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PubMed1996

Triple-quantum MAS-NMR of quadrupolar nuclei.

From two-dimensional multiquantum NMR spectra of quadrupolar nuclei, it is now possible to obtain much greater resolution than in a classical single-quantum magic-angle spinning or variable-angle spinning spectrum. We describe here a very simple pulse scheme which efficiently excites the desired multiquantum NMR coherence and a new acquisition procedure which yields to pure-absorption mode 2D spectra. Experimental spectra for 87Rb in polycrystalline rubidium nitrate illustrate the method.

Magnetic Resonance Spectroscopy↗

PubMed2001

Control of exciton dynamics in nanodots for quantum operations.

We present a theory to further a new perspective of proactive control of exciton dynamics in the quantum limit. Circularly polarized optical pulses in a semiconductor nanodot are used to control the dynamics of two interacting excitons of opposite polarizations. Shaping of femtosecond laser pulses keeps the quantum operation within the decoherence time. Computation of the fidelity of the operations and application to the complete solution of a minimal quantum computing algorithm demonstrate in theory the feasibility of quantum control.

Journal Article↗

PubMed1991

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗

PubMed2004

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers.

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.

Catalysis↗

PubMed1980

A theoretical study of the interaction of guanine and cytosine with specific amino acid side chains.

Quantum-mechanical computations are performed on the in vacuo and in water interactions between the purine bases guanine and cytosine and the side chains of the amino acids arginine, lysine, glutamic acid and glutamine. The results predict that while guanine should be the more strongly interacting base both in vacuo and in water, lysine should be the most strongly interacting amino acid in vacuo and arginine the most strongly interacting amino acid in water solvent. The theoretical results on the interactions in water agree satisfactorily with experimentation.

Amino Acids↗

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↗

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↗

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↗

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↗

PubMed1996

Vibrational coupling between the nitro groups in 1,4-dinitrobenzene and 1,3-dinitrobenzene molecules: ab initio and normal coordinate analyses treatments.

Ab initio quantum chemical computations have been performed for 1,4-dinitrobenzene and 1,3-dinitrobenzene and their (15)N isotope-labeled derivatives at the 3-21G, 6-31G and 6-31G(*) basis set levels. The results have been compared with the experiment: the best coincidence has been obtained by the 6-31G method for 1,4-dinitrobenzene and by the 6-31G(*) method for 1,3-dinitrobenzene. The isotopic frequency shifts of the nitro group bands, induced by (14)N-(15)N labeling and the vibrational coupling between the nitro groups, calculated with GAMESS software, have been in accordance with the measured ones. A normal coordinate analysis has been carried out for the 1,4-dinitro- benzene molecule using a slightly modified force field of 1,3-dinitrobenzene, reasonable fit between the observed and calculated frequencies has been obtained. The results support the conclusion that the electronic contribution to the vibrational coupling between the two nitro groups in the studied dinitrobenzenes is negligible: thus, it may be suggested that the dynamical coupling will predominate.

Journal Article↗