Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

On the quantum mechanical scattering statistics of many particles

The probability of a quantum particle being detected in a given solid angle is determined by the S-matrix. The explanation of this fact in time-dependent scattering theory is often linked to the quantum flux, since the quantum flux integrated against a (detector-) surface and over a time interval can be viewed as the probability that the particle crosses this surface within the given time interval. Regarding many particle scattering, however, this argument is no longer valid, as each particle arrives at the detector at its own random time. While various treatments of this problem can be envisaged, here we present a straightforward Bohmian analysis of many particle potential scattering from which the S-matrix probability emerges in the limit of large distances.

Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modelled using RRKM theory, based on Eo values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k∞ values in the range 1.9 to 4.5 × 10-10 cm3 molecule-1 s-1. These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16 and 67% of the collision rates for these reactions. In the reaction of SiH2 + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalysed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H2O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

The reaction between silylene and ammonia: some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH3. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ/pulse) fitted the Arrhenius equation: log(k/cm3 molecule-1 s-1) = (-10.37 ± 0.17) + (0.36 ± 1.12 kJ mol-1)/RTln10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10-100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ/pulse. Ab initio calculations at the G3 level of theory, show that SiH2 + NH3 should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH2 + NH3 should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH2 decays are better explained by reaction of SiH2 with the amino radical, NH2, formed by photodissociation of NH3 at 193 nm. The mechanism of this previously unstudied reaction is discussed.

Multivariate analysis of the dielectric response of materials modeled using networks of resistors and capacitors

We discuss the modeling of dielectric responses of electromagnetically excited networks which are composed of a mixture of capacitors and resistors. Such networks can be employed as lumped-parameter circuits to model the response of composite materials containing conductive and insulating grains. The dynamics of the excited network systems are studied using a state space model derived from a randomized incidence matrix. Time and frequency domain responses from synthetic data sets generated from state space models are analyzed for the purpose of estimating the fraction of capacitors in the network. Good results were obtained by using either the time-domain response to a pulse excitation or impedance data at selected frequencies. A chemometric framework based on a Successive Projections Algorithm (SPA) enables the construction of multiple linear regression (MLR) models which can efficiently determine the ratio of conductive to insulating components in composite material samples. The proposed method avoids restrictions commonly associated with Archie’s law, the application of percolation theory or Kohlrausch-Williams-Watts models and is applicable to experimental results generated by either time domain transient spectrometers or continuous-wave instruments. Furthermore, it is quite generic and applicable to tomography, acoustics as well as other spectroscopies such as nuclear magnetic resonance, electron paramagnetic resonance and, therefore, should be of general interest across the dielectrics community.

Fractional quantum Hall effect in second subband of a 2DES

In the present paper we report on the experimental electron sheet density vs. magnetic field diagram for the magnetoresistance R(xx) of a two-dimensional electron system (2DES) with two occupied subbands. For magnetic fields above 9T, we found fractional quantum Hall levels centered around the filing factor v = 3/2 in both the two occupied electric subbands. We focused specially on the fractional levels of the second subband, whose experimental values of the magnetic field B of their minima do not obey a periodicity law in 1/|B-B(c)|, where B(c) is the critical field at the filling factor v = 3/2, and we explain this fact entirely in the framework of the composite fermions theory. We use a simple theoretical model to give a possible explanation for the fact. Copyright (c) EPLA, 2011

The effect of confinement on the temperature dependence of the excitonic transition energy in GaAs/Al(x)Ga(1-x)As quantum wells

We determined by means of photoluminescence measurements the dependence on temperature of the transition energy of excitons in GaAs/Al(x)Ga(1-x)As quantum wells with different alloy concentrations (with different barrier heights). Using a fitting procedure, we determined the parameters which describe the behavior of the excitonic transition energy as a function of temperature according to three different theoretical models. We verified that the temperature dependence of the excitonic transition energy does not only depend on the GaAs material but also depends on the barrier material, i.e. on the alloy composition. The effect of confinement on the temperature dependence of the excitonic transition is discussed.

Surface and Quantum Confinement Effects in ZnO Nanocrystals

ZnO nanocrystals are studied using theoretical calculations based on the density functional theory. The two main effects related to the reduced size of the nanocrystals are investigated: quantum confinement and a large surface:volume ratio. The effects of quantum confinement are studied by saturating the surface dangling bonds of the nanocrystals with hypothetical H atoms. To understand the effects of the surfaces of the nanocrystals, all saturation is removed and the system is relaxed to its minimum energy position. Several different surface motifs are reported, which should be observed experimentally. Spin-polarized calculations are performed in the nonsaturated nanocrystals, leading to different magnetic moments. We propose that this magnetic moment can be responsible for the intrinsic magnetism observed in ZnO nanostructures.

Weak antilocalization in HgTe quantum wells near a topological transition

The anomalous alternating magnetoresistivity in HgTe quantum wells with thicknesses of 5.8 and 8.3 nm, i.e., near the transition from the direct band spectrum to an inverted spectrum, has been revealed and analyzed. It has been shown that the revealed anomalous alternating magnetoresistivity in wells with an inverted spectrum is well described by the theory developed by S.V. Iordanskii et al. [JETP Lett. 60, 206 (1994)] and W. Knap et al. [Phys. Rev. B 53, 3912 (1996)]. A detailed comparison of the experimental data with the theory indicates the presence of only the cubic term in the spin splitting of the electronic spectrum. The applicability conditions of the mentioned theory are not satisfied in a well with a direct gap and, for this reason, such a certain conclusion is impossible. The results indicate the existence of a strong spin-orbit interaction in symmetric HgTe quantum wells near the topological transition.

QUANTUM HALL FERROMAGNET IN A DOUBLE WELL WITH VANISHING g-FACTOR.

We have studied the quantum Hall effect in Al(x)Ga(1-x)As-double well structure with vanishing g-factor. We determined the density-magnetic field n(s) - B diagrams for the longitudinal resistance R(xx). In spite of the fact that the n(s) - B diagram for conventional GaAs double wells shows a striking similarity with the theory, we observed the strong difference between these diagrams for double wells with vanishing g-factor. We argue that the electron-electron interaction is responsible for unusual behavior of the Landau levels in such a system.

MAGNETORESISTANCE OSCILLATIONS IN DOUBLE QUANTUM WELLS UNDER MICROWAVE IRRADIATION

We report in detail oscillatory magnetoresistance in double quantum wells under microwave irradiation. The experimental investigation contains measurements of frequency, power and temperature dependence. In theory, the observed interference oscillations are explained in terms of the influence of subband coupling on the frequency-dependent photoinduced part of the electron distribution function. Thus, the magnetoresistance shows the interference of magneto-intersubband and conventional microwave induced resistance oscillations.

Effects of confinement on the electron-phonon interaction in Al(0.18)Ga(0.82)As/GaAs quantum wells

Photoluminescence measurements at different temperatures have been performed to investigate the effects of confinement on the electron-phonon interaction in GaAs/AlGaAs quantum wells (QWs). A series of samples with different well widths in the range from 150 up to 750 A was analyzed. Using a fitting procedure based on the Passler-p model to describe the temperature dependence of the exciton recombination energy, we determined a fit parameter which is related to the strength of the electron-phonon interaction. On the basis of the behavior of this fit parameter as a function of the well width thickness of the samples investigated, we verified that effects of confinement on the exciton recombination energy are still present in QWs with well widths as large as 450 angstrom. Our findings also show that the electron-phonon interaction is three times stronger in GaAs bulk material than in Al(0.18)Ga(0.82)As/GaAs QWs.

Path integral representations in noncommutative quantum mechanics and noncommutative version of Berezin-Marinov action

It is known that the actions of field theories on a noncommutative space-time can be written as some modified (we call them theta-modified) classical actions already on the commutative space-time (introducing a star product). Then the quantization of such modified actions reproduces both space-time noncommutativity and the usual quantum mechanical features of the corresponding field theory. In the present article, we discuss the problem of constructing theta-modified actions for relativistic QM. We construct such actions for relativistic spinless and spinning particles. The key idea is to extract theta-modified actions of the relativistic particles from path-integral representations of the corresponding noncommutative field theory propagators. We consider the Klein-Gordon and Dirac equations for the causal propagators in such theories. Then we construct for the propagators path-integral representations. Effective actions in such representations we treat as theta-modified actions of the relativistic particles. To confirm the interpretation, we canonically quantize these actions. Thus, we obtain the Klein-Gordon and Dirac equations in the noncommutative field theories. The theta-modified action of the relativistic spinning particle is just a generalization of the Berezin-Marinov pseudoclassical action for the noncommutative case.

CONSTRUCTING QUANTUM OBSERVABLES AND SELF-ADJOINT EXTENSIONS OF SYMMETRIC OPERATORS. III. SELF-ADJOINT BOUNDARY CONDITIONS

This paper completes the review of the theory of self-adjoint extensions of symmetric operators for physicists as a basis for constructing quantum-mechanical observables. It contains a comparative presentation of the well-known methods and a newly proposed method for constructing ordinary self-adjoint differential operators associated with self-adjoint differential expressions in terms of self-adjoint boundary conditions. The new method has the advantage that it does not require explicitly evaluating deficient subspaces and deficiency indices (these latter are determined in passing) and that boundary conditions are of explicit character irrespective of the singularity of a differential expression. General assertions and constructions are illustrated by examples of well-known quantum-mechanical operators like momentum and Hamiltonian.

Semiclassical and quantum motions on the non-commutative plane

We study the canonical and the coherent state quantizations of a particle moving in a magnetic field on the non-commutative plane. Using a theta-modified action, we perform the canonical quantization and analyze the gauge dependence of the theory. We compare coherent states quantizations obtained through Malkin-Man`ko states and circular squeezed states. The relation between these states and the ""classical"" trajectories is investigated, and we present numerical explorations of some semiclassical quantities. (C) 2009 Elsevier B.V. All rights reserved.