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Due to formal and computational advances in coupled-cluster theory over the past few years, it is now possible to obtain very accurate molecular geometries, vibrational frequencies, heats of formation, binding energies, and vertical electronic excitation energies. The present monograph reviews the advances that have lead to the current state-of-the art, and also summarizes selected examples from the published literature.
We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.
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.
A computational method was devised to explore the relationship between charge separation, geometry, molecular dipole moment, polarizability, and hyperpolarizabilities in comjugated organic molecules. It is shown that bond length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimizaton of molecules and materials.
In a high temperature combustion situation such as a gas turbine or rocket engine, combustion products include water vapor. This water vapor reacts with oxides in the hot-gas-path to form volatile hydroxides and oxyhydroxides. The oxides may be structural oxide components or protective oxides on alloys or non-oxide ceramics. In either case, this enhanced volatilization leads to degradation of components. Reliable thermochemical data for many metal hydroxides and oxyhydroxides has not been available. We review a database put together at NASA over many years based on experimental and ab initio computations for thermochemical data of Al, Si, Ti, Cr, Mn, Y, Zr, La, Ta, Gd, and Yb hydroxides and oxyhydroxides. Experimental methods for measuring thermodynamic quantities of metal hydroxides and oxyhydroxides are limited since the required high temperatures and high pressures preclude many conventional methods. Nonetheless, transpiration has proven a valuable tool in our laboratories for the Si-O-H, Cr-O-H, and Ti-O-H systems. Data are analyzed with second and third law methods. These data can be leveraged with quantum chemistry to provide reliable free energy functions for the third law calculation and comparison to the derived enthalpies of formation. Both wave function and DFT methods can be utilized for deriving the thermodynamic functions for the various metal hydroxides and oxyhydroxides. We have found that, in general, reasonable molecular geometries and spectroscopic data can be derived with a relatively low level of theory, i.e. DFT with the B3LYP functional. Accurate calculations of the enthalpy of formation require higher levels of theory, such as the Coupled Cluster, Singles, Doubles, and perturbative Triples CCSD(T) approach with complete basis sets (CBS). Also, corrections for hindered rotations and anharmonicity are necessary. For some symmetries, the anharmonic correction has proven to be a challenge and we have found that this is only treated properly by certain codes. The database lists the fHo(298), So(298), and Cp in the form Cp = A + BT + CT2 + D/T + E/T2, where A, B, C, D, and E are the fitting constants. Thus, it can be easily used in any of the common computational thermochemistry codes. To date, the database contains 51 gaseous species of the formula MOx(OH)y.
High spatial and spectral resolution observations of the distribution, physical parameters, and kinematics of the molecular interstellar medium toward the nucleus of the Seyfert 2 galaxy NGC 1068 are reported. The data consist of 2.4 by 3.4 arcseconds resolution interferometry of the 88.6 GHz HCN J = 1 towards 0 line at 17 km/s spectral resolution, single dish observations of several mm/submm isotopic lines of CO and HCN, and 0.85 arcseconds imaging spectroscopy of the 2.12 micron H2 S(1) line at a velocity resolution of 110 km/s. The central few hundred parsecs of NGC 1068 contain a system of dense (N(H2) approximately 10(exp 5) cm(exp -3)), warm (T greater than or equal to 70 K) molecular cloud cores. The low density molecular envelopes have probably been stripped by the nuclear wind and radiation. The molecular gas layer is located in the plane of NGC 1068's large scale disk (inclination approximately 35 deg) and orbits in elliptical streamlines in response to the central stellar bar. The spatial distribution of the 2 micron H2 emission suggests that gas is shocked at the leading edge of the bar, probably resulting in gas influx into the central 100 pc at a rate of a few solar mass per year. In addition to large scale streaming (with a solid body rotation curve), the HCN velocity field requires the presence of random motions of order 100 km/s. We interpret these large random motions as implying the nuclear gas disk to be very thick (scale height/radius approximately 1), probably as the result of the impact of nuclear radiation and wind on orbiting molecular clouds. Geometry and column density of the molecular cloud layer between approximately 30 pc to 300 pc from the nucleus can plausibly account for the nuclear obscuration and anisotropy of the radiation field in the visible and UV.
Physical forces of gravity, hemodynamic stresses, and movement play a critical role in tissue development. Yet, little is known about how cells convert these mechanical signals into a chemical response. This review attempts to place the potential molecular mediators of mechanotransduction (e.g. stretch-sensitive ion channels, signaling molecules, cytoskeleton, integrins) within the context of the structural complexity of living cells. The model presented relies on recent experimental findings, which suggests that cells use tensegrity architecture for their organization. Tensegrity predicts that cells are hard-wired to respond immediately to mechanical stresses transmitted over cell surface receptors that physically couple the cytoskeleton to extracellular matrix (e.g. integrins) or to other cells (cadherins, selectins, CAMs). Many signal transducing molecules that are activated by cell binding to growth factors and extracellular matrix associate with cytoskeletal scaffolds within focal adhesion complexes. Mechanical signals, therefore, may be integrated with other environmental signals and transduced into a biochemical response through force-dependent changes in scaffold geometry or molecular mechanics. Tensegrity also provides a mechanism to focus mechanical energy on molecular transducers and to orchestrate and tune the cellular response.
Utilizing Lyman-alpha emission cross sections for H2 as secondary standards, absolute values of Lyman-alpha emission cross sections for CH4 have been obtained for electron impact energies varying from threshold to 100 eV. A crossed electron beam-molecular beam geometry was employed and the Lyman-alpha radiation was detected at 90 deg and 45 deg with respect to the incident electron beam by a solar blind photomultiplier in tandem with an oxygen filter. The results are compared with previous measurements. Appreciable differences among the various experimental data are found.
The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. The time development of ordering is quantified and a novel freezing mechanism is observed. The liquid forms layers and subsequent in-plane ordering within a layer is accompanied by a sharpening of the layer in the transverse direction. The effects of channel size, the methods of quench, the liquid-wall interaction and the roughness of walls on the freezing mechanism are elucidated. Comparison with recent experiments on freezing in confined geometries is presented.
Utilizing a crossed electron beam-molecular beam collision geometry, mass spectra of C(sub 60) and C(sub 70) ions have been obtained for an electron impact energy range of 20 eV to 600 eV.
We have constructed three-dimensional models for the equilibrium abundance of molecular hydrogen in diffuse interstellar clouds of arbitrary geometry that are illuminated by ultraviolet radiation. The position-dependent photodissociation rate of H2 in such clouds was computed with a 26 ray approximation to model the attenuation of the incident ultraviolet radiation field by dust and by H2 line absorption. We have applied our modeling technique to the isolated diffuse cloud G236+39, assuming that the cloud has a constant density and that the thickness of the cloud along the line of sight is at every point proportional to the 100 micron continuum intensity measured by IRAS. We find that our model can successfully account for observed variations in the ratio of 100 micron continuum intensity to H I column density, with larger values of that ratio occurring along lines of sight in which the molecular hydrogen fraction is expected to be the largest. Using a standard chi square analysis to assess the goodness of fit of our models, we find (at the 60 a level) that a three-dimensional model is more successful in matching the observational data than a one-dimensional model in which the geometrical extent of the cloud along the line of sight is assumed to be much smaller than its extent in the plane of the sky. If D is the distance to G236 + 39, and given standard assumptions about the rate of grain-catalyzed H2 formation, we find that the cloud has an extent along the line of sight that is 0.9 +/- 0.1 times its mean extent projected onto the plane of the sky and a gas density of 53 +/- 8 (100 pc/D) H nuclei/cc and is illuminated by a radiation field of 1.1 +/- 0.2 (100 pc/D) times the mean interstellar radiation field. The derived 100 micron emissivity per nucleon is 1.13 +/- 0.06 x 10(exp -20) MJy/sr sq cm.
Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Intro: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication.
Using a crossed electron beam-molecular beam scattering geometry and a relative-flow technique, ratios of elastic differential cross sections of CO to those of He have been measured at electron impact energies of 3, 5, 7.5, 9.9, 15, 20, 30, 50, 75, and 100 eV. At each energy, an angular range of 15 to 130 deg has been covered. These ratios have been multiplied by previously known He elastic differential cross sections to obtain elastic differential cross sections for CO. Since pure rotational excitations were not resolved, the elastic differential cross sections are a sum of elastic and pure rotational excitations at room temperature. From a knowledge of differential cross sections (DCS), integral and momentum transfer cross sections have been calculated. Both the DCS and integral cross sections are compared at 50, 75, and 100 eV to a recent two-potential theory of e-molecule scattering. Present results show that the isoelectronic molecules CO and N2 have very similar magnitudes and shapes of their differential cross sections.
Utilizing a crossed electron-beam-molecular-beam scattering geometry, relative values of differential electron scattering cross sections for cesium chloride at 5 and 20 eV electron impact energies and at scattering angles between 10 and 120 deg have been measured. These relative cross sections have been normalized to the cross section at 15 deg scattering angle calculated by the hybrid S-matrix technique. In the angular range between 0 and 10 deg and between 120 and 180 deg extrapolations have been made to obtain integral and momentum transfer cross sections. An energy-loss spectrum is also presented which gives various spectral features lying between the 4 and 10 eV regions in CsCl.
A crossed electron beam-molecular beam scattering geometry and the relative-flow technique are used to measure the ratios of the elastic differential cross sections of SO2 to those of He at electron impact energies of 12, 20, 50, 100, 150, and 200 eV. At each energy, an angular range of 15-150 deg is covered. The ratios are multiplied by previously known He elastic differential cross sections to obtain elastic differential cross sections for SO2. Integral and momentum transfer cross sections are then determined from a knowledge of differential cross sections. With the aid of the two-potential theory of e-molecule scattering, calculations are also performed and compared with the measurements.
A crossed electron beam-molecular beam collision geometry is used to measure cross sections for the production of positive ions by electron impact on NH3 and CS2. Ionization cross-section data for NH3 and the values of various cross sections are presented, as well as ionization efficiency curves for CS2. Considerable differences are found between the various results on NH3. The present values are close to the data of Djuric et al. (1981). The semiempirical calculations of Hare and Meath (1987) differ considerably in the absolute values of cross sections. Discrepancies were observed in comparisons of cross sections of other fragment ions resulting from the ionization and dissociate ionization of NH3.
Using a crossed electron beam-molecular beam collision geometry and the relative flow technique measurements have been made to generate a uniform set of electron impact ionization cross-section data for O2 for electron impact energies from threshold to 1000 eV. Present values of total, partial and dissociative ionization cross-sections are compared with previously published data. Cross-sections for the formation of O2(+) from O2 have been measured for the first time.
An experimental investigation of the non-reactive mixing processes associated with a lobed fuel injector in a coflowing air stream is presented. The lobed fuel injector is a device which generates streamwise vorticity, producing high strain rates which can enhance the mixing of reactants while delaying ignition in a controlled manner. The lobed injectors examined in the present study consist of two corrugated plates between which a fuel surrogate, CO2, is injected into coflowing air. Acetone is seeded in the CO2 supply as a fuel marker. Comparison of two alternative lobed injector geometries is made with a straight fuel injector to determine net differences in mixing and strain fields due to streamwise vorticity generation. Planar laser-induced fluorescence (PLIF) of the seeded acetone yields two-dimensional images of the scalar concentration field at various downstream locations, from which local mixing and scalar dissipation rates are computed. It is found that the lobed injector geometry can enhance molecular mixing and create a highly strained flowfield, and that the strain rates generated by scalar energy dissipation can potentially delay ignition in a reacting flowfield.