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PubMedDate not supplied

Experimental realization of Shor's quantum factoring algorithm using nuclear magnetic resonance.

The number of steps any classical computer requires in order to find the prime factors of an l-digit integer N increases exponentially with l, at least using algorithms known at present. Factoring large integers is therefore conjectured to be intractable classically, an observation underlying the security of widely used cryptographic codes. Quantum computers, however, could factor integers in only polynomial time, using Shor's quantum factoring algorithm. Although important for the study of quantum computers, experimental demonstration of this algorithm has proved elusive. Here we report an implementation of the simplest instance of Shor's algorithm: factorization of N = 15 (whose prime factors are 3 and 5). We use seven spin-1/2 nuclei in a molecule as quantum bits, which can be manipulated with room temperature liquid-state nuclear magnetic resonance techniques. This method of using nuclei to store quantum information is in principle scalable to systems containing many quantum bits, but such scalability is not implied by the present work. The significance of our work lies in the demonstration of experimental and theoretical techniques for precise control and modelling of complex quantum computers. In particular, we present a simple, parameter-free but predictive model of decoherence effects in our system.

Journal Article↗

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

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↗

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↗

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↗

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↗