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PubMed2000

Quantum information processing with semiconductor macroatoms.

An all optical implementation of quantum information processing with semiconductor macroatoms is proposed. Our quantum hardware consists of an array of quantum dots and the computational degrees of freedom are energy-selected interband optical transitions. The quantum-computing strategy exploits exciton-exciton interactions driven by ultrafast multicolor laser pulses. Contrary to existing proposals based on charge excitations, our approach does not require time-dependent electric fields, thus allowing for a subpicosecond, decoherence-free, operation time scale in realistic semiconductor nanostructures.

Journal Article↗

PubMedDate not supplied

[Input and output channels of quantum biocomputers].

It is proposed that "Quantum Molecular" computer of a neuron consists of the cell cytoskeleton serving as calculating media and input ionic channel sending a hypersound signal to observe these media. The sound spreads through the media travelling along microtubules and microfilaments and switching between those via molecular bridges which serve as elementary switches. The whole system works like a wave guiding net connecting input ionic channels (which generate different sound signals) and output ionic channels (which are controlled by the processed sound signals). Thus the output of such systems depends on the input (controlled by synaptic activity) and on the construction and state of these calculating media. We think that the sound waves spreading through different calculating media solve different physical problems. The construction of the calculating part of the cytoskeleton, according to the hypothesis, is different in different neurons. It is defined by special protein which is produced by DNA, RNA and protein molecular word processor (during brain development and, may be, education). We comment on how the existence of an extremal computer produces an impact on physics and mathematics exemplified by the optimality principle as substitution of physical relativity principle for a complex problem.

Brain↗

PubMed2003

Spin dynamics from majorana fermions.

Using the Majorana fermion representation of spin-1/2 local moments, we show how the dynamic spin correlation and susceptibility are obtained directly from the one-particle Majorana propagator. We illustrate our method by applying it to the spin dynamics of a nonequilibrium quantum dot, computing the voltage-dependent spin relaxation rate and showing that, at weak coupling, the fluctuation-dissipation relation for the spin of a quantum dot is voltage dependent. We confirm the voltage-dependent Curie susceptibility recently found by Parcollet and Hooley [Phys. Rev. B 66, 085315 (2002)]].

Journal Article↗

PubMed2003

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.

Journal Article↗

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↗

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↗

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↗

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↗

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↗

PubMed2004

Calculated volume and energy profiles for water exchange on t2g6 rhodium(III) and iridium(III) hexaaquaions: conclusive evidence for an Ia mechanism.

An I(a) mechanism was assigned for water exchange on the hexaaquaions Rh(OH(2))(6)(3+) and Ir(OH(2))(6)(3+) on the basis of negative Delta V(++) experimental values (-4.2 and -5.7 cm(3) mol(-1), respectively). The use of Delta V(++) as a mechanistic criterion was open to debate primarily because Delta V(++) could be affected by extension or compression of the nonparticipating ligand bond lengths on going to the transition state of an exchange process. In this paper, volume and energy profiles for two distinct water exchange mechanisms (D and I(a)) have been computed using quantum chemical calculations which include hydration effects. The activation energy for Ir(OH(2))(6)(3+) is 32.2 kJ mol(-1) in favor of the I(a) mechanism (127.9 kJ mol(-1)), as opposed to a D pathway; the value for the I(a) mechanism being close to Delta H(++) and Delta G(++) experimental values (130.5 kJ mol(-1) and 129.9 kJ mol(-1) at 298 K, respectively). Volumes of activation, computed using Connolly surfaces and for the I(a) pathway (DeltaV(++)(calc) = -3.9 and -3.5 cm(3) mol(-1), respectively, for Rh(3+) and Ir(3+)), are in agreement with the experimental values. Further, it is demonstrated for both mechanisms that the contribution to the volume of activation due to the changes in bond lengths between Ir(III) and the spectator water molecules is negligible: -1.8 for the D, and -0.9 cm(3) mol(-1) for I(a) mechanism. This finding clarifies the debate about the interpretation of Delta V(++) and unequivocally confirms the occurrence of an I(a) mechanism with retention of configuration and a small a character for both Rh(III) and Ir(III) hexaaquaions.

Journal Article↗

PubMed2002

Electron density of semi-bridging carbonyls. Metamorphosis of CO ligands observed via experimental and theoretical investigations on [FeCo(CO)(8)](-).

The electron density distribution in a transition-metal dimer containing a semibridging carbonyl is determined through experimental X-ray diffraction and quantum chemical computations. The changes occurring during the evolution from terminal to bridging coordinations are described by a "structure-correlation-like" approach and by a theoretical investigation along the conversion path. The smooth continuum of conformations observed in the solid state is explained in terms of the mutual interplay of direct M-M and M-CO and indirect M- - -M and M- - -C interactions, which can be characterized by interatomic delocalization indexes, within the framework of Quantum Theory of Atoms in Molecules.

Journal Article↗

PubMed2000

Neural network methods for identification and optimization of quantum mechanical features needed for bioactivity.

This paper presents a new approach to the discovery and design of bioactive compounds. The focus of this application will be on the analysis of enzymatic inhibitors. At present the discovery of enzymatic inhibitors for therapeutic use is often accomplished through random searches. The first phase of discovery is a random search through a large pre-fabricated chemical library. Many molecules are tested with refined enzyme for signs of inhibition. Once a group of lead compounds have been discovered the chemical intuition of biochemists is used to find structurally related compounds that are more effective. This step requires new molecules to be conceived and synthesized, and it is the most time-consuming and expensive step. The development of computational and theoretical methods for prediction of the molecular structure that would bind most tightly prior to synthesis and testing, would facilitate the design of novel inhibitors. In the past, our work has focused on solving the problem of predicting the bioactivity of a molecule prior to synthesis. We used a neural network trained with the bioactivity of known compounds to predict the bioactivity of unknown compounds. In our current work, we use a separate neural network in conjunction with a trained neural network in an attempt to gain insight as to how to modify existing compounds and increase their bioactivity.

Enzyme Inhibitors↗

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↗

PubMed2004

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy.

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.

Algorithms↗

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↗