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At least 865 records · Page 48
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DOE OSTI2011

INTERSTELLAR ICES AS WITNESSES OF STAR FORMATION: SELECTIVE DEUTERATION OF WATER AND ORGANIC MOLECULES UNVEILED

Observations of star-forming environments revealed that the abundances of some deuterated interstellar molecules are markedly larger than the cosmic D/H ratio of 10{sup -5}. Possible reasons for this pointed to grain surface chemistry. However, organic molecules and water, which are both ice constituents, do not enjoy the same deuteration. For example, deuterated formaldehyde is very abundant in comets and star-forming regions, while deuterated water rarely is. In this paper, we explain this selective deuteration by following the formation of ices (using the rate equation method) in translucent clouds, as well as their evolution as the cloud collapses to form a star. Ices start with the deposition of gas-phase CO and O onto dust grains. While reaction of oxygen with atoms (H or D) or molecules (H{sub 2}) yields H{sub 2}O (HDO), CO only reacts with atoms (H and D) to form H{sub 2}CO (HDCO, D{sub 2}CO). As a result, the deuteration of formaldehyde is sensitive to the gas D/H ratio as the cloud undergoes gravitational collapse, while the deuteration of water strongly depends on the dust temperature at the time of ice formation. These results reproduce well the deuterium fractionation of formaldehyde observed in comets and star-forming regions and can explain the wide spread of deuterium fractionation of water observed in these environments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

SULFUR MOLECULE CHEMISTRY IN SUPERNOVA EJECTA RECORDED BY SILICON CARBIDE STARDUST

We studied about 3400 presolar silicon carbide (SiC) grains from the Murchison CM2 meteorite for C- and Si-isotopic compositions. Among these grains we identified 7 unusual or type C SiC (U/C) grains, characterized by isotopically heavy Si, and 36 supernova type X SiC grains, characterized by isotopically light Si. Selected U/C and X grains were also measured for S-, Mg-Al-, and Ca-Ti-isotopic compositions. We show that the U/C grains incorporated radioactive {sup 44}Ti, which is evidence that they formed in the ejecta of Type II supernova (SNII) explosions. Abundances of radioactive {sup 26}Al and {sup 44}Ti are compatible with those observed in X grains. U/C and X grains carry light S with enrichments in {sup 32}S of up to a factor of 2.7. The combination of heavy Si and light S observed in U/C grains is not consistent with abundance predictions of simple supernova models. The isotope data suggest preferential trapping of S from the innermost supernova zones, the production site of radioactive {sup 44}Ti, by the growing silicon carbide particles. A way to achieve this is by sulfur molecule chemistry in the still unmixed ejecta. This confirms model predictions of molecule formation in SNII ejecta and shows that sulfur molecule chemistry operates in the harsh and hot environments of stellar explosions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

MOLECULES IN {eta} CARINAE

We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Fast calculation of diffraction patterns from an ensemble of aligned molecules

We report an algorithm to calculate electron diffraction patterns for molecules with anisotropic angular distribution, which is significantly faster than existing methods. The algorithm uses a transform to convert the molecular orientation distribution, which is a function of three Euler angles, to the atom-pair distribution functions which depend on the polar and azimuthal angles. The diffraction signal can then be calculated from the atom-pair distributions. We demonstrate the computation method numerically by calculating electron diffraction patterns for a symmetric top molecule (trifluoroiodomethane) and an asymmetric top molecule (formaldehyde) and show that it reduces the calculation time by approximately two orders of magnitude compared to the standard brute-force method. Here, the method can also be applied to the calculation of x-ray diffraction patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Quantum membrane phases in synthetic lattices of cold molecules or Rydberg atoms

Here, we calculate properties of dipolar interacting ultracold molecules or Rydberg atoms in a semisynthetic three-dimensional configuration—one synthetic dimension plus a two-dimensional real-space optical lattice or periodic microtrap array—using the stochastic Green's function quantum Monte Carlo method. Through a calculation of thermodynamic quantities and appropriate correlation functions, along with their finite-size scalings, we show that there is a second-order transition to a low-temperature phase in which two-dimensional “sheets” form in the synthetic dimension of internal rotational or electronic states of the molecules or Rydberg atoms, respectively. Simulations for different values of the interaction V, which acts between atoms or molecules that are adjacent both in real and synthetic space, allow us to compute a phase diagram. We find a finite-temperature transition at sufficiently large V as well as a quantum phase transition—a critical value V c below which the transition temperature vanishes.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Berry connection in atom-molecule systems

In the mean-field theory of atom-molecule systems, where bosonic atoms combine to form molecules, there is no usual U(1) symmetry, presenting an apparent hurdle for defining the Berry phase and Berry curvature for these systems. We define a Berry connection for this system, with which the Berry phase and Berry curvature can be naturally computed. We use a three-level atom-molecule system to illustrate our results. In particular, we have computed the mean-field Berry curvature of this system analytically, and compared it to the Berry curvature computed with the second-quantized model of the same system. An excellent agreement is found, indicating the validity of our definition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Second-order Born approximation for the ionization of molecules by electron and positron impact

Second-order Born approximation is applied to study the ionization of molecules. The initial and final states are described by single-center wave functions. For the initial state a Gaussian wave function is used while for the ejected electron it is a distorted wave. Results of the present model are compared with recent (e,2e) experiments on the water molecule. Preliminary results are also presented for the ionization of the thymine molecule by electrons and positrons.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Electron-impact study of the S{sub 2} molecule using the R-matrix method

The present study deals with the calculation of elastic [integrated and differential cross section (DCS)], momentum-transfer, excitation, and ionization cross sections for electron impact on S{sub 2} molecules using the R-matrix method. The target states are represented by including correlations via a configuration-interaction technique. We used a double zeta plus polarization Gaussian basis set contracted as (12,8,1)/(6,4,1) for S atoms. The results of the static exchange, correlated one-state, and 20-state close-coupling approximations are presented. We have detected a stable anionic bound state {sup 2}{Pi}{sub g} of S{sub 2}{sup -} having the configuration 1{sigma}{sub g}{sup 2}{center_dot}{center_dot}{center_dot}5{sigma}{sub g}{sup 2} 1{sigma}{sub u}{sup 2}{center_dot}{center_dot}{center_dot}4{sigma}{sub u}{sup 2} 1{pi}{sub u}{sup 4} 1{pi}{sub g}{sup 4} 2{pi}{sub u}{sup 4} 2{pi}{sub g}{sup 3}. The vertical electron affinity value is 1.42 eV, which is comparable with the experimental value of 1.67{+-}0.015 eV. We detected two shape resonances, both of {sup 2}{Pi}{sub u} symmetry in the excitation cross sections of the {sup 1}{Delta}{sub g} and {sup 1}{Sigma}{sub g}{sup +} excited states. The dissociative nature of these resonances is explored by performing scattering calculations in which the S-S bond is stretched. These resonances support dissociative attachment, yielding S and S{sup -}. We have also predicted six resonances of various symmetries ({sup 2}A{sub u}, {sup 2}B{sub 1g},{sup 4}A{sub u}, {sup 4}B{sub 1g}) in the X {sup 3}{Sigma}{sub g}{sup -} {yields} B {sup 3}{Sigma}{sub u}{sup -} transition. We have calculated the DCS, in a correlated one-state model, by using the polydcs program of Sanna and Gianturco. The data from the momentum-transfer cross section, generated from DCS, are used to compute effective collision frequencies over a wide electron temperature range (200-30 000 K). The ionization cross sections are calculated in the binary-encounter Bethe model in which Hartree-Fock molecular orbitals at a self-consistent level are used to calculate kinetic and binding energies of the occupied molecular orbitals. We have included up to g-partial wave (l=4) in the scattering calculations. For this molecule we have used a Born-closure top-up procedure to account for the higher partial waves for the convergence of the cross section for the dipole-allowed excitation from the ground state. We have also evaluated the scattering length of the S{sub 2} molecule, which is equal to 2.615a{sub 0}.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Magnetic-field effects in transitions of X Li molecules (X: even isotopes of group II atoms)

We analyze the Zeeman shift in the (v,N)=(0,0){yields}(1,0) transition frequency of X Li molecules (X: even isotopes of group II atoms), which is of interest in metrology. The Zeeman shift in the transition frequency between stretching states is found to be less than 1 mHz with a magnetic field of 1 G. X {sup 6}Li molecules are more advantageous than X {sup 7}Li molecules for measuring the transition frequency without the Zeeman shift because of the smaller g factor of the Li nuclear spin.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Spectroscopic prescription for optimal stimulated Raman transfer of ultracold heteronuclear molecules to the lowest rovibronic level

We show that the multiplicative product of a molecular-beam excitation spectrum and an ultracold-molecule excitation spectrum, with a frequency offset appropriate to the initial ultracold-molecule level, provides the relative rate of stimulated Raman transfer (SRT) from a given high rovibrational level to the lowest rovibronic level, i.e., the v{sup ''}=0,J{sup ''}=0 level of the ground electronic state for photoassociated (and magnetoassociated) ultracold molecules. This product spectrum clearly indicates the optimal pathways for SRT, even when the two component spectra are completely unassigned. We illustrate this specifically for the case of KRb.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Prospects for rapid deceleration of small molecules by optical bichromatic forces

We examine the prospects for utilizing the optical bichromatic force (BCF) to greatly enhance laser deceleration and cooling for near-cycling transitions in small molecules. We discuss the expected behavior of the BCF in near-cycling transitions with internal degeneracies, then consider the specific example of decelerating a beam of calcium monofluoride molecules. We have selected CaF as a prototype molecule both because it has an easily accessible near-cycling transition and because it is well suited to studies of ultracold molecular physics and chemistry. We also report experimental verification of one of the key requirements, the production of large bichromatic forces in a multilevel system with significant energy level splittings, by performing tests in an atomic beam of metastable helium.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Thermalization of atom-molecule Bose gases in a double-well potential

We study the nonequiliribium dynamics of atom-molecule Bose gases in a double-well potential. In this system, the internal atom-molecule tunneling has significant influence on the dynamics. We investigate the regularity of dynamics by studying the level statistics of the quantum system. We find that chaotic energy eigenstates arise from the competition between the interwell and the atom-molecule internal tunnelings. Furthermore, we show that the physical quantities relax to the microcanonical averages in the full-quantum dynamics when the system is chaotic. This thermalization is caused by the verification of the eigenstate thermalization hypothesis (ETH). We show numerically that the onset of ETH occurs simultaneously with that of chaos. In addition, we show that the energy eigenstates become exponentially localized states simultaneously with the onset of chaos.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

d-wave superfluidity in optical lattices of ultracold polar molecules

Recent work on ultracold polar molecules, governed by a generalization of the t-J Hamiltonian, suggests that molecules may be better suited than atoms for studying d-wave superfluidity due to stronger interactions and larger tunability of the system. We compute the phase diagram for polar molecules in a checkerboard lattice consisting of weakly coupled square plaquettes. In the simplest experimentally realizable case where there is only tunneling and an XX-type spin-spin interaction, we identify the parameter regime where d-wave superfluidity occurs. We also find that the inclusion of a density-density interaction destroys the superfluid phase and that the inclusion of a spin-density or an Ising-type spin-spin interaction can enhance the superfluid phase. We also propose schemes for experimentally realizing the perturbative calculations exhibiting enhanced d-wave superfluidity.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate and two molecules of inorganic phosphate

A co-crystal structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate, YS0470, and two molecules of inorganic phosphate has been determined. The identity of the phosphate ligands was confirmed by anomalous diffraction data. Human farnesyl pyrophosphate synthase (hFPPS) produces farnesyl pyrophos@@phate, an isoprenoid essential for a variety of cellular processes. The enzyme has been well established as the molecular target of the nitrogen-containing bisphosphonates (N-BPs), which are best known for their antiresorptive effects in bone but are also known for their anticancer properties. Crystal structures of hFPPS in ternary complexes with a novel bisphosphonate, YS0470, and the secondary ligands inorganic phosphate (P{sub i}), inorganic pyrophosphate (PP{sub i}) and isopentenyl pyrophosphate (IPP) have recently been reported. Only the co-binding of the bisphosphonate with either PP{sub i} or IPP resulted in the full closure of the C-@@terminal tail of the enzyme, a conformational change that is required for catalysis and that is also responsible for the potent in vivo efficacy of N-BPs. In the present communication, a co-crystal structure of hFPPS in complex with YS0470 and two molecules of P{sub i} is reported. The unusually close proximity between these ligands, which was confirmed by anomalous diffraction data, suggests that they interact with one another, with their anionic charges neutralized in their bound state. The structure also showed the tail of the enzyme to be fully disordered, indicating that simultaneous binding of two P{sub i} molecules with a bisphosphonate cannot induce the tail-closing conformational change in hFPPS. Examination of homologous FPPSs suggested that this ligand-dependent tail closure is only conserved in the mammalian proteins. The prevalence of P{sub i}-bound hFPPS structures in the PDB raises a question regarding the in vivo relevance of P{sub i} binding to the function of the enzyme.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Plasma-free atomic layer deposition of Ru thin films using H{sub 2} molecules as a nonoxidizing reactant

The ruthenium (Ru) thin films were grown by atomic layer deposition (ALD) using a sequential supply of dicarbonyl-bis(5-methyl-2,4-hexanediketonato) Ru(II) (C{sub 16}H{sub 22}O{sub 6}Ru) and H{sub 2} as a reactant at a substrate temperature of 250 °C. Deposition was possible using H{sub 2} molecules without a plasma by increasing the chamber pressure to above 10 Torr. Specifically, high-quality Ru films with a low resistivity of ∼40 μΩ cm and few amount of oxygen (∼1.2 at. %) were obtained under a chamber pressure of 300 Torr though the oxygen was contained in the precursor. Under the optimized conditions, self-limited film growth with regard to the precursor and reactant pulsing times was confirmed under elevated chamber pressures. The ALD-Ru process proposed in this study showed one of the highest growth rates of 0.12 nm/cycle on a thermally grown SiO{sub 2} substrate, as well as a very low number of incubation cycles (approximately 12 cycles). Cross-sectional view transmission electron microscopy showed that no interfacial oxide had formed during the deposition of the ALD-Ru films on a W surface using H{sub 2} molecules, whereas ∼7 nm thick interfacial oxide was formed when O{sub 2} molecules were used as a reactant. The step coverage of the ALD-Ru film onto very small-sized trenches (aspect ratio: ∼4.5 and the top opening size of 25 nm) and holes (aspect ratio: ∼40 and top opening size of 40 nm) was excellent (∼100%).

36 MATERIALS SCIENCE↗
DOE OSTI2018

X-ray Crystallographic Characterization of the Swine MHC I Molecule SLA-3*0202 Complexed with IAV-HA Nonapeptide

The swine major histocompatibility complex (MHC) class I molecules are also called swine leukocyte antigen (SLA), and most of the highly polymorphic SLA genes are associated with swine diseases. However, the well documented structural reports on swine MHC I molecules remain quite limited. In order to clarify the structural characteristics of the Chinese heishan wild boar MHC class I molecule, SLA-3*0202 and swine β2-microglobulin (sβ2m) with a KMNTQFTAV nonapeptide derived from Influenza A virus Hemagglutinin protein (IAV-HA) were assembled and crystallized. The crystal diffracted at 1.55 Å resolution and belonged to the sp. gr. C121, with the unit-cell parameters a = 206.46 Å, b = 41.47 Å, c = 106.74 Å. The Matthews coefficient and solvent content were calculated to be 2.30 Å{sup 3} Da{sup –1} and 46.64%, respectively. The availability of the structure, which is being solved by molecular replacement, will provide new insights into swine MHC I presenting IAV peptides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Dispersion of Lifetimes of Excited States of Single Molecules in Organic Matrices at Ultralow Temperatures

Fluorescence excitation spectra of single terrylene molecules in transparent naphthalene and polyethylene matrices at ultralow (30–100 mK) temperatures have been studied under the conditions where the widths of zero-phonon spectral lines are determined only by the lifetime T{sub 1} of the excited electronic state. The experimentally observed dispersion of T{sub 1} values for identical molecules is attributed to local field effects, which are responsible for the dependence of T{sub 1} on the effective value of refractive index n of the matrix, which is characteristic of the localization region of each molecule. It has been shown that the dependence T{sub 1}(n) for ensembles of point emitters in organic matrices is satisfactorily explained within the model of a “virtual cavity” around the emitter inside a continuous medium, as well as within the developed quantum kinetic approach including various contributions of the local environment to the lifetime T{sub 1}. The recalculation of average T{sub 1} values to the corresponding n values with the use of the expressions obtained for T{sub 1}(n) has shown that the difference of the calculated refractive indices of naphthalene and polyethylene from the well-known tabulated n values is less than 1%.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Intercalation of C{sub 60} Fullerene Molecules under Single-Layer Graphene on Molybdenum Carbide

It is shown that heating of a fullerite film several monomolecular layers thick deposited onto single-layer graphene formed on a substrate of molybdenum carbide Mo{sub 2}C at T = 700–800 K leads to the intercalation of C{sub 60} molecules under the graphene layer. The direct deposition of C{sub 60} molecules at T = 650 K also leads to the intercalation of C{sub 60} molecules under graphene; the maximal amount of fullerene accumulated under graphene is one single layer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗