Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Extremal k *-Cycle Resonant Hexagonal Chains

Denote by ^* _n the set of all k ^*-cycle resonant hexagonal chains with n hexagons. For any B _n ^* _n , let m(B _n ) and i(B _n ) be the numbers of matchings (=the Hosoya index) and the number of independent sets (=the Merrifield–Simmons index) of B _n , respectively. In this paper, we give a characterization of the k ^*-cycle resonant hexagonal chains, and show that for any B _n ^* _n , m(H _n )m(B _n ) and i(H _n )i(B _n ), where H _n is the helicene chain. Moreover, equalities hold only if B _n =H _n .     

Semi‐classical formulation of time‐dependent discrete variable representation method

In this article, we apply a novel time‐dependent discrete variable representation (TDDVR) method proposed by Barkakaty and Adhikari to investigate tunneling through an Eckart barrier. This semi‐classical method is theoretically rigorous and straightforward to implement. Among the TDDVR formulations, this report presents the first derivation of a rigorous form of quantum force (QF) for the present perspective. The validity of this semi‐classical approach is demanded based on the excellent agreement of the tunneling probability with the corresponding quantum results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

EPR Study on the complex formed by charge-transfer process between ground-state acceptor chloranil and nine donors

EPR study showed that the semi-quinone radical anion of chloranil (TCQ) was formed in a charge-transfer process between ground state chloranil as acceptor and each one of the following ground state donors,i.e.,N,N'-diethyl aniline (DEA),phenothiazine (PTZ),carbazole (CBZ),pyrene (PY),ferrocene (FRO),triphenylphosphine (TPP),triethylamine (TEA),anthracene (AN) and N,N-diethyl-3-aminophenyl ester of palmitic acid (DPP).Our results indicate that there is a tunneling effect for the ground-state charge-transfer process between chloranil and the donor.     

Characterization of the organization in shear layers via the Proper Orthogonal Decomposition

Experiments are performed in an incompressible plane turbulent mixing layer, using various hot wire rake configurations. From these experiments, the Proper Orthogonal Decomposition is applied for kernels where the space-time correlation tensor is evaluated over different spatial meshes and velocity components configurations. The resulting decompositions are then discussed in terms of characterization of the organization of the flow for various scalar or vectorial approaches of the POD. An incrtial range law is evidenced. The instantaneous contribution of the first modes of the POD to the organization of the flow is analyzed. A dynamical behavior for the organization of the flow is observed from the correlation between the first two modes contribution.     

Enhancement of activated decay of metastable states by resonant pumping

We consider the effect of a high-frequency pumping cost on the escape rate of a classical underdamped Brownian particle out of a deep potential well. The energy dependence of the oscillation frequency(E) is assumed to be weak on the scale of thermal energy,_E(0)T(0)T/V₀ (0)[_E(0) is the derivative of(E) atE= 0,V ₀ is the barrier height,V ₀ T]. The quadratic-in- contribution to the decay rate is calculated in two different regimes: (1) for the case of resonance of the pumping frequency with the nth harmonic of the internal motion at an energye, when = n(e); (2) for a rollout region of the basic resonance near the bottom of the potential well, when ¦-(0)¦ and is the damping coefficient. In the latter case the absorption spectrum and the enhancement of the decay rate are calculated as functions of two reduced parameters, the anharmonicity of the potential,v _E (0)T/, and the resonance mismatch, [ —(0)]/. It is shown that the effect of the pumping increases with diminishing ¦v¦ and at small v is proportional tov ^–1. In this regime, the dependence on is stepwise: the pumping contribution is large for v > 0 and small for v < 0. In the frame of our theory, the decay rate is invariant against the simultaneous alternation of the signs of andv. The spectrum of the energy absorption has the standard Lorentzian shape in the absence of anharmonicity,v=0, and with increasing of ¦v¦ shifts and widens retaining its bell-shape form.     

Theory of electron tunneling through a bridge molecule with two electronic levels at low temperatures

A theory of electron tunneling through a single-center bridge redox group that has two electronic levels participating in the electron transfer process is presented. The temperature is presumed to be low enough to ignore activation redox conversions of the bridge group. Salient features of this system are due both to the presence of two electroactive states of the bridge group and to relaxation processes along the reaction coordinate. The processes in question make the tunneling current time-dependent at fixed potentials and can bring about hysteresis in current-voltage curves when cycling the bias potential. Effects of inelastic tunneling with excitation of vibrations of a local quantum degree of freedom are considered.     

Ligand dynamics and reactivity in trimetallic clusters

The general relationships between trinuclear cluster reactivity and the ligand dynamical processes in these systems are explored. Three specific mechanistic studies are presented: (1) the rate and stereochemistry of ligand addition to ₃-imidoyl complexes, (2) the factors influencing the rate of carbon-hydrogen bond activation in ₃-alkyne complexes, and (3) the origin of anomalously large kinetic deuterium isotope effect in metal to ligand and ligand to metal hydrogen transfer in trinuclear and binuclear complexes. In all three cases, the current state of the mechanistic studies are summarized and the possible rate of specific ligand dynamical processes in controlling the mechanism are put forth.     

PHOTOEMISSION WITHIN AND BEYOND THE ONE-STEP MODEL

Photoemission in the vacuum ultraviolet photon regime has proved to be an effective tool for the investigation of valence band surface electronic structure. The interpretation cannot be exclusively confined to the valence bands but has to consider cross sections with realistic final states consistently designed within the one-step model. Therefore especially in the surface sensitive photoemission, several effects hide the final goal of deducing the energetic and wavefunction structure together with microscopic potential parameters through a convincing agreement of calculated with measured spectra. The final states band structure is much less well understood than the valence band structure under consideration. The optical potential, which controls the surface sensitivity through the underlying damping mechanisms, widely relies on empirical assumptions. Furthermore, the photon field is not only strongly influenced but in the vicinity of the plasma frequency also deteriorated by the electronic response. In view of high resolution spectroscopy the accuracy of the data interpretation is affected, and in fact, band-mapping methods are no longer valid. Examples of recent calculations to account for these effects are reviewed.     

Palladium(II) complexes of the reducing sugars D-arabinose,D-ribose,rac-mannose,and D-galactose

The cellulose solvent Pd-en, an aqueous solution of [(en)Pd(II)(OH)(2)] (en=ethylenediamine), reacts with the monosaccharides D-arabinose (D-Ara), D-ribose (D-Rib), rac-mannose (rac-Man), and D-galactose (D-Gal) under formation of dimetalated aldose complexes, if the molar ratio of Pd and sugar is 2:1 or larger. In the Pd(2) complexes, the aldoses are tetra-deprotonated and act as bisdiolato ligands. Two crystalline pentose complexes were isolated: [(en)(2)Pd(2)(beta-D-Arap1,2,3,4 H(-4))].5 H(2)O (1) and [(en)(2)Pd(2)(beta-D-Ribp1,2,3,4 H(-4))].6.5 H(2)O (2), along with two hexose complexes. With rac-Man, the major solution species is crystallized as the 9.4-hydrate [(en)(2)Pd(2)(beta-rac-Manp1,2,3,4 H(-4))].9.4 H(2)O (3). From the respective D-Gal solutions, [(en)(2)Pd(2)(beta-D-Galf1,3,5,6 H(-4))].5 H(2)O.C(2)H(5)OH (4), with the sugar tetraanion in its furanose form, is crystallized though it is not the major species, rather the second most abundant in purely aqueous solutions. The Galf species is enriched in the mother liquors to the extent of 25 % of total sugar content. Substitution of the en ligand by two molecules of ammonia, methylamine, or isopropylamine, respectively, results in the formation of different solution species. With the bulkiest ligand, isopropylamine, monometalation of the aldoses in the 1,2-position is exclusively observed.