Ab initio molecular orbital calculations on ion-molecule and ion pair-molecule complexes of the water-lithium cyanide system

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets were performed on a series of ion-molecule and ion pair-molecule complexes for the H2O + LiCN system. Stabilisation energies (with counter-poise corrections), geometrical parameters, internal force constants and harmonic vibrational frequencies were evaluated for 16 structures of interest. Although the interaction energies are smaller, the geometries and relative stabilities of the monohydrated contact ion pair are reminiscent of those computed for the complexes of the individual ions. Thus, interaction of the oxygen lone pair with lithium leads to a highly stabilised C2v structure, while the coordination of water to the cyanide ion involves a slightly non-linear hydrogen bond. Symmetrical bifurcated structures are computed to be saddle points on the potential energy surface, and to have an imaginary frequency for the rocking mode of the water molecule. On optimisation the geometries of the solvent shared ion pair structures (e.g. Li+cdots, three dots, centered OH2cdots, three dots, centered CN−) revealed a proton transfer from the water molecule leading to hydrogen bonded forms such as Li-O-Hcdots, three dots, centered HCN. The variation in the force constants and harmonic frequencies in the various structures considered are discussed in terms of ion-molecular and ion pair-molecule interactions.

Top-spin analysis of new scalar and tensor interactions in e(+)e(-) collisions with beam polarization

We utilize top polarization in the process e(+)e(-) -> t (t) over bar at the International Linear Collider ( ILC) with transverse beam polarization to probe interactions of the scalar and tensor type beyond the standard model and to disentangle their individual contributions. Ninety percent confidence level limits on the interactions with realistic integrated luminosity are presented and are found to improve by an order of magnitude compared to the case when the spin of the top quark is not measured. Sensitivities of the order of a few times 10(-3) TeV-2 for real and imaginary parts of both scalar and tensor couplings at root s = 500 and 800 GeV with an integrated luminosity of 500 fb(-1) and completely polarized beams are shown to be possible. A powerful model-independent framework for inclusive measurements is employed to describe the spin-momentum correlations, and their C, P, and T properties are presented in a technical appendix.

Single-molecule thermodynamics: the heat distribution function of a charged particle in a static magnetic field

Interest in the applicability of fluctuation theorems to the thermodynamics of single molecules in external potentials has recently led to calculations of the work and total entropy distributions of Brownian oscillators in static and time-dependent electromagnetic fields. These calculations, which are based on solutions to a Smoluchowski equation, are not easily extended to a consideration of the other thermodynamic quantity of interest in such systems-the heat exchanges of the particle alone-because of the nonlinear dependence of the heat on a particle's stochastic trajectory. In this paper, we show that a path integral approach provides an exact expression for the distribution of the heat fluctuations of a charged Brownian oscillator in a static magnetic field. This approach is an extension of a similar path integral approach applied earlier by our group to the calculation of the heat distribution function of a trapped Brownian particle, which was found, in the limit of long times, to be consistent with experimental data on the thermal interactions of single micron-sized colloids in a viscous solvent.

Sequential Assembly of an Active RNA Polymerase Molecule at the Air-Water Interface

At the heart of understanding cellular processes lies our ability to explore the specific nature of communication between sequential information carrying biopolymers. However, the data extracted from conventional solution phase studies may not reflect the dynamics of communication between recognized partners as they occur in the crowded cellular milieu. We use the principle of immobilization of histidine-tagged biopolymers at a Ni(II)-encoded Langmuir monolayer to study sequence-specific protein-protein interactions in an artificially crowded environment The advantage of this technique lies in increasing the surface density of one of the interacting partners that allows us to study macromolecular interactions in a controlled crowded environment, but without compromising the speed of the reactions. We have taken advantage of this technique to follow the sequential assembly process of the multiprotein complex Escherichia coil RNA polymerase at the interface and also deciphered the role of one of the proteins, omega (omega), in the assembly pathway. Our reconstitution studies indicate that in the absence of molecular chaperones or other cofactors, omega (omega) plays a decisive role in refolding the largest protein beta prime (beta') and its recruitment into the multimeric assembly to reconstitute an active RNA polymerase. It was also observed that the monolayer had the ability to distinguish between sequence-specific and -nonspecific interactions despite the immobilization of one of the biomacromolecules. The technique provides a universal two-dimensional template for studying protein-ligand interactions while mimicking molecular crowding.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Persistent passive hopping and juggling is possible even with plastic collisions

We describe simple one-dimensional models of passive (no energy input, no control), generally dissipative, vertical hopping and one-ball juggling. The central observation is that internal passive system motions can conspire to eliminate collisions in these systems. For hopping, two point masses are connected by a spring and the lower mass has inelastic collisions with the ground. For juggling, a lower point-mass hand is connected by a spring to the ground and an upper point-mass ball is caught with an inelastic collision and then re-thrown into gravitational free flight. The two systems have identical dynamics. Despite inelastic collisions between non-zero masses, these systems have special symmetric energy-conserving periodic motions where the collision is at zero relative velocity. Additionally, these special periodic motions have a non-zero sized, one-sided region of attraction on the higher-energy side. For either very large or very small mass ratios, the one-sided region of attraction is large. These results persist for mildly non-linear springs and non-constant gravity. Although non-collisional damping destroys the periodic motions, small energy injection makes the periodic motions stable, with a two-sided region of attraction. The existence of such special energy conserving solutions for hopping and juggling points to possibly useful strategies for both animals and robots. The lossless motions are demonstrated with a table-top experiment.

A Passive Hopper With Lossless Collisions

A passive vertical hopping robot is here highly idealised as two vertically arranged masses acted on by gravity and coupled by a linear spring. The lower mass makes dead (e = 0) collisions with the rigid ground. The equations of motion can be reduced to a one dimensional map. Fixed points of the map are found in which case the robot hops incessantly. For these conservative solutions the lower mass collides with the ground with zero impact velocity. The interval of attraction for these conservative fixed points depends on system parameters.

The absolute orientation of a molecule in space: Extension of the 'CIP' system

A scheme for denoting the absolute spatial orientation of molecules and molecular fragments is presented; this is based on three angular deviations - one for each spatial dimension - with respect to a reference orientation, which is itself defined with the help of certain features of the Cahn-Ingold-Prelog stereochemical notation. The new scheme helps in reconstructing the three-dimensional characteristics of molecules from purely verbal descriptors, and may thus find application in various information storage and retrieval processes (e.,-. encrypting holograms, etc.).

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M.similar to tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Barrier crossing by a flexible long chain molecule - The kink mechanism

The problem and related earlier work All the above problems involve the passage of a long chain molecule, through a region in space, where the free energy per segment is higher, thus effectively presenting a barrier for the motion of the molecule. This is what we refer to as the Kramers proble...

Segregation into Chiral Enantiomeric Conformations of an Achiral Molecule by Concomitant Polymorphism

An analogue of the green fluorescent protein (GFP) luminophore crystallizes from a methanol solution impregnated with dichloromethane, into a pair of chiral crystals. Thermal analysis, fluorescence emission studies, and crystal packing analysis show that the two crystals are different materials. The two polymorphs arise from the rotation of a monosubstituted benzene ring about a C-N bond which results in the formation of two strong bifurcated C-H center dot center dot center dot O intermolecular bonds to oxygen O(6). The color difference has been ascribed to a difference in the packing of the two crystal forms. Theoretical studies supported by low temperature NMR show low kinetic energy barriers (similar to 10 kJ mol(-1)) separating the asymmetric units of the two crystal structures, suggesting that the driving force for the polymorphism could be the result of packing of two different asymmetric units.