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Investigations were carried out in two major areas during the last reporting period. Energy- and structure-related properties of small gold clusters deposited on the GaAs(110) surface were investigated using a molecular dynamics procedure. Additionally, a comparative study of the many-body potentials of silicon systems was performed.
We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions.
The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth. One Sentence Summary: Small metal-binding peptides were the likely precursors of modern enzymes.
We present the first results obtained with our new imaging Fabry-Perot spectrometer, KWIC. We obtained a fully sampled 9.8 sec. spatial resolution image of the inner 8 min. x 12 min. region of the Orion Nebula in the 37 micro m continuum and a somewhat smaller scale image in the (SiII) 35 micro m line. The continuum image traces out the structure of the interface region between the molecular cloud and the Orion A HII region, as well picking out embedded sources such as the BN-KL star cluster. The continuum directly yields the luminosity of the sources and is used to deduce dust mass and grain parameters. Our (SiII) image both reveals the clumpy structure of the interface region and signals the presence of a dissociative J-shock in the high velocity outflow from IRc2.
The accuracy of current molecular-structure calculations is illustrated with examples of quantum mechanical solutions for chemical problems. Two approaches are considered: (1) the coupled-cluster singles and doubles (CCSD) with a perturbational estimate of the contribution of connected triple excitations, or CCDS(T); and (2) the multireference configuration-interaction (MRCI) approach to the correlation problem. The MRCI approach gains greater applicability by means of size-extensive modifications such as the averaged-coupled pair functional approach. The examples of solutions to chemical problems include those for C-H bond energies, the vibrational frequencies of O3, identifying the ground state of Al2 and Si2, and the Lewis-Rayleigh afterglow and the Hermann IR system of N2. Accurate molecular-wave functions can be derived from a combination of basis-set saturation studies and full configuration-interaction calculations.
A survey is reported of the J = 1 - 0 2.6-mm transition of CO, covering 11.5 square degrees toward the Taurus dark cloud complex, including Heiles Cloud 2 and DL 2. The main finding is the presence of systematic velocity structure in the Barnard 18 region of DL 2. This structure is tentatively interpreted as an expanding shell of molecular gas of diameter about 3 pc centered on a cluster of young T Tauri stars. The estimated momentum of the shell is consistent with that expected from winds from the young stars seen in the shell.
The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.
The S140 molecular cloud was observed in five transitions of CS with resolutions of 11 to 45 arcsec. The data were analyzed with both the LVG and microturbulent models of radiative transfer to derive the density structure. It was found that the CS emission comes from three components of gas: a spherical component centered on the infrared cluster, an arc component along the ionization front between the S140 H II region and the dense molecular cloud core, and a high-velocity component from the dense part of a molecular outflow. The spherical component contributes most to the CS emission and was analyzed in more detail than the other components. Using a temperature distribution derived from an analysis of the dust emission from S140, we fit a power-law density distribution of n(r) = n(sub i)(r/r(sub i))(exp -alpha) to the spherical component. The best fit was for n(sub i) = 1.4 x 10(exp 6) (density at r(sub i) = 0.026 pc) and alpha = 0.8. The density (n(sub i)) was found to be greater than or equal to the density required to account for the dust emission, depending on the dust opacity laws adopted. The presence of optical emission (Dinerstein, Lester, & Rank 1979) suggests a clumpy structure for the dense gas. Considerations of the virial mass and the lowest amount of column density required to produce dust emission put the volume filling factor (f(sub nu)) of the dense gas at approximately 0.14-0.5. We compared S140 with other regions of star formation where the density structure has been derived from excitation analysis. Source-source variations in density gradients and clumpiness clearly exist, ranging from alpha = 2 and f(sub nu) approximately 1 in B335 to alpha approximately 0, f(sub nu) approximately 0.1 in M17. There is a tendency for more massive star-forming regions to have a flatter density distribution, a more clumpy structure, and a large number of young stars. The implications of this tendency are discussed.
Analytic derivative techniques are utilized to determine molecular geometries, vibration spectra, molecular force field, proton affinity, and energetics of clustering of protonated methane. It is observed that the geometries are gradient optimized, while the harmonic force fields and IR intensities are also determined analytically at the SCF level. It is determined that the frequency of the torsional model for rotation of the H2 about the pseudothreefold axis of the CH3(+) group is extremely low, and the proton affinity of CH4 is calculated as 129.0 kcal/mol.
The thermodynamic properties of (CO2)N molecular aggregates of size N between 2 and 13 have been investigated. These crystallites exhibit well defined orientational order-disorder rotational transitions accompanied by a structural transition into a plastic crystallite phase. In addition, they exhibit melting and disassociation transitions. It is shown that the interpretation of experimental data, based upon dimer properties, depends crucially on these results. Equilibrium structures and orientations are also given.
The central field empirical pair potential model is applied to studying the effects of kinks, ledges, and vacancies on the absorption of water molecules from the vapor. Molecular dynamics simulations indicate that cluster and/or surface modes play a primary role in the absorption process, the flexibility of the hydrogen bond serves to decrease the energy required for structural interconversion, and the rapid distribution of added energy in a hydrogen bonded system lead to aggregate stability which greatly exceeds that predicted by static energy calculations.
Winds from T-Tauri stars may provide an important dynamical input into cold molecular clouds. If the frequency of T-Tauri stars exceeds 20/cu pc, wind-driven shells collide and form ram-pressure-confined clumps. The supersonic clump motions can account for cloud line widths. Clumps collide inelastically, coalescing and eventually becoming Jeans unstable. For characteristic dark cloud temperatures low-mass stars form, and it is speculated that in this manner clouds can be self-sustaining for 10 million to 100 million yr. Only when either the gas supply is exhausted or an external trigger stimulates massive star formation (for example, by heating the cloud or enhancing the clump collision rate), will the cloud eventually be disrupted. A natural consequence of this model is that dark cloud lifetimes are identified with the duration of low-mass star formation, inferred to exceed 10 million yr from studies of nearby star clusters. Other implications include the prediction of the existence of embedded low-mass stars in turbulent cloud cores, the presence of an internal source of radiation in dark clouds, and a clumpy structure for cold molecular clouds.
The present conference on heterogeneous atmospheric chemistry considers such topics concerning clusters, particles and microparticles as common problems in nucleation and growth, chemical kinetics, and catalysis, chemical reactions with aerosols, electron beam studies of natural and anthropogenic microparticles, and structural studies employing molecular beam techniques, as well as such gas-solid interaction topics as photoassisted reactions, catalyzed photolysis, and heterogeneous catalysis. Also discussed are sulfur dioxide absorption, oxidation, and oxidation inhibition in falling drops, sulfur dioxide/water equilibria, the evidence for heterogeneous catalysis in the atmosphere, the importance of heterogeneous processes to tropospheric chemistry, soot-catalyzed atmospheric reactions, and the concentrations and mechanisms of formation of sulfate in the atmospheric boundary layer.
From intermolecular force studies, it is now known that the overall non-additive contribution to the lattice enegy is positive so that analysis based on only pairwise additivity suggests a shallower intermolecular potential than the true value. Two body contributions alone are also known to be categorically unable to even qualitatively describe some configurations of molecular clusters in the gas phase or the general relaxation and reconstruction of fcc crystal surfaces. In addition, the many-body contribution was shown to play a key role in the stability of certain crystal structures. In these recent analyses, a relatively simple potential energy function (PEF), comprising only a two-body Mie-type potential plus a three-body Axilrod-Teller-type potential, was found to be extremely effective. This same parametric PEF is applied to describe the bulk stability and surface energy for the diamond cubic structure. To test the stability condition, the FCC, BCC, diamond cubic, graphite and beta-tin structures were considered.
Consideration is given to HST observations of late-type stars, molecular absorption in the UV spectrum of Alpha Ori, EUV emission from late-type stars, Rosat observations of the Pleiades cluster, a deep ROSAT observation of the Hyades cluster, optical spectroscopy detected by EXOSAT, stellar photospheric convection, a structure of the solar X-ray corona, magnetic surface images of the BY Dra Star HD 82558, a Zebra interpretatin of BY Dra stars, optical flares on II Peg, a low-resolution spectroscopic survey of post-T tauri candidates, millimeter and sub-millimeter emission from flare stars, and activity in tidally interacting binaries. Attention is also given to modeling stellar angular momentum evolution, extended 60-micron emission from nearby Mira variables, the PANDORA atmosphere program, the global properties of active regions, oscillations in a stratified atmosphere, lithium abundances in northern RS CVn binaries, a new catalog of cool dwarf stars, the Far UV Spectrograph Explorer, and development of reflecting coronagraphs.
The southern H II region G333.6-0.2, which has a total luminosity of 3.3 million solar luminosities (for an assumed distance of 4 kpc) was mapped at 2.2, 10, 30, 50, and 100 microns. At all wavelengths, the surface brightness of the infrared radiation is unusually high and the structure of the source is compact and symmetrical. The present observations, along with previous data, suggest that G333.6-0.2 is excited by a single luminous object or a very compact cluster, which has formed on the front surface of a dense molecular cloud as seen from the earth. It is shown that the spectral and spatial characteristics of the infrared radiation can be understood in terms of this blister model.
DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from > 100 Mbp down to < 0.01 Mbp, is modeled using computer simulations and analytic equations. A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. The chromatin model neglects molecular details but systematically incorporates an increase in average spatial separation between two DNA loci as the number of base-pairs between the loci increases. Fragment-size distributions obtained using DNAbreak match data on large fragments about as well as distributions previously obtained with a less mechanistic approach. Dose-response relations, linear at small doses of high linear energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data.