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At least 379 records · Page 21Linked to original sources
PubMed1996

Effects of the phi[NHCO] retromodification on dehydroalanine dipeptide.

The potential energy surface of the phi [NHCO] delta Ala dipeptide has been computed using ab initio quantum mechanical calculations at different theoretical levels. Three degenerate minima were found and characterized. The most favoured conformation is stabilized by an intramolecular hydrogen bonding interaction. The other two minima correspond to helical and malonamide-like conformations, being 4.6 kcal/mol and 6.9 kcal/mol less stable than the lowest energy conformation, respectively. Influence of solvent effects on the relative stabilities of the different conformations have been accounted using SCRF calculations. Two implicit solvent models have been considered: water and CCl4. The results indicate that in the both cases the conformation with an intramolecular hydrogen bonding interaction retains its lowest energy.

Alanine↗
PubMed2003

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure.

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.

Binding Sites↗
PubMed2002

Carbon-13 NMR shielding in the twenty common amino acids: comparisons with experimental results in proteins.

We have used ab initio quantum chemical techniques to compute the (13)C(alpha) and (13)C(beta) shielding surfaces for the 14 amino acids not previously investigated (R. H. Havlin et al., J. Am. Chem. Soc. 1997, 119, 11951-11958) in their most popular conformations. The spans (Omega = sigma(33) - sigma(11)) of all the tensors reported here are large ( approximately 34 ppm) and there are only very minor differences between helical and sheet residues. This is in contrast to the previous report in which Val, Ile and Thr were reported to have large ( approximately 12 ppm) differences in Omega between helical and sheet geometries. Apparently, only the beta-branched (beta-disubstituted) amino acids have such large CSA span (Omega) differences; however, there are uniformly large differences in the solution-NMR-determined CSA (Deltasigma = sigma(orth) - sigma(par)) between helices and sheets in all amino acids considered. This effect is overwhelmingly due to a change in shielding tensor orientation. With the aid of such shielding tensor orientation information, we computed Deltasigma values for all of the amino acids in calmodulin/M13 and ubiquitin. For ubiquitin, we find only a 2.7 ppm rmsd between theory and experiment for Deltasigma over an approximately 45 ppm range, a 0.96 slope, and an R(2) = 0.94 value when using an average solution NMR structure. We also report C(beta) shielding tensor results for these same amino acids, which reflect the small isotropic chemical shift differences seen experimentally, together with similar C(beta) shielding tensor magnitudes and orientations. In addition, we describe the results of calculations of C(alpha), C(beta), C(gamma)1, C(gamma)2, and C(delta) shifts in the two isoleucine residues in bovine pancreatic trypsin inhibitor and the four isoleucines in a cytochrome c and demonstrate that the side chain chemical shifts are strongly influenced by chi(2) torsion angle effects. There is very good agreement between theory and experiment using either X-ray or average solution NMR structures. Overall, these results show that both C(alpha) backbone chemical shift anisotropy results as well as backbone and side chain (13)C isotropic shifts can now be predicted with good accuracy by using quantum chemical methods, which should facilitate solution structure determination/refinement using such shielding tensor surface information.

Amino Acids↗
PubMed1997

Computer simulation study on the conversion of spirolactone to enones over H-Y zeolite.

We report here the results of computer modeling studies and quantum chemical calculations on the spirolactone-to-enone conversion reaction over the zeolite catalysts, especially H-Y zeolite. We studied the adsorption mode of the molecules inside the supercage of H-Y and the mechanism of electron transfer between organic molecules and the framework of zeolite H-Y by density functional theory (DFT) calculations. Because the organic molecules considered in the present study are less symmetrical we docked the molecule inside the supercage of H-Y and energy minimization was then applied to these docked structures to yield representative low-energy binding sites for the molecules within the host structure. The interaction energy results show that the major interaction is between the methylene hydrogen of the molecule and the oxygen of the framework. The molecular electrostatic potential maps show that the ketonic oxygen of the reactant molecules abstract proton from Brönsted acid site. Thus the mechanism proposed by DFT calculation matches well with the experimental observations.

Computer Simulation↗
PubMed2026

Electromagnetic Radiation Stimulated Learning in Perovskite Nickelates.

Biological plasticity refers to the ability of synapses to strengthen or weaken over time. These adaptive properties play a fundamental role in learning and memory, spanning many orders of magnitude in timescales. Short-term plasticity (STP) arises from rapid correlative activity, while long-term plasticity (LTP) is governed by slower biochemical processes. Here, we investigate electromagnetically driven relaxation dynamics in perovskite nickelate thin films as an analogue of biological learning behaviors. By comparing radio frequency (RF), infrared (IR), visible, and ultraviolet (UV) radiation as stimuli, we find that RF excitation primarily induces STP, while visible and IR illumination lead to reversible relaxation on behavioral timescales. In contrast, UV illumination results in persistent, non-thermal changes in conductivity over extended timescales. Notably, UV-exposed nickelate films exhibit glass-like dynamics, characterized by stretched exponential relaxation and aging phenomena. The films display habituation to repeated stimuli, along with sensitization and spontaneous recovery under controlled environments. A minimal dynamical systems model captures key qualitative features of the UV-induced resistance changes. Our results demonstrate that electromagnetic frequency enables multi-timescale relaxation spanning nearly nine orders of magnitude, suggesting perovskite nickelates as promising platforms for adaptive optoelectronic hardware and for linking computational neuroscience with emerging quantum technologies.

electromagnetic radiation↗
PubMed1995

Microscopic computation in human brain evolution.

When human psychological performance is viewed in terms of cognitive modules, our species displays remarkable differences in computational power. Algorithmically simple computations are generally difficult to perform, whereas optimal routing or "Traveling Salesman" Problems (TSP) of far greater complexity are solved on an everyday basis. It is argued that even "simple" instances of TSP are not purely Euclidian problems in human computations, but involve emotional, autonomic, and cognitive constraints. They therefore require a level of parallel processing not possible in a macroscopic system to complete the algorithm within a brief period of time. A microscopic neurobiological model emphasizing the computational power of excited atoms within the neuronal membrane is presented as an alternative to classical connectionist approaches. The evolution of the system is viewed in terms of specific natural selection pressures driving satisfying computations toward global optimization. The relationship of microscopic computation to the nature of consciousness is examined, and possible mathematical models as a basis for simulation studies are briefly discussed.

Algorithms↗
PubMed1995

Potential energy functions.

When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.

Electrochemistry↗
PubMed2002

Passive water transport in biological pores.

Three kinds of membrane proteins have been shown to have water channels properties: the aquaporins, the cotransporters, and the uniports. A molecular-kinetic description of water transport in pores is compared to analytical models based on macroscopic parameters such as pore diameter and length. The use and limitations of irreversible thermodynamics is discussed. Experimental data on water and solute permeability in aquaporins are reviewed. No unifying transport model based on macroscopic parameters can be set up; for example, there is no correlation between solute diameter and permeability. Instead, the influence of hydrogen bonds between solute and pore, and the pH dependence of permeability, point toward a model based upon chemical interactions. The atomic model for AQP1 based on electron crystallographic data defines the dimensions and chemical nature of the aqueous pore. These structural data combined with quantum mechanical modeling and computer simulation might result in a realistic description of water transport. Data on water and solute permeability in cotransporters and uniports are reviewed. The function of these proteins as substrate transporters involves a series of conformational changes. The role of conformational equilibria on the water permeability will be discussed.

Animals↗
PubMed2002

A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces.

Although the denaturing of adsorbed proteins on biomaterials surfaces is believed to lead to adverse tissue reactions to implanted materials, very little is currently known of the actual mechanisms involved. These mechanisms must be understood if surfaces are to be proactively designed to control protein adsorption behavior. Concepts widely employed in rational drug design and in protein and RNA folding predictions provide a means to approach this problem. Accordingly, a theoretical analysis has been conducted to estimate the thermodynamic contributions (changes in enthalpy, entropy, and Gibbs free energy) for the adsorption of selected individual mid-chain protein residues to functionalized surfaces. Enthalpic contributions from residue-surface interactions were calculated using semi-empirical quantum mechanical-based computational chemistry methods in a simulated aqueous environment (MOPAC/COSMO), and enthalpic and entropic contributions due to water restructuring effects assumed to occur during adsorption were estimated from experimental data for functional group wetting and calculated changes in solvent accessible surface area as each protein residue approached each surface. When combined with intraprotein residue-residue interactions, the understanding of residue-surface adsorption energy relationships provides a means to begin to predict protein adsorption behavior as a function of biomaterials surface chemistry. It is recognized that several assumptions have been made in this approach that could be challenged, and that truncations necessary due to programming limitations have been applied that may neglect potentially important interactions. Therefore, it must be understood that the modeling predictions may not be directly applicable to biomaterials for surface design under actual physiologic conditions at this stage. However, this attempt at modeling fundamental components of protein adsorption is presented as an initial approach to understanding these complex events.

Adsorption↗
PubMed1999

The Galton-Watson branching process as a quantitative tool in parasitology.

Stochastic growth processes abound in the biology of parasitism, and one mathematical tool that is particularly well suited for describing such phenomena is the Galton-Watson branching process. Introduced more than a century ago to settle a debate over the rate of disappearance of surnames in the British peerage, branching processes are applied today in fields as diverse as quantum physics and theoretical computer science. In this article, Dale Taneyhill, Alison Dunn and Melanie Hatcher provide a simple introduction to branching processes, and demonstrate their uses in quantitative parasitology.

Animals↗
PubMed2002

Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR.

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.

Adenine↗
PubMed2002

23Na NMR study of the interaction between hyaluronan and the bications Ca(++), Mg(++) and Cu(++).

The relaxation rate R = pi Delta nu(1/2) of the quadrupolar (23)Na nucleus was measured at pH approximately 7 using a 200 MHz NMR spectrometer with a view to observe the interaction between hyaluronan and its natural counterion Na(+) and the bications Ca(++), Mg(++) and Cu(++). An interpretation of our results, by means of the "entropy of fluctuations" concept of Na(+), is presented. We show that Cu(++) ions are more effective than Ca(++) and Mg(++). A possible model of complexation of Cu(++) in a cage formed by the 1-4 glycosidic bond, the carboxylate side-chain and the acetoamide side-chain is proposed, according to electrostatic potential computations using the ZINDO1 quantum semi empirical method.

Calcium↗
PubMed1981

Theoretical approach for radiosensitizers. Correlation between calculated electroaffinity and sensitization factors of nitro-compounds.

The electron affinity of eight well-known nitroaromatic and nitroheterocyclic radiosensitizers is computed resorting to a quantum mechanical approach. Four of the compounds studied were nitroimidazoles; but p-nitroacetophenone and some 5-nitrofuran derivatives were also investigated for comparison. A good correlation between the theoretical electroaffinity values and the radiosensitization efficiencies is found in the case of the nitroimidazoles, in which the pi-electron system appears to be limited to the aromatic ring, except for small side groups. In the case of molecules where the pi-electron system spreads out on the side-chain the theoretical procedure seems to fail.

Acetophenones↗
PubMed2002

Efficacy of proton pump inhibitor drugs against Plasmodium falciparum in vitro and their probable pharmacophores.

The substituted benzimidazoles omeprazole, lansoprazole, rabeprazole, and pantoprazole were found to have in vitro activity against three different isolates of Plasmodium falciparum: D6 (which is chloroquine and pyrimethamine sensitive), W2 (chloroquine and pyrimethamine resistant), and TM91C235 (multidrug resistant). Lansoprazole and rabeprazole were the most effective against all three isolates, with a 50% inhibitory concentration (IC(50)) range of 7 to 11 microM. Omeprazole showed intermediate activity against D6 and W2 isolates, with IC(50)s of 27 to 28 microM, but had poor activity against TM91C235, with an IC(50) of 76 microM. Pantoprazole was the least effective, with IC(50)s of 73 microM against D6, 53 microM against W2, and 39 microM against TM91C235. A pharmacophore model describing the important features responsible for potent activity of the drugs was developed using computational techniques of semiempirical quantum chemical methods and the three-dimensional QSAR procedure of the CATALYST software. The important features of the pharmacophore, according to the findings based on the CATALYST procedures, are the hydrogen bond acceptor and donor sites at the benzimidine nitrogen atoms and the two aromatic hydrophobic sites in the molecules. AM1 quantum chemical calculations identified the electrostatic potential surface surrounding the sulfoxide atom as crucial for potent activity.

Animals↗
PubMed1989

Determination of electron density, mass density and calcium fraction by mass of soft and osseous tissues by dual energy CT.

Techniques of CT analysis of trabecular regions are concerned with bone mineral assessment, with considerable attention being paid to the effect of unknown fat content. Information concerning mass density and electron density might provide a more complete picture but is not normally obtained. A method for the calculation of mass and electron density, as well as the fraction of calcium by mass, is described and requires only a measurement of effective beam energy on the skin in addition to the CT numbers from a dual energy scan. The method uses the six major elements, H, C, N, O, P and Ca as compartments for the analysis and can also be applied to soft tissue by using only the first four. The calculated mass fraction of Ca is found to be sensitive to fat content and difference between surface and internal energies which can lead to serious underestimates below a fraction of about 0.04. Mass and electron density results are independent of fat content and only marginally affected by energy differences. Results were obtained with simple materials confirming mass density can be calculated to the order of 3% and electron density to considerably better than 1%.

Body Composition↗
PubMedDate not supplied

A two-stage shift register for clocked Quantum-Dot Cellular Automata.

Quantum-Dot Cellular Automata (QCA) is a computational scheme utilizing the position of interacting single electrons within arrays of quantum dots ("cells") to encode and process binary information. Clocked QCA architectures can provide power gain, logic level restoration, and memory features. Using arrays of micron-sized metal dots, we experimentally demonstrate operation of a QCA latch-inverter and a two-stage shift register.

Aluminum↗
PubMed1999

Test of semiclassical amplitudes for quantum ray-splitting systems.

We compute semiclassically and numerically the weights of ray-splitting orbits in the density of states of a rectangular and an annular ray-splitting billiard. The agreement between the semiclassical and the numerical results is very good, confirming the necessity of including reflection and transmission coefficients of non-Newtonian ray-splitting orbits in semiclassical expressions for the density of states of ray-splitting systems.

Journal Article↗