR) have been developed as a new approach in constructing models for estimating physicochemical, biomedicinal, and toxicological properties of interest. This approach uses increasingly more complex molecular descriptors in a graduated approach to model building. In this study, statistical and neural network methods have been applied to the development of H-QSAR models for estimating the acute aquatic toxicity (LC50) of 69 benzene derivatives to Pimephales promelas (fathead minnow). Topostructural, topochemical, geometrical, and quantum chemical indices were used as the four levels of the hierarchical method. It is clear from both the statistical and neural network models that topostructural indices alone cannot adequately model this set of congeneric chemicals. Not surprisingly, topochemical indices greatly increase the predictive power of both statistical and neural network models. Quantum chemical indices also add significantly to the modeling of this set of acute aquatic toxicity data.

Animals↗

PubMed2001

Quantum mechanical designs toward planar delocalized cyclooctatetraene: a new target for synthesis.

Ab initio and hybrid density functional quantum mechanical computation are applied to the structure and energetics of a series of annelated cyclooctatetraenes. Tetrakis-cyclobuteno, perfluorocyclobuteno or bicyclo[2.1.1]hexeno annelations result in planar structures with distinct exo and endo valence tautomers of the double bonded cycle. The contribution of each basic annelation to the exo/endo relative energy is estimated. An additivity scheme for approximating the energy of a mixed system is developed and compared to the quantum mechanical prediction. Bis bicyclic annelation to the a and d positions creates "valence tautomeric frustration" and strongly perturbs the molecular structure. This phenomenon leads to a general design for a planar cyclooctatetraenes where the "delocalized" diradicaloid state is the minimum energy form. These compounds are seen as excellent targets for chemical synthesis.

Alkenes↗