Suggested Binding Mechanism of the HIV-gp120 to its CD4 Receptor

The molecular recognition and attachment of the CD4 molecule and the HIV envelope glycoprotein (gp120) might be described as a consecutive three-step molecular recognition process. 1. (a) Long range interaction: electrostatic pre-orientation, 2. (b) short range interaction: electronic attachment followed by a ‘Locking-in’ (via aromatic ring orientation) and 3. (c) internal interaction (induced fit): conformational readjustment of the protein molecules. On the basis of the preliminary investigations (X-ray structures of CD4 and biological studies of CD4 and gp120 point mutants) we described a computational model. This approach consists of empirical calculations as well as ab initio level of quantum chemistry. The conformational analysis of the wild type and mutant CD4 molecules was supported by molecular mechanics and dynamics (Amber force field). The latter analysis involves the application of a novel method, the Amino Acid Conformation Assignment of Proteins (ACAP) software, developed for the notation of secondary protein structures. According to the cardinal role of the electrostatic factors during this interaction, several ab initio investigations were performed for better understanding of the recognition process on submolecular level. Using the above mentioned computational model, we could interpret the basic behaviours and predict some additional features of CD4-gp120 interaction, in spite of the missing gp120 X-ray structure.

On the treatment of singularities of the Watson Hamiltonian for nonlinear molecules

The applicability of the Watson Hamiltonian for the description of nonlinear molecules—especially triatomic ones—has always been questioned, as the Jacobian of the transformation that leads to the Watson Hamiltonian, vanishes at the linear configuration. This results in singular behavior of the Watson Hamiltonian, giving rise to serious numerical problems in the computation of vibrational spectra, with unphysical, spurious vibrational states appearing among the physical vibrations, especially in the region of highly excited states. In this work, we analyze the problem and propose a simple way to confine the nuclear wavefunction in such a way that the spurious solutions are eliminated. We study the water molecule and observe an improvement compared with previous results. We also apply the method to the van der Walls molecule XeHe2.

Electronic states and spin-forbidden cooling transitions of AlH and AlF

The feasibility of laser cooling AlH and AlF is investigated using ab initio quantum chemistry. All the electronic states corresponding to the ground and lowest two excited states of the Al atom are calculated using multi-reference configuration interaction (MRCI) and the large AV6Z basis set for AlH. The smaller AVQZ basis set is used to calculate the valence electronic states of AlF. Theoretical Franck-Condon factors are determined for the A(1)Pi -> X(1)Sigma(+) transitions in both radicals and found to agree with the highly diagonal factors found experimentally, suggesting computational chemistry is an effective method for screening suitable laser cooling candidates. AlH does not appear to have a transition quite as diagonal as that in SrF (which has been laser cooled) but the A(1)Pi -> X(1)Sigma(+) transition transition of AlF is a strong candidate for cooling with just a single laser, though the cooling frequency is deep in the UV. Furthermore, the a (3)Pi -> X(1)Sigma(+) transitions are also strongly diagonal and in AlF is a practical method for obtaining very low final temperatures around 3 mu K.

Prospects for ultracold carbon via charge exchange reactions and laser cooled carbides

Strategies to produce an ultracold sample of carbon atoms are explored and assessed with the help of quantum chemistry. After a brief discussion of the experimental difficulties using conventional methods, two strategies are investigated. The first attempts to exploit charge exchange reactions between ultracold metal atoms and sympathetically cooled C+ ions. Ab initio calculations including electron correlation have been conducted on the molecular ions [LiC]+ and [BeC]+ to determine whether alkali or alkaline earth metals are a suitable buffer gas for the formation of C atoms but strong spontaneous radiative charge exchange ensure they are not ideal. The second technique involves the stimulated production of ultracold C atoms from a gas of laser cooled carbides. Calculations on LiC suggest that the alkali carbides are not suitable but the CH radical is a possible laser cooling candidate thanks to very favourable Frank-Condon factors. A scheme based on a four pulse STIRAP excitation pathway to a Feshbach resonance is outlined for the production of atomic fragments with near zero centre of mass velocity.

Effect of positron-atom interactions on the annihilation gamma spectra of molecules

Calculations of ?-spectra for positron annihilation on a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The annihilation ?-spectra characterise the momentum distribution of the electron-positron pair at the instant of annihilation. The contribution to the ?-spectra from individual molecular orbitals is obtained from electron momentum densities calculated using modern computational quantum chemistry density functional theory tools. The calculation, in its simplest form, effectively treats the low-energy (thermalised, room-temperature) positron as a plane wave and gives annihilation ?-spectra that are about 40% broader than experiment, although the main chemical trends are reproduced. We show that this effective 'narrowing' of the experimental spectra is due to the action of the molecular potential on the positron, chiefly, due to the positron repulsion from the nuclei. It leads to a suppression of the contribution of small positron-nuclear separations where the electron momentum is large. To investigate the effect of the nuclear repulsion, as well as that of short-range electron-positron and positron-molecule correlations, a linear combination of atomic orbital description of the molecular orbitals is employed. It facilitates the incorporation of correction factors which can be calculated from atomic many-body theory and account for the repulsion and correlations. Their inclusion in the calculation gives -spectrum linewidths that are in much better agreement with experiment. Furthermore, it is shown that the effective distortion of the electron momentum density, when it is observed through positron annihilation -spectra, can be approximated by a relatively simple scaling factor. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Ultracold radiative charge transfer in hybrid ion-atom traps

We present ab initio quantum chemistry calculations for elastic scattering and the radiative charge transfer reaction process and collision rates for trapped ytterbium ions immersed in a quantum degenerate rubidium vapor.
The collision of the ion (or ions) with the quasiatom is the key mechanism to transfer quantum coherences between the systems. We use first-principles
quantum chemistry codes to obtain the potential surfaces and coupling terms for the two-body interaction of Yb^+ with Rb. We find that the low energy collision has an inelastic radiative charge transfer process in agreement with recent experiments.
The charge transfer cross section agrees well with the semiclassical Langevin model at higher energies but is dominated by resonances at submillikelvin temperatures.

Strong electronic correlation in the hydrogen chain: A variational Monte Carlo study

In this paper, we report a fully ab initio variational Monte Carlo study of the linear and periodic chain of hydrogen atoms, a prototype system providing the simplest example of strong electronic correlation in low dimensions. In particular, we prove that numerical accuracy comparable to that of benchmark density-matrix renormalization-group calculations can be achieved by using a highly correlated Jastrow-antisymmetrized geminal power variational wave function. Furthermore, by using the so-called "modern theory of polarization" and by studying the spin-spin and dimer-dimer correlations functions, we have characterized in detail the crossover between the weakly and strongly correlated regimes of this atomic chain. Our results show that variational Monte Carlo provides an accurate and flexible alternative to highly correlated methods of quantum chemistry which, at variance with these methods, can be also applied to a strongly correlated solid in low dimensions close to a crossover or a phase transition.

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice-leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point. 

Formation and characterization of carbon-radical precursors in char steam gasification

Highly reactive radicals play an important role in high-temperature gasification processes. However, the effect of radicals on gasification has not been systematically investigated. In the present study, the formation of carbon-radical precursors using atomic radicals such as OH, O, and H and molecules such as H₂ and O₂ was characterized, and the effect of the precursors on the adsorption step of steam char gasification was studied using quantum chemistry methods. The results revealed that the radicals can be chemisorbed exothermically on char active sites, and the following order of reactivity was observed: O > H₂ > H > OH > O ₂. Moreover, hydrogen bonds are formed between steam molecules and carbon-radical complexes. Steam molecule adsorption onto carbon-O and carbon-OH complexes is easier than adsorption onto clean carbon surfaces. Alternatively, adsorption on carbon-O₂, carbon-H₂, and carbon-H complexes is at the same level with that of clean carbon surfaces; thus, OH and O radicals accelerate the physical adsorption of steam onto the char surface, H radical and O₂ and H₂ molecules do not have a significant effect on adsorption. © 2010 American Chemical Society.

Ultracold, radiative charge transfer in hybrid Yb ion – Rb atom traps

Ultracold hybrid ion–atom traps offer the possibility of microscopic manipulation of quantum coherences in the gas using the ion as a probe. However, inelastic processes, particularly charge transfer can be a significant process of ion loss and has been measured experimentally for the ${\rm Y}{{{\rm b}}^{+}}$ ion immersed in a Rb vapour. We use first-principles quantum chemistry codes to obtain the potential energy curves and dipole moments for the lowest-lying energy states of this complex. Calculations for the radiative decay processes cross sections and rate coefficients are presented for the total decay processes; ${\rm Y}{{{\rm b}}^{+}}(6{\rm s}{{\;}^{2}}{\rm S})+{\rm Rb}(5{\rm s}{{\;}^{2}}{\rm S})\to {\rm Yb}(6{{{\rm s}}^{2}}{{\;}^{1}}{\rm S})+{\rm R}{{{\rm b}}^{+}}(4{{{\rm p}}^{6}}{{\;}^{1}}{\rm S})+h\nu $ and ${\rm Y}{{{\rm b}}^{+}}(6{\rm s}{{\;}^{2}}{\rm S})+{\rm Rb}(5{\rm s}{{\;}^{2}}{\rm S})\to {\rm YbR}{{{\rm b}}^{+}}({{X}^{1}}{{\Sigma }^{+}})+h\nu $. Comparing the semi-classical Langevin approximation with the quantum approach, we find it provides a very good estimate of the background at higher energies. The results demonstrate that radiative decay mechanisms are important over the energy and temperature region considered. In fact, the Langevin process of ion–atom collisions dominates cold ion–atom collisions. For spin-dependent processes [1] the anisotropic magnetic dipole–dipole interaction and the second-order spin–orbit coupling can play important roles, inducing coupling between the spin and the orbital motion. They measured the spin-relaxing collision rate to be approximately five orders of magnitude higher than the charge-exchange collision rate [1]. Regarding the measured radiative charge transfer collision rate, we find that our calculation is in very good agreement with experiment and with previous calculations. Nonetheless, we find no broad resonances features that might underly a strong isotope effect. In conclusion, we find, in agreement with previous theory that the isotope anomaly observed in experiment remains an open question.

Radiative charge transfer in cold and ultracold sulphur atoms colliding with protons

Radiative decay processes at cold and ultra cold temperatures for sulfur atoms colliding with protons are investigated. The MOLPRO quantum chemistry suite of codes was used to obtain accurate potential energies and transition dipole moments, as a function of internuclear distance, between low-lying states of the SH+ molecular cation. A multi-reference configuration-interaction approximation together with the Davidson correction is used to determine the potential energy curves and transition dipole moments, between the states of interest, where the molecular orbitals are obtained from state-averaged multi-configuration-self-consistent field calculations. The collision problem is solved approximately using an optical potential method to obtain radiative loss, and a fully two-channel quantum approach for radiative charge transfer. Cross sections and rate coefficients are determined for the first time for temperatures ranging from 10 μK up to 10 000 K. Results are obtained for all isotopes of sulfur, colliding with H+ and D+ ions and comparison is made to a number of other collision systems.

Production of ultracold hydrogen and deuterium via Doppler-cooled Feshbach molecules

A counterintuitive scheme to produce ultracold hydrogen via fragmentation of laser cooled diatomic hydrides is presented where the final atomic H temperature is inversely proportional to the mass of the molecular parent. In addition, the critical density for formation of a Bose-Einstein condensate (BEC) at a fixed temperature is reduced by a factor (mH/mMH)3/2 over directly cooled hydrogen atoms. The narrow Feshbach resonances between a S01 atom and hydrogen are well suited to a tiny center of mass energy release necessary during fragmentation. With the support of ab initio quantum chemistry, it is demonstrated that BaH is an ideal diatomic precursor that can be laser cooled to a Doppler temperature of ∼26μK with just two rovibronic transitions, the simplest molecular cooling scheme identified to date. Preparation of a hydrogen atom gas below the critical BEC temperature Tc is feasible with present cooling technology, with optical pulse control of the condensation process.

Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy

Transcriptome analysis using microarray technology represents a powerful unbiased approach for delineating pathogenic mechanisms in disease. Here molecular mechanisms of renal tubulointerstitial fibrosis (TIF) were probed by monitoring changes in the renal transcriptome in a glomerular disease-dependent model of TIF ( adriamycin nephropathy) using Affymetrix (mu74av2) microarray coupled with sequential primary biological function-focused and secondary

Two-dimensional images of dissolved sulfide and metals in anoxic sediments by a novel diffusive gradients in thin film probe and optical scanning techniques

A novel diffusive gradients in thin film probe developed comprises diffusive gel layer of silver iodide (AgI) and a back-up Microchelex resin gel layer. 2D high-resolution images of sulfide and trace metals were determined respectively on the AgI gel by densitometric analysis and on the Microchelex resin layer with laser-ablation-inductively-coupled plasma mass spectrometry (LA-ICP-MS).We investigated the validity of the analytical procedures used for the determination of sulfide and trace metals. We found low relative standard deviations on replicate measurements, linear trace-metal calibration curves between the LA-ICP-MS signal and the true trace-metal concentration in the resin gel, and a good agreement of the sulfide results obtained with the AgI resin gel and with other analytical methods. The method was applied on anoxic sediment pore waters in an estuarine and marine system. Simultaneous remobilization of sulfide and trace metals was observed in the marine sediment.

Thermodynamics of trajectories of a quantum harmonic oscillator coupled to N baths

We undertake a thorough analysis of the thermodynamics of the trajectories followed by a quantum harmonic oscillator coupled to $N$ dissipative baths by using a new approach to large-deviation theory inspired by phase-space quantum optics. As an illustrative example, we study the archetypal case of a harmonic oscillator coupled to two thermal baths, allowing for a comparison with the analogous classical result. In the low-temperature limit, we find a significant quantum suppression in the rate of work exchanged between the system and each bath. We further show how the presented method is capable of giving analytical results even for the case of a driven harmonic oscillator. Based on that result, we analyse the laser cooling of the motion of a trapped ion or optomechanical system, illustrating how the emission statistics can be controllably altered by the driving force.