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PubMed1998

Five quantum coherence of I=5/2 nuclei: 27Al in polycrystalline AlCl3.

Optimal conditions were calculated for the excitation and detection of the five quantum coherence of quadrupolar nuclei with I = 5/2 in powder samples, observed by the two-pulse sequence (theta1)x - tau1 - (theta2)alpha - tau2, where alpha is the phase cycling angle. We varied the pulse lengths and the relative values of the nutation frequency omega1 = gammaB1 and the quadrupolar frequency omegaQ. Also, the effect of the resonance offset was studied under optimal conditions. Besides, the conditions for obtaining the maximal echo amplitude after the two-pulse sequence with alpha = y were found. Theoretical results were compared with experiments on 27Al nuclei in polycrystalline AlCl3.

Aluminum Chloride↗

PubMed2006

Femtosecond time-resolved transient absorption spectroscopy of xanthophylls.

Xanthophylls are a major class of photosynthetic pigments that participate in an adaptation mechanism by which higher plants protect themselves from high light stress. In the present work, an ultrafast time-resolved spectroscopic investigation of all the major xanthophyll pigments from spinach has been performed. The molecules are zeaxanthin, lutein, violaxanthin, and neoxanthin. beta-Carotene was also studied. The experimental data reveal the inherent spectral properties and ultrafast dynamics including the S(1) state lifetimes of each of the pigments. In conjunction with quantum mechanical computations the results address the molecular features of xanthophylls that control the formation and decay of the S* state in solution. The findings provide compelling evidence that S* is an excited state with a conformational geometry twisted relative to the ground state. The data indicate that S* is formed via a branched pathway from higher excited singlet states and that its yield depends critically on the presence of beta-ionylidene rings in the polyene system of pi-electron conjugated double bonds. The data are expected to be beneficial to researchers employing ultrafast time-resolved spectroscopic methods to investigate the mechanisms of both energy transfer and nonphotochemical quenching in higher plant preparations.

Electrons↗

PubMedDate not supplied

Prediction of enzyme binding: human thrombin inhibition study by quantum chemical and artificial intelligence methods based on X-ray structures.

Thrombin is a serine protease which plays important roles in the human body, the key one being the control of thrombus formation. The inhibition of thrombin has become a target for new antithrombotics. The aim of our work was to (i) construct a model which would enable us to predict Ki values for the binding of an inhibitor into the active site of thrombin based on a database of known X-ray structures of inhibitor-enzyme complexes and (ii) to identify the structural and electrostatic characteristics of inhibitor molecules crucially important to their effective binding. To retain as much of the 3D structural information of the bound inhibitor as possible, we implemented the quantum mechanical/molecular mechanical (QM/MM) procedure for calculating the molecular electrostatic potential (MEP) at the van der Waals surfaces of atoms in the protein's active site. The inhibitor was treated quantum mechanically, while the rest of the complex was treated by classical means. The obtained MEP values served as inputs into the counter-propagation artificial neural network (CP-ANN), and a genetic algorithm was subsequently used to search for the combination of atoms that predominantly influences the binding. The constructed CP-ANN model yielded Ki values predictions with a correlation coefficient of 0.96, with Ki values extended over 7 orders of magnitude. Our approach also shows the relative importance of the various amino acid residues present in the active site of the enzyme for inhibitor binding. The list of residues selected by our automatic procedure is in good correlation with the current consensus regarding the importance of certain crucial residues in thrombin's active site.

Algorithms↗

PubMed2005

Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.

Full quantum mechanical computational study has been carried out to study binding of efavirenz (EFZ), a second generation FDA approved nonnucleoside inhibitor, to HIV-1 reverse transcriptase (RT) and its K103N and Y181C mutants using the MFCC (molecular fractionation with conjugate caps) method. The binding interaction energies between EFZ and each protein fragment are calculated using a combination of HF/3-21G, B3LYP/6-31G* and MP2/6-31G* ab initio levels. The present computation shows that Efavirenz binds to HIV-1 RT predominantly through strong electrostatic interaction with the Lys101 residue. The small loss of binding to K103N mutant by Efavirenz can be attributed to a slightly weakened attractive interaction between the drug and Lys101 due to a conformational change of mutation. The small loss of binding to Y181C mutant by efavirenz can be attributed to the Glu698 residue moving closer to EFZ due to conformational change, which results in an increase of repulsive energy relative to the wild type (WT). The binding of efavirenz-derived DPC961 to HIV-1 RT is enhanced by an additional attractive interaction to residue Hid235 and reduced repulsion to Glu698, resulting in an increase of binding energy by about 4 kcal/mol.

Alkynes↗

PubMed2006

Crystal density predictions for nitramines based on quantum chemistry.

An efficient and convenient method for predicting the crystalline densities of energetic materials was established based on the quantum chemical computations. Density functional theory (DFT) with four different basis sets (6-31G(**), 6-311G(**), 6-31+G(**), and 6-311++G(**)) and various semiempirical molecular orbital (MO) methods have been employed to predict the molecular volumes and densities of a series of energetic nitramines including acyclic, monocyclic, and polycyclic/cage molecules. The relationships between the calculated values and experimental data were discussed in detail, and linear correlations were suggested and compared at different levels. The calculation shows that if the selected basis set is larger, it will expend more CPU (central processing unit) time, larger molecular volume and smaller density will be obtained. And the densities predicted by the semiempirical MO methods are all systematically larger than the experimental data. In comparison with other methods, B3LYP/6-31G(**) is most accurate and economical to predict the solid-state densities of energetic nitramines. This may be instructive to the molecular designing and screening novel HEDMs.

Aniline Compounds↗

PubMed2002

Directing power of cyclobutenoid annelations on the double bonds of planar cyclooctatetraenes.

Ab initio and hybrid density functional quantum mechanical computations are applied to the structure and energetics of a series of two-atom-bridge annelated cyclooctatetraenes. The contribution of each annelation to the exo/endo relative energy is estimated. Key directing factors for a given type of annelation, such as strain, electronegativity, or cyclic electron count, can be sorted out by comparison of various bridge compositions. Overall, electron count and the essential components of the Clar/Robinson rule work well to predict the exo/endo preferences. Specifically, three 4-e(-) Hückel systems (CH-CH, NH-BH and NH-C(O)) display dominant exo forms whereas the three 4n + 2 Hückel counterparts (C(O)-C(O), BH-BH, and planar NH-NH) display a common preference for endo. These endo systems act like four independent four-membered "aromatic" rings linked by "single" bonds. An analysis based on the effective hybridization of carbon atoms in the annulene (Bent's rule) provides a rationale for subtle trends in their specific annulene geometry.

Alkenes↗

PubMed1997

Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair.

Recent experiments have shown that difluorotoluene (F), a nonpolar isostere for thymine (T), codes efficiently and specifically for adenine (A) in DNA replication. F has almost the same shape as thymine but it is unable to form conventional hydrogen bonds with adenine. Therefore, it has been claimed that not hydrogen bonding but shape complementary may be important for the selection of the correct bases by DNA-replicating enzymes. In order to gain deeper insight into structure, charge distribution and energetics of the A-F and A-T base pairs we have performed quantum-chemical ab initio and density functional calculations at the HF, MP2 and B3LYP levels. The interaction energy of the A-F complex amounts to -3.8 kcal/mol (MP2) and is thus substantially smaller than typical ab initio interaction energies for Watson-Crick or non-canonical base pairs. The A-T and A-F complexes are planar and their overall geometries are similar (root-mean-square deviation: 0.4 A). The calculated donor acceptor atom distances in A-T are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. However, A-F shows a base pair opening as compared to A-T. Even though the interaction energy in the A-F base pair is small, the distances for the N6-H...F and N1...H-C3 contacts are still below the sum of the van-der-Waals radii, which means that the interaction is not governed by van-der-Waals forces alone. If the experimental findings can be confirmed, then our results indicate that DNA polymerase is able to retain high fidelity with base pairs of much smaller interaction energies than found for the conventional Watson-Crick and non-canonical base pairs.

Adenine↗

PubMed1999

Cell adhesion to polymeric surfaces: experimental study and simple theoretical approach.

In a medium without serum, the initial adhesion of L1210 cells to nonsulfonated and sulfonated polymer surfaces was investigated. In the case of sulfonated polymer surfaces, the relative number of adhering cells strongly increases with an increase of the interfacial surface tension; that is, adhesion strongly depends on the surface density of sulfonic groups. However, in the case of nonsulfonated polymer surfaces, the relative number of adhering cells is high and independent of the interfacial surface tension. To extend the basic knowledge of these phenomena, a semi-empirical quantum chemical computational study was undertaken. Simple probe molecules were chosen that mimic the chemical properties of functional groups present on polymeric surfaces. The energies of interaction between these molecules and ones representing the midchain polypeptide building blocks were calculated. To discuss the steric effects involved in similar interactions on real surfaces, a simple model of polymeric surfaces was proposed. Also the interactions among such surfaces and the short hydrated polypeptide chain were studied at the molecular mechanics level of theory. The derived intermolecular energy parameter was found to change in parallel to the number of adhered cells within the two groups of substrata under study: nonsulfonated and sulfonated. The computational results suggest the possible existence of differently arranged cell membrane protein centers responsible for docking to these two types of surfaces.

Biocompatible Materials↗

PubMed2000

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues.

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

Alcohol Dehydrogenase↗

PubMed2001

Synthesis of radialene-shaped pyrroles by multiple-anion-capture reactions of 1,3-dianions.

A new multicomponent reaction (multiple-anion-capture reaction) of 1,3-dianions with nitriles and oxalic acid-bis(imidoyl)chlorides is reported. This process allows for an efficient and regioselective synthesis of a variety of radialene-shaped pyrroles which constitute structurally new and interesting heterocyclic systems. The cyclization products can be considered as aza-analogues of the pharmacologically relevant substance class of 3-acetyltetramic acids. A rationalization of the experimental results is given based on quantum chemical computations.

Anions↗

PubMed2004

Enhanced fluorescence of remote functionalized diaminodicyanoquinodimethanes in the solid state and fluorescence switching in a doped polymer by solvent vapors.

Remote functionalized zwitterionic diaminodicyanoquinodimethanes are found to exhibit a dramatic enhancement of light emission in the solid state and when doped in polymer films, as compared to the solution state. Crystal structure analysis of prototypical molecules reveals the role of the remote functionality in the solid state molecular organization. Semiempirical quantum chemical computations provide a viable model to explain the interesting phenomenon of fluorescence enhancement as arising from the inhibition of geometry relaxation of the vertical excited state to a nonemitting state. The reversible switching of a doped polymer film fluorescence triggered by solvent vapors is demonstrated.

Journal Article↗

PubMed2006

Rational design of aziridine-containing cysteine protease inhibitors with improved potency: studies on inhibition mechanism.

To enable a rational design of improved cysteine protease inhibitors, the present work investigates trends in the inhibition potency of aziridine derivatives with a substituted nitrogen center. To predict the influence of electron-withdrawing substituents, quantum chemical computations of the ring opening of N-formylated, N-methylated, and N-unsubstituted aziridines with thiolate were performed. They revealed that the N-formyl group leads to a strong decrease of the reaction barrier and a considerable increase in exothermicity due to stabilization of the transition state. In contrast, a nucleophilic attack at the carbonyl carbon atom is characterized by very low reaction barriers, suggesting a reversible reaction, thus providing the theoretical background for the reversible inhibition of cysteine proteases by peptidyl aldehydes. Reactions of aziridine building blocks (diethyl aziridine-2,3-dicarboxylate 1, diethyl 1-formyl aziridine-2,3-dicarboxylate 2) with a model thiolate in aqueous solution which were followed by NMR spectroscopy and mass spectrometry, showed the N-formylated compound 2 to readily undergo a ring-opening reaction. In contrast, the reaction of 1 with the thiolate is much slower. Enzyme assays with the cysteine protease cathepsin L showed 2 to be a 5000-fold better enzyme inhibitor than 1. Dialysis assays clearly proved irreversible inhibition. These experiments, together with the results obtained with the model thiolate, indicate that the main inhibition mechanism of the N-formylated aziridine 2 is the ring-opening reaction rather than the reversible attack of the active site cysteine residue at the carbonyl carbon atom.

Aziridines↗

PubMed2007

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Calcium↗

PubMed2004

13C NMR fingerprint characterizes long time-scale structure of Sc3N@C80 endohedral fullerene.

(13)C NMR chemical shifts of Sc(3)N@C(80) were computed using quantum Born-Oppenheimer molecular dynamics simulations, followed by DFT-NMR calculations on a large series of snapshots. Whereas calculations of the C(3) static gas-phase optimized structure fail to reproduce the two-line experimental spectrum, long-time molecular dynamics simulations quantitatively reproduce the experiment.

Journal Article↗

PubMed2001

Aqueous Suspensions of Poly(ethylene Glycol)/Pyrocarbon/Fumed Silica.

Aqueous suspensions of fumed silica and pyrocarbon/silica (CS) in the presence of dissolved poly(ethylene glycol) (PEG) were studied using (1)H NMR spectroscopy with freezing-out of bulk water and quantum chemical computations of the chemical shifts. The freezing effect for PEG/water is akin to that for low-molecular organics, as formation of solid phases of water (ice) and PEG occurs, and their mixture forms at the eutectic temperature. In the aqueous suspensions of fumed silica or CS, PEG molecules are localized at the solid-liquid interfaces and do not form the bulk solution even at large concentrations; however, the amount of bulk undisturbed water rises due to formation of the immobilized PEG layer. For such suspensions of silica or CS at a low amount of pyrocarbon (C(C)=4 wt%), there is a portion of the graph of the surface free energy (gamma(S)) increasing nearly linearly with the PEG concentration (C(PEG)); however, in the case of large C(C)=40 wt% in CS, a similar effect is not observed, as gamma(S) is maximal at low C(PEG)=0.1 wt%. Copyright 2001 Academic Press.

Journal Article↗

PubMed2000

Theoretical Study of the Collision-Induced Double Transition CO(2) (nu(3) = 1) + N(2) (nu(1) = 1) <-- CO(2) (nu(3) = 0) + N(2) (nu(1) = 0) at 296 K.

A procedure is presented for the calculation of the double vibrational collision-induced absorption CO(2) (nu(3) = 1) + N(2) (nu(1) = 1) <-- CO(2) (nu(3) = 0) + N(2) (nu(1) = 0) on the basis of quantum lineshapes computed using an isotropic potential and dipole-induced dipole functions. The linestrengths and energies of the vibration-rotation transitions are treated explicitly for N(2), utilizing the HITRAN database for CO(2). The theoretical absorption profile is compared to recent experimental results. By narrowing the width of the individual lines contributing to the overall absorption profile relative to their values determined for N(2)-N(2) collision-induced absorption, excellent agreement between theory and experiment is obtained. Copyright 2000 Academic Press.

Journal Article↗

PubMed2001

Theoretical Study of Collision-Induced Double Transitions in CO(2)-X(2) (X(2) = H(2), N(2), and O(2)) Pairs.

The double vibrational collision-induced absorptions CO(2) (nu(3) = 1) + X(2) (nu(1) = 1) <-- CO(2) (nu(3) = 0) + X(2) (nu(1) = 0), for X(2) = H(2), N(2), and O(2) are studied on the basis of quantum lineshapes computed using isotropic potentials and dipole-induced dipole functions. The linestrengths and energies of the vibration-rotation transitions are treated explicitly for X(2) and utilizing the HITRAN database for CO(2). From the frequency-dependent absorption profiles, the integrated absorption intensities are determined to be 7.2 +/- 1.2, 1.2 +/- 0.1, and 1.1 +/- 0.2 (10(-4) cm(-2) amagat(-2)) for the H(2), N(2), and O(2) collision partners, respectively. The integrated intensities for H(2) and N(2) agree well with previously measured and calculated results, while the value for O(2), which represents the first theoretical determination for this absorption, is approximately four times greater than the only experimental measurement (0.29 x 10(-4) cm(-2) amagat(-2)). Copyright 2001 Academic Press.

Journal Article↗

PubMed1996

Tautomerism of xanthine and alloxanthine: a model for substrate recognition by xanthine oxidase.

Tautomerism of neutral xanthine and alloxanthine has been examined both in the gas phase and in aqueous solution. The tautomeric preference in the gas phase has been studied by means of semiempirical and ab initio quantum-mechanical computations with inclusion of correlation effects at the Møller-Plesset level, and from density-functional calculations. The influence of solvent on the relative stability between tautomers has been estimated from self-consistent reaction field calculations performed with different models. The results provide a detailed picture of tautomerism for these biologically relevant purine bases. The functional implications in the recognition by xanthine oxidase are analyzed from inspection of the interaction patterns of the most stable tautomeric forms. A model for the recognition of these purine derivatives in the enzyme binding site is discussed.

Binding Sites↗