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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Definition and determination of the triplet-triplet energy transfer reaction coordinate

A definition of the triplet-triplet energy transfer reaction coordinate within the very weak electronic coupling limit is proposed, and a novel theoretical formalism is developed for its quantitative determination in terms of internal coordinates The present formalism permits (i) the separation of donor and acceptor contributions to the reaction coordinate, (ii) the identification of the intrinsic role of donor and acceptor in the triplet energy transfer process, and (iii) the quantification of the effect of every internal coordinate on the transfer process. This formalism is general and can be applied to classical as well as to nonvertical triplet energy transfer processes. The utility of the novel formalism is demonstrated here by its application to the paradigm of nonvertical triplet-triplet energy transfer involving cis-stilbene as acceptor molecule. In this way the effect of each internal molecular coordinate in promoting the transfer rate, from triplet donors in the low and high-energy limit, could be analyzed in detail.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

An ab initio investigation of the ground and low-lying singlet and triplet electronic states of XNO{sub 2} and XONO (X = Cl, Br, and I)

A systematic ab initio treatment of the nitryl halides (XNO{sub 2}) and the cis- and trans- conformers of the halide nitrites (XONO), where X = Cl, Br, and I, have been carried out using highly correlated methods with sequences of correlation consistent basis sets. Equilibrium geometries and harmonic frequencies have been accurately calculated in all cases at the explicitly correlated CCSD(T)-F12b level of theory, including the effects of core-valence correlation for the former. Where experimental values are available for the equilibrium structures (ClNO{sub 2} and BrNO{sub 2}), the present calculations are in excellent agreement; however, the X-O distances are slightly too long by about 0.01 Å due to missing multireference effects. Accurate predictions for the iodine species are made for the first time. The vertical electronic excitation spectra have been calculated using equation-of-motion coupled cluster methods for the low-lying singlet states and multireference configuration interaction for both singlet and triplet states. The latter also included the effects of spin-orbit coupling to provide oscillator strengths for the ground state singlet to excited triplet transitions. While for ClNO{sub 2} the transitions to excited singlet states all occur at wavelengths shorter than 310 nm, there is one longer wavelength singlet transition in BrNO{sub 2} and two in the case of INO{sub 2}. The long wavelength tail in the XNO{sub 2} species is predicted to be dominated by transitions to triplet states. In addition to red-shifting from X = Cl to I, the triplet transitions also increase in oscillator strength, becoming comparable to many of the singlet transitions in the case of INO{sub 2}. Hence in particular, the latter species should be very photolabile. Similar trends are observed and reported for the halogen nitrites, many of which for the first time.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Interaction of photosensitive surfactant with DNA and poly acrylic acid

In this paper, we investigate interactions and phase transitions in polyelectrolyte-surfactant complexes formed between a cationic azobenzene-containing surfactant and two types of polyelectrolytes: natural (DNA) or synthetic (PAA: poly acrylic acid). The construction of a phase diagram allowed distancing between four major phases: extended coil conformation, colloidally stable compacted globules, colloidal instability range, and surfactant-stabilized compact state. Investigation on the complexes’ properties in different phases and under irradiation with UV light provides information about the role of the surfactant's hydrophobic trans isomers both in the formation and destruction of DNA and PAA globules as well as in their colloidal stabilization. The trans isomer shows much stronger affinity to the polyelectrolytes than the hydrophilic cis counterpart. There is no need for complete compensation of the polyelectrolyte charges to reach the complete compaction. On contrary to the findings previously reported in the literature, we demonstrate – for the first time – complete polyelectrolyte compaction which occurs already at 20% of DNA (and at 50% of PAA) charge compensation. The trans isomer plays the main role in the compaction. The aggregation between azobenzene units in the photosensitive surfactant is a driving force of this process. The decompaction can be realized during UV light irradiation and is strongly influenced by the interplay between surfactant-surfactant and surfactant-DNA interactions in the compacted globules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Percolation network in resistive switching devices with the structure of silver/amorphous silicon/p-type silicon

Conducting pathway of percolation network was identified in resistive switching devices (RSDs) with the structure of silver/amorphous silicon/p-type silicon (Ag/a-Si/p-Si) based on its gradual RESET-process and the stochastic complex impedance spectroscopy characteristics (CIS). The formation of the percolation network is attributed to amounts of nanocrystalline Si particles as well as defect sites embedded in a-Si layer, in which the defect sites supply positions for Ag ions to nucleate and grow. The similar percolation network has been only observed in Ag-Ge-Se based RSD before. This report provides a better understanding for electric properties of RSD based on the percolation network.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Tetrazole acetic acid: Tautomers, conformers, and isomerization

Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0–8 kJ mol{sup −1} energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol{sup −1}) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol{sup −1}). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm{sup −1}, where the first OH stretching overtone vibrations of 1ccc and 2pcc occur. The reverse transformations could be induced by irradiations at 7010 and 7030 cm{sup −1}, transforming 1cct and 2pct back to 1ccc and 2pcc, also selectively. Besides the NIR-induced transformations, the photogenerated 1cct and 2pct forms also decay in N{sub 2} matrices back to 1ccc and 2pcc spontaneously, with characteristic decay times of hours (1H) and tens of minutes (2H). The decay mechanism is rationalized in terms of the proton tunneling. In crystals, TAA exists exclusively as 1H-tautomer. By contrast, the tautomeric composition of the matrix-isolated monomers was found to consist of both 1H- and 2H-tautomers, in comparable amounts. A mechanistic discussion of the tautomerization process occurring during sublimation, accounting also for the observed minor decomposition of TAA leading to CO{sub 2} and 5-methyl-tetrazole, is proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Multi-reference vibration correlation methods

State-specific vibration correlation methods beyond the vibrational multi-configuration self-consistent field (VMCSCF) approximation have been developed, which allow for the accurate calculation of state energies for systems suffering from strong anharmonic resonances. Both variational multi-reference configuration interaction approaches and an implementation of approximate 2nd order vibrational multi-reference perturbation theory are presented. The variational approach can be significantly accelerated by a configuration selection scheme, which leads to negligible deviations in the final results. Relaxation effects due to the partitioning of the correlation space and the performance of a VMCSCF modal basis in contrast to a standard modal basis obtained from vibrational self-consistent field theory have been investigated in detail. Benchmark calculations based on high-level potentials are provided for the propargyl cation and cis-diazene.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Assessment of mode-mixing and Herzberg-Teller effects on two-photon absorption and resonance hyper-Raman spectra from a time-dependent approach

A time-dependent approach is presented to simulate the two-photon absorption (TPA) and resonance hyper-Raman scattering (RHRS) spectra including Duschinsky rotation (mode-mixing) and Herzberg-Teller (HT) vibronic coupling effects. The computational obstacles for the excited-state geometries, vibrational frequencies, and nuclear derivatives of transition dipole moments, which enter the expressions of TPA and RHRS cross sections, are further overcome by the recently developed analytical excited-state energy derivative approaches in the framework of time-dependent density functional theory. The excited-state potential curvatures are evaluated at different levels of approximation to inspect the effects of frequency differences, mode-mixing and HT on TPA and RHRS spectra. Two types of molecules, one with high symmetry (formaldehyde, p-difluorobenzene, and benzotrifluoride) and the other with non-centrosymmetry (cis-hydroxybenzylidene-2,3-dimethylimidazolinone in the deprotonated anion state (HDBI{sup −})), are used as test systems. The calculated results reveal that it is crucial to adopt the exact excited-state potential curvatures in the calculations of TPA and RHRS spectra even for the high-symmetric molecules, and that the vertical gradient approximation leads to a large deviation. Furthermore, it is found that the HT contribution is evident in the TPA and RHRS spectra of HDBI{sup −} although its one- and two-photon transitions are strongly allowed, and its effect results in an obvious blueshift of the TPA maximum with respect to the one-photon absorption maximum. With the HT and solvent effects getting involved, the simulated blueshift of 1291 cm{sup −1} agrees well with the experimental measurement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Molecular-dynamics simulations of thin polyisoprene films confined between amorphous silica substrates

Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 < H/R{sub g} < 8, where R{sub g} is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Chemical reactions of conformationally selected 3-aminophenol molecules in a beam with Coulomb-crystallized Ca{sup +} ions

Many molecules exhibit multiple conformers that often easily interconvert under thermal conditions. Therefore, single conformations are difficult to isolate which renders the study of their distinct chemical reactivities challenging. We have recently reported a new experimental method for the characterization of conformer-specific effects in chemical reactions [Y.-P. Chang, K. Długołęcki, J. Küpper, D. Rösch, D. Wild, and S. Willitsch, “Specific chemical reactivities of spatially separated 3-aminophenol conformers with cold Ca{sup +} ions,” Science 342, 98–101 (2013)]. Different conformers are spatially separated using inhomogeneous electric fields and reacted with a Coulomb crystal of cold, spatially localized ions in a trap. As a first application, we studied reactions between the two conformers of 3-aminophenol and Ca{sup +}. We observed a twofold larger rate constant for the cis compared to the trans conformer which was rationalized in terms of the differences in the long-range ion-molecule interactions. The present article provides a detailed description of the new method and a full account of the experimental results as well as the accompanying theoretical calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Simulation of polyethylene glycol and calcium-mediated membrane fusion

We report on the mechanism of membrane fusion mediated by polyethylene glycol (PEG) and Ca{sup 2+} by means of a coarse-grained molecular dynamics simulation approach. Our data provide a detailed view on the role of cations and polymer in modulating the interaction between negatively charged apposed membranes. The PEG chains cause a reduction of the inter-lamellar distance and cause an increase in concentration of divalent cations. When thermally driven fluctuations bring the membranes at close contact, a switch from cis to trans Ca{sup 2+}-lipid complexes stabilizes a focal contact acting as a nucleation site for further expansion of the adhesion region. Flipping of lipid tails induces subsequent stalk formation. Together, our results provide a molecular explanation for the synergistic effect of Ca{sup 2+} and PEG on membrane fusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Laser induced rovibrational cooling of the linear polyatomic ion C{sub 2}H{sub 2}{sup +}

The laser-induced blackbody-assisted rotational cooling of a linear polyatomic ion, C{sub 2}H{sub 2}{sup +}, in its {sup 2}Π ground electronic state in the presence of the blackbody radiation field at 300 K and 77 K is investigated theoretically using a rate-equations model. Although pure rotational transitions are forbidden in this non-polar species, the ν{sub 5} cis-bending mode is infrared active and the (1-0) band of this mode strongly overlaps the 300 K blackbody spectrum. Hence the lifetimes of state-selected rotational levels are found to be short compared to the typical timescale of ion trapping experiments. The ν{sub 5} (1-0) transition is split by the Renner-Teller coupling of vibrational and electronic angular momentum, and by the spin-orbit coupling, into six principal components and these effects are included in the calculations. In this paper, a rotational-cooling scheme is proposed that involves simultaneous pumping of a set of closely spaced Q-branch transitions on the {sup 2}Δ{sub 5/2} − {sup 2}Π{sub 3/2} band together with two Q-branch lines in the {sup 2}Σ{sup +} − {sup 2}Π{sub 1/2} band. It is shown that this should lead to >70% of total population in the lowest rotational level at 300 K and over 99% at 77 K. In principle, the multiple Q-branch lines could be pumped with just two broad-band (∼Δν = 0.4–3 cm{sup −1}) infrared lasers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Photoisomerization action spectrum of retinal protonated Schiff base in the gas phase

The photophysical behaviour of the isolated retinal protonated n-butylamine Schiff base (RPSB) is investigated in the gas phase using a combination of ion mobility spectrometry and laser spectroscopy. The RPSB cations are introduced by electrospray ionisation into an ion mobility mass spectrometer where they are exposed to tunable laser radiation in the region of the S{sub 1} ← S{sub 0} transition (420–680 nm range). Four peaks are observed in the arrival time distribution of the RPSB ions. On the basis of predicted collision cross sections with nitrogen gas, the dominant peak is assigned to the all-trans isomer, whereas the subsidiary peaks are assigned to various single, double and triple cis geometric isomers. RPSB ions that absorb laser radiation undergo photoisomerization, leading to a detectable change in their drift speed. By monitoring the photoisomer signal as a function of laser wavelength an action spectrum, extending from 480 to 660 nm with a clear peak at 615 ± 5 nm, is obtained. The photoisomerization action spectrum is related to the absorption spectrum of isolated retinal RPSB molecules and should help benchmark future electronic structure calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Charge transfer from an adsorbed ruthenium-based photosensitizer through an ultra-thin aluminium oxide layer and into a metallic substrate

The interaction of the dye molecule N3 (cis-bis(isothiocyanato)bis(2,2-bipyridyl-4,4′-dicarbo-xylato) -ruthenium(II)) with the ultra-thin oxide layer on a AlNi(110) substrate, has been studied using synchrotron radiation based photoelectron spectroscopy, resonant photoemission spectroscopy, and near edge X-ray absorption fine structure spectroscopy. Calibrated X-ray absorption and valence band spectra of the monolayer and multilayer coverages reveal that charge transfer is possible from the molecule to the AlNi(110) substrate via tunnelling through the ultra-thin oxide layer and into the conduction band edge of the substrate. This charge transfer mechanism is possible from the LUMO+2 and 3 in the excited state but not from the LUMO, therefore enabling core-hole clock analysis, which gives an upper limit of 6.0 ± 2.5 fs for the transfer time. This indicates that ultra-thin oxide layers are a viable material for use in dye-sensitized solar cells, which may lead to reduced recombination effects and improved efficiencies of future devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Fragment transition density method to calculate electronic coupling for excitation energy transfer

A general approach, the Fragment Transition Density (FTD) scheme, is introduced to estimate electronic coupling for excitation energy transfer in a molecular system. Within this method, the excitation energies and transition densities of the system are used to derive the coupling matrix element. The scheme allows one to treat systems where exciton donor and acceptor are close together and their exchange interaction and orbital overlap are significant. The FTD method can be applied in combination with any quantum mechanical approach to treat excited states of general nature including single-, double-, and higher excitations. Using FTD approach, we derive excitonic couplings for several systems computed with the CIS, TD DFT and MS-CASPT2 methods. In particular, it is shown that the estimated coupling values in DNA π-stacks are strongly affected by the short-range electronic interaction of adjacent nucleobases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Photosensitive response of azobenzene containing films towards pure intensity or polarization interference patterns

In this paper, we report on differences in the response of photosensitive azobenzene containing films upon irradiation with the intensity or polarization interference patterns. Two materials are studied differing in the molecular weight: an azobenzene-containing polymer and a molecular glass formed from a much smaller molecule consisting of three connected azobenzene units. Topography changes occurring along with the changes in irradiation conditions are recorded using a homemade set-up combining an optical part for generation and shaping of interference patterns and an atomic force microscope for acquiring the kinetics of film deformation. In this way, we could reveal the unique behavior of photosensitive materials during the first few minutes of irradiation: the change in topography is initially driven by an increase in the azobenzene free volume along with the trans-cis isomerization, followed by the mass transport finally resulting in the surface relief grating. This study demonstrates the great potential of our setup to experimentally highlight puzzling processes governing the formation of surface relief gratings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗