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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Tuning the optical emission of MoS{sub 2} nanosheets using proximal photoswitchable azobenzene molecules

We report photoluminescence measurements performed on monolayer- and two-layer-MoS{sub 2} placed on two types of mixed self-assembled monolayers (mSAMs) of photoswitchable azobenzene molecules. The two mSAMs differ via the electronegative character of the azobenzene derivatives. Thin layers of a transition metal dichalcogenide—MoS{sub 2}—were mechanically exfoliated on mSAM to allow for direct interaction between the molecules and the MoS{sub 2} layers. When the MoS{sub 2} nanosheet is in contact with the electropositive azobenzene molecules in trans configuration, an emission side band at lower energies and at low excitation powers suggest n-type doping. The photoisomerization of the molecules from trans to cis configuration lowers the doping, quenching the side band and enhancing the overall PL efficiency by a factor of ∼3. Opposite results were observed with the chlorinated, more electronegative molecules, exhibiting a reversed trend in the PL efficiency between trans and cis, but with an overall larger intensity. The type of doping induced by the two types of mSAMs was determined by Kelvin probe force microscopy technique.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes

The evaporation/condensation coefficient (β) and the evaporation rate (γ) for n-dodecane vs. temperature, gas pressure, gas and liquid density, and solvation effects at a droplet surface are analysed using quantum chemical density functional theory calculations of several ensembles of conformers of n-dodecane molecules in the gas phase (hybrid functional ωB97X-D with the cc-pVTZ and cc-pVDZ basis sets) and in liquid phase (solvation method: SMD/ωB97X-D). It is shown that β depends more strongly on a number of neighbouring molecules interacting with an evaporating molecule at a droplet surface (this number is estimated through changes in the surface Gibbs free energy of solvation) than on pressure in the gas phase or conformerisation and cross-conformerisation of molecules in both phases. Thus, temperature and the surrounding effects at droplet surfaces are the dominant factors affecting the values of β for n-dodecane molecules. These values are shown to be similar (at reduced temperatures T/T{sub c} < 0.8) or slightly larger (at T/T{sub c} > 0.8) than the values of β calculated by the molecular dynamics force fields (MD FF) methods. This endorses the reliability of the previously developed classical approach to estimation of β by the MD FF methods, except at temperatures close to the critical temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Solving the Schrödinger equation of molecules by relaxing the antisymmetry rule: Inter-exchange theory

The Schrödinger equation (SE) and the antisymmetry principle constitute the governing principle of chemistry. A general method of solving the SE was presented before as the free complement (FC) theory, which gave highly accurate solutions for small atoms and molecules. We assume here to use the FC theory starting from the local valence bond wave function. When this theory is applied to larger molecules, antisymmetrizations of electronic wave functions become time-consuming and therefore, an additional breakthrough is necessary concerning the antisymmetry principle. Usually, in molecular calculations, we first construct the wave function to satisfy the antisymmetry rule, “electronic wave functions must be prescribed to be antisymmetric for all exchanges of electrons, otherwise bosonic interference may disturb the basis of the science.” Starting from determinantal wave functions is typical. Here, we give an antisymmetrization theory, called inter-exchange (iExg) theory, by dividing molecular antisymmetrizations to those within atoms and between atoms. For the electrons belonging to distant atoms in a molecule, only partial antisymmetrizations or even no antisymmetrizations are necessary, depending on the distance between the atoms. So, the above antisymmetry rule is not necessarily followed strictly to get the results of a desired accuracy. For this and other reasons, the necessary parts of the antisymmetrization operations become very small as molecules become larger, leading finally to the operation counts of lower orders of N, the number of electrons. This theory creates a natural antisymmetrization method that is useful for large molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Mechanism of charge transfer and its impacts on Fermi-level pinning for gas molecules adsorbed on monolayer WS{sub 2}

Density functional theory calculations were performed to assess changes in the geometric and electronic structures of monolayer WS{sub 2} upon adsorption of various gas molecules (H{sub 2}, O{sub 2}, H{sub 2}O, NH{sub 3}, NO, NO{sub 2}, and CO). The most stable configuration of the adsorbed molecules, the adsorption energy, and the degree of charge transfer between adsorbate and substrate were determined. All evaluated molecules were physisorbed on monolayer WS{sub 2} with a low degree of charge transfer and accept charge from the monolayer, except for NH{sub 3}, which is a charge donor. Band structure calculations showed that the valence and conduction bands of monolayer WS{sub 2} are not significantly altered upon adsorption of H{sub 2}, H{sub 2}O, NH{sub 3}, and CO, whereas the lowest unoccupied molecular orbitals of O{sub 2}, NO, and NO{sub 2} are pinned around the Fermi-level when these molecules are adsorbed on monolayer WS{sub 2}. The phenomenon of Fermi-level pinning was discussed in light of the traditional and orbital mixing charge transfer theories. The impacts of the charge transfer mechanism on Fermi-level pinning were confirmed for the gas molecules adsorbed on monolayer WS{sub 2}. The proposed mechanism governing Fermi-level pinning is applicable to the systems of adsorbates on recently developed two-dimensional materials, such as graphene and transition metal dichalcogenides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Polarization properties of light scattered off solutions of chiral molecules in non-forward direction

Measuring the optical activity from an ensemble of chiral molecules is a common tool to know their stereo-structure. These measurements are done in the same propagation direction of the probe beam of light, because that is the direction where most signal is emitted. We provide experimental and theoretical evidence that, even though other interesting information may be gathered when collecting light emitted in other directions, for most molecules, the phenomenon of optical activity is only present in the forward scattering direction. The fundamental reason behind this is that forward scattered light preserves the circular polarization states due to the cylindrical symmetry of the system, an essential requirement for optical activity. An important exemption happens in dual molecules, i.e., molecules which present the same response to electric and magnetic fields. We present a series of experiments measuring the optical activity and the scattering of chiral solutions in the forward and perpendicular directions. We experimentally show that these molecules present optical activity and preservation of circular polarization in the forward direction, while the polarization pattern in non-forward directions is much more complex and, in particular, does not preserve the circular polarization. Finally, we show that when probing the particle with different wavelengths, the scattering in non-forward directions presents some interesting structural features which are hidden in the forward measurements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence of a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Gauge-invariant expectation values of the energy of a molecule in an electromagnetic field

In this paper, we show that the full Hamiltonian for a molecule in an electromagnetic field can be separated into a molecular Hamiltonian and a field Hamiltonian, both with gauge-invariant expectation values. The expectation value of the molecular Hamiltonian gives physically meaningful results for the energy of a molecule in a time-dependent applied field. In contrast, the usual partitioning of the full Hamiltonian into molecular and field terms introduces an arbitrary gauge-dependent potential into the molecular Hamiltonian and leaves a gauge-dependent form of the Hamiltonian for the field. With the usual partitioning of the Hamiltonian, this same problem of gauge dependence arises even in the absence of an applied field, as we show explicitly by considering a gauge transformation from zero applied field and zero external potentials to zero applied field, but non-zero external vector and scalar potentials. We resolve this problem and also remove the gauge dependence from the Hamiltonian for a molecule in a non-zero applied field and from the field Hamiltonian, by repartitioning the full Hamiltonian. It is possible to remove the gauge dependence because the interaction of the molecular charges with the gauge potential cancels identically with a gauge-dependent term in the usual form of the field Hamiltonian. We treat the electromagnetic field classically and treat the molecule quantum mechanically, but nonrelativistically. Our derivation starts from the Lagrangian for a set of charged particles and an electromagnetic field, with the particle coordinates, the vector potential, the scalar potential, and their time derivatives treated as the variables in the Lagrangian. We construct the full Hamiltonian using a Lagrange multiplier method originally suggested by Dirac, partition this Hamiltonian into a molecular term H{sub m} and a field term H{sub f}, and show that both H{sub m} and H{sub f} have gauge-independent expectation values. Any gauge may be chosen for the calculations; but following our partitioning, the expectation values of the molecular Hamiltonian are identical to those obtained directly in the Coulomb gauge. As a corollary of this result, the power absorbed by a molecule from a time-dependent, applied electromagnetic field is equal to the time derivative of the non-adiabatic term in the molecular energy, in any gauge.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

H{sub 2} MOLECULAR CLUSTERS WITH EMBEDDED MOLECULES AND ATOMS AS THE SOURCE OF THE DIFFUSE INTERSTELLAR BANDS

We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ({sup s}eed{sup )}, embedded in a single-layer shell of H{sub 2} molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H{sub 2} molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H{sub 2} shell. We refer to these clusters as contaminated H{sub 2} clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectral profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from {approx}centimeter-sized, dirty H{sub 2} ice balls, called contaminated H{sub 2} ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H{sub 2} molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the {approx}10-100 GHz spectral region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

DISSOCIATIVE PHOTOIONIZATION OF POLYCYCLIC AROMATIC HYDROCARBON MOLECULES CARRYING AN ETHYNYL GROUP

The life cycle of the population of interstellar polycyclic aromatic hydrocarbon (PAH) molecules depends partly on the photostability of the individual species. We have studied the dissociative photoionization of two ethynyl-substituted PAH species, namely, 9-ethynylphenanthrene and 1-ethynylpyrene. Their adiabatic ionization energy and the appearance energy of fragment ions have been measured with the photoelectron photoion coincidence spectroscopy technique. The adiabatic ionization energy has been found at 7.84 ± 0.02 eV for 9-ethynylphenanthrene and at 7.41 ± 0.02 eV for 1-ethynylpyrene. These values are similar to those determined for the corresponding non-substituted PAH molecules phenanthrene and pyrene. The appearance energy of the fragment ion indicative of the loss of a H atom following photoionization is also similar for either ethynyl-substituted PAH molecule and its non-substituted counterpart. The measurements are used to estimate the critical energy for the loss of a H atom by the PAH cations and the stability of ethynyl-substituted PAH molecules upon photoionization. We conclude that these PAH derivatives are as photostable as the non-substituted species in H i regions. If present in the interstellar medium, they may play an important role in the growth of interstellar PAH molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Probing Dipolar Interactions between Rydberg Atoms and Ultracold Polar Molecules

Here, we probe resonant dipolar interactions between ultracold 40 K ⁢ 87 Rb molecules and Rydberg 87 Rb atoms in an optically trapped ensemble. Through state-selective ionization detection of the KRb molecules, we observe resonant energy transfer at 2.227 GHz from Rydberg atoms to molecules under a tunable external electric field. We measure a broadening up to 3.5 MHz, for the Rb Rydberg excitation spectrum, which matches a Monte Carlo simulation that describes a Rydberg atom and neighboring molecules evolving under a dipole-dipole interacting Hamiltonian. The demonstrated interspecies dipolar interaction is a key ingredient for hybrid Rydberg-polar molecule systems, where the advantages of each system can be leveraged and combined.

dipolar Rydberg atoms↗
DOE OSTI2021

Towards C P -violation studies on superheavy molecules: Theoretical and experimental perspectives

Molecules containing superheavy atoms can be artificially created to serve as sensitive probes to study symmetry-violating phenomena. Here, we provide detailed theoretical studies of quantities relevant to the electron electric dipole moment (eEDM) and nucleus-electron scalar-pseudoscalar interactions in diatomic molecules containing superheavy lawrencium nuclei. The sensitivity to parity and time (or, equivalently, CP) reversal violating properties is studied for different neutral and ionic molecules. The effective electric fields in these systems are found to be about 3–4 times larger than other known molecules on which eEDM experiments are being performed. Similarly, these superheavy molecules exhibit an enhancement of more than 3 times for CP-violating scalar-pseudoscalar nucleus-electron interactions. Our preliminary analysis using the Woods-Saxon nuclear model also demonstrates that these results are sensitive to the diffuse surface interactions inside the Lr nucleus. We also briefly comment on some experimental aspects by discussing the production of these systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Sensitivity of transitions in internal rotor molecules to a possible variation of the proton-to-electron mass ratio

Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio {mu}[Jansen et al., Phys. Rev. Lett. 106, 100801 (2011)]. The high sensitivity of methanol originates from the interplay between overall rotation and hindered internal rotation of the molecule; that is, transitions that convert internal rotation energy into overall rotation energy, or vice versa, have an enhanced sensitivity coefficient, K{sub {mu}}. As internal rotation is a common phenomenon in polyatomic molecules, it is likely that other molecules display similar or even larger effects. In this paper we generalize the concepts that form the foundation of the high sensitivity in methanol and use this to construct an approximate model which makes it possible to estimate the sensitivities of transitions in internal rotor molecules with C{sub 3v} symmetry, without performing a full calculation of energy levels. We find that a reliable estimate of transition sensitivities can be obtained from the three rotational constants (A, B, and C) and three torsional constants (F, V{sub 3}, and {rho}). This model is verified by comparing obtained sensitivities for methanol, acetaldehyde, acetamide, methyl formate, and acetic acid with a full analysis of the molecular Hamiltonian. Of the molecules considered, methanol is by far the most suitable candidate for laboratory and cosmological tests searching for a possible variation of {mu}.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2013

Study of collisional deactivation of O{sub 2}(b{sup 1}{Sigma}{sub g}{sup +}) molecules in a hydrogen-oxygen mixture at high temperatures using laser-induced gratings

Collisional deactivation of O{sub 2}(b{sup 1}{Sigma}{sub g}{sup +}) molecules resonantly excited by a 10 ns pulse of laser radiation with a wavelength of 762 nm in H{sub 2}/O{sub 2} mixtures is experimentally studied. The radiation intensity and hence the molecule excitation efficiency have a spatially periodic modulation that leads to the formation of laser-induced gratings (LIGs) of the refractive index. The study of LIG temporal evolution allows collisional relaxation rates of molecular excited states and gas temperature to be determined. In this work, the b{sup 1}{Sigma}{sub g}{sup +} state of O{sub 2} molecules deactivation rates are measured in a 4.3 vol % H{sub 2} mixture at the number density of 2 amg in the temperature range 291-850 K. The physical deactivation is shown to dominate in the collisions of H{sub 2} with O{sub 2}(b{sup 1}{Sigma}{sub g}{sup +}) and O{sub 2}(a{sup 1}{Delta}{sub g}) up to temperatures of 780-790 K at time delays up to 10 {mu}s after the excitation pulse. The parameters of the obtained temperature dependence of the (b{sup 1}{Sigma}{sub g}{sup +} state deactivation rate agree well with the data of independent measurements performed earlier at lower temperatures (200-400 K). Tunable diode laser absorption spectroscopy is used to measure the temperature dependence of the number density of the H{sub 2}O molecules which appear as the mixture, as the result of the dark gross reaction with O{sub 2} molecules in the ground state, O{sub 2} + 2H{sub 2} {yields} 2H{sub 2}O. The measurements show that this reaction results in complete transformation of H{sub 2} into H{sub 2}O at temperatures of 790-810 K.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Rotation dynamics of C{sub 60} molecules in a monolayer fullerene film on the WO{sub 2}/W(110) surface near the rotational phase transition

The rotation dynamics of C{sub 60} molecules in monolayer fullerene films grown on the WO{sub 2}/W(110) surface is studied by scanning tunneling microscopy. The formation of molecule clusters, which have a high libron vibration amplitude, is detected near the rotational phase transition temperature. The energy parameters that determine a change in the molecule orientation, namely, the energy difference between the nearest minima of the C{sub 60} molecule energy (30 meV) as a function of the molecule orientation and the potential barrier between them (610 meV), are determined. The results are discussed in terms of the mean-field approximation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Electron attachment to the SF{sub 6} molecule

Various models for transition between electron and nuclear subsystems are compared in the case of electron attachment to the SF{sub 6} molecule. Experimental data, including the cross section of electron attachment to this molecule as a function of the electron energy and vibrational temperature, the rate constants of this process in swarm experiments, and the rates of the chemionization process involving Rydberg atoms and the SF{sub 6} molecule, are collected and treated. Based on the data and on the resonant character of electron capture into an autodetachment ion state in accordance with the Breit–Wigner formula, we find that intersection of the molecule and negative ion electron terms proceeds above the potential well bottom of the molecule with the barrier height 0.05–0.1 eV, and the transition between these electron terms has both the tunnel and abovebarrier character. The limit of small electron energies e for the electron attachment cross section at room vibrational temperature takes place at ε ≪ 2 meV, while in the range 2 meV ≪ ε ≪ 80 meV, the cross section is inversely proportional to ε. In considering the attachment process as a result of the interaction between the electron and vibrational degrees of freedom, we find the coupling factor f between them to be f = aT at low vibrational temperatures T with a ≈ 3 × 10{sup −4} K{sup −1}. The coupling factor is independent of the temperature at T > 400 K.

74 ATOMIC AND MOLECULAR PHYSICS↗