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PubMed2004

Quantum-dot quantum-interference infrared design proposal photodetector: and modeling of performance characteristics.

A novel design of an IR photodetector operating at wavelengths around 10 microm is presented. It is based on a three-level quantum coherence effect in semiconductor quantum dots as measured in balanced-homodyne detection in a Mach-Zehnder interferometer. The advantage of this design is the combination of room-temperature operation and fast response time, whereas the major drawback is the high noise-equivalent power.

Computer Simulation↗
PubMed2002

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis.

Haloalkane dehalogenases catalyze cleavage of the carbon-halogen bond in halogenated aliphatic compounds, resulting in the formation of an alcohol, a halide, and a proton as the reaction products. Three structural features of haloalkane dehalogenases are essential for their catalytic performance: (i) a catalytic triad, (ii) an oxyanion hole, and (iii) the halide-stabilizing residues. Halide-stabilizing residues are not structurally conserved among different haloalkane dehalogenases. The level of stabilization of the transition state structure of S(N)2 reaction and halide ion provided by each of the active site residues in the enzymes DhlA, LinB, and DhaA was quantified by quantum mechanic calculations. The residues that significantly stabilize the halide ion were assigned as the primary (essential) or the secondary (less important) halide-stabilizing residues. Site-directed mutagenesis was conducted with LinB enzyme to confirm location of its primary halide-stabilizing residues. Asn38Asp, Asn38Glu, Asn38Phe, Asn38Gln, Trp109Leu, Phe151Leu, Phe151Trp, Phe151Tyr, and Phe169Leu mutants of LinB were constructed, purified, and kinetically characterized. The following active site residues were classified as the primary halide-stabilizing residues: Trp125 and Trp175 of DhlA; Asn38 and Trp109 of LinB; and Asn41 and Trp107 of DhaA. All these residues make a hydrogen bond with the halide ion released from the substrate molecule, and their substitution results in enzymes with significantly modified catalytic properties. The following active site residues were classified as the secondary halide-stabilizing residues: Phe172, Pro223, and Val226 of DhlA; Trp207, Pro208, and Ile211 of LinB; and Phe205, Pro206, and Ile209 of DhaA. The differences in the halide stabilizing residues of three haloalkane dehalogenases are discussed in the light of molecular adaptation of these enzymes to their substrates.

Amino Acids↗
PubMed2005

Development of a quantum molecular dynamic (QMD) model to describe fission and fragment production.

In this paper is presented the development of a QMD model for the description of the spallation reaction at energies from a few MeV to a few hundred MeV. The QMD model is developed using a new evaporation-fission model, the generalised evaporation model (GEM2). The spectrum of particles and residual nuclide mass and charge distributions in reactions of protons and neutrons with heavy targets (238U, 208Pb, 207Pb and 2206Pb) has been calculated using the QMD+GEM2 model.

Computer Simulation↗
PubMed2001

Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations.

The structure and the conformational behavior of the HIV-1 reverse transcriptase inhibitor, 11-cyclopropyl-5,11dihydro-4-methyl-6H-dipyrido[3,2-b2',3'-e][1,4]diazepin-6-one (nevirapine), is investigated by semiempirical (MNDO, AMI and PM3) method, ab initio at the HF/3-21G and HF/6-31G** levels and density functional theory at the B3LYP/6-31G** level. The fully optimized structure and rotational potential of the nitrogen and carbon bond in the cyclopropyl ring were examined in detail. A similar geometrical minimum is obtained from all methods which shows an almost identical structure to the geometry of the molecule in the complex structure with HIV-1 reverse transcriptase. To get some information on the structure in solution, NMR chemical shift calculations were also performed by a density functional theory at the B3LYP/6-31G** level, using GIAO approximation. The calculated 1H-NMR and 13C-NMR spectra for the energy minimum geometry agree well with the experimental results, which indicated that the geometry of nevirapine in solution is very similar to that of the molecule in the inhibition complex. Furthermore, the obtained results are compared to the conformational studies of other non-nucleoside reverse transcriptase inhibitors and reveal a common agreement of the non-nucleoside reverse transcriptase inhibitors. The specific butterfly-like shape and conformational flexibility within the side chain of the non-nucleoside reverse transcriptase inhibitors play an important role inducing conformational change of HIV-1 reverse transcriptase structure and are essential for the association at the inhibition pocket.

Anti-HIV Agents↗
PubMed1996

Computed radiography X-ray exposure trends.

RATIONALE AND OBJECTIVES: Computed radiography provides correct optical density on film, independent of the incident radiation exposure, but it can result in under- or overexposure of the imaging plate. In the current study, we evaluated the radiation exposure trends of computed radiography over a 2-year period for portable chest examinations to determine and compare the radiographic techniques of the computed radiography system relative to conventional screen-film detectors. METHODS: A Fuji computed radiography system was interfaced to a digital workstation to track system usage and examination demographics, including examination type and sensitivity number. Hard-copy films were used for diagnosis. The sensitivity number, a value inversely related to incident exposure on the imaging plate, was used to determine whether the proper techniques were used by the technologists. RESULTS: The initial use of the computed radiography system revealed a broad distribution of exposures being used; complaints regarding noisy films (e.g., underexposure) resulted in subsequent overexposure for a significant number of films. A quality-control audit indicating excessive exposure resulted in educational feedback and a tighter distribution of exposures within the optimal range as determined by our radiologists. The average technique was approximately equivalent to a 200-speed system. CONCLUSION: Computed radiography provides excellent dynamic range and rescaling capabilities for proper film optical density, and thus fewer repeat examinations. However, underexposure results in suboptimal image quality that is related to excessive quantum mottle. Overexposure requires film audits to limit unnecessary radiation exposure. In general, the optimal exposures are achieved with approximately 1.5-2 times the incident detector exposure of a 400-speed rare-earth system. The ability of computed radiography to reduce radiation exposure is unlikely when compared with a typical rare-earth screen-film combination (400 speed) in terms of adequate image quality for the diagnosis of subtle, low-contrast findings. For certain diagnostic procedures (e.g., nasogastric tube placement verification), lower exposures can be tolerated.

Humans↗
PubMed2005

Quantum drag forces on a sphere moving through a rarefied gas.

As an application of quantum fluid mechanics, we consider the drag force exerted on a sphere by an ultradilute gas. Quantum mechanical diffraction scattering theory enters in that regime wherein the mean free path of a molecule in the gas is large compared with the sphere radius. The drag force is computed in a model specified by the "sticking fraction" of events in which a gaseous molecule is adsorbed by the spherical surface. Classical inelastic scattering theory is shown to be inadequate for physically reasonable sticking fraction values. The quantum mechanical scattering drag force is exhibited theoretically and compared with experimental data.

Journal Article↗
PubMed2002

Synthesis, structure, electronic and vibrational spectra of 9-(Diethylamino)-benzo(a)phenoxazin-7-ium-5-N-methacrylamide.

The electronic and vibrational spectra of 9-(Diethylamino)-benzo(a)phenoxazin-7-ium-5-N-methacrylamide (Nile Blue-5-N-methacrylamide) are measured, and the results are compared with the theoretical values obtained by quantum chemical calculations. The geometry, electronic transitions, charge distribution, and the IR normal modes of this new dye and of its precursor Nile Blue have been computed by using Density Functional Theory (DFT) method with the functional B3LYP and the 6-31G(d) Gaussian basis set. The molecular properties of the two dyes, predicted and observed, are very similar in the electronic ground state. In the excited state, however, the longer lifetime and larger fluorescence quantum yield of the Nile Blue-5-methacrylamide is ascribed to an inhibition of the twisted intramolecular charge transfer (TICT) process, when the NH2 is substituted by the methacrylamide in the 5-position of the aromatic extended ring of the dye. The change in charge density of the N atom in 5-position, as well as the difference in dipole moment and ionization potential of the two dyes molecules, explain the attenuation of TICT process. The vibration spectra of both dyes are simulated properly by using the DFT method.

Lasers↗
PubMed2001

Quantum chemical study of ester aminolysis catalyzed by a single adenine: a reference reaction for the ribosomal peptide synthesis.

Herein we report the results of a HF/6-31+G** and B3LYP/6-31+G** computational investigation of the title reaction for the peptide bond synthesis catalyzed by a single adenine. This system constitutes a reference reaction to study the basic chemical events that have been proposed to occur at the peptidyl transferase active site of ribosomes on the basis of structural determinations (Science 2000, 239, 920--931). Thus, the analysis of the geometry, charge distribution, and energetics of the critical structures involved in this title reaction yields insight into the catalytic mode of action of RNA molecules. Our computational results give further support to the hypotheses that the activated nucleotide A2451 in the ribosome acts as a base catalyst and that this role is similar to that of the His residue in the catalytic triad of serine proteases.

Acetates↗
PubMed1999

Ergodic properties of a generic nonintegrable quantum many-body system in the thermodynamic limit.

We study a generic but simple nonintegrable quantum many-body system of locally interacting particles, namely, a kicked-parameter (t,V) model of spinless fermions on a one-dimensional lattice (equivalent to a kicked Heisenberg XX-Z chain of 1/2 spins). The statistical properties of the dynamics (quantum ergodicity and quantum mixing) and the nature of quantum transport in the thermodynamic limit are considered as the kick parameters (which control the degree of nonintegrability) are varied. We find and demonstrate ballistic transport and nonergodic, nonmixing dynamics (implying infinite conductivity at all temperatures) in the integrable regime of zero or very small kick parameters, and more generally and importantly, also in the nonintegrable regime of intermediate values of kicked parameters, whereas only for sufficiently large kick parameters do we recover quantum ergodicity and mixing implying normal (diffusive) transport. We propose an order parameter (charge stiffness D) which controls the phase transition from nonmixing and nonergodic dynamics (ordered phase, D>0) to mixing and ergodic dynamics (disordered phase, D=0) in the thermodynamic limit. Furthermore, we find exponential decay of time correlation functions in the regime of mixing dynamics. The results are obtained consistently within three different numerical and analytical approaches: (i) time evolution of a finite system and direct computation of time correlation functions, (ii) full diagonalization of finite systems and statistical analysis of stationary data, and (iii) algebraic construction of quantum invariants of motion of an infinite system, in particular the time-averaged observables.

Journal Article↗
PubMed2003

Network visualization system for computational chemistry.

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.

Journal Article↗
PubMed2006

Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes.

Mammalian cytochromes P450 (CYP) are enzymes of great biological and pharmaco-toxicological relevance. Due to their membrane-bound nature, the structural characterization of these proteins is extremely difficult, and therefore computational techniques, such as comparative modeling, may help obtaining reliable structures of members of this family. An important feature of CYP is the presence of an iron-containing porphyrin group at the enzyme active site. This calls for quantum chemical calculations to derive charges and parameters suitable for classical force field-based investigations of this proteins family. In this report, we first carried out density functional theory (DFT) computations to derive suitable charges for the Fe2+-containing heme group of P450 enzymes. Then, by means of the homology modeling technique, and taking advantage of the recently published crystal structure of the human CYP2C9, we built a new model of the human aromatase (CYP19) enzyme. Furthermore, to study the thermal stability of the new model as well as to test the suitability of the new DFT-based heme parameters, molecular dynamics (MD) simulations were carried out on both CYP2C9 and CYP19. Finally, the last few ns of aromatase MD trajectories were investigated following the essential dynamics protocol that allowed the detection of some correlated motions among some protein domains.

Animals↗
PubMed2005

A kinetic study of the reactions of Fe+ with N2O, N2, O2, CO2 and H2O, and the ligand-switching reactions Fe+.X + Y --> Fe+.Y + X (X = N2, O2, CO2; Y = O2, H2O).

A series of reactions involving Fe(+) ions were studied by the pulsed laser ablation of an iron target, with detection of ions by quadrupole mass spectrometry at the downstream end of a fast flow tube. The reactions of Fe(+) with N(2)O, N(2) and O(2) were studied in order to benchmark this new technique. Extending measurements of the rate coefficient for Fe(+) + N(2)O from 773 K to 185 K shows that the reaction exhibits marked non-Arrhenius behaviour, which appears to be explained by excitation of the N(2)O bending vibrational modes. The recombination of Fe(+) with CO(2) and H(2)O in He was then studied over a range of pressure and temperature. The data were fitted by RRKM theory combined with ab initio quantum calculations on Fe(+).CO(2) and Fe(+).H(2)O, yielding the following results (120-400 K and 0-10(3) Torr). For Fe(+) + CO(2): k(rec,0) = 1.0 x 10(-29) (T/300 K)(-2.31) cm(6) molecule(-2) s(-1); k(rec,infinity) = 8.1 x 10(-10) cm(3) molecule(-1) s(-1). For Fe(+) + H(2)O: k(rec,0) = 5.3 x 10(-29) (T/300 K)(-2.02) cm(6) molecule(-2) s(-1); k(rec,infinity) = 2.1 x 10(-9) (T/300 K)(-0.41) cm(3) molecule(-1) s(-1). The uncertainty in these rate coefficients is determined using a Monte Carlo procedure. A series of exothermic ligand-switching reactions were also studied at 294 K: k(Fe(+).N(2) + O(2)) = (3.17 +/- 0.41) x 10(-10), k(Fe(+).CO(2) + O(2)) = (2.16 +/- 0.35) x 10(-10), k(Fe(+).N(2) + H(2)O) = (1.25 +/- 0.14) x 10(-9) and k(Fe(+).O(2) + H(2)O) = (8.79 +/- 1.30) x 10(-10) cm(3) molecule(-1) s(-1), which are all between 36 and 52% of their theoretical upper limits calculated from long-range capture theory. Finally, the role of these reactions in the chemistry of meteor-ablated iron in the upper atmosphere is discussed. The removal rates of Fe(+) by N(2), O(2), CO(2) and H(2)O at 90 km altitude are approximately 0.1, 0.07, 3 x 10(-4) and 1 x 10(-6) s(-1), respectively. The initially formed Fe(+).N(2) and Fe(+).O(2) are converted into the H(2)O complex at approximately 0.05 s(-1). Fe(+).H(2)O should therefore be the most abundant single-ligand Fe(+) complex in the mesosphere below 90 km.

Carbon Dioxide↗
PubMed2006

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath.

A hybrid quantum/classical molecular dynamics approach is applied to a proton transfer reaction represented by a symmetric double well system coupled to a dissipative bath. In this approach, the proton is treated quantum mechanically and all bath modes are treated classically. The transition state theory rate constant is obtained from the potential of mean force, which is generated along a collective reaction coordinate with umbrella sampling techniques. The transmission coefficient, which accounts for dynamical recrossings of the dividing surface, is calculated with a reactive flux approach combined with the molecular dynamics with quantum transitions surface hopping method. The hybrid quantum/classical results agree well with numerically exact results in the spatial-diffusion-controlled regime, which is most relevant for proton transfer in proteins. This hybrid quantum/classical approach has already been shown to be computationally practical for studying proton transfer in large biological systems. These results have important implications for future applications to hydrogen transfer reactions in solution and proteins.

Biophysics↗
PubMed2006

Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis.

The transport of ammonium across the cell membrane represents an important biological process in all living organisms. The mechanisms for ammonium translocation were analyzed by computer simulations based on first principles. Intermolecular interaction energies between the differentially methylated ammonium and the ammonium channel protein AmtB were calculated by means of the supermolecular approach at the MP2/6-311+G* level based on the high-resolution crystal structures of ligand-bound protein complexes. Our analysis attributes the molecular determinants for protein-ligand recognition in ammonium transporter AmtB to the aromatic cage formed by three aromatic residues Phe103, Phe107, and Trp148, as well as Ser219. The former residues are involved in cation-pi interactions with the positively charged methylated ammoniums. The latter residue acts as a hydrogen bond acceptor to ammonium. Thus, this work provides directly the missing evidence for the hypothesized role played by the wider vestibule site of AmtB at the periplasmic side of the membrane in "recruiting" NH(4)(+) or methylammonium ions as proposed by Khademi et al. (Science 2004, 305, 1587). In addition, a hybrid quantum mechanics/molecular mechanics scheme was applied to optimize the structures of differentially methylated ammoniums in the AmtB protein, which generated structural and energetic data that provide a satisfactory explanation to the experimental observation that tetramethylammonium is not inhibitory to conducting ammonium and methylammonium in the ammonium transport channel.

Journal Article↗
PubMed2002

Transportable automated ammonia sensor based on a pulsed thermoelectrically cooled quantum-cascade distributed feedback laser.

A compact ammonia sensor based on a 10-microm single-frequency, thermoelectrically cooled, pulsed quantum-cascade laser with an embedded distributed feedback structure has been developed. To measure NH3 concentrations, we scanned the laser over two absorption lines of its fundamental v2 band. A sensitivity of better than 0.3 parts per million was achieved with just a 1-m optical path length. The sensor is computer controlled and automated to monitor NH3 concentrations continuously for extended periods of time and to store data in the computer memory.

Ammonia↗
PubMed1999

Quantum mechanical analysis of oxygenated and deoxygenated states of hemocyanin: theoretical clues for a plausible allosteric model of oxygen binding.

In this work with ab initio computations, we describe relevant interactions between protein active sites and ligands, using as a test case arthropod hemocyanins. A computational analysis of models corresponding to the oxygenated and deoxygenated forms of the hemocyanin active site is performed using the Density Functional Theory approach. We characterize the electron density distribution of the binding site with and without bound oxygen in relation to the geometry, which stems out of the crystals of three hemocyanin proteins, namely the oxygenated form from the horseshoe crab Limulus polyphemus, and the deoxygenated forms, respectively, from the same source and from another arthropod, the spiny lobster Panulirus interruplus. Comparison of the three available crystals indicate structural differences at the oxygen binding site, which cannot be explained only by the presence and absence of the oxygen ligand, since the geometry of the ligand site of the deoxygenated Panulirus hemocyanin is rather similar to that of the oxygenated Limulus protein. This finding was interpreted in the frame of a mechanism of allosteric regulation for oxygen binding. However, the cooperative mechanism, which is experimentally well documented, is only partially supported by crystallographic data, since no oxygenated crystal of Panulirus hemocyanin is presently available. We address the following question: is the local ligand geometry responsible for the difference of the dicopper distance observed in the two deoxygenated forms of hemocyanin or is it necessary to advocate the allosteric regulation of the active site conformations in order to reconcile the different crystal forms? We find that the difference of the dicopper distance between the two deoxygenated hemocyanins is not due to the small differences of ligand geometry found in the crystals and conclude that it must be therefore stabilized by the whole protein tertiary structure.

Allosteric Regulation↗
PubMed2002

Biological adaptabilities and quantum entropies.

The entropy-based theory of adaptability set forth by Michael Conrad in the early 1970s continued to appear in his work for over two decades, and was the subject of the only book he published in his lifetime. He applied this theory to a host of subjects ranging from enzyme dynamics to sociology. This paper reviews the formalism of adaptability theory, clarifying some of its mathematical and interpretive difficulties. The theory frames the computational tradeoff principle, a thesis that was the most frequently recurring claim in his work. The formulation of adaptability theory presented here allows the introduction of quantum entropy functions into the theory, revealing an interesting relationship between adaptability and another one of Conrad's deep preoccupations, the role of quantum processes in life.

Adaptation, Physiological↗