[Chemical structure-biological activity relationship].
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Computers↗
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Results for “quantum computing”
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[The possible role of rare tautomers of DNA bases in mutagenesis: study of the effect of hydration on tautomeric equilibrium by the Monte-Carlo method].
Monte Carlo simulation of hydration of keto and enol tautomers of 9-methylguanine (G) and 1-methyluracil (U) has been performed in relation to a possible role of tautomer transitions of DNA bases in mutagenesis. The comparison of the simulation results with published experimental data and results of quantum mechanical computations leads us to conclusion about difference in the origins of keto-form prevalence in water solutions of G and U. Such a reason for uracil (thymine) is a greater intrinsic stability of keto tautomer while the more preferable hydration of keto form of G is the reason of its predominance. As a consequence, during biosynthesis less hydrophylic environment (as compared to water solution) can be a reason for guanine transition into enol form and can result in mispair formation. Such a mutation mechanism is of a minor probability through thymine (uracil) tautomerization.
DNA↗
[The hydration of acetylcholine and its conformation in solution].
Quantum-mechanical computations performed by the ab initio self-consistent field molecular orbital method have been used for the determination of the principal hydration sites of acetylcholine in its gauche et trans conformations. The hydration destabilizes the gauche form with respect to the trans one by about 2 kcal/mole. Taking into account, however, that the gauche form is 3 kcal/mole intrinsically more stable, this form still remains the most stable one of acetylcholine in solution.
Acetylcholine↗
The Dirac equation in quantum chemistry: strategies to overcome the current computational problems.
A perspective on the use of the relativistic Dirac equation in quantum chemistry is given. It is demonstrated that many of the computational problems that plague the current implementations of the different electronic structure methods can be overcome by utilizing the locality of the small component wave function and density. Possible applications of such new and more efficient formulations are discussed.
Journal Article↗
Bio-computational model of object-recognition: quantum Hebbian processing with neurally shaped Gabor wavelets.
Theoretical and simulational evidence, as well as experimental indications, are accumulating that quantum associative memory and imaging are possible. We compare these data with biological evidence, since we find them to a significant extent compatible. This paper presents a computationally implementable integrative model of appearance-based viewpoint-invariant recognition of objects. The neuro-quantum hybrid model incorporates neural processing up to V1 and quantum associative processing in V1, achieving together an object-recognition result in V2 and ITC. Results of our simulation of the central quantum-like parts of the bio-model, receiving neurally pre-processed inputs, are presented. This part contains our original simulated storage by multiple quantum interference of image-encoding Gabor wavelets done in a Hebbian way, especially using the Griniasty et al. pose-sequence learning rule.
Humans↗
[Toward observing chemical reactions of proteins with quantum chemistry].
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Computers↗
Salt or ion bridges in biological systems: a study employing quantum and molecular mechanics.
Equilibrium geometries and binding energies of model "salt" or "ion" bridge systems have been computed by ab initio quantum chemistry techniques (GAUSSIAN82) and by empirical force field techniques (AMBER2.0). Formate and dimethyl phosphate served as anions in the model compounds while interacting with several organic cations, including methyl ammonium, methyl guanidinium, and divalent metal ion (either Mg2+ or Ca2+) without and with an additional chloride; and a divalent metal ion (either Mg2+ or Ca2+), chloride, and four water molecules of hydration about the metal ion. The majority of the quantum chemical computations were performed using a split-valence basis set. For the model compounds studied we find that the ab initio optimized geometries are in remarkably good agreement with the molecular mechanics geometries. Several calculations were also performed using diffuse fractions. The formate anion binds these model cations more strongly than does dimethyl phosphate, while the organic cation methyl ammonium binds model anions more strongly than does methyl guanidinium. Finally, in model compounds including organic anions, Mg2+ or Ca2+ and four molecules of water, and a chloride anion, we find that the equilibrium structure of the magnesium complex involves a solvent separated ion pair (the magnesium ion is six coordinate), whereas the calcium ion complex remains seven coordinate. Molecular mechanics overestimates binding energies, but the estimates may be close enough to actual binding energies to give useful insight into the details of salt bridges in biological systems.
Chemical Phenomena↗
Electron-attachment resonances of glycine zwitterions from quantum scattering calculations: modeling macrosolvation effects.
A computational study of the quantum dynamics for low-energy electrons scattered by the isolated zwitterionic species of the glycine molecule is carried out using a model interaction potential described in the main text. The macroscopic effects of water solvation on the target molecule in the electron scattering problem are described through a continuum polarizable model (CPCM) which modifies the target molecular structure. In such a way, realistic molecular orbitals depicting the glycine zwitterion in solution are used to model the electron-molecule interaction. The results of the calculations indicate the presence of five different transient negative ions (TNIs) formed at energies from the threshold and up to about 6 eV. Although no nuclear motion was explicitly considered in the ensuing decay processes, the analysis of the nodal structures and density distributions for the resonant excess electron wavefunctions over the molecular space suggests possible anionic fragmentations that produce (Gly-H)-, H-, -CO2-, and -NH3. The likely consequences of such releases into the medium are briefly discussed.
Electrons↗
Experimental implementation of an adiabatic quantum optimization algorithm.
We report the realization of a nuclear magnetic resonance computer with three quantum bits that simulates an adiabatic quantum optimization algorithm. Adiabatic quantum algorithms offer new insight into how quantum resources can be used to solve hard problems. This experiment uses a particularly well-suited three quantum bit molecule and was made possible by introducing a technique that encodes general instances of the given optimization problem into an easily applicable Hamiltonian. Our results indicate an optimal run time of the adiabatic algorithm that agrees well with the prediction of a simple decoherence model.
Journal Article↗
Consciousness, the brain, and spacetime geometry.
What is consciousness? Conventional approaches see it as an emergent property of complex interactions among individual neurons; however these approaches fail to address enigmatic features of consciousness. Accordingly, some philosophers have contended that "qualia," or an experiential medium from which consciousness is derived, exists as a fundamental component of reality. Whitehead, for example, described the universe as being composed of "occasions of experience." To examine this possibility scientifically, the very nature of physical reality must be re-examined. We must come to terms with the physics of spacetime--as described by Einstein's general theory of relativity, and its relation to the fundamental theory of matter--as described by quantum theory. Roger Penrose has proposed a new physics of objective reduction: "OR," which appeals to a form of quantum gravity to provide a useful description of fundamental processes at the quantum/classical borderline. Within the OR scheme, we consider that consciousness occurs if an appropriately organized system is able to develop and maintain quantum coherent superposition until a specific "objective" criterion (a threshold related to quantum gravity) is reached; the coherent system then self-reduces (objective reduction: OR). We contend that this type of objective self-collapse introduces non-computability, an essential feature of consciousness which distinguishes our minds from classical computers. Each OR is taken as an instantaneous event--the climax of a self-organizing process in fundamental spacetime--and a candidate for a conscious Whitehead "occasion of experience." How could an OR process occur in the brain, be coupled to neural activities, and account for other features of consciousness? We nominate a quantum computational OR process with the requisite characteristics to be occurring in cytoskeletal micro-tubules within the brain's neurons. In this model, quantum-superposed states develop in microtubule subunit proteins ("tubulins") within certain brain neurons, remain coherent, and recruit more superposed tubulins until a mass-time-energy threshold (related to quantum gravity) is reached. At that point, self-collapse, or objective reduction (OR), abruptly occurs. We equate the pre-reduction, coherent superposition ("quantum computing") phase with pre-conscious processes, and each instantaneous (and non-computable) OR, or self-collapse, with a discrete conscious event. Sequences of OR events give rise to a "stream" of consciousness. Microtubule-associated proteins can "tune" the quantum oscillations of the coherent superposed states; the OR is thus self-organized, or "orchestrated" ("Orch OR"). Each Orch OR event selects (non-computably) microtubule subunit states which regulate synaptic/neural functions using classical signaling. The quantum gravity threshold for self-collapse is relevant to consciousness, according to our arguments, because macroscopic superposed quantum states each have their own spacetime geometries. These geometries are also superposed, and in some way "separated," but when sufficiently separated, the superposition of spacetime geometries becomes significantly unstable and reduces to a single universe state. Quantum gravity determines the limits of the instability; we contend that the actual choice of state made by Nature is non-computable. Thus each Orch OR event is a self-selection of spacetime geometry, coupled to the brain through microtubules and other biomolecules. If conscious experience is intimately connected with the very physics underlying spacetime structure, then Orch OR in microtubules indeed provides us with a completely new and uniquely promising perspective on the difficult problems of consciousness.
Brain↗
Demonstration of a quantum teleportation network for continuous variables.
Quantum teleportation involves the transportation of an unknown quantum state from one location to another, without physical transfer of the information carrier. Although quantum teleportation is a naturally bipartite process, it can be extended to a multipartite protocol known as a quantum teleportation network. In such a network, entanglement is shared between three or more parties. For the case of three parties (a tripartite network), teleportation of a quantum state can occur between any pair, but only with the assistance of the third party. Multipartite quantum protocols are expected to form fundamental components for larger-scale quantum communication and computation. Here we report the experimental realization of a tripartite quantum teleportation network for quantum states of continuous variables (electromagnetic field modes). We demonstrate teleportation of a coherent state between three different pairs in the network, unambiguously demonstrating its tripartite character.
Journal Article↗
Computer studies on the stereostructure and quantum chemical properties of 6-pyruvoyl tetrahydropterin, the key intermediate of tetrahydrobiopterin biosynthesis.
The optimized geometry of the conformation of atoms constituting the 6-pyruvoyl tetrahydropterin molecule, the labile key intermediate of tetrahydrobiopterin biosynthesis, was obtained by molecular orbital calculations within the MINDO/3 framework. The stereostructure of the molecule showing the preferred mode for binding to sepiapterin reductase or pyruvoyl tetrahydropterin reductase was drawn in perspective. The resulting structure with the equatorial staggered configuration of the 6-1',2'-dioxopropyl (pyruvoyl) side chain indicated that O(1') and H(6) were located in the trans position around the C(6)-C(1') bond and that the two vicinal carbonyls in the side chain were fixed in the incomplete trans form. The calculation of atomic charges and LUMO coefficients of these carbonyls suggests that the C2'-carbonyl may be more reactive toward NADPH than the C1'-carbonyl in the enzymatic reaction.
Alcohol Oxidoreductases↗
Subsecond multi-slice computed tomography: basics and applications.
The recent advent of multislice-scanning is the first real quantum leap in computed tomography since the introduction of spiral CT in the early 90s. We discuss basic theoretical considerations important for the design of multislice scanners. Then, specific issues, like the design of the detector and spiral interpolation schemes are addressed briefly for the SOMATOM PLUS 4 Volume Zoom. The theoretical concepts are validated with phantom measurements. We finally show the large potential of the new technology for clinical applications. The concurrent acquisition of multiple slices results in a dramatic reduction of scan time for a given scan technique. This allows scanning volumes previously inaccessible. Similarly, given volumes can be scanned at narrower collimation, i.e. higher axial resolution in a given time. From data acquired at narrow collimation, both high-resolution studies and standard images can be reconstructed in the so-called Combi-Mode. This on the one hand reduces dose exposure to the patient because repeated scanning of a patient is no longer required. On the other hand, standard reconstructions benefit from narrow collimation as Partial Volume Artifacts are drastically suppressed. The rotational speed of 0.5 s of the SOMATOM PLUS 4 Volume Zoom furthermore opens up a whole range of new applications in cardiac CT. For the first time, virtually motion-free images can be acquired even for large volumes in a single breathhold by the combination of fast rotation and ECG triggering, respectively gating. We explain the underlying concepts and present initial results. The paper concludes with a brief discussion of the impact of the new technique on image display and postprocessing.
Artifacts↗
A neural networks-based drug discovery approach and its application for designing aldose reductase inhibitors.
A novel approach that combines neural networks, computer docking and quantum mechanical method is developed to design potent aldose reductase inhibitors (ARIs). Neural networks is employed to determine the quantitative structure-activity relationship (QSAR) among the known ARIs. The physical descriptors of the neural networks, such as electronegativity and molar volume, are evaluated with first-principles quantum mechanical method. Based on the QSAR, new candidates for ARI are predicted, and subsequently screened via computer docking technique. The surviving candidates are further tested via quantum mechanical calculation for their bindings to aldose reductase. We find that the best 49 predicted ARI candidates have better calculated binding energies than those of experimentally known drug candidates.
Aldehyde Reductase↗
Electronic structure of 3d[M(H2O)6](3+) ions from Sc(III) to Fe(III): a quantum mechanical study based on DFT computations and natural bond orbital analyses.
The metal-donor atom bonding along the series of 3d[M(H2O)6](3+) ions from Sc(3+) to Fe(3+) has been investigated by density-functional calculations combined with natural localized bond orbital analyses. The M-OH(2) bonds were considered as donor-acceptor bonds, and the contributions coming from the metal ion's 3d sigma-, 3d pi-, and 4s sigma-interactions were treated individually. In this way, the total amount of charge transferred from the water oxygen-donor atoms toward the appropriate metal orbitals could be analyzed in a straightforward manner. One result obtained along these lines is that the overall extent of ligand-to-metal charge transfer shows a strong correlation to the hydration enthalpies of the aqua metal ions. If the contributions to the total ligand-to-metal ion charge transfer are divided into sigma- and pi-contributions, it turns out that Cr(3+) is the best sigma-acceptor, but its pi-accepting abilities are the weakest along the series. Fe(3+) is found to be the best pi-acceptor among the 3d hexaaqua ions studied. Its aptitude to accept sigma-electron density is the second weakest along the series and only slightly higher than that of Sc(3+) (the least sigma-acceptor of all ions) because of the larger involvement of the Fe(3+) 4s orbital in sigma-bonding. The strengths of the three types of bonding interactions have been correlated with the electron affinities of the different metal orbitals. Deviations from the regular trends of electron affinities along the series were found for those [M(H2O)6](3+) ions that are subject to Jahn-Teller distortions. In these cases (d(1) = [Ti(H2O)6](3+), d(2) = [V(H2O)6](3+), and d(4) = [Mn(H2O)6](3+)), ligand-to-metal charge transfer is prevented to go into those metal orbitals that contain unpaired d electrons. A lowering of the complex symmetry is observed and coupled with the following variations: The Ti(3+)- and V(3+)-hexaaqua ions switch from T(h)() to C(i)() symmetry while the Mn(3+)-hexaaqua ion moves to D(2)(h)() symmetry. The loss of orbital overlap leading to a diminished ligand-to-metal charge transfer toward the single occupied metal orbitals is compensated by amplified bonding interactions of the ligand orbitals with the unoccupied metal orbitals to some extent.
Journal Article↗
Nonadiabatic quantum-classical reaction rates with quantum equilibrium structure.
Time correlation function expressions for quantum reaction-rate coefficients are computed in a quantum-classical limit. This form for the correlation function retains the full quantum equilibrium structure of the system in the spectral density function but approximates the time evolution of the operator by quantum-classical Liouville dynamics. Approximate analytical expressions for the spectral density function, which incorporate quantum effects in the many-body environment and reaction coordinate, are derived. The results of numerical simulations of the reaction rate are presented for a reaction model in which a two-level system is coupled to a bistable oscillator which is, in turn, coupled to a bath of harmonic oscillators. The nonadiabatic quantum-classical dynamics is simulated in terms of an ensemble of surface-hopping trajectories and the effects of the quantum equilibrium structure on the reaction rate are discussed.
Journal Article↗
Computational study of many-dimensional quantum energy flow: From action diffusion to localization.
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Journal Article↗
Rational design of anticonvulsants: a quantum pharmacologic study of the ion channel-modulating FMRFamide tetrapeptide as an endogenous anticonvulsant.
We applied the computational techniques of quantum pharmacology to examine molecular conformations (shapes and geometries) of the tetrapeptide FMR-Famide (L-Phe-L-Met-L-Arg-L-Phe-NH2), determining the geometric features necessary for anticonvulsant activity. The rigorous tiered hierarchical approach used molecular mechanics, molecular dynamics, and semiempirical quantum mechanics calculational methods. Low-energy conformations showed pertinent conformational information to be considered in the rational design of novel anticonvulsants. The FMRFamide peptide backbone assumes a bent but primary planar geometry. Distinct polar and nonpolar regions are created as the two Phe residues occupy one "face" of the bent conformation, while the Met and Arg residues occupy the opposite face. The aromatic rings point away from each other along the backbone, and this separation is consistent among the low-energy conformations at approximately 11-12 A. The Met side chain interacts with neither the peptide backbone nor the side chains of other residues. Molecular mechanics and semiempirical quantum mechanics calculations predict limited variation in the orientation of the Arg side chain.
Algorithms↗