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At least 109 records · Page 6

Ab initio Potential Energy Surface for H-H2

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

Partridge, Harry↗

Non-Equilibrium Properties from Equilibrium Free Energy Calculations

Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

Pohorille, Andrew↗

Line Mixing in Parallel and Perpendicular Bands of CO2: A Further Test of the Refined Robert-Bonamy Formalism

Starting from the refined Robert-Bonamy formalism [Q. Ma, C. Boulet, and R. H. Tipping, J. Chem. Phys. 139, 034305 (2013)], we propose here an extension of line mixing studies to infrared absorptions of linear polyatomic molecules having stretching and bending modes. The present formalism does not neglect the internal degrees of freedom of the perturbing molecules, contrary to the energy corrected sudden (ECS) modeling, and enables one to calculate the whole relaxation matrix starting from the potential energy surface. Meanwhile, similar to the ECS modeling, the present formalism properly accounts for roles played by all the internal angular momenta in the coupling process, including the vibrational angular momentum. The formalism has been applied to the important case of CO2 broadened by N2. Applications to two kinds of vibrational bands (sigma yields sigma and sigma yields pi) have shown that the present results are in good agreement with both experimental data and results derived from the ECS model.

Semiclassical theories↗

Evidence for the Protection of N-heterocycles from Gamma Radiation by Mars Analogue Minerals

Organic compounds have been delivered to the surface of Mars via meteorites, comets and interplanetary dust particles for billions of years. Determining the effects of high energy radiation and galactic cosmic radiation (GCR) on these organic compounds is critical for understanding the potential for the preservation of organic molecules associated with past or present life, and where to look for possible chemical bio- signatures during future Mars missions. Understanding how these effects are attenuated by the mineral matrix and the depth at which they are buried have been challenging to determine in situ on Mars. There have been very few experimental studies on the survival of organic compounds under radiation from a gamma source under realistic conditions, and their interpretation until now has been difficult due to the lack of data for actual radiation levels on Mars. Using the in-situ data obtained by the MSL/RAD instrument to anchor the dose calculations, here we show that the N-heterocycles purine and uracil, crucial components of biochemical processes in extant living systems, mixed with calcite, anhydrite, and kaolinite as Mars analogue minerals can survive the effects of radiation with a dose corresponding to ~500,000 years on the Martian surface. The extent of survival varied not only with the nature of the organic compound, but its depth from the surface. These results provide new experimental data for the degree of protection offered by the regolith, in conjunction with minerals, for organic compounds that may be present on Mars.

mars↗

Performance of a CW double electric discharge for supersonic CO lasers

The results of an experimental investigation of a CW double discharge in supersonic CO mixtures are reported. Stable discharges in CO/N2 and CO/Ar mixtures, with a maximum energy loading of 0.5 eV/CO molecule, were achieved in a small-scale continuous-flow supersonic channel. Detailed measurements of the discharge characteristics were performed, including electrostatic probe measurements of floating potential and electron number density and spectroscopic measurements of the CO vibrational population distributions. The results of these measurements indicate that the vibrational excitation efficiency of the discharge is approximately 60%, for moderate levels of main discharge current. These experiments, on a small scale, demonstrate that the double-discharge scheme provides adequate vibrational energy loading for efficient CO laser operation under CW supersonic flow conditions.

Stanton, A. C.↗

Stabilities of nitrogen containing heterocyclic radicals and geometrical influences on non-radiative processes in organic molecules

Stabilities of nitrogen containing heterocyclic radicals were studied to detect radicals of the type R-N-R, and to theoretically rationalize their electronic structure. The computation of simple potential energy surfaces for ground and excited states is discussed along with the photophysical properties of indolizine. Methods of calculation and problems associated with the calculations are presented. Results, tables, diagrams, discussions, and references are included.

Evleth, E. M.↗

Effect of Electronic Excitation on Hydrogen Atom Transfer (Tautomerization) Reactions for the DNA Base Adenine

Geometrical structures and energetic properties for four different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest single excited state potential energy surface are studied. The energetic order of the tautomers on the ground state potential surface is 9H less than 7H less than 3H less than 1H, while on the excited state surface this order is found to be different: 3H less than 1H less than 9H less than 7H. Minimum energy reaction paths are obtained for hydrogen atom transfer (9 yields 3 tautomerization) reactions in the ground and the lowest excited electronic state. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic state, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. The barrier for this reaction in the excited state may become very low in the presence of water or other polar solvent molecules, and therefore such tautomerization reaction may play an important role in the solution phase photochemistry of adenine.

Chaban, Galina M.↗

A quantum model for bending vibrations and thermodynamic properties of C3.

The investigation reported was conducted to clarify the thermodynamic properties of C3 by further developing the limit to the partition function suggested by Strauss and Thiele (1967). A quantum solution for the energy levels of a quadratically perturbed square well potential is presented and the consistency of this limit with observed energy levels is established. In the process a more complete physical picture of the bending C3 molecules emerges. The values of entropy deduced from various measurements of graphite pressure are compared with this limit, and the thermodynamic properties predicted for the limiting case are evaluated.

Hansen, C. F.↗

Hydrogen bonding in the benzene-ammonia dimer

High-resolution optical and microwave spectra of the gas-phase benzene-ammonia dimer were obtained, showing that the ammonia molecule resides above the benzene plane and undergoes free, or nearly free, internal rotation. To estimate the binding energy (De) and other global properties of the intermolecular potential, theoretical calculations were performed for the benzene-ammonia dimer, using the Gaussian 92 (Fritsch, 1992) program at the MP2/6-31G** level. The predicted De was found to be at the lowest end of the range commonly accepted for hydrogen bonding and considerably below that of C6H6-H2O, consistent with the gas-phase acidities of ammonia and water. The observed geometry greatly resembles the amino-aromatic interaction found naturally in proteins.

Rodham, David A.↗

Dissociative Ionization of Aromatic and Heterocyclic Molecules

Space radiation poses a major health hazard to humans in space flight. The high-energy charged particles in space radiation ranging from protons to high atomic number, high-energy (HZE) particles, and the secondary species they produce, attack DNA, cells, and tissues. Of the potential hazards, long-term health effects such as carcinogenesis are likely linked to the DNA lesions caused by secondary electrons in the 1 - 30 eV range. Dissociative ionization (DI) is one of the electron collision processes that can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. To understand this process, we have developed a theoretical model for DI. Our model makes use of the fact that electron motion is much faster than nuclear motion and assumes DI proceeds through a two-step process. The first step is electron-impact ionization resulting in a particular state of the molecular ion in the geometry of the neutral molecule. In the second step the ion undergoes unimolecular dissociation. Thus the DI cross section sigma(sup DI)(sub a) for channel a is given by sigma(sup DI)(sub a) = sigma(sup I)(sub a) P(sub D) with sigma(sup I)(sub a) the ionization cross section of channel a and P(sub D) the dissociation probability. This model has been applied to study the DI of H2O, NH3, and CH4, with results in good agreement with experiment. The ionization cross section sigma(sup I)(sub a) was calculated using the improved binary encounter-dipole model and the unimolecular dissociation probability P(sub D) obtained by following the minimum energy path determined by the gradients and Hessians of the electronic energy with respect to the nuclear coordinates of the ion. This model is used to study the DI from the low-lying channels of benzene and pyridine to understand the different product formation in aromatic and heterocyclic molecules. DI study of the DNA base thymine is underway. Solvent effects will also be discussed.

Huo, Winifred M.↗

Studies of H2O on beta-AgI surfaces - An effective pair potential model

The adsorption of a water molecule on surfaces of beta-AgI, the hexagonal crystal believed to be primarily responsible for the ice-nucleating properties of AgI, is studied on the basis of an effective pair potential model. The water molecule is represented by a rigid point charge ST-2 model and the AgI substrate by an array of point atoms, and maximal binding energy surfaces and optimal H2O configurations are generated for the water molecule adsorbed on the rigid and unrelaxed basal and prism faces. Modeling of H2O adsorption above a two-layer ledge, an iodine vacancy and an H2O molecule trapped in the vacancy indicates that H2O adsorption is favored at interstitial sites where no substrate atoms lie directly below. The prism face is found to attract the water molecule more strongly and provide larger energy barriers to surface diffusion than basal face sites, with the ideal basal faces providing hexagonal patterns of adsorption sites for the H2O with preferred dipole moments aligned.

Hale, B. N.↗

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Dzegilenko, Fedor N.↗

A molecular dynamics study of chloride binding by the cryptand SC24

The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.

NASA Discipline Exobiology↗

Electron impact cross sections for v = 0-1 vibrational excitation in CO at electron energies of 3 to 100 eV

The paper discusses the measurements of normalized, absolute differential cross-sections for electron-impact vibrational transition in CO. Integral and momentum-transfer cross-sections were obtained from these differential results; incident electron energies were in the 3 to 100 eV range, and the scattering angles were 10 to 135 deg. A comparison of these results with measurements made with pure vibrationally elastic cross-sections in N2, and with the data based on a two-potential theory for electron scattering from diatomic molecules showed that the present CO cross-sections are similar to those in N2. This indicates that the long-range effect of the small CO dipole moment is negligible in promoting vibrational excitation; moreover, a significant peak in the integral and momentum-transfer cross-sections is observed at 20 eV. Finally, the low-energy integral cross-sections are compared with a recent set of swarm data for vibrational excitation.

Chutjian, A.↗

Cubanes: Super explosives and potential pharmaceutical intermediates

The cubane molecule, in which eight carbon atoms are locked in a cubic framework, shows great potential for both military and pharmaceutical applications. Octanitrocubane, with a predicted density of 2.1 g/cc and strain energy of more than 165 kcal/mol, is considered to be the 'super-explosive', while cubane derivatives submitted to the National Institutes of Health for preliminary biological activity screening have displayed promising anti-cancer and anti-HIV activity.

Bashir-Hashemi, A.↗

Collisional excitation of interstellar molecules - Deuterated water, HDO

Using an accurate theoretical interacting potential and coupled-channel molecular scattering calculations, excitation rates for deuterated water (HDO) in collisions with He atoms were computed. Data are presented for rates among the 34 rotational levels with energy below 400/cm for temperatures between 50 and 500 K. Excitation rate constants were determined using data from fixed energy cross sections averaged over thermal (Boltzmann) distributions of collision energies. Based on the agreement (for H2O) of rates from two different theoretical potentials and on agreement with the limited experimental data, the larger rates for HDO were estimated to be generally accurate to better than 50 percent.

Green, Sheldon↗

Nanostructure Engineered Chemical Sensors for Hazardous Gas and Vapor Detection

A nanosensor technology has been developed using nanostructures, such as single walled carbon nanotubes (SWNTs) and metal oxides nanowires or nanobelts, on a pair of interdigitated electrodes (IDE) processed with a silicon based microfabrication and micromachining technique. The IDE fingers were fabricated using thin film metallization techniques. Both in-situ growth of nanostructure materials and casting of the nanostructure dispersions were used to make chemical sensing devices. These sensors have been exposed to hazardous gases and vapors, such as acetone, benzene, chlorine, and ammonia in the concentration range of ppm to ppb at room temperature. The electronic molecular sensing in our sensor platform can be understood by electron modulation between the nanostructure engineered device and gas molecules. As a result of the electron modulation, the conductance of nanodevice will change. Due to the large surface area, low surface energy barrier and high thermal and mechanical stability, nanostructured chemical sensors potentially can offer higher sensitivity, lower power consumption and better robustness than the state-of-the-art systems, which make them more attractive for defense and space applications. Combined with MEMS technology, light weight and compact size sensors can be made in wafer scale with low cost.

Li, Jing↗

On the Use of Quartic Force Fields in Variational Calculations

The use of quartic force fields (QFFs) has been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this paper we outline and discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine(-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can effectively describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods. Cases are referenced where variational computations coupled with transformed QFFs produce accuracies compared to experiment for fundamental frequencies on the order of 5 cm(exp −1) and often as good as 1 cm(exp −1).

quartic force field↗