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Sample records for crystal nonequilibrium molecular

  1. Nonequilibrium molecular dynamics of liquid crystals

    NASA Astrophysics Data System (ADS)

    Sarman, S. S.; Cummings, P. T.; Evans, D. J.

    1994-11-01

    During the last 15 years, noneyuilibrium molecular dynamics (NEMD) has been successfully applied to study transport phenomena in fluids that are isotropic at equilibrium. A natural extension is therefore to study liquid crystals, which are anisotropic al equilibrium. The lower symmetry of these systems means that the linear transport coefficients are considerably more complicated than in an isotropic system. Part of the reason for this is that there are crosscouplings between tensors of different rank and parity. Such couplings arc symmetry-forbidden in isotropic phases. In this paper. we review some of fundamental theoretical results we have derived concerning the rheology of liquid crystals. report NEMD simulations of thermal conductivity and shear viscosity of liquid crystals, and present NEMD simulations of shear cessation phenomena. All of the NEMD results are presented for a model liquid crystal fluid which is a modification of the Gay-Borne fluid. The results obtained are in qualitative agreement with experimental measurements on liquid crystal systems.

  2. Nonequilibrium-molecular-dynamics measurement of the Leslie coefficients of a Gay-Berne nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Qian, Tiezheng

    2007-03-01

    We carried out nonequilibrium molecular dynamics (MD) simulations to measure the six Leslie coefficients of a nematic liquid crystal composed of molecules interacting via the Gay-Berne potential. In the presence of a simple shear flow, an external field is applied to control the molecular orientation, and a uniform director is stabilized in the central region of the channel in which the liquid crystal is confined and sheared. With the director tuned by varying the applied field, a number of orientational states are stabilized in the presence of a shear flow, and various viscous stress components are measured in these states of different directors. The six Leslie coefficients αi are determined by interpreting the MD measurement data for viscous stress according to the constitutive relations in the Ericksen-Leslie-Parodi (ELP) theory. The Parodi relation α2+α3=α6-α5 is well satisfied. Given the values of the Leslie coefficients, liquid crystal orientations are evaluated for different field directions and shear rates. Comparison with those directly measured in MD simualtions demonstrates a quantitative agreement, showing that in the Gay-Berne nematic liquid crystal, the viscous stress and the coupling between orientation and flow are well described by the ELP theory.

  3. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    Hoover, W.G. |

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.

  4. Specific mass increment and nonequilibrium crystal growth

    NASA Astrophysics Data System (ADS)

    Martyushev, Leonid M.; Terentiev, Pavel S.

    2013-09-01

    Unsteady nonequilibrium crystallization of ammonium chloride from an aqueous solution resulting in the formation of irregular, so-called seaweed, structures is experimentally investigated. It is shown that specific increment of mass for the coexisting structures (or parts thereof) is the same and changes with time (t) according to the power law a/t-b, where the factor a=1.87±0.09 and the factor b is determined by the system relaxation time. The normalization of the power law to the total time of structure growth allows obtaining a universal law that describes the specific mass increment with time for both seaweed and dendrite structures (including the non-coexisting ones).

  5. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

    Bubbles pushed through a quasi-two-dimensional channel self-organize into a variety of periodic lattices. The structures of these lattices correspond to local minima of the interfacial energy. The "flowing crystals" are long-lived metastable states, a small subset of possible local minima of confined quasi-two-dimensional foams [P. Garstecki and G. M. Whitesides, Phys. Rev. E 73, 031603 (2006)10.1103/PhysRevE.73.031603]. Experimental results suggest that the choice of the structures that we observe is dictated by the dynamic stability of the cyclic processes of their formation. Thus, the dynamic system that we report provides a unique example of nonequilibrium self-organization that results in structures that correspond to local minima of the relevant energy functional. PMID:16907453

  6. Density Functional Theory for Steady-State Nonequilibrium Molecular Junctions

    PubMed Central

    Liu, Shuanglong; Nurbawono, Argo; Zhang, Chun

    2015-01-01

    We present a density functional theory (DFT) for steady-state nonequilibrium quantum systems such as molecular junctions under a finite bias. Based on the steady-state nonequilibrium statistics that maps nonequilibrium to an effective equilibrium, we show that ground-state DFT (GS-DFT) is not applicable in this case and two densities, the total electron density and the density of current-carrying electrons, are needed to uniquely determine the properties of the corresponding nonequilibrium system. A self-consistent mean-field approach based on two densities is then derived. The theory is implemented into SIESTA computational package and applied to study nonequilibrium electronic/transport properties of a realistic carbon-nanotube (CNT)/Benzene junction. Results obtained from our steady-state DFT (SS-DFT) are compared with those of conventional GS-DFT based transport calculations. We show that SS-DFT yields energetically more stable nonequilibrium steady state, predicts significantly lower electric current, and is able to produce correct electronic structures in local equilibrium under a limiting case. PMID:26472080

  7. Nonequilibrium molecular motion in a hypersonic shock wave.

    PubMed

    Pham-Van-Diep, G; Erwin, D; Muntz, E P

    1989-08-11

    Molecular velocities have been measured inside a hypersonic, normal shock wave, where the gas experiences rapid changes in its macroscopic properties. As first hypothesized by Mott-Smith, but never directly observed, the molecular velocity distribution exhibits a qualitatively bimodal character that is derived from the distribution functions on either side of the shock. Quantitatively correct forms of the molecular velocity distribution function in highly nonequilibrium flows can be calculated, by means of the Direct Simulation Monte Carlo technique.

  8. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W. G.; Hoover, C. G.

    1993-08-01

    Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

  9. Welding Molecular Crystals.

    PubMed

    Adolf, Cyril R R; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2015-12-16

    Both for fundamental and applied sciences, the design of complex molecular systems in the crystalline phase with strict control of order and periodicity at both microscopic and macroscopic levels is of prime importance for development of new solid-state materials and devices. The design and fabrication of complex crystalline systems as networks of crystals displaying task-specific properties is a step toward smart materials. Here we report on isostructural and almost isometric molecular crystals of different colors, their use for fabrication of core-shell crystals, and their welding by 3D epitaxial growth into networks of crystals as single-crystalline entities. Welding of crystals by self-assembly processes into macroscopic networks of crystals is a powerful strategy for the design of hierarchically organized periodic complex architectures composed of different subdomains displaying targeted characteristics. Crystal welding may be regarded as a first step toward the design of new hierarchically organized complex crystalline systems.

  10. Non-equilibrium phase transitions in a liquid crystal

    NASA Astrophysics Data System (ADS)

    Dan, K.; Roy, M.; Datta, A.

    2015-09-01

    The present manuscript describes kinetic behaviour of the glass transition and non-equilibrium features of the "Nematic-Isotropic" (N-I) phase transition of a well known liquid crystalline material N-(4-methoxybenzylidene)-4-butylaniline from the effects of heating rate and initial temperature on the transitions, through differential scanning calorimetry (DSC), Fourier transform infrared and fluorescence spectroscopy. Around the vicinity of the glass transition temperature (Tg), while only a change in the baseline of the ΔCp vs T curve is observed for heating rate (β) > 5 K min-1, consistent with a glass transition, a clear peak for β ≤ 5 K min-1 and the rapid reduction in the ΔCp value from the former to the latter rate correspond to an order-disorder transition and a transition from ergodic to non-ergodic behaviour. The ln β vs 1000/T curve for the glass transition shows convex Arrhenius behaviour that can be explained very well by a purely entropic activation barrier [Dan et al., Eur. Phys. Lett. 108, 36007 (2014)]. Fourier transform infrared spectroscopy indicates sudden freezing of the out-of-plane distortion vibrations of the benzene rings around the glass transition temperature and a considerable red shift indicating enhanced coplanarity of the benzene rings and, consequently, enhancement in the molecular ordering compared to room temperature. We further provide a direct experimental evidence of the non-equilibrium nature of the N-I transition through the dependence of this transition temperature (TNI) and associated enthalpy change (ΔH) on the initial temperature (at fixed β-values) for the DSC scans. A plausible qualitative explanation based on Mesquita's extension of Landau-deGennes theory [O. N. de Mesquita, Braz. J. Phys. 28, 257 (1998)] has been put forward. The change in the molecular ordering from nematic to isotropic phase has been investigated through fluorescence anisotropy measurements where the order parameter, quantified by the

  11. Non-equilibrium phase transitions in a liquid crystal.

    PubMed

    Dan, K; Roy, M; Datta, A

    2015-09-01

    The present manuscript describes kinetic behaviour of the glass transition and non-equilibrium features of the "Nematic-Isotropic" (N-I) phase transition of a well known liquid crystalline material N-(4-methoxybenzylidene)-4-butylaniline from the effects of heating rate and initial temperature on the transitions, through differential scanning calorimetry (DSC), Fourier transform infrared and fluorescence spectroscopy. Around the vicinity of the glass transition temperature (Tg), while only a change in the baseline of the ΔCp vs T curve is observed for heating rate (β) > 5 K min(-1), consistent with a glass transition, a clear peak for β ≤ 5 K min(-1) and the rapid reduction in the ΔCp value from the former to the latter rate correspond to an order-disorder transition and a transition from ergodic to non-ergodic behaviour. The ln β vs 1000/T curve for the glass transition shows convex Arrhenius behaviour that can be explained very well by a purely entropic activation barrier [Dan et al., Eur. Phys. Lett. 108, 36007 (2014)]. Fourier transform infrared spectroscopy indicates sudden freezing of the out-of-plane distortion vibrations of the benzene rings around the glass transition temperature and a considerable red shift indicating enhanced coplanarity of the benzene rings and, consequently, enhancement in the molecular ordering compared to room temperature. We further provide a direct experimental evidence of the non-equilibrium nature of the N-I transition through the dependence of this transition temperature (TNI) and associated enthalpy change (ΔH) on the initial temperature (at fixed β-values) for the DSC scans. A plausible qualitative explanation based on Mesquita's extension of Landau-deGennes theory [O. N. de Mesquita, Braz. J. Phys. 28, 257 (1998)] has been put forward. The change in the molecular ordering from nematic to isotropic phase has been investigated through fluorescence anisotropy measurements where the order parameter, quantified by the

  12. Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Galperin, Michael

    2016-05-01

    We consider optical spectroscopy of molecular junctions from the quantum transport perspective when radiation field is quantized and optical response of the system is simulated as photon flux. Using exact expressions for photon and electronic fluxes derived within the nonequilibrium Green function (NEGF) methodology and utilizing fourth order diagrammatic perturbation theory (PT) in molecular coupling to radiation field, we perform simulations employing realistic parameters. Results of the simulations are compared to the bare PT which is usually employed in studies on nonlinear optical spectroscopy to classify optical processes. We show that the bare PT violates conservation laws, while flux conserving NEGF formulation mixes optical processes.

  13. Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective.

    PubMed

    Gao, Yi; Galperin, Michael

    2016-05-01

    We consider optical spectroscopy of molecular junctions from the quantum transport perspective when radiation field is quantized and optical response of the system is simulated as photon flux. Using exact expressions for photon and electronic fluxes derived within the nonequilibrium Green function (NEGF) methodology and utilizing fourth order diagrammatic perturbation theory (PT) in molecular coupling to radiation field, we perform simulations employing realistic parameters. Results of the simulations are compared to the bare PT which is usually employed in studies on nonlinear optical spectroscopy to classify optical processes. We show that the bare PT violates conservation laws, while flux conserving NEGF formulation mixes optical processes. PMID:27155631

  14. Molecular Simulation of Nonequilibrium Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Schwartzentruber, T. E.; Valentini, P.; Tump, P.

    2011-08-01

    Large-scale conventional time-driven molecular dynam- ics (MD) simulations of normal shock waves are performed for monatomic argon and argon-helium mixtures. For pure argon, near perfect agreement between MD and direct simulation Monte Carlo (DSMC) results using the variable-hard-sphere model are found for density and temperature profiles as well as for velocity distribution functions throughout the shock. MD simulation results for argon are also in excellent agreement with experimental shock thickness data. Preliminary MD simulation results for argon-helium mixtures are in qualitative agreement with experimental density and temperature profile data, where separation between argon and helium density profiles due to disparate atomic mass is observed. Since conventional time-driven MD simulation of di- lute gases is computationally inefficient, a combined Event-Driven/Time-Driven MD algorithm is presented. The ED/TD-MD algorithm computes impending collisions and advances molecules directly to their next collision while evaluating the collision using conventional time-driven MD with an arbitrary interatomic potential. The method timestep thus approaches the mean-collision- time in the gas, while also detecting and simulating multi- body collisions with a small approximation. Extension of the method to diatomic and small polyatomic molecules is detailed, where center-of-mass velocities and extended cutoff radii are used to advance molecules to impending collisions. Only atomic positions are integrated during collisions and molecule sorting algorithms are employed to determine if atoms are bound in a molecule after a collision event. Rotational relaxation to equilibrium for a low density diatomic gas is validated by comparison with large-scale conventional time-driven MD simulation, where the final rotational distribution function is verified to be the correct Boltzmann rotational energy distribution.

  15. Fluxes of nonequilibrium photo-excited phonons along surfaces of crystals without an inversion center

    SciTech Connect

    Blokh, M.D.

    1988-01-01

    The flux of nonequilibrium phonons excited by light in the near-surface domain of a crystal or a thin plate is investigated. An exact expression is obtained for the phonon energy flux for a crystal with a polar direction and its polarization dependence is analyzed. The magnitude of the energy flux can reach the incident light intensity. The temperature difference produced by the flux of nonequilibrium photo-excited phonons is found.

  16. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

    The Direct Simulation Monte Carlo (DSMC) method typically used to model thermochemical nonequilibrium rarefied gases requires accurate total collision cross sections, reaction probabilities, and molecular internal energy exchange models. However, the baseline total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, reaction probabilities are defined such that experimentally determined equilibrium reaction rates are replicated, and internal energy relaxation models are phenomenological in nature. Therefore, these models have questionable validity in modeling strongly nonequilibrium gases with temperatures greater than those possible in experimental test facilities. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method can be used to accurately compute total collision cross sections, reaction probabilities, and internal energy exchange models based on first principles for hypervelocity collision conditions. In this thesis, MD/QCT-based models were used to improve simulations of two unique nonequilibrium rarefied gas systems: the Ionian atmosphere and hypersonic shocks in Earth's atmosphere. The Jovian plasma torus flows over Io at ≈ 57 km/s, inducing high-speed collisions between atmospheric SO2 and the hypervelocity plasma's O atoms and ions. The DSMC method is well-suited to model the rarefied atmosphere, so MD/QCT studies are therefore conducted to improve DSMC collision models of the critical SO2-O collision pair. The MD/QCT trajectory simulations employed a new potential energy surface that was developed using a ReaxFF fit to a set of ab initio calculations. Compared to the MD/QCT results, the baseline DSMC models are found to significantly under-predict total cross sections, use reaction probabilities that are unrealistically high, and give unphysical internal energies above the dissociation energy for non-reacting inelastic collisions and under-predicts post

  17. Shock and Laser Induced Non-Equilibrium Chemistry in Molecular Energetics

    NASA Astrophysics Data System (ADS)

    Wood, Mitchell; Cherukara, Mathew; Kober, Edward; Strachan, Alejandro

    2015-06-01

    In this study, we have used large scale reactive molecular dynamics (MD) simulations to study how contrasting initiation mechanisms from either shock or electromagnetic insults compare to traditional thermal initiation. We will show how insults of equal strength but different character can yield vastly different reaction profiles and thus the evolution of hot-spots. For shocked RDX (Up = 2km/s), we find that the collapse of a cylindrical 40 nm diameter pore leads to a significant amount of non-equilibrium reactions followed by the formation of a sustained deflagration wave. In contrast, a hot spot that is seeded into a statically compressed crystal with matching size and temperature will quench over the same timescale, highlighting the importance of insult type. Furthermore, MD simulations of electromagnetic insults coupled to intramolecular vibrations have shown, in some cases, mode specific initial chemistry and altered kinetics of the subsequent decomposition. By leveraging spectroscopic and chemical information gathered in our MD simulations, we have been able to identify and track non-equilibrium vibrational states of these materials and correlate them to these observed changes. Implications of insult dependent reactivity and non-equilibrium chemistry will be discussed.

  18. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Radak, Brian K.; Roux, Benoît

    2016-10-01

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  19. Thermal conductivity of silicon nanowire by nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Shuai-chuang; Liang, Xin-gang; Xu, Xiang-hua; Ohara, Taku

    2009-01-01

    The thermal conductivity of silicon nanowires was predicted using the nonequilibrium molecular dynamics method using the Stillinger-Weber potential model and the Nose-Hoover thermostat. The dependence of the thermal conductivity on the wire length, cross-sectional area, and temperature was investigated. The surface along the longitudinal direction was set as a free boundary with potential boundaries in the other directions. The cross-sectional areas of the nanowires ranged from about 5 to 19 nm2 with lengths ranging from 6 to 54 nm. The thermal conductivity dependence on temperature agrees well with the experimental results. The reciprocal of the thermal conductivity was found to be linearly related to the nanowire length. These results quantitatively show that decreasing the cross-sectional area reduces the phonon mean free path in nanowires.

  20. Plasticity induced by shock waves in nonequilibrium molecular-dynamics simulation

    SciTech Connect

    Holian, B.L.

    1998-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations of shock waves in single crystals have shown that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. Later calculations quantified the apparent threshold strength, namely the yield strength of the perfect crystal. Subsequently, pulsed x-ray experiments on shocked single crystals showed relative shifts in diffraction peaks, confirming the authors NEMD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, the authors have been able to simulate shock waves in 10-million atom crystals with cross sectional dimensions of 100 x 100 fcc unit cells (compared to earlier 6 x 6 systems). They have seen that the increased cross-section allows the system to slip along all of the available {l_brace}111{r_brace} slip planes, in different places along the now non-planar shock front. These simulations conclusively eliminate the worry that the kind of slippage they have observed is somehow an artifact of transverse periodic boundary conditions. Moreover, they have introduced a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, and show that for weaker shock waves (below the perfect crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

  1. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene.

    PubMed

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-09-09

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties.

  2. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene

    PubMed Central

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-01-01

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties. PMID:27609305

  3. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene.

    PubMed

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-01-01

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties. PMID:27609305

  4. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-09-01

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties.

  5. Shockwave-induced plasticity via large-scale nonequilibrium molecular dynamics

    SciTech Connect

    Holian, B.L.

    1998-07-01

    Nonequilibrium molecular-dynamics (MD) simulations of shock waves in single crystals have shown that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. Later calculations quantified the apparent threshold strength, namely the yield strength of the perfect crystal. Subsequently, pulsed x-ray experiments on shocked single crystals showed relative shifts in diffraction peaks, confirming our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have been able to simulate shock waves in 10-million atom crystals with cross-sectional dimensions of 100{times}100 fcc unit cells (compared to earlier 6{times}6 systems). We have seen that the increased cross-section allows the system to slip along all of the available {l_brace}111{r_brace} slip planes, in different places along the now non-planar shock front. These simulations conclusively eliminate the worry that the kind of slippage we have observed is somehow an artifact of transverse periodic boundary conditions. Thus, future simulations are much more likely to show that weak-shock plasticity is nucleated by pre-existing extended defects embedded in the sample. {copyright} {ital 1998 American Institute of Physics.}

  6. Nonequilibrium melting and crystallization of a model Lennard-Jones system.

    PubMed

    Luo, Sheng-Nian; Strachan, Alejandro; Swift, Damian C

    2004-06-22

    Nonequilibrium melting and crystallization of a model Lennard-Jones system were investigated with molecular dynamics simulations to quantify the maximum superheating/supercooling at fixed pressure, and over-pressurization/over-depressurization at fixed temperature. The temperature and pressure hystereses were found to be equivalent with regard to the Gibbs free energy barrier for nucleation of liquid or solid. These results place upper bounds on hysteretic effects of solidification and melting in high heating- and strain-rate experiments such as shock wave loading and release. The authors also demonstrate that the equilibrium melting temperature at a given pressure can be obtained directly from temperatures at the maximum superheating and supercooling on the temperature hysteresis; this approach, called the hysteresis method, is a conceptually simple and computationally inexpensive alternative to solid-liquid coexistence simulation and thermodynamic integration methods, and should be regarded as a general method. We also found that the extent of maximum superheating/supercooling is weakly pressure dependent, and the solid-liquid interfacial energy increases with pressure. The Lindemann fractional root-mean-squared displacement of solid and liquid at equilibrium and extreme metastable states is quantified, and is predicted to remain constant (0.14) at high pressures for solid at the equilibrium melting temperature. PMID:15268198

  7. Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

    SciTech Connect

    Bresme, F.; Armstrong, J.

    2014-01-07

    We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.

  8. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states

    NASA Astrophysics Data System (ADS)

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2016-04-01

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  9. Adiabatic Hamiltonian deformation, linear response theory, and nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G.

    1980-05-28

    Although Hamiltonians of various kinds have previously been used to derive Green-Kubo relations for the transport coefficients, the particular choice described is uniquely related to thermodynamics. This nonequilibrium Hamiltonian formulation of fluid flow provides pedagogically simple routes to nonequilibrium fluxes and distribution functions, to theoretical understanding of long-time effects, and to new numerical methods for simulating systems far from equilibrium. The same methods are now being applied to solid-phase problems. At the relatively high frequencies used in the viscous fluid calculations described, solids typically behave elastically. Lower frequencies lead to the formation of dislocations and other defects, making it possible to study plastic flow. A property of the nonequilibrium equations of motion which might be profitably explored is their effective irreversibility. Because only a few particles are necessary to generate irreversible behavior, simulations using adiabatic deformations of the kind described here could perhaps elucidate the instability in the equations of motion responsible for irreversibility.

  10. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states.

    PubMed

    Bjorgaard, J A; Velizhanin, K A; Tretiak, S

    2016-04-21

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited statemolecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited statemolecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission. PMID:27389206

  11. Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space

    NASA Astrophysics Data System (ADS)

    Glowacki, David R.; Lightfoot, Robert; Harvey, Jeremy N.

    2013-03-01

    The ability to characterise and control matter far away from equilibrium is a frontier challenge facing modern science. In this article, we sketch out a heuristic structure for thinking about the different ways in which non-equilibrium phenomena can impact molecular reaction dynamics. Our analytical schema includes three different regimes, organised according to increasing dynamical resolution: at the lowest resolution, we have conformer phase space, at an intermediate resolution, we have energy space; and at the highest resolution, we have mode space. Within each regime, we discuss practical definitions of non-equilibrium phenomena, mostly in terms of the corresponding relaxation timescales. Using this analytical framework, we discuss some recent non-equilibrium reaction dynamics studies spanning isolated small-molecule ensembles, gas-phase ensembles and solution-phase ensembles. This includes new results that provide insight into how non-equilibrium phenomena impact the solution-phase alkene-hydroboration reaction. We emphasise that interesting non-equilibrium dynamical phenomena often occur when the relaxation timescales characterising each regime are similar. In closing, we reflect on outstanding challenges and future research directions to guide our understanding of how non-equilibrium phenomena impact reaction dynamics.

  12. Molecular dynamics of biaxial nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Sarman, Sten

    1996-01-01

    We devise a constraint algorithm that makes the angular velocity of the director of a liquid crystal a constant of motion. When the angular velocity is set equal to zero, a director based coordinate system becomes an inertial frame. This is a great advantage because most thermodynamic properties and time correlation functions of a liquid crystal are best expressed relative to a director based coordinate system. One also prevents the director reorientation from interfering with the tails of the time correlation functions. When the angular velocity is forced to be zero the constraints do not do any work on the system. This makes it possible to prove that ensemble averages of phase functions and time correlation functions are unaffected by the director constraint torques. The constraint algorithm also facilitates generalization of nonequilibrium molecular dynamics algorithms to liquid crystal phases. In order to test the algorithm numerically we have simulated a biaxial nematic phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)]. The director constraint algorithm works very well. We have calculated the velocity autocorrelation functions and the self diffusion coefficients. In a biaxial nematic liquid crystal there are three independent components of the self-diffusion tensor. They have been found to be finite and different thus proving that we really simulate a liquid rather than a solid and that the symmetry is biaxial. Simulation of biaxial liquid crystals requires fairly large systems. We have therefore developed an algorithm that we run on a parallel computer instead of an ordinary work station.

  13. Molecular gas dynamics observations of Chapman-Enskog behavior and departures there from in nonequilibrium gases.

    PubMed

    Gallis, M A; Torczynski, J R; Rader, D J

    2004-04-01

    Bird's direct simulation Monte Carlo method is used to compute the molecular velocity distribution of a gas with heat flow. At continuum nonequilibrium conditions (small heat flux), Chapman-Enskog behavior is obtained for inverse-power-law molecules (hard-sphere through Maxwell): the Sonine-polynomial coefficients away from walls (i.e., the normal solution) agree with theory. At noncontinuum nonequilibrium conditions (large heat flux), these coefficients differ systematically from their continuum values as the local Knudsen number (nondimensional heat flux) is increased.

  14. High-Pressure Unconditionally Stable Nonequilibrium Molecular Plasmas

    NASA Astrophysics Data System (ADS)

    Palm, Peter; Ploenjes, Elke; Adamovich, Igor; Rich, J. William

    2000-10-01

    A novel method of sustaining unconditionally stable, large-volume, high-pressure nonequilibrium plasmas is suggested. The plasma is initiated by resonance absorption of CO laser radiation by carbon monoxide gas mixed with nitrogen and oxygen or nitric oxide in an absorption cell followed by overpopulation of high vibrational levels of CO in vibration-vibration (V-V) energy exchange collisions, [ CO(v) + CO(w) leftharpoons CO(v-1) + CO(w+1) ] and subsequent ionization by an associative ionization mechanism, [ CO(v) + CO(w) arrow (CO)_2^+ + e^-, Ev + Ew >= E_ion. ] Free electrons produced by associative ionization are heated by a sub-breakdown RF field applied to the optically pumped plasma. The heated electrons lose their energy primarily in collisions with the molecules, thereby vibrationally exciting all molecules. This is followed by overpopulation of high vibrational levels of the molecules by the V-V exchange process and further associative ionization. Unconditional stability is enabled by a negative feedback between gas heating and ionization due to an increase of vibration-translation relaxation rates with temperature leading to rapid depopulation of high vibrational levels needed for associative ionization.

  15. Understanding Nonequilibrium and Correlated Electron Behavior in Molecular Junctions

    NASA Astrophysics Data System (ADS)

    Wegewijs, Maarten

    2010-03-01

    I present an overview of the effects of the strong correlations in single-molecule junctions on non-linear transport, focusing on theory while comparing with several recent experiments. In the brief introduction I outline our real-time diagrammatic transport theory and its renormalization group extensions. In this approach a kinetic equation (generalized master equation) for the molecular density matrix incorporates both the quantum coherence and the strong correlations between electronic, vibrational and spin degrees of freedom of the device. The molecular state and non-linear current are calculated perturbatively beyond the lowest order in the coupling to the electrodes. As a first example, a detailed comparison with recent measurements on carbon-nanotube ``peapod'' devices is presented, indicating non-trivial hybridization and Coulomb interaction with the host nanotube quantum dot. The remainder of the talk focuses on predictions for specific electromechanical (electron-vibration coupling) and magnetic effects (spin-orbit coupling). I discuss non-linear transport signatures of vibrations when going beyond the simplified pictures of sequential tunneling (which breaks down due to quantum fluctuations) and the Born-Oppenheimer separation (its breakdown resulting in pseudo-Jahn-Teller coupling). Both effects have recently been observed. Finally, I address the interplay of transport with various aspects of molecular magnetism, such as antisymmetric (Dzyaloshinskii-Moriya) exchange and magnetic anisotropy. A comparison with recent transport experiments reveals the possibility of electric-field tunable molecular magnetism in an ``ferric-star'' molecular device.

  16. Effect of external drive on strongly coupled Yukawa systems: a nonequilibrium molecular dynamics study.

    PubMed

    J, Ashwin; Ganesh, R

    2009-11-01

    Using nonequilibrium molecular dynamics (MD) simulations behavior of three-dimensional (3D) Yukawa system has been studied in the presence of a small amplitude drive along one direction (say z[over ] ). This drive has the general form V=V_{0} cos(k_{L}z)Theta(t-t_{0}) , where Theta(t-t_{0}) is a Heaviside step function in time at t=t_{0} and k_{L}=2pi/L , L being the size of the system; V0 is considered small compared to average interparticle potential energy. In particular, a 3D equilibrated Yukawa crystal (bcc) near solid-liquid transition is subjected to an external drive at times t> or =t_{0} at the largest possible scale. For a given k_{L} it is observed that there exists a critical amplitude (V_{0};{c}) of the external drive below which the crystalline order is preserved and above which (V_{0}> or =V_{0};{c}) the transition from bcc to strongly coupled Yukawa liquid is observed. This critical amplitude (V_{0};{c}) is sensitive to the location of the Yukawa solid in the (kappa,Gamma) phase space. Various signatures of melting, transients, and steady state in the presence of this drive are elucidated using extensive MD diagnostics such as loss of long-range crystalline order, change in diffusion from subnormal to normal, and the fall of transversal shear peak in the Fourier transform of the velocity autocorrelation function. The mechanism of heating in the transient state is attributed to the local heating of the system where the forces are maximum. It is shown that these local hot regions dissipate heat into surrounding regions ultimately leading to a uniform temperature throughout the system. Ion streaming due to external field has been neglected.

  17. Thermal Transport in C60 Molecular Crystals Above Room Temperature

    NASA Astrophysics Data System (ADS)

    Gorham, Caroline S.; McGaughey, Alan J. H.

    2015-03-01

    The thermal conductivity of solid fullerene molecular systems has garnered significant interest as an example of materials whose thermal transport is dominated by Einstein-type oscillators. Using classical molecular dynamics simulations, this study isolates the roles of intramolecular and intermolecular vibrational degrees of freedom on the bulk thermal conductivity of the face-centered cubic C60 molecular crystal. The Green-Kubo method is used to predict the bulk thermal conductivity. The contributions to thermal transport resulting from collective motions of the molecules, molecular rotations, and intramolecular vibrations are isolated using non-equilibrium methods. These contributions are interpreted using a Debye model, a nearest-neighbor resistance network, and Allen-Feldman theory. C.S.G. is grateful for funding from the NASA Office of Graduate Research through the Space Technology Research Fellowship.

  18. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    SciTech Connect

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-09-29

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.

  19. Nonequilibrium chemistry in shocked molecular clouds. [interstellar gases

    NASA Technical Reports Server (NTRS)

    Iglesias, E. R.; Silk, J.

    1978-01-01

    The gas-phase chemistry is studied behind a 10-km/s shock propagating into a dense molecular cloud. The principal conclusions are that: the concentrations of certain molecules (CO, NH3, HCN, N2) are unperturbed by the shock; other molecules (H2CO, CN, HCO(+)) are greatly decreased in abundance; and substantial amounts of H2O, HCO, and CH4 are produced. Approximately 1 million yr (independent of the density) must elapse after shock passage before chemical equilibrium is attained.

  20. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

  1. Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

    PubMed Central

    2016-01-01

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys.2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD–MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD–MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

  2. Exciton coupling in molecular crystals

    NASA Technical Reports Server (NTRS)

    Ake, R. L.

    1976-01-01

    The implications of perfect exciton coupling and molecular vibrations were investigated, as well as the effect they have on the lifetime of singlet and triplet excitons coupled in a limiting geometry. Crystalline bibenzyl, Cl4Hl4, provided a situation in which these mechanisms involving exciton coupling can be studied in the limit of perfect coupling between units due to the crystal's geometry. This geometry leads to a coupling between the two halves of the molecule resulting in a splitting of the molecular excited states. The study reported involves an experimental spectroscopic approach and begins with the purification of the bibenzyl. The principal experimental apparatus was an emission spectrometer. A closed cycle cryogenic system was used to vary the temperature of the sample between 20 K and 300 K. The desired results are the temperature-dependent emission spectra of the bibenzyl; in addition, the lifetimes and quantum yields measured at each temperature reveal the effect of competing radiationless processes.

  3. Synthesis of calcium oxalate crystals in culture medium irradiated with non-equilibrium atmospheric-pressure plasma

    NASA Astrophysics Data System (ADS)

    Kurake, Naoyuki; Tanaka, Hiromasa; Ishikawa, Kenji; Nakamura, Kae; Kajiyama, Hiroaki; Kikkawa, Fumitaka; Mizuno, Masaaki; Yamanishi, Yoko; Hori, Masaru

    2016-09-01

    Octahedral particulates several tens of microns in size were synthesized in a culture medium irradiated through contact with a plume of non-equilibrium atmospheric-pressure plasma (NEAPP). The particulates were identified in the crystalline phase as calcium oxalate dihydrate (COD). The original medium contained constituents such as NaCl, d-glucose, CaCl2, and NaHCO3 but not oxalate or oxalic acid. The oxalate was clearly synthesized and crystallized in the medium as thermodynamically unstable COD crystals after the NEAPP irradiation.

  4. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics—Monte Carlo simulations

    SciTech Connect

    Chen, Yunjie; Roux, Benoît

    2015-01-14

    A family of hybrid simulation methods that combines the advantages of Monte Carlo (MC) with the strengths of classical molecular dynamics (MD) consists in carrying out short non-equilibrium MD (neMD) trajectories to generate new configurations that are subsequently accepted or rejected via an MC process. In the simplest case where a deterministic dynamic propagator is used to generate the neMD trajectories, the familiar Metropolis acceptance criterion based on the change in the total energy ΔE, min[1,  exp( − βΔE)], guarantees that the hybrid algorithm will yield the equilibrium Boltzmann distribution. However, the functional form of the acceptance probability is more complex when the non-equilibrium switching process is generated via a non-deterministic stochastic dissipative propagator coupled to a heat bath. Here, we clarify the conditions under which the Metropolis criterion remains valid to rigorously yield a proper equilibrium Boltzmann distribution within hybrid neMD-MC algorithm.

  5. Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Clarke, Elaine T.

    2013-09-01

    Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

  6. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

    The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials. PMID:27325090

  7. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    PubMed

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation.

  8. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    PubMed

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation. PMID:27121070

  9. Mesoscale modeling of dislocations in molecular crystals

    NASA Astrophysics Data System (ADS)

    Lei, Lei; Koslowski, Marisol

    2011-02-01

    Understanding the inelastic deformation of molecular crystals is of fundamental importance to the modeling of the processing of drugs in the pharmaceutical industry as well as to the initiation of detonation in high energy density materials. In this work, we present dislocation dynamics simulations of the deformation of two molecular crystals of interest in the pharmaceutical industry, sucrose and paracetamol. The simulations calculate the yield stress of sucrose and paracetamol in good agreement with experimental observation and predict the anisotropy in the mechanical response observed in these materials. Our results show that dislocation dynamics is an effective tool to study plastic deformation in molecular crystals.

  10. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    PubMed

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-01

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches. PMID:26539729

  11. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    PubMed

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-01

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

  12. A localized momentum constraint for non-equilibrium molecular dynamics simulations.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2015-02-21

    A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case.

  13. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    NASA Astrophysics Data System (ADS)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  14. Shear viscosity of molten alkali halides from equilibrium and nonequilibrium molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Galamba, N.; Nieto de Castro, C. A.; Ely, James F.

    2005-06-01

    The shear viscosity of molten NaCl and KCl was calculated through equilibrium (EMD) and nonequilibrium molecular-dynamics (NEMD) simulations in the canonical (N,V,T) ensemble. Two rigid-ion potentials were investigated, namely, the Born-Mayer-Huggins-Tosi-Fumi potential and the Michielsen-Woerlee-Graaf-Ketelaar potential with the parameters proposed by Ladd. The NEMD simulations were performed using the SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] with a Gaussian isokinetic thermostat and the results are compared with those obtained from Green-Kubo EMD (N,V,T) simulations and experimental shear viscosity data. The NEMD zero strain rate shear viscosity, η(0), was obtained by fitting a simplified Carreau-type equation and by application of mode-coupling theory, i.e., a η-γ1/2 linear relationship. The values obtained from the first method are found to be significantly lower than those predicted by the second. The agreement between the EMD and NEMD results with experimental data is satisfactory for the two potentials investigated. The ion-ion radial distribution functions obtained with the two rigid-ion potentials for both molten salts are discussed in terms of the differences between the two models.

  15. Shear viscosity of polar liquid mixtures via non-equilibrium molecular dynamics: water, methanol, and acetone

    NASA Astrophysics Data System (ADS)

    Wheeler Richard, Dean R.; Rowley, L.

    Non-equilibrium molecular dynamics (NEMD) with isobaric and isokinetic controls were used to simulate the shear viscosity for binary mixtures of water, methanol and acetone, and for ternary mixtures. In all, 22 different liquid composition points were simulated at 298.15 K and 0.1 MPa. A new set of acetone potential parameters was developed, while slight variants to existing water and methanol models were used. Long range Coulombic interactions were computed with the Ewald sum adapted to Lees-Edwards boundary conditions as formulated in Wheeler, D. R., Fuller, N. G., and Rowley, R. L., 1997, Molec. Phys., 92, 55. The attractive (dispersive) part of the Lennard-Jones (LJ) interactions also was handled by a lattice sum. A hybrid mixing rule was used for the LJ cross interactions. Viscosities extrapolated to zero shear compared well with experimental results, having a mean absolute error of 14% and no errors greater than 30%. Although the simulations successfully predicted viscosity maxima for mixtures high in water content, the peak heights tended to be too low, probably due to the limitations of the water model. The results suggest that NEMD may be a viable means of estimating viscosities for polar liquid mixtures with an unrestricted number of components.

  16. Non-equilibrium molecular dynamics simulation of the unstirred layer in the osmotically driven flow

    NASA Astrophysics Data System (ADS)

    Konno, Keito; Itano, Tomoaki; Seki, Masako

    2015-11-01

    We studied the solvent flows driven by the osmotic pressure difference across the semi-permeable membrane. The flow penetrating from the low concentration side transports away solutes adjacent of the membrane, so that the concentration is reduced significantly only at the vicinity of the membrane. It is expected that the relatively low solute concentration develops into a thin boundary layer in the vicinity of the membrane in the case of absence of external stirring process, which is termed as un-stirred layer (USL). To investigate concentration distribution in USL, we carried out non-equilibrium molecular dynamics simulations. The flows driven by th osmotic pressure are idealized as 2 dimensional hard disk model, which is composed of solvent and solute molecules. The membrane is modeled as a medium composed of stationary parallel rods distributed by a spatial interval, which is less than the diameter of the solute molecules. The following results were obtained from the numerical simulation. First, the thickness of USL, which was estimated from the obtained concentration distribution, is on the order of a length determined by mean free path. Second, USL was semicircle the center of which is on the end of pore of membrane.

  17. Methodology for determining the electronic thermal conductivity of metals via direct nonequilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Yue, Sheng-Ying; Zhang, Xiaoliang; Stackhouse, Stephen; Qin, Guangzhao; Di Napoli, Edoardo; Hu, Ming

    2016-08-01

    Many physical properties of metals can be understood in terms of the free electron model, as proven by the Wiedemann-Franz law. According to this model, electronic thermal conductivity can be inferred from the Boltzmann transport equation (BTE). However, the BTE does not perform well for some complex metals, such as Cu. Moreover, the BTE cannot clearly describe the origin of the thermal energy carried by electrons or how this energy is transported in metals. The charge distribution of conduction electrons in metals is known to reflect the electrostatic potential of the ion cores. Based on this premise, we develop a methodology for evaluating electronic thermal conductivity of metals by combining the free electron model and nonequilibrium ab initio molecular dynamics simulations. We confirm that the kinetic energy of thermally excited electrons originates from the energy of the spatial electrostatic potential oscillation, which is induced by the thermal motion of ion cores. This method directly predicts the electronic thermal conductivity of pure metals with a high degree of accuracy, without explicitly addressing any complicated scattering processes of free electrons. Our methodology offers a route to understand the physics of heat transfer by electrons at the atomistic level. The methodology can be further extended to the study of similar electron-involved problems in materials, such as electron-phonon coupling, which is underway currently.

  18. Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew

    2014-11-01

    This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box deforms with the flow, and it is possible for image particles to become arbitrarily close, causing a breakdown in the simulation. The KR boundary conditions avoid this problem for planar elongational flow and general planar mixed flow [T. A. Hunt, S. Bernardi, and B. D. Todd, J. Chem. Phys. 133, 154116 (2010)] through careful choice of the initial simulation box and by periodically remapping the simulation box in a way that conserves image locations. In this work, the ideas are extended to a large class of three-dimensional flows by using multiple remappings for the simulation box. The simulation box geometry is no longer time-periodic (which was shown to be impossible for uniaxial and biaxial stretching flows in the original work by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)]. The presented algorithm applies to all flows with nondefective flow matrices, and in particular, to uniaxial and biaxial flows.

  19. Nonequilibrium molecular dynamics calculation of the thermal conductivity based on an improved relaxation scheme.

    PubMed

    Cao, Bing-Yang

    2008-08-21

    A nonequilibrium molecular dynamics (NEMD) method using stochastic energy injection and removal as uniform heat sources and sinks is developed to calculate the thermal conductivity. The stochastic energy is generated by a Maxwell function generator and is imposed on only a few individual molecules each time step. The relaxation of the thermal perturbation is improved compared to other NEMD algorithms because there are no localized heat source and sink slab regions in the system. The heat sources are uniformly distributed in the right half of the system while the sinks are in the left half, which leads to a periodically quadratic temperature distribution that is almost sinusoidal. The thermal conductivity is then easily calculated from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. This improved relaxation NEMD scheme is used to calculate the thermal conductivities of liquid and solid argons. It shows that the present algorithm gives accurate results with fast convergence and small size effects. Other stochastic energy perturbation, e.g., thermal noise, can be used to replace the Maxwell-type perturbation used in this paper to make the improved relaxation scheme more effective. PMID:19044759

  20. Computationally efficient dielectric calculations of molecular crystals

    SciTech Connect

    Schwarz, Kathleen A.; Sundararaman, Ravishankar; Arias, T. A.

    2015-06-07

    The microscopic dielectric response is a key quantity for electronic materials such as organic semiconductors. Calculations of this response for molecular crystals are currently either expensive or rely on extreme simplifications such as multipole expansions which lack microscopic detail. We present an alternate approach using a microscopic analogue of the Clausius-Mossotti equation, which constructs the dielectric response of a crystal from an eigenvalue decomposition of the dielectric response of individual molecules. This method can potentially be used to examine the effects of defects, disorder, and surfaces on the dielectric properties of molecular solids.

  1. Molecular-weight-dependent changes in morphology of solution-grown polyethylene single crystals.

    PubMed

    Zhang, Bin; Chen, Jingbo; Baier, Moritz C; Mecking, Stefan; Reiter, Renate; Mülhaupt, Rolf; Reiter, Günter

    2015-01-01

    Polymer single crystals consisting of folded chains are always in a nonequilibrium state, even if they are faceted with a well-defined envelope reflecting the parameters of the crystal unit cell. Heterogeneities like small variations in the degree of chain folding within such crystals are responsible for a rather broad range in melting temperature. Consequently, upon annealing at a given temperature, some parts may be above and some below their respective melting temperatures, inducing a lamellar thickening process, which may vary locally. To emphasize such variations, controlled annealing experiments are performed at comparatively low temperatures and for long times. For single crystals of low-molecular-weight polyethylene, the formation of the well-known "Swiss-cheese"-like morphology with randomly distributed holes of varying sizes within the annealed single crystal is observed. However, for high-molecular-weight polyethylene, a regular pattern appeared upon annealing, characterized by branches of equal width that are oriented perpendicular to the crystal edge. All branches end at the nucleation site. Interestingly, the resulting pattern depends sensitively on both crystallization and annealing conditions. These thermally induced regular patterns within a single crystal are attributed to a stable crystalline framework formed within polyethylene single crystals in the course of growth.

  2. Protein crystallization facilitated by molecularly imprinted polymers

    PubMed Central

    Saridakis, Emmanuel; Khurshid, Sahir; Govada, Lata; Phan, Quan; Hawkins, Daniel; Crichlow, Gregg V.; Lolis, Elias; Reddy, Subrayal M.; Chayen, Naomi E.

    2011-01-01

    We present a previously undescribed initiative and its application, namely the design of molecularly imprinted polymers (MIPs) for producing protein crystals that are essential for determining high-resolution 3D structures of proteins. MIPs, also referred to as “smart materials,” are made to contain cavities capable of rebinding protein; thus the fingerprint of the protein created on the polymer allows it to serve as an ideal template for crystal formation. We have shown that six different MIPs induced crystallization of nine proteins, yielding crystals in conditions that do not give crystals otherwise. The incorporation of MIPs in screening experiments gave rise to crystalline hits in 8–10% of the trials for three target proteins. These hits would have been missed using other known nucleants. MIPs also facilitated the formation of large single crystals at metastable conditions for seven proteins. Moreover, the presence of MIPs has led to faster formation of crystals in all cases where crystals would appear eventually and to major improvement in diffraction in some cases. The MIPs were effective for their cognate proteins and also for other proteins, with size compatibility being a likely criterion for efficacy. Atomic force microscopy (AFM) measurements demonstrated specific affinity between the MIP cavities and a protein-functionalized AFM tip, corroborating our hypothesis that due to the recognition of proteins by the cavities, MIPs can act as nucleation-inducing substrates (nucleants) by harnessing the proteins themselves as templates. PMID:21690356

  3. Shear viscosity of a supercooled polymer melt via nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Varnik, F.; Binder, K.

    2002-10-01

    Using nonequilibrium molecular dynamics simulations, we compute the shear viscosity, ηs, of a glass forming polymer melt at temperatures ranging from the normal liquid state down to the supercooled state. For this purpose, the polymer melt is confined between two solid walls and a constant force pointing in direction parallel to the walls is applied on each monomer thus giving rise to a Poiseuille flow. It is shown that ηs(T) does not exhibit an Arrhenius-type behavior but can be described both by a power law (mode coupling theory) and by a Vogel-Fulcher-Tammann law. A similar behavior is observed in recent experiments above the glass transition temperature. The diffusion coefficient is computed using the mean square displacements in direction perpendicular to the flow. Combined with the knowledge of ηs(T), it is then shown that the Stokes-Einstein relation is valid at high temperatures, whereas deviations are observed in the supercooled regime in agreement with experiments. Moreover, the local viscosity, η(z), is also computed and its reliability is discussed. Using the sharp rise of η(z) close to the wall, we estimate zwall, the effective position of the wall. It is found that zwall moves towards the film center at lower T thus leading to a decrease of the (hydrodynamic) width of the system. Furthermore, we observe that the curves for η(z)/ηs at various temperatures superimpose if the data are depicted versus z-zwall(T). This suggests that the spatial and temperature dependence of the local viscosity separate if the effective position of the wall is chosen as a new reference plane.

  4. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  5. Nonequilibrium Molecular Dynamics Simulations of Organic Friction Modifiers Adsorbed on Iron Oxide Surfaces.

    PubMed

    Ewen, James P; Gattinoni, Chiara; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

    2016-05-10

    For the successful development and application of lubricants, a full understanding of the nanoscale behavior of complex tribological systems is required, but this is difficult to obtain experimentally. In this study, we use nonequilibrium molecular dynamics (NEMD) simulations to examine the atomistic structure and friction properties of commercially relevant organic friction modifier (OFM) monolayers adsorbed on iron oxide surfaces and lubricated by a thin, separating layer of hexadecane. Specifically, acid, amide, and glyceride OFMs, with saturated and Z-unsaturated hydrocarbon tail groups, are simulated at various surface coverages and sliding velocities. At low and medium coverage, the OFMs form liquidlike and amorphous monolayers, respectively, which are significantly interdigitated with the hexadecane lubricant, resulting in relatively high friction coefficients. At high coverage, solidlike monolayers are formed for all of the OFMs, which, during sliding, results in slip planes between well-defined OFM and hexadecane layers, yielding a marked reduction in the friction coefficient. When present at equal surface coverage, OFMs with saturated and Z-unsaturated tail groups are found to yield similar structure and friction behavior. OFMs with glyceride head groups yield significantly lower friction coefficients than amide and particularly carboxylic acid head groups. For all of the OFMs and coverages simulated, the friction coefficient is found to increase linearly with the logarithm of sliding velocity; however, the gradient of this increase depends on the coverage. The structure and friction details obtained from these simulations agree well with experimental results and also shed light on the relative tribological performance of these OFMs through nanoscale structural variations. This has important implications in terms of the applicability of NEMD to aid the development of new formulations to control friction.

  6. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  7. Star formation and molecular hydrogen in dwarf galaxies: a non-equilibrium view

    NASA Astrophysics Data System (ADS)

    Hu, Chia-Yu; Naab, Thorsten; Walch, Stefanie; Glover, Simon C. O.; Clark, Paul C.

    2016-06-01

    We study the connection of star formation to atomic (H I) and molecular hydrogen (H2) in isolated, low-metallicity dwarf galaxies with high-resolution (mgas = 4 M⊙, Nngb = 100) smoothed particle hydrodynamics simulations. The model includes self-gravity, non-equilibrium cooling, shielding from a uniform and constant interstellar radiation field, the chemistry of H2 formation, H2-independent star formation, supernova feedback and metal enrichment. We find that the H2 mass fraction is sensitive to the adopted dust-to-gas ratio and the strength of the interstellar radiation field, while the star formation rate is not. Star formation is regulated by stellar feedback, keeping the gas out of thermal equilibrium for densities n < 1 cm-3. Because of the long chemical time-scales, the H2 mass remains out of chemical equilibrium throughout the simulation. Star formation is well correlated with cold (T ≤ 100 K) gas, but this dense and cold gas - the reservoir for star formation - is dominated by H I, not H2. In addition, a significant fraction of H2 resides in a diffuse, warm phase, which is not star-forming. The interstellar medium is dominated by warm gas (100 K < T ≤ 3 × 104 K) both in mass and in volume. The scaleheight of the gaseous disc increases with radius while the cold gas is always confined to a thin layer in the mid-plane. The cold gas fraction is regulated by feedback at small radii and by the assumed radiation field at large radii. The decreasing cold gas fractions result in a rapid increase in depletion time (up to 100 Gyr) for total gas surface densities Σ _{H I+H_2} ≲ 10 M⊙ pc-2, in agreement with observations of dwarf galaxies in the Kennicutt-Schmidt plane.

  8. Pulse FT NMR of non-equilibrium states of half-integer spin quadrupolar nuclei in single crystals.

    PubMed

    Nakashima, Thomas T; Harris, Kristopher J; Wasylishen, Roderick E

    2010-02-01

    For quadrupolar nuclei with spin quantum numbers equal to 3/2, 5/2 and 7/2, the intensities of the NMR transitions in a single crystal are examined as a function of the rf excitation flip angle. Single-quantum NMR intensities are calculated using density matrix theory beginning under various non-equilibrium conditions and are compared with those determined experimentally. As a representative spin-3/2 system, the flip-angle dependence of the (23)Na NMR intensities of a single crystal of NaNO(3) was investigated beginning with the inversion of the populations associated with one of the satellite transitions. Subsequently, the populations of both satellite transitions were inverted using highly frequency-selective hyperbolic secant pulses. Calculated and experimental intensities are in good agreement. As an example of a spin-5/2 system, the flip-angle dependence of the (27)Al NMR transition intensities was determined using a single crystal of sapphire, Al(2)O(3), starting under different nuclear spin population conditions. The experimental trends mimicked those predicted by the density matrix calculations but the agreement was not as good as for the spin-3/2 case. Some SIMPSON simulations were also carried out to confirm the results generated by our density matrix calculations. The theoretical flip-angle behavior of the NMR transition intensities obtained from a spin-7/2 spin system is also discussed.

  9. Nonequilibrium phenomena in N{sub 2}-cluster-surface collisions: A molecular-dynamics study of fragmentation, lateral jetting, and nonequilibrium energy distributions

    SciTech Connect

    Zimmermann, Steffen; Urbassek, Herbert M.

    2006-12-15

    Using molecular-dynamics simulation, we study the impact of (N{sub 2}){sub 2869} clusters on a flat rigid wall. We study the cluster fragmentation process, the formation of lateral jets, the energy redistribution among the resulting fragments, and the ratio of internal and translational energy of the emerging free molecules as a function of cluster impact energy in the range of 0.076-1520 meV/molecule. We find the fragmentation threshold energy to be in agreement with that found previously for (N{sub 2}){sub 13} clusters; the (scaled) number of fragments, however, increases more slowly with impact energy. Also the energy redistribution of the cluster impact energy among the internal and translational energy of the fragments is similar to that found for the small cluster. This means in particular that free molecules show a strong nonequilibrium energy partitioning in which the internal degrees of freedom are considerably less excited than the translational degrees of freedom. We also find that at impact energies above the fragmentation threshold the angular distribution of fragments is peaked parallel to the surface--i.e., the formation of lateral surface jets.

  10. Crystallization of nickel nanoclusters by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Gaminchev, K.

    2012-12-01

    We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.

  11. Molecular Models of Liquid Crystal Elastomers

    NASA Astrophysics Data System (ADS)

    Rajshekhar

    Liquid crystal elastomers combine the elastic properties of conventional rubbers with the optical properties of liquid crystals. This dual nature gives rise to unusual physical properties, including the stress induced transition from a polydomain state, consisting of multiple nematic regions with independent orientations, to a monodomain state consisting of a single nematic region with a uniform director. We propose several molecular-scale coarse-grained models of liquid crystal elastomers with varying degrees of resolution. The models employ the Gay-Berne soft potential, and exhibit the chain connectivity of a diamond network. Simulation results show that these models are able to capture the polydomain state exhibited by liquid crystal elastomers in the absence of any external stress. When subjected to uniaxial stress, our models exhibit a polydomain to monodomain transition. We explain that the polydomain state occurs through the aggregation of liquid crystal molecules assisted by crosslinking sites, and conclude that the transition mechanism to the monodomain state is based on the reorientation of nematic domains along the direction of applied stress. Our modeling efforts are primarily focused on three models. The first two models consider the effects of rigid and flexible crosslinkers in liquid crystal elastomers with a diamond topology for chain connectivity. The third model deviates from the diamond network topology and adopts a random network topology.

  12. Rheological and structural studies of liquid decane, hexadecane, and tetracosane under planar elongational flow using nonequilibrium molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Baig, C.; Edwards, B. J.; Keffer, D. J.; Cochran, H. D.

    2005-05-01

    We report for the first time rheological and structural properties of liquid decane, hexadecane, and tetracosane using nonequilibrium molecular-dynamics (NEMD) simulations under planar elongational flow (PEF). The underlying NEMD algorithm employed is the so-called p-SLLOD algorithm [C. Baig, B. J. Edwards, D. J. Keffer, and H. D. Cochran, J. Chem. Phys. 122, 114103 (2005)]. Two elongational viscosities are measured, and they are shown not to be equal to each other, indicating two independent viscometric functions in PEF. With an appropriate definition, it is observed that the two elongational viscosities converge to each other at very low elongation rates, i.e., in the Newtonian regime. For all three alkanes, tension-thinning behavior is observed. At high elongation rates, chains appear to be fully stretched. This is supported by the result of the mean-square end-to-end distance of chains ⟨Rete2⟩ and the mean-square radius of gyration of chains ⟨Rg2⟩, and further supported by the result of the intramolecular Lennard-Jones (LJ) potential energy. It is also observed that ⟨Rete2⟩ and ⟨Rg2⟩ show a different trend as a function of strain rate from those in shear flow: after reaching a plateau value, ⟨Rete2⟩ and ⟨Rg2⟩ are found to increase further as elongation rate increases. A minimum in the hydrostatic pressure is observed for hexadecane and tetracosane at about ɛ˙(mσ2/ɛ)1/2=0.02. This phenomenon is shown to be associated with the intermolecular LJ potential energy. The bond-bending and torsional energies display similar trends, but a different behavior is observed for the bond-stretching energy. An important observation common in these three bonded-intramolecular interactions is that all three modes are suppressed to a small value at high elongation rates. We conjecture that a liquid-crystal-like, nematic structure is present in these systems at high elongation rates, which is characterized by a strong chain alignment with a fully

  13. Linear optical response of current-carrying molecular junction: a nonequilibrium Green's function-time-dependent density functional theory approach.

    PubMed

    Galperin, Michael; Tretiak, Sergei

    2008-03-28

    We propose a scheme for calculation of linear optical response of current-carrying molecular junctions for the case when electronic tunneling through the junction is much faster than characteristic time of external laser field. We discuss relationships between nonequilibrium Green's function (NEGF) and time-dependent density functional theory (TDDFT) approaches and derive expressions for optical response and linear polarizability within NEGF-TDDFT scheme. Corresponding results for isolated molecule, derived within TDDFT approach previously, are reproduced when coupling to contacts is neglected. PMID:18376958

  14. Thermal conductivity behavior of superatom molecular crystals

    NASA Astrophysics Data System (ADS)

    Ong, Wee-Liat; O'Brien, Evan; Dougherty, Patrick; Epstein, Jillian; Higgs, C. Fred; McGaughey, Alan; Roy, Xavier; Malen, Jonathan

    The room temperature thermal conductivity of several superatom molecular crystals (SMCs) are measured and found to be below 0.3 W/mK. The trend of room temperature thermal conductivity of the different crystals agree well with their sound speeds obtained independently using nano-indentation. These crystals, however, can exhibit non-crystalline thermal conductivity behavior depending on their constituent elements. A superatom is a cluster of atoms that acts as a stable entity [e.g., fullerenes (C60)]. By careful mixing and assembling these nano-sized superatoms, the resulting superatom-assembled materials hold promises for improving various technological devices. Organic-inorganic superatoms can assemble into unary SMCs or co-crystallized with C60 superatoms into binary SMCs. Thermal transport is of considerable interest with possible new physics in these hierarchically atomic precise crystals in the low temperature regime. The thermal conductivity of the SMCs are measured using the frequency domain thermoreflectance setup. Unary SMCs exhibit an almost invariant thermal conductivity down to a temperature of 150 K. Binary SMCs, however, can either show a crystalline-like increase or an amorphous-like decrease with decreasing temperature.

  15. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  16. Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. Final report, September 15, 1987--March 14, 1997

    SciTech Connect

    Murad, S.

    1997-05-01

    Computer Simulation Studies were carried out using the method of equilibrium and nonequilibrium molecular dynamics (NEMD) to examine a wide range of transport processes in both fluids and fluid mixtures. This included testing a wide range of mixing rules for thermal conductivity and viscosity. In addition a method was developed to calculate the internal rotational contributions to thermal conductivity and the accuracy of current methods for predicting these contributions were examined. These comparisons were then used to suggest possible ways of improving these theories. The method of NEMD was also used to examine the critical enhancements of thermal conductivity. Finally, molecular simulations were carried out to study the various transport coefficients of fluids confined by membranes, as well as important transport processes such as osmosis, and reverse osmosis.

  17. Modeling magma flow in volcanic conduit with non-equilibrium crystallization

    NASA Astrophysics Data System (ADS)

    Yulia, Tsvetkova

    2010-05-01

    Modeling magma flow in volcanic conduit including with non -equilibrium crystallization There is a set of models of magma flow in volcanic conduits which predicts oscillations in magma discharge during extrusion of lava domes. These models neglect heating of surrounding rocks and use 1D approximation of the flow in the conduit. Here magma flow is investigated with an account of heat exchange between surrounding rocks and magma and different dependences viscosity on temperature and crystal concentration. Stick-slip conditions were applied at the wall. The flow is assumed to be quasi-static and quasi 1D. Only vertical component of velocity vector is present, thus, we do not consider horizontal momentum balance. At the top of the conduit the pressure is assumed to be fixed, chamber pressure changes according with magma influx and outflux. First set of simulation was made for the viscosity that depends on cross-section average crystal concentration and parabolic velocity profile. In earlier models that account for crystal growth kinetics the temperature was allowed to change only due to the release of latent heat of crystallization. Heat transfer leads to cooling of the outer parts of the conduit leading to high crystal contents and high magma viscosities. Changes in viscosity result in changes in discharge rate. For the non-isothermal case there is no motion during most part of the cycle and a portion of magma solidifies at the top of the conduit forming a plug. During repose period chamber pressure is growing due to influx of fresh magma, and magma discharge rate starts to increase. Influx of hot magma into the conduit leads to decrease in friction resulting in a jump in discharge rate that lead to depressurization of magma chamber. Discharge rate decreases and magma solidifies again. For isothermal model with the same parameters discharge rate monotonically tends to the value of Qin. Simulation reveal that crystal content changes significantly across the conduit

  18. Pressure-induced transformations in molecular crystals

    SciTech Connect

    Taylor, R.D.; Hearne, G.R. |; Pasternak, M.P.

    1995-09-01

    A review is given on the unique features of the Moessbauer spectroscopy (MS) which by virtue of the quadrupole interaction and the lattice dynamics allows one to characterize some structural properties in the pressure-induced amorphous state of molecular crystals. Experiments were performed in GeI{sub 4}, SnI{sub 4} and SnBr{sub 4} by means of {sup 119}Sn and {sup 129}I MS with pressures to 35 GPa at cryogenic temperatures using diamond anvil cells.

  19. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    SciTech Connect

    Zhang, Z. D.; Wang, J.

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  20. Curl flux, coherence, and population landscape of molecular systems: nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics.

    PubMed

    Zhang, Zhedong; Wang, Jin; Zhang, Z D; Wang, J

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  1. New zinc-glycine-iodide complexes as a product of equilibrium and non-equilibrium crystallization in the Gly - ZnI2 - H2O system

    NASA Astrophysics Data System (ADS)

    Tepavitcharova, S.; Havlíček, D.; Matulková, I.; Rabadjieva, D.; Gergulova, R.; Plocek, J.; Němec, I.; Císařová, I.

    2016-09-01

    Equilibrium crystallization of two anhydrous complex compounds, [Zn(gly)2I2] and [Zn(gly)I2], and non-equilibrium crystallization of the [Zn3(H2O)4(μ-gly)2I6] complex have been observed in the Gly - ZnI2 - H2O system at 25°C. Different mixed zinc-glycine-iodide-aqua complexes exist in the studied solutions and those with the highest activity are responsible for the crystallization process. The stable [ZnI2O2(2Gly)]0 complexes are responsible for the large equilibrium crystallization field of the compound [Zn(gly)2I2] (monoclinic system, C2/c space group), in whose crystal structure they are incorporated as discrete distorted electroneutral tetrahedra. In zinc-iodide solutions with a low water activity it is more probable that the glycine zwitterions act as bidentate ligands and form polynuclear complexes. We assume the [ZnI2O2(2/2Gly)]0 infinite chains build the compound [Zn(gly)I2], for which we have found a narrow equilibrium crystallization field. We have failed to describe the crystal structure of this compound because of its limited stability in the air. Non-equilibrium crystallization of [Zn3(H2O)4(μ-gly)2I6] (triclinic system, P-1 space group) was demonstrated, with crystal structure built by trinuclear complexes [ZnI3O(1/2Gly)] [ZnO4(4H2O)O2(2/2Gly)(trans)][ZnI3O(1/2Gly)]. The FTIR and Raman spectra and also the thermal behaviour of the three compounds were discussed.

  2. Nonlinear vibrational excitations in molecular crystals molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Pumilia, P.; Abbate, S.; Baldini, G.; Ferro, D. R.; Tubino, R.

    1992-03-01

    The coupling constant for vibrational solitons χ has been examined in a molecular mechanics model for acetanilide (ACN) molecular crystal. According to A.C. Scott, solitons can form and propagate in solid acetanilide over a threshold energy value. This can be regarded as a structural model for the spines of hydrogen bond chains stabilizing the α helical structure of proteins. A one dimensional hydrogen bond chain of ACN has been built, for which we have found that, even though experimental parameters are correctly predicted, the excessive rigidity of the isolated chain prevents the formation of a localized distortion around the excitation. Yet, C=O coupling value with softer lattice modes could be rather high, allowing self-trapping to take place.

  3. Molecular kinetic theory of strongly nonequilibrium processes of mass, momentum, and energy transfer: Local equilibrium criteria

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2015-09-01

    Consequences of the complete system of transfer equations of the properties (momentum, energy, and mass) of particles and their pairs are considered under local equilibrium conditions with regard to the Bogoliubov hierarchy of relaxation times between the first and second distribution functions (DFs) and distinctions in the characteristic relaxation times of particle momentum, energy, and mass. It is found that even under the local equilibrium condition in the Bogoliubov hierarchy of relaxation times between the first and second DFs, pair correlations are maintained between all dynamic variables (velocity, temperature, and density) whose values are proportional to the gradients of transferable properties. A criterion is introduced requiring there be no local equilibrium condition upon reaching the critical value at which the description of the transfer process becomes incorrect in classical nonequilibrium thermodynamics. External forces are considered in the equations for strongly nonequilibrium processes. Along with allowing for intermolecular potentials, it becomes possible to discuss the concept of passive forces (introduced in thermodynamics by Gibbs) from the standpoint of the kinetic theory. It is shown that use of this concept does not reflect modern representations of real processes.

  4. Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Solomentsev, Gleb Y.; English, Niall J.; Mooney, Damian A.

    2010-12-01

    Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å-1. A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-à-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

  5. Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Palla, Pier Luca; Pierleoni, Carlo; Ciccotti, Giovanni

    2008-08-01

    Nonequilibrium molecular dynamics (NEMD) calculations of the bulk viscosity of the triple point Lennard-Jones fluid are performed with the aim of investigating the origin of the observed disagreement between Green-Kubo estimates and previous NEMD data. We show that a careful application of the Doll’s perturbation field, the dynamical NEMD method, the instantaneous form of the perturbation and the “subtraction technique” provides a NEMD estimate of the bulk viscosity at zero field in full agreement with the value obtained by the Green-Kubo formula. As previously reported for the shear viscosity, we find that the bulk viscosity exhibits a large linear regime with the field intensity.

  6. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Garate, José-A.

    2016-08-01

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ˜0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

  7. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics.

    PubMed

    English, Niall J; Garate, José-A

    2016-08-28

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region. PMID:27586951

  8. Decoherence in crystals of quantum molecular magnets.

    PubMed

    Takahashi, S; Tupitsyn, I S; van Tol, J; Beedle, C C; Hendrickson, D N; Stamp, P C E

    2011-07-20

    Quantum decoherence is a central concept in physics. Applications such as quantum information processing depend on understanding it; there are even fundamental theories proposed that go beyond quantum mechanics, in which the breakdown of quantum theory would appear as an 'intrinsic' decoherence, mimicking the more familiar environmental decoherence processes. Such applications cannot be optimized, and such theories cannot be tested, until we have a firm handle on ordinary environmental decoherence processes. Here we show that the theory for insulating electronic spin systems can make accurate and testable predictions for environmental decoherence in molecular-based quantum magnets. Experiments on molecular magnets have successfully demonstrated quantum-coherent phenomena but the decoherence processes that ultimately limit such behaviour were not well constrained. For molecular magnets, theory predicts three principal contributions to environmental decoherence: from phonons, from nuclear spins and from intermolecular dipolar interactions. We use high magnetic fields on single crystals of Fe(8) molecular magnets (in which the Fe ions are surrounded by organic ligands) to suppress dipolar and nuclear-spin decoherence. In these high-field experiments, we find that the decoherence time varies strongly as a function of temperature and magnetic field. The theoretical predictions are fully verified experimentally, and there are no other visible decoherence sources. In these high fields, we obtain a maximum decoherence quality-factor of 1.49 × 10(6); our investigation suggests that the environmental decoherence time can be extended up to about 500 microseconds, with a decoherence quality factor of ∼6 × 10(7), by optimizing the temperature, magnetic field and nuclear isotopic concentrations.

  9. THE ABUNDANCE OF MOLECULAR HYDROGEN AND ITS CORRELATION WITH MIDPLANE PRESSURE IN GALAXIES: NON-EQUILIBRIUM, TURBULENT, CHEMICAL MODELS

    SciTech Connect

    Mac Low, Mordecai-Mark; Glover, Simon C. O. E-mail: glover@uni-heidelberg.de

    2012-02-20

    Observations of spiral galaxies show a strong linear correlation between the ratio of molecular to atomic hydrogen surface density R{sub mol} and midplane pressure. To explain this, we simulate three-dimensional, magnetized turbulence, including simplified treatments of non-equilibrium chemistry and the propagation of dissociating radiation, to follow the formation of H{sub 2} from cold atomic gas. The formation timescale for H{sub 2} is sufficiently long that equilibrium is not reached within the 20-30 Myr lifetimes of molecular clouds. The equilibrium balance between radiative dissociation and H{sub 2} formation on dust grains fails to predict the time-dependent molecular fractions we find. A simple, time-dependent model of H{sub 2} formation can reproduce the gross behavior, although turbulent density perturbations increase molecular fractions by a factor of few above it. In contradiction to equilibrium models, radiative dissociation of molecules plays little role in our model for diffuse radiation fields with strengths less than 10 times that of the solar neighborhood, because of the effective self-shielding of H{sub 2}. The observed correlation of R{sub mol} with pressure corresponds to a correlation with local gas density if the effective temperature in the cold neutral medium of galactic disks is roughly constant. We indeed find such a correlation of R{sub mol} with density. If we examine the value of R{sub mol} in our local models after a free-fall time at their average density, as expected for models of molecular cloud formation by large-scale gravitational instability, our models reproduce the observed correlation over more than an order-of-magnitude range in density.

  10. A steady-state non-equilibrium molecular dynamics approach for the study of evaporation processes.

    PubMed

    Zhang, Jianguo; Müller-Plathe, Florian; Yahia-Ouahmed, Méziane; Leroy, Frédéric

    2013-10-01

    Two non-equilibrium methods (called bubble method and splitting method, respectively) have been developed and tested to study the steady state evaporation of a droplet surrounded by its vapor, where the evaporation continuously occurs at the vapor-liquid interface while the droplet size remains constant. In the bubble method, gas molecules are continuously reinserted into a free volume (represented by a bubble) located at the centre of mass of the droplet to keep the droplet size constant. In the splitting method, a molecule close to the centre of mass of the droplet is split into two: In this way, the droplet size is also maintained during the evaporation. By additional local thermostats confined to the area of insertion, the effect of frequent insertions on properties such as density and temperature can be limited to the immediate insertion area. Perturbations are not observed in other parts of the droplet. In the end, both the bubble method and the splitting method achieve steady-state droplet evaporation. Although these methods have been developed using an isolated droplet, we anticipate that they will find a wide range of applications in the study of the evaporation of isolated films and droplets or thin films on heated substrates or under confinement. They can in principle also be used to study the steady-state of other physical processes, such as the diffusion or permeation of gas molecules or ions in a pressure gradient or a concentration gradient. PMID:24116576

  11. In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1

    PubMed Central

    Frentrup, Hendrik; Hart, Kyle E.; Colina, Coray M.; Müller, Erich A.

    2015-01-01

    We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers. PMID:25764366

  12. Nonlocal heat transfer in two-dimensional Lennard-Jones crystal: Application of the molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Ovchinnikov, M. N.; Kushtanova, G. G.

    The redistribution of heat between two subsystems in the two-dimensional crystal consisting of particles interacting by means of the Lennard-Jones potential with argon parameters is considered in the frame of molecular dynamics method. Calculations of heat flux, its time derivative and kinetic temperature gradient showed that the characteristic relaxation times of the nonequilibrium flux within the nonlocal Cattaneo model at temperatures 10K < T < 40K are very small (τv <10-11s) and, comparable with the time of phonons free path.

  13. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    SciTech Connect

    Okumura, Hisashi

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  14. Flow alignment phenomena in liquid crystals studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2009-10-01

    The flow alignment of a nematic liquid crystal has been studied as a function of temperature, beginning at high temperature in the nematic phase and down to the nematic-smectic A phase transition. The alignment angle is obtained by estimating the twist viscosities by nonequilibrium molecular dynamics (NEMD) methods. These estimates are cross-checked by evaluating the corresponding equilibrium fluctuation relations. As a further comparison, shear flow simulations are carried out by application of the SLLOD equations of motion (so named because of their close relationship to the Doll's equation of motion, which can be derived from the Doll's tensor Hamiltonian), whereby the alignment angle is obtained directly. All these methods give consistent results for the alignment angle. At low temperatures near the nematic-smectic A transition the system becomes flow unstable. In this region the alignment angle has been calculated as a function of time.

  15. Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

    SciTech Connect

    Ghatage, Dhairyashil; Tomar, Gaurav Shukla, Ratnesh K.

    2015-03-28

    Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.

  16. Thermal conductivity of carbon nanotube—polyamide-6,6 nanocomposites: Reverse non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Alaghemandi, Mohammad; Müller-Plathe, Florian; Böhm, Michael C.

    2011-11-01

    The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from naïve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.

  17. Non-equilibrium molecular dynamics simulation of nanojet injection with adaptive-spatial decomposition parallel algorithm.

    PubMed

    Shin, Hyun-Ho; Yoon, Woong-Sup

    2008-07-01

    An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size.

  18. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. I. From space Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Zhang, Xiaoliang; Hu, Ming

    2015-11-01

    Probing detailed spectral dependence of phonon transport properties in bulk materials is critical to improve the function and performance of structures and devices in a diverse spectrum of technologies. Currently, such information can only be provided by the phonon spectral energy density (SED) or equivalently, time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics simulations (EMD), but has not been realized in nonequilibrium molecular dynamics simulations (NEMD) so far. In this paper we generate a scheme directly based on NEMD and lattice dynamics theory, called the time domain direct decomposition method (TDDDM), to predict the phonon mode specific thermal conductivity. Two benchmark cases of Lennard-Jones (LJ) argon and Stillinger-Weber (SW) Si are studied by TDDDM to characterize contributions of individual phonon modes to overall thermal conductivity and the results are compared with that predicted using SED and TDNMA. Similar trends are found for both cases, which indicate that our TDDDM approach captures the major phonon properties in NEMD run. The biggest advantage of TDDDM is that it can be used to investigate the size effect of individual phonon modes in NEMD simulations, which cannot be tackled by SED and TDNMA in EMD simulations currently. We found that the phonon modes with mean free path larger than the system size are truncated in NEMD and contribute little to the overall thermal conductivity. The TDDDM provides direct physical origin for the well-known strong size effects in thermal conductivity prediction by NEMD. Moreover, the well-known common sense of the zero thermal conductivity contribution from the Γ point is rigorously proved by TDDDM. Since TDDDM inherently possesses the nature of both NEMD simulations and lattice dynamics, we anticipate that TDDDM is particularly useful for offering a deep understanding of phonon behaviors in nanostructures or under strong confinement, especially when the

  19. Screened dipolar interactions in some molecular crystals

    NASA Astrophysics Data System (ADS)

    Munn, R. W.; Hurst, M.

    1990-10-01

    Screened dipole energies and dipole electric fields are calculated for the crystals of HCN, meta- and para-nitroaniline, the nonlinear optical compounds POM, MAP and DAN, meta-dinitrobenzene, and acetanilide. Only para-nitroaniline is centrosymmetric, but all the crystals have significant negative dipole energies (of the order of -20 kJ mol -1) except for POM and metadinitrobenzene, where they are positive but small in magnitude. Local dipole fields are of the order of 10 GV m -1. The results assume that surface charge annuls any macroscopic dipole field. It is speculated that the observed preponderance of centrosymmetric crystals of polar molecules may reflect a favourable dipole energy in the initial crystal nucleus rather than the macroscopic crystal.

  20. Molecular-dynamics simulation of crystallization in helical polymers.

    PubMed

    Yamamoto, Takashi; Sawada, Kaoru

    2005-12-15

    The molecular mechanism of crystallization in helical polymers is a fascinating but very difficult subject of research. We here report our recent efforts toward better understanding of the crystallization in helical polymers by use of molecular-dynamics simulation. With straightforward approaches to the problem being quite difficult, we adopt a different strategy of categorizing the helical polymers into two distinct types: one type is a simple bare helix which is essentially made of backbone atomic groups only and has smoother molecular contours, and the other is a more general helix having large side groups that would considerably hamper molecular motion and crystallization. Both types of helical polymers are here constructed by use of the united atom model, but they show quite distinct crystallization behavior; the crystallization of the former-type polymer is rather fast, while that of the latter-type polymer is extremely slow. We find that the bare helix, when rapidly cooled in free three-dimensional space, freezes into partially ordered state with limited intramolecular and intermolecular orders, and that remarkable improvement of order and growth of an ordered chain-folded crystallite occurs by very long-time annealing of the partially ordered state around the apparent freezing temperature. We also study crystallization of the bare helix upon a growth surface; the crystallization in this case proceeds much faster through highly cooperative process of the intermolecular and the intramolecular degrees of freedom. On the other hand, crystallization of the realistic model of isotactic polypropylene (iPP) having pendant methylene groups is found to be extremely sluggish. By restricting the spatial dimension of the system thereby fully disentangling the chain, we observe that the molecule of iPP crystallizes very quickly onto the crystal substrate made of the same iPP chain. Quite remarkable is that the molecule of iPP strictly recognizes the helical sense of the

  1. Between Crystal and Glass: Thermal Transport in C60 Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Lu, Simon; Kumar, Sushant; McGaughey, Alan

    Molecular crystals of the fullerene C60 and its derivatives [e.g., phenyl-C61-butyric acid methyl ester (PCBM)] are candidate materials for use in photovoltaics and thermoelectrics. In thermoelectrics, their usefulness is due in part to their exceptionally low thermal conductivities (0.4 W/m-K for C60 and 0.05 W/m-K for PCBM) at room temperature. Little is known regarding the microscopic physics underlying these low thermal conductivities. An important question is whether thermal transport in the C60 molecular crystal is (i) crystal-like, where energy is transported as collective vibrations of the centers of mass of the molecules, or (ii) amorphous-like, where energy diffuses from molecule to molecule. We use molecular dynamics (MD) simulations and the Green-Kubo method to probe this question by predicting the relative contributions of crystal-like and amorphous-like transport to the thermal conductivity of the C60 molecular crystal. To isolate crystal-like transport, we perform simulations on C60 crystals where molecular rotations and intra-molecular vibrations are prohibited. To isolate amorphous-like transport, we fix the centers of mass of the molecules. We compare the MD results to predictions from a fully diffusive network resistance model. This work is supported by the National Science Foundation (Grant DMR-1507325).

  2. Two-dimensional molecular crystals of phosphonic acids on graphene.

    PubMed

    Prado, Mariana C; Nascimento, Regiane; Moura, Luciano G; Matos, Matheus J S; Mazzoni, Mario S C; Cancado, Luiz G; Chacham, Helio; Neves, Bernardo R A

    2011-01-25

    The synthesis and characterization of two-dimensional (2D) molecular crystals composed of long and linear phosphonic acids atop graphene is reported. Using scanning probe microscopy in combination with first-principles calculations, we show that these true 2D crystals are oriented along the graphene armchair direction only, thereby enabling an easy determination of graphene flake orientation. We have also compared the doping level of graphene flakes via Raman spectroscopy. The presence of the molecular crystal atop graphene induces a well-defined shift in the Fermi level, corresponding to hole doping, which is in agreement with our ab initio calculations.

  3. A general set of order parameters for molecular crystals

    NASA Astrophysics Data System (ADS)

    Santiso, Erik E.; Trout, Bernhardt L.

    2011-02-01

    Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.

  4. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  5. Quantum dissipative effects on non-equilibrium transport through a single-molecular transistor: The Anderson-Holstein-Caldeira-Leggett model

    PubMed Central

    Raju, Ch. Narasimha; Chatterjee, Ashok

    2016-01-01

    The Anderson-Holstein model with Caldeira-Leggett coupling with environment is considered to describe the damping effect in a single molecular transistor (SMT) which comprises a molecular quantum dot (with electron-phonon interaction) mounted on a substrate (environment) and coupled to metallic electrodes. The electron-phonon interaction is first eliminated using the Lang-Firsov transformation and the spectral density function, charge current and differential conductance are then calculated using the non-equilibrium Keldysh Green function technique. The effects of damping rate, and electron-electron and electron-phonon interactions on the transport properties of SMT are studied at zero temperature. PMID:26732725

  6. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    SciTech Connect

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  7. Hole localization in molecular crystals from hybrid density functional theory.

    PubMed

    Sai, Na; Barbara, Paul F; Leung, Kevin

    2011-06-01

    We use first-principles computational methods to examine hole trapping in organic molecular crystals. We present a computational scheme based on the tuning of the fraction of exact exchange in hybrid density functional theory to eliminate the many-electron self-interaction error. With small organic molecules, we show that this scheme gives accurate descriptions of ionization and dimer dissociation. We demonstrate that the excess hole in perfect molecular crystals forms self-trapped molecular polarons. The predicted absolute ionization potentials of both localized and delocalized holes are consistent with experimental values.

  8. Photoinduced Ratchet-Like Rotational Motion of Branched Molecular Crystals.

    PubMed

    Zhu, Lingyan; Al-Kaysi, Rabih O; Bardeen, Christopher J

    2016-06-13

    Photomechanical molecular crystals can undergo a variety of light-induced motions, including expansion, bending, twisting, and jumping. The use of more complex crystal shapes may provide ways to turn these motions into useful work. To generate such shapes, pH-driven reprecipitation has been used to grow branched microcrystals of the anthracene derivative 4-fluoroanthracenecarboxylic acid. When these microcrystals are illuminated with light of λ=405 nm, an intermolecular [4+4] photodimerization reaction drives twisting and bending of the individual branches. These deformations drive a rotation of the overall crystal that can be repeated over multiple exposures to light. The magnitude and direction of this rotation vary because of differences in the crystal shape, but a typical branched crystal undergoes a 50° net rotation after 25 consecutive irradiations for 1 s. The ability of these crystals to undergo ratchet-like rotation is attributed to their chiral shape.

  9. Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

    NASA Astrophysics Data System (ADS)

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2012-01-01

    The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.

  10. Photoinduced Ratchet-Like Rotational Motion of Branched Molecular Crystals.

    PubMed

    Zhu, Lingyan; Al-Kaysi, Rabih O; Bardeen, Christopher J

    2016-06-13

    Photomechanical molecular crystals can undergo a variety of light-induced motions, including expansion, bending, twisting, and jumping. The use of more complex crystal shapes may provide ways to turn these motions into useful work. To generate such shapes, pH-driven reprecipitation has been used to grow branched microcrystals of the anthracene derivative 4-fluoroanthracenecarboxylic acid. When these microcrystals are illuminated with light of λ=405 nm, an intermolecular [4+4] photodimerization reaction drives twisting and bending of the individual branches. These deformations drive a rotation of the overall crystal that can be repeated over multiple exposures to light. The magnitude and direction of this rotation vary because of differences in the crystal shape, but a typical branched crystal undergoes a 50° net rotation after 25 consecutive irradiations for 1 s. The ability of these crystals to undergo ratchet-like rotation is attributed to their chiral shape. PMID:27150819

  11. Nonequilibrium kinetics of the electron–phonon sybsystem of a crystal in a strong electric field as a base of the electroplastic effect

    SciTech Connect

    Karas, V. I. Vlasenko, A. M.; Sokolenko, V. I.; Zakharov, V. E.

    2015-09-15

    We present the results of a kinetic analysis of nonequilibrium dynamics of the electron–phonon system of a crystal in a strong electric field based on the proposed method of numerically solving a set of Boltzmann equations for electron and phonon distribution functions without expanding the electron distribution function into a series in the phonon energy. It is shown that the electric field action excites the electron subsystem, which by transferring energy to the phonon subsystem creates a large amount of short-wave phonons that effectively influence the lattice defects (point, lines, boundaries of different phases), which results in a redistribution of and decrease in the lattice defect density, in damage healing, in a decrease in the local peak stress, and a decrease in the degradation level of the construction material properties.

  12. Nonequilibrium kinetics of the electron-phonon sybsystem of a crystal in a strong electric field as a base of the electroplastic effect

    NASA Astrophysics Data System (ADS)

    Karas, V. I.; Vlasenko, A. M.; Sokolenko, V. I.; Zakharov, V. E.

    2015-09-01

    We present the results of a kinetic analysis of nonequilibrium dynamics of the electron-phonon system of a crystal in a strong electric field based on the proposed method of numerically solving a set of Boltzmann equations for electron and phonon distribution functions without expanding the electron distribution function into a series in the phonon energy. It is shown that the electric field action excites the electron subsystem, which by transferring energy to the phonon subsystem creates a large amount of short-wave phonons that effectively influence the lattice defects (point, lines, boundaries of different phases), which results in a redistribution of and decrease in the lattice defect density, in damage healing, in a decrease in the local peak stress, and a decrease in the degradation level of the construction material properties.

  13. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

  14. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition.

    PubMed

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G; Mpourmpakis, Giannis; Asplin, John R; Rimer, Jeffrey D

    2016-08-25

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization--citrate and hydroxycitrate--exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation of

  15. Lattice modes in molecular crystals measured with nuclear inelastic scattering

    SciTech Connect

    Kohn, V. G.; Chumakov, A. I.; Rueffer, R.

    2006-03-01

    We reveal an important property of nuclear inelastic scattering in a molecular crystal with well-separated lattice and molecular modes: The presence of the molecular modes does not change the shape but merely rescales the lattice part of the energy dependence of nuclear inelastic scattering. Therefore, the density of states (DOS) of the lattice vibrations can be properly derived even from the lattice part of nuclear inelastic scattering alone. In this case, one has to substitute the mean recoil energy of a nucleus by the effective recoil energy of the molecule. In first approximation, the ratio of the recoil energies is close to the ratio of the nuclear and molecular masses. More precisely, it is given by the relative area of the lattice part in the entire DOS. The theoretical analysis is verified with numerical calculations for a model DOS and with the experimental data for the decamethyl ferrocene molecular crystal. More generally, the analysis is valid for any region of nuclear inelastic scattering around the central elastic peak with sufficiently narrow lines beyond it. Therefore, the demonstrated property of nuclear inelastic scattering allows for a much shorter measuring time in studies of lattice modes in molecular crystals, low-energy molecular modes in proteins, and in investigations of glass dynamics with molecular probes.

  16. Defect-induced solid state amorphization of molecular crystals

    NASA Astrophysics Data System (ADS)

    Lei, Lei; Carvajal, Teresa; Koslowski, Marisol

    2012-04-01

    We investigate the process of mechanically induced amorphization in small molecule organic crystals under extensive deformation. In this work, we develop a model that describes the amorphization of molecular crystals, in which the plastic response is calculated with a phase field dislocation dynamics theory in four materials: acetaminophen, sucrose, γ-indomethacin, and aspirin. The model is able to predict the fraction of amorphous material generated in single crystals for a given applied stress. Our results show that γ-indomethacin and sucrose demonstrate large volume fractions of amorphous material after sufficient plastic deformation, while smaller amorphous volume fractions are predicted in acetaminophen and aspirin, in agreement with experimental observation.

  17. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  18. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition

    NASA Astrophysics Data System (ADS)

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G.; Mpourmpakis, Giannis; Asplin, John R.; Rimer, Jeffrey D.

    2016-08-01

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization—citrate and hydroxycitrate—exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation

  19. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition

    NASA Astrophysics Data System (ADS)

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G.; Mpourmpakis, Giannis; Asplin, John R.; Rimer, Jeffrey D.

    2016-08-01

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor–crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization—citrate and hydroxycitrate—exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor–crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of

  20. Resonant four wave mixing in molecular crystals

    NASA Astrophysics Data System (ADS)

    Hochstrasser, R. M.; Meredith, G. R.; Trommsdorff, H. P.

    1980-08-01

    Experimental studies are presented of the Raman and two-photon resonant effects in the third order susceptibility for benzene, naphthalene, and biphenyl crystals at 1.6 °K. The experiments consist of measurements of the polarized coherent light dispersion at ω3=2ω1-ω2 when the crystals are irradiated with two tunable lasers at ω1 and ω2. The frequencies ω1 and ω2 are chosen such that ω1-ω2 and 2ω1 match vibrational and electronic resonances, respectively, of the materials. The four wave mixing results obtained under definite polarization conditions are used in association with Raman scattering cross sections to find values for the nonresonant background third-order susceptibilities of the crystals and the two-photon absorption coefficients of various vibronic transitions. In addition the large dynamic range of these experiments has allowed us to obtain homogeneous (Lorenzian) damping parameters (Γ) for a number of vibrational levels of the electronic ground and excited states. In terms of the trace (αt2) and the anisotropy (βt) the following results were obtained: Benzene 154501, αt2 =8.6×10-51 (cm6 mol-1), βt2?0, Γ=0.7 cm-1; naphthalene 154201, αt2=2.8×10-50, βt2 =4.1×10-50, Γ=5.5 cm-1; biphenyl B3g←Ag, 0-0, βt2=3.6×10-49, Γ=0.9 cm-1. These calibration points can be utilized to obtain the absolute strengths of each of the many two-photon vibronic transitions observed previously in the two-photon fluorescence of these crystals. The damping parameters yield vibrational relaxation times in the range 0.4 ps for naphthalene 1542, to longer than 12.5 ps for the naphthalene ground state mode at 1383 cm-1. It is proposed that 1542 relaxes by fission into an electronic and vibrational exciton.

  1. Molecular theory of liquid crystal thin films

    NASA Astrophysics Data System (ADS)

    Meng, Shihong

    A molecular theory has been developed to describe the isotropic-nematic transitoon of model nematogens in bulk and in thin films. The surfaces of thin films can be hard surfaces or coated with surfactant monolayers. The theory only includes hard body interactions between all molecule species: solvent, nematogens and surfactants. We have studied the influence of the separation between confining walls, concentration of nematogens, as well as the surface anchoring and areal density of surfactant at the interface upon the phases of nematogens. We have explained the possible existence of planar degenerate phase through entropic pictures and have confirmed close to the bulk isotropic-nematic transition point, the order of the phases of nematogens from isotropic to nematic then back to isotropic when varying the areal density of surfactant monolayers at interfaces. From the results obtained, we believe that we have captured the main competing interactions between surfactants and nematogens and our molecular level theory is capable of describing these two interactions of different natures. Our results can provide a guideline for molecular design of biosensors. We have modeled the molecular systems with as much simplification as possible while retaining the main features. The thesis is arranged into introduction, results on bulk, thin films confined between hard walls and between surfactant monolayers.

  2. Modelling transient heat conduction in solids at multiple length and time scales: A coupled non-equilibrium molecular dynamics/continuum approach

    SciTech Connect

    Jolley, Kenny; Gill, Simon P.A.

    2009-10-20

    A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nose-Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.

  3. Model for photoinduced bending of slender molecular crystals.

    PubMed

    Nath, Naba K; Pejov, Ljupčo; Nichols, Shane M; Hu, Chunhua; Saleh, Na'il; Kahr, Bart; Naumov, Panče

    2014-02-19

    The growing realization that photoinduced bending of slender photoreactive single crystals is surprisingly common has inspired researchers to control crystal motility for actuation. However, new mechanically responsive crystals are reported at a greater rate than their quantitative photophysical characterization; a quantitative identification of measurable parameters and molecular-scale factors that determine the mechanical response has yet to be established. Herein, a simple mathematical description of the quasi-static and time-dependent photoinduced bending of macroscopic single crystals is provided. This kinetic model goes beyond the approximate treatment of a bending crystal as a simple composite bilayer. It includes alternative pathways for excited-state decay and provides a more accurate description of the bending by accounting for the spatial gradient in the product/reactant ratio. A new crystal form (space group P21/n) of the photoresponsive azo-dye Disperse Red 1 (DR1) is analyzed within the constraints of the aforementioned model. The crystal bending kinetics depends on intrinsic factors (crystal size) and external factors (excitation time, direction, and intensity).

  4. Molecular Dynamics Simulations of Spinodal-Assisted Polymer Crystallization

    SciTech Connect

    Gee, R H; Lacevic, N M; Fried, L

    2005-07-08

    Large scale molecular dynamics simulations of bulk melts of polar (poly(vinylidene fluoride) (pVDF)) polymers are utilized to study chain conformation and ordering prior to crystallization under cooling. While the late stages of polymer crystallization have been studied in great detail, recent theoretical and experimental evidence indicates that there are important phenomena occurring in the early stages of polymer crystallization that are not understood to the same degree. When the polymer melt is quenched from a temperature above the melting temperature to the crystallization temperature, crystallization does not occur instantaneously. This initial interval without crystalline order is characterized as an induction period. It has been thought of as a nucleation period in the classical theories of polymer crystallization, but recent experiments, computer simulations, and theoretical work suggest that the initial period in polymer crystallization is assisted by a spinodal decomposition type mechanism. In this study we have achieved physically realistic length scales to study early stages of polymer ordering, and show that spinodal-assisted ordering prior to crystallization is operative in polar polymers suggesting general applicability of this process.

  5. Phase transitions in molecular crystals: looking backwards, glancing sideways

    NASA Astrophysics Data System (ADS)

    Dunitz, Jack D.

    2016-11-01

    After a gap of a quarter century, I try to look back on problems that I may have discussed in my Aminoff Award Lecture in 1990. It was entitled: Phase Transitions in Molecular Crystals; a Chemical Viewpoint. To the best of my knowledge, not much progress has been made with those problems since then.

  6. Molecular resolution imaging of macromolecular crystals by atomic force microscopy.

    PubMed Central

    Kuznetsov YuG; Malkin, A J; Land, T A; DeYoreo, J J; Barba, A P; Konnert, J; McPherson, A

    1997-01-01

    Atomic force microscopy (AFM) images at the molecular level have been obtained for a number of different protein and virus crystals. They can be utilized in some special cases to obtain information useful to crystal structure analyses by x-ray diffraction. In particular, questions of space group enantiomer, the packing of molecules within a unit cell, the number of molecules per asymmetric unit, and the dispositions of multiple molecules within the asymmetric unit may be resolved. In addition, because of the increasing sensitivity and resolution of the AFM technique, some molecular features of very large asymmetric units may be within reach. We describe here high-resolution studies, using AFM, to visualize individual molecules and viruses in their crystal lattices. These investigations included fungal lipase, lysozyme, thaumatin, canavalin, and satellite tobacco mosaic virus (STMV). Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 PMID:9129839

  7. Exciton polariton dispersion for molecular crystal with isotopic replacement defects.

    NASA Astrophysics Data System (ADS)

    Rumyantsev, Vladimir; Fedorov, Stanislav; Shtaerman, Esfir

    2001-03-01

    This summary presents peculiarities of exciton polariton spectrum conditional by availability of isotopic replacement defects in molecular crystal. In the examined case of binary crystal configuration dependence of molecular currents, energies and intermolecular resonance interaction matrix W is weak as well as W-components are small. It enabled to describe main exciton spectrum peculiarities in approach similar to orientated gas model and to obtain polariton dispersion low in analytical form. The specific of dispersion curves is that the pair of curves reflecting isotopic replacement effect is added to the typical polariton curves for perfect crystal. The value of "the bottle throat" of added curves has been evaluated. Non-collinearity of the molecule dipole moments in crystalline matrix and the moments of isotopic replacement admixture determines it.

  8. Fundamental gap of molecular crystals via constrained density functional theory

    NASA Astrophysics Data System (ADS)

    Droghetti, Andrea; Rungger, Ivan; Das Pemmaraju, Chaitanya; Sanvito, Stefano

    2016-05-01

    The energy gap of a molecular crystal is one of the most important properties since it determines the crystal charge transport when the material is utilized in electronic devices. This is, however, a quantity difficult to calculate and standard theoretical approaches based on density functional theory (DFT) have proven unable to provide accurate estimates. In fact, besides the well-known band-gap problem, DFT completely fails in capturing the fundamental gap reduction occurring when molecules are packed in a crystal structures. The failure has to be associated with the inability of describing the electronic polarization and the real space localization of the charged states. Here we describe a scheme based on constrained DFT, which can improve upon the shortcomings of standard DFT. The method is applied to the benzene crystal, where we show that accurate results can be achieved for both the band gap and also the energy level alignment.

  9. Two-dimensional van der Waals C60 molecular crystal

    PubMed Central

    Reddy, C. D.; Gen Yu, Zhi; Zhang, Yong-Wei

    2015-01-01

    Two-dimensional (2D) atomic crystals, such as graphene and transition metal dichalcogenides et al. have drawn extraordinary attention recently. For these 2D materials, atoms within their monolayer are covalently bonded. An interesting question arises: Can molecules form a 2D monolayer crystal via van der Waals interactions? Here, we first study the structural stability of a free-standing infinite C60 molecular monolayer using molecular dynamic simulations, and find that the monolayer is stable up to 600 K. We further study the mechanical properties of the monolayer, and find that the elastic modulus, ultimate tensile stress and failure strain are 55–100 GPa, 90–155 MPa, and 1.5–2.3%, respectively, depending on the stretching orientation. The monolayer fails due to shearing and cavitation under uniaxial tensile loading. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the monolayer are found to be delocalized and as a result, the band gap is reduced to only 60% of the isolated C60 molecule. Interestingly, this band gap can be tuned up to ±30% using strain engineering. Owing to its thermal stability, low density, strain-tunable semi-conducting characteristics and large bending flexibility, this van der Waals molecular monolayer crystal presents aplenty opportunities for developing novel applications in nanoelectronics. PMID:26183501

  10. suPAR: The Molecular Crystal Ball

    PubMed Central

    Thunø, Maria; Macho, Betina; Eugen-Olsen, Jesper

    2009-01-01

    soluble urokinase Plasminogen Activator Receptor (suPAR) levels reflect inflammation and elevated suPAR levels are found in several infectious diseases and cancer. suPAR exists in three forms; suPARI-III, suPARII-III and suPARI which show different properties due to structural differences. Studies suggest that full-length suPAR is a regulator of uPAR/uPA by acting as uPA-scavenger, whereas the cleaved suPARII-III act as a chemotactic agent promoting the immune response via the SRSRY sequence in the linker-region. This review focus on the various suPAR fragments and their involvement in inflammation and pathogenic processes. We focus on the molecular mechanisms of the suPAR fragments and the link to the inflammatory process, as this could lead to medical applications in infectious and pathological conditions. PMID:19893210

  11. Theoretical characterization of charge transport in organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Sanchez-Carrera, Roel S.

    The rapid growth in the interest to explore new synthetic crystalline organic semiconductors and their subsequent device characterization has revived the debate on the development of theoretical models to better understand the intrinsic charge transport mechanisms in organic materials. At the moment, several charge-transport theories for organic molecular crystals have been proposed and have observed a comparable agreement with experimental results. However, these models are limited in scope and restricted to specific ranges of microscopic parameters and temperatures. A general description that is applicable in all parameter regimes is still unavailable. The first step towards a complete understanding of the problem associated with the charge transport in organic molecular crystals includes the development of a first-principles theoretical methodology to evaluate with high accuracy the main microscopic charge-transport parameters and their respective couplings with intra- and intermolecular vibrational degrees of freedom. In this thesis, we have developed a first-principles methodology to investigate the impact of electron-phonon interactions on the charge-carrier mobilities in organic molecular crystals. Well-known organic materials such as oligoacene and oligothienoacene derivatives were studied in detail. To predict the charge-transport phenomena in organic materials, we rely on the Marcus theory of electron-transfer reactions. Within this context, the nature of the intramolecular vibronic coupling in oligoacenes was studied using an approach that combines high-resolution gas-phase photo-electron spectroscopy measurements with first-principles quantum-mechanical calculations. This further led to investigation of the electron interactions with optical phonons in oligoacene single crystals. The lattice phonon modes were computed at both density functional theory (DFT) and empirical force field levels. The low-frequency optical modes are found to play a significant

  12. How molecular interactions affect crystal morphology: the case of haloperidol.

    PubMed

    Li Destri, Giovanni; Marrazzo, Agostino; Rescifina, Antonio; Punzo, Francesco

    2011-11-01

    The tableting behaviour of drugs can be dramatically affected by changes in the crystal habit of the drug molecule. Pharmaceutical companies are therefore interested in the morphology prediction as a possible tool to optimise the industrial process. Molecular mechanics calculations embedded in dedicated software together with X-ray diffraction analysis were used to enlighten the structural properties of 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one-whose commercial name is haloperidol--an antipsychotic drug that contributed to the progress and revolution of psychiatric care. We defined, by means of X-ray powder diffraction, which--or how much--of the two crystallographic structures present in the Cambridge Crystallographic Database represents the commercial crystalline powder. Once the correct structure was selected, the whole structural analysis was carried out as a comparison with the already deposited structures. The available single crystal structure was used to model the X-ray powder diffraction pattern. The "real" structure was then optimised by means of molecular mechanics and the crystal morphology of the compounds was predicted with different computational methods. Analogies and differences among the different morphologies, together with the potential role of several solvents were used to try to bridge the gap between the molecular structure--that is, the atomic point of view--and the crystal habit. PMID:21656519

  13. Design of ferroelectric organic molecular crystals with ultrahigh polarization.

    PubMed

    Chen, Shuang; Zeng, Xiao Cheng

    2014-04-30

    Inspired by recent successful synthesis of room-temperature ferroelectric supramolecular charge-transfer complexes, i.e., tetrathiafulvalene (TTF)- and pyromellitic diimide (PMDI)-based crystals (Tayi et al. Nature 2012, 488, 485-489), three new ferroelectric two-component organic molecular crystals are designed based on the TTF and PMDI motifs and an extensive polymorph search. To achieve energetically favorable packing structures for the crystals, a newly developed computational approach that combines polymorph predictor with density functional theory (DFT) geometry optimization is employed. Tens of thousands of packing structures for the TTF- and PMDI-based crystals are first generated based on the limited number of asymmetric units in a unit cell as well as limited common symmetry groups for organocarbon crystals. Subsequent filtering of these packing structures by comparing with the reference structures yields dozens of promising crystal structures. Further DFT optimizations allow us to identify several highly stable packing structures that possess the space group of P2₁ as well as high to ultrahigh spontaneous polarizations (23-127 μC/cm(2)) along the crystallographic b axis. These values are either comparable to or much higher than the computed value (25 μC/cm(2)) or measured value (55 μC/cm(2)) for the state-of-the-art organic supramolecular systems. The high polarization arises from the ionic displacement. We further construct surface models to derive the electric-field-switched low-symmetry structures of new TTF- and PMDI-based crystals. By comparing the high-symmetry and low-symmetry crystal structures, we find that the ferroelectric polarization of the crystals is very sensitive to atomic positions, and a small molecular displacement may result in relatively high polarizations along the a and c axes, polarity reversal, and/or electronic contribution to polarization. If these newly designed TTF- and PMDI-based crystals with high polarizations are

  14. Shear-strain-induced chemical reactivity of layered molecular crystals

    SciTech Connect

    M. M. Kuklja; Sergey N. Rashkeev

    2007-04-01

    A density-functional-theory study of shear-related dissociation of two molecular crystals, diamino-dinitroethylene (FOX-7) and triamino-trinitrobenzine (TATB), is presented. A detailed explanation is proposed for the fact that FOX-7 is more sensitive than TATB while their sensitivities to initiation of chemistry have been expected to be comparable. We suggest that shear plays a crucial role in dissociation of molecules in organic energetic crystals and may be imperative in providing specific recommendations on ways for materials design.

  15. Nonlinear Optical Investigations of Vibrational Relaxation in Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Decola, Philip Lawrence

    Experimental studies of four-wave mixing have been used to obtain novel spectroscopic information in molecular crystals. This work can be separated into singly resonant and multiresonant investigations. One effort was to exploit the frequency and time domain capabilities of singly resonant coherent anti-Stokes Raman spectroscopy (CARS) to study vibrational dynamics in naphthalene and benzene single crystals at liquid Helium temperatures. To a large extent vibrational energy is chemical energy, so to understand the flow of vibrational energy in molecules and molecular aggregates can enhance our understanding of chemical reaction rates and pathways. Some of the salient results are: (1) the existence of motional narrowing in molecular crystals makes it possible for lifetime (T _1) broadening to dominate the linewidth of the vibrational transition even when the intrinsic disorder width is much larger than 1/T_1, (2) relaxation in molecular crystals can be surprisingly slow, ranging from subnanosecond to nanosecond, (3) substantial mode dependent contribution to relaxation from ^{13}C impurities in benzene, and (4) evidence of mode specific energy relaxation observed in a systematic study of benzene Raman active modes. The results obtained here are applied to the problems of understanding the contributions to residual low-temperature vibron linewidths and of developing simple mechanical intuitions to explain systematically the kinetic pathways for vibrational relaxation in molecular crystals. These results are discussed in light of the current theories of excitation dynamics in condensed phases. The other area of study was multiresonant nonlinear spectroscopic investigations of mixed organic crystals. The first multiresonant CARS and its Stokes analogue (CSRS) have been obtained in a mixed crystal of pentacene in benzoic acid allowing the simultaneous observation of ground and excited state Raman spectra. These spectra contain lines that are much sharper than expected

  16. High Throughput Profiling of Molecular Shapes in Crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Peter R.; Thomas, Sajesh P.; Jayatilaka, Dylan

    2016-02-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design.

  17. Controlling Molecular Growth between Fractals and Crystals on Surfaces.

    PubMed

    Zhang, Xue; Li, Na; Gu, Gao-Chen; Wang, Hao; Nieckarz, Damian; Szabelski, Paweł; He, Yang; Wang, Yu; Xie, Chao; Shen, Zi-Yong; Lü, Jing-Tao; Tang, Hao; Peng, Lian-Mao; Hou, Shi-Min; Wu, Kai; Wang, Yong-Feng

    2015-12-22

    Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpiński triangle (ST) fractals and 2D molecular crystals that were formed by 4,4″-dihydroxy-1,1':3',1″-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block.

  18. High Throughput Profiling of Molecular Shapes in Crystals

    PubMed Central

    Spackman, Peter R.; Thomas, Sajesh P.; Jayatilaka, Dylan

    2016-01-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. PMID:26908351

  19. Controlling Molecular Growth between Fractals and Crystals on Surfaces.

    PubMed

    Zhang, Xue; Li, Na; Gu, Gao-Chen; Wang, Hao; Nieckarz, Damian; Szabelski, Paweł; He, Yang; Wang, Yu; Xie, Chao; Shen, Zi-Yong; Lü, Jing-Tao; Tang, Hao; Peng, Lian-Mao; Hou, Shi-Min; Wu, Kai; Wang, Yong-Feng

    2015-12-22

    Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpiński triangle (ST) fractals and 2D molecular crystals that were formed by 4,4″-dihydroxy-1,1':3',1″-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block. PMID:26502984

  20. High Throughput Profiling of Molecular Shapes in Crystals.

    PubMed

    Spackman, Peter R; Thomas, Sajesh P; Jayatilaka, Dylan

    2016-01-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. PMID:26908351

  1. Growth of oriented molecular sieve crystals on organophosphonate films

    NASA Astrophysics Data System (ADS)

    Feng, S.; Bein, T.

    1994-04-01

    THE successful construction of complex organic/inorganic bio-mimetic systems1-3has demonstrated the great power of supra-molecular pre-organization and templating in controlling crystal growth4. For instance, polar organic surfaces or surface-attached polar groups can induce the formation of thin films of iron oxide5. It would be of great interest, for the design of novel devices such as sensors or catalyst membranes6, to be able to control the growth on surfaces of porous crystals with oriented channels: such channels could, for example, control the access of molecules to the surface of a field-effect transistor in a sensor device. Films and membranes with non-oriented channels have been prepared by depositing or growing zeolite7-12 crystals on metal or metal-oxide supports13-21 in one case21, pre-grown crystals of an aluminophosphate zeolite were oriented by application of an electric field. Here we report the oriented growth of crystals of a zinco-phosphate zeolite on gold surfaces modified with metal phosphonate multilayer films. We attribute the high degree of orientation (>90%) to a strong affinity between the phosphonic acid groups of the phosphate multilayer and the (111) faces of the growing crystals.

  2. Molecular dynamics simulations of glycine crystal-solution interface

    NASA Astrophysics Data System (ADS)

    Banerjee, Soumik; Briesen, Heiko

    2009-11-01

    Glycine is an amino acid that has several applications in the pharmaceutical industry. Hence, growth of α-glycine crystals through solution crystallization is an important process. To gain a fundamental understanding of the seeded growth of α-glycine from aqueous solution, the (110) face of α-glycine crystal in contact with a solution of glycine in water has been simulated with molecular dynamics. The temporal change in the location of the interface of the α-glycine crystal seed has been characterized by detecting a density gradient. It is found that the α-glycine crystal dissolves with time at a progressively decreasing rate. Diffusion coefficients of glycine adjacent to (110) face of α-glycine crystal have been calculated at various temperatures (280, 285, 290, 295, and 300 K) and concentrations (3.6, 4.5, and 6.0 mol/l) and compared to that in the bulk solution. In order to gain a fundamental insight into the nature of variation in such properties at the interface and the bulk, the formation of hydrogen bonds at various temperatures and concentrations has been investigated. It is found that the nature of interaction between various atoms of glycine molecules, as characterized by radial distribution functions, can provide interesting insight into the formation of hydrogen bonds that in turn affect the diffusion coefficients at the interface.

  3. Molecular dynamics simulations of polymer crystallization in highly supercooled melt: Primary nucleation and cold crystallization

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takashi

    2010-07-01

    Molecular mechanisms of crystallization at large supercooling and structure of supercooled melt are investigated in our polyethylenelike polymer through molecular dynamics simulations. Three representative crystallization processes are here considered: (1) isothermal homogeneous nucleation in the melt, (2) crystallization by rapid cooling of the melt, and (3) cold crystallization during slow heating of an amorphous state. Molecular level structures of the melt and the emerging crystallites are characterized by the use of the specific parameters, the effective segment length Lp and the radius of gyration Rg of the molecules, together with the overall crystallinity χc. In quasiequilibrium melt of moderate supercooling, the chains have random-coil conformations. However, the temperature dependence of the averaged Lp in the melt is found to show quite unexpected transition around the bulk melting temperature. At larger supercooling of 330 K, the homogeneous nucleation takes place after an induction period of about 4 ns. Characteristic conformational changes are here described by multimodal distributions of Rg, the main components of which correspond to relaxed random-coil chains in the melt and once-folded chains in the crystallites; the former chains transform continuously into the latter, having similar chain extension Rg. Rapid cooling of the melt is found to give poorly crystallized states having fringed-micellar organization. The effective segment length Lp shows considerably faster increase than Rg, resulting in peculiar conformational frustration. Nearly amorphous samples obtained by very rapid cooling show pronounced cold crystallization by slow heating over the glass transition temperature, where crystallites of random orientations form a granular texture due to steric collisions of the growing lamellae. The generated crystal texture is only metastable and readily reorganizes by annealing at high temperatures, where the chains are found to make large

  4. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Tanaka, Kouichi; Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki; Kitsunezuka, Masashi; Shinma, Atsushi

    2013-11-01

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  5. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    SciTech Connect

    Tanaka, Kouichi; Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki; Kitsunezuka, Masashi; Shinma, Atsushi

    2013-11-21

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  6. Subnanometer replica molding of molecular steps on ionic crystals.

    PubMed

    Elhadj, Selim; Rioux, Robert M; Dickey, Michael D; DeYoreo, James J; Whitesides, George M

    2010-10-13

    Replica molding with elastomeric polymers has been used routinely to replicate features less than 10 nm in size. Because the theoretical limit of this technique is set by polymer-surface interactions, atomic radii, and accessible volumes, replication at subnanometer length scales should be possible. Using polydimethylsiloxane to create a mold and polyurethane to form the replica, we demonstrate replication of elementary steps 3-5 Å in height that define the minimum separation between molecular layers in the lattices of the ionic crystals potassium dihydrogen phosphate and calcite. This work establishes the operation of replica molding at the molecular scale.

  7. Diffusion on (110) Surface of Molecular Crystal Pentaerythritol Tetranitrate

    SciTech Connect

    Wang, J; Golfinopoulos, T; Gee, R H; Huang, H

    2007-01-25

    Using classical molecular dynamics simulations, we investigate the diffusion mechanisms of admolecules on the (110) surface of molecular crystal pentaerythritol tetranitrate. Our results show that (1) admolecules are stable at off lattice sites, (2) admolecules diffuse along close-packed [1{bar 1}1] and [{bar 1}11] directions, and (3) admolecules detach from the surface at 350K and above. Based on the number of diffusion jumps as a function of temperature, we estimate the jump frequency to be v=1.14 x 10{sup 12} e{sup -0.08eV/kT} per second.

  8. Non-equilibrium Dynamics of DNA Nanotubes

    NASA Astrophysics Data System (ADS)

    Hariadi, Rizal Fajar

    Can the fundamental processes that underlie molecular biology be understood and simulated by DNA nanotechnology? The early development of DNA nanotechnology by Ned Seeman was driven by the desire to find a solution to the protein crystallization problem. Much of the later development of the field was also driven by envisioned applications in computing and nanofabrication. While the DNA nanotechnology community has assembled a versatile tool kit with which DNA nanostructures of considerable complexity can be assembled, the application of this tool kit to other areas of science and technology is still in its infancy. This dissertation reports on the construction of non-equilibrium DNA nanotube dynamic to probe molecular processes in the areas of hydrodynamics and cytoskeletal behavior. As the first example, we used DNA nanotubes as a molecular probe for elongational flow measurement in different micro-scale flow settings. The hydrodynamic flow in the vicinity of simple geometrical objects, such as a rigid DNA nanotube, is amenable to rigorous theoretical investigation. We measured the distribution of elongational flows produced in progressively more complex settings, ranging from the vicinity of an orifice in a microfluidic chamber to within a bursting bubble of Pacific ocean water. This information can be used to constrain theories on the origin of life in which replication involves a hydrodynamically driven fission process, such as the coacervate fission proposed by Oparin. A second theme of this dissertation is the bottom-up construction of a de novo artificial cytoskeleton with DNA nanotubes. The work reported here encompasses structural, locomotion, and control aspects of non-equilibrium cytoskeletal behavior. We first measured the kinetic parameters of DNA nanotube assembly and tested the accuracy of the existing polymerization models in the literature. Toward recapitulation of non-equilibrium cytoskeletal dynamics, we coupled the polymerization of DNA

  9. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    SciTech Connect

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-07

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  10. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  11. Molecular dynamics simulation of shocks in porous TATB crystals

    SciTech Connect

    Fried, L.E.; Tarver, C.

    1995-08-01

    We report molecular dynamics results on the shock structure of 2-D crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approx. 30 nm in materials with a 20% random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock equilibration times increase from 1 ps to greater than 10 ps.

  12. Collective aspects of singlet fission in molecular crystals

    SciTech Connect

    Teichen, Paul E.; Eaves, Joel D.

    2015-07-28

    We present a model to describe collective features of singlet fission in molecular crystals and analyze it using many-body theory. The model we develop allows excitonic states to delocalize over several chromophores which is consistent with the character of the excited states in many molecular crystals, such as the acenes, where singlet fission occurs. As singlet states become more delocalized and triplet states more localized, the rate of singlet fission increases. We also determine the conditions under which the two triplets resulting from fission are correlated. Using the Bethe Ansatz and an entanglement measure for indistinguishable bipartite systems, we calculate the triplet-triplet entanglement as a function of the biexciton interaction strength. The biexciton interaction can produce bound biexciton states and provides a source of entanglement between the two triplets even when the triplets are spatially well separated. Significant entanglement between the triplet pair occurs well below the threshold for bound pair formation. Our results paint a dynamical picture that helps to explain why fission has been observed to be more efficient in molecular crystals than in their covalent dimer analogues and have consequences for photovoltaic efficiency models that assume that the two triplets can be extracted independently.

  13. Molecular aspects of flow-induced crystallization of polypropylene

    NASA Astrophysics Data System (ADS)

    Thurman, Derek W.

    Using a novel shearing device, we investigate-flow-induced crystallization of bimodal blends of polypropylenes (PP) in which we vary the molecular character (concentration, molecular weight, regularity) of the high molecular weight mode. We apply a number of in situ characterization tools (rheo-optics, rheo-WAXD) to the development of transient structure and interpret our findings in light of ex situ microscopic examination of the final morphology. Blending a well-characterized high molecular weight isotactic polypropylene into a "base iPP" at various concentrations (c), we determined that less than 1% of long chains with Mw five times larger than the Mw of the base resin profoundly affected the flow-induced crystallization kinetics and morphology. Varying the concentration from below to above c* indicated that the effect of the long chains involves cooperative interactions enhanced by long chain-long chain overlap. The long chains particularly influence the formation of anisotropic nuclei. Studying a series of bimodal blends in which the long chain molecular weight (ML) was varied, we found that increasing ML increased the tendency to form threadlike precursors to oriented crystallization. This was highlighted by a marked decrease in the threshold stress (sigma*) necessary to induce oriented crystallization. A minimum separation in relaxation time scales (˜100 times slower) between the long chains and the average was necessary to form long lived oriented precursor structures. A novel "depth sectioning" analysis technique allowed us to gain depth dependent information from real-time rheo-optical and rheo-WAXD experiments. We identify a promising set of conditions that may be used to measure the thread propagation velocity for this material if the appropriate length scale can be assigned by microscopy. Threads first form near the channel wall and grow in length with prolonged flow until thread length per unit volume saturates. Prior to saturation, the thread

  14. Unusually Large Young's Moduli of Amino Acid Molecular Crystals.

    PubMed

    Azuri, Ido; Meirzadeh, Elena; Ehre, David; Cohen, Sidney R; Rappe, Andrew M; Lahav, Meir; Lubomirsky, Igor; Kronik, Leeor

    2015-11-01

    Young's moduli of selected amino acid molecular crystals were studied both experimentally and computationally using nanoindentation and dispersion-corrected density functional theory. The Young modulus is found to be strongly facet-dependent, with some facets exhibiting exceptionally high values (as large as 44 GPa). The magnitude of Young's modulus is strongly correlated with the relative orientation between the underlying hydrogen-bonding network and the measured facet. Furthermore, we show computationally that the Young modulus can be as large as 70-90 GPa if facets perpendicular to the primary direction of the hydrogen-bonding network can be stabilized. This value is remarkably high for a molecular solid and suggests the design of hydrogen-bond networks as a route for rational design of ultra-stiff molecular solids.

  15. Transport properties of cholesteric liquid crystals studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten

    We have studied the transport properties of a cholesteric liquid crystal by molecular dynamics simulation. The molecules consist of six soft ellipsoids of revolution, the axes of which are perpendicular to the line connecting their centres of symmetry. The angle between the symmetry axes of two adjacent ellipsoids is 7.5°, so the molecules are twisted. At high densities they form a cholesteric phase where their twist axes are oriented around the cholesteric axis and the symmetry axes of the ellipsoids are approximately parallel to the local director. We have been particularly interested in thermomechanical coupling or the Lehmann effect, which arises when a temperature gradient parallel to the cholesteric axis induces a torque that rotates the director. The converse is also possible: rotation of the director can drive a heat current. The thermal conductivity, the twist viscosity, the cross-coupling coefficient between the temperature gradient and the torque, and the cross-coupling coefficient between the director angular velocity and the heat current have been calculated by non-equilibrium molecular dynamics simulation methods (NEMD) and by evaluation of the Green-Kubo relations from equilibrium simulations. Two ensembles have been utilized: the ordinary canonical ensemble and another ensemble where the director angular velocity is constrained to be a constant of motion. All the methods give consistent results for the twist viscosity and the thermal conductivity. The NEMD estimates of the cross-coupling coefficients agree within a relative error of 20%. This is consistent with the Onsager reciprocity relations that state that the two cross-coupling coefficients should be equal. The relative error of the Green-Kubo estimates is about 100% even though the order of magnitude is the same as that of the NEMD estimates.

  16. Absorbate-Induced Piezochromism in a Porous Molecular Crystal

    PubMed Central

    2015-01-01

    Atmospherically stable porous frameworks and materials are interesting for heterogeneous solid–gas applications. One motivation is the direct and selective uptake of pollutant/hazardous gases, where the material produces a measurable response in the presence of the analyte. In this report, we present a combined experimental and theoretical rationalization for the piezochromic response of a robust and porous molecular crystal built from an extensively fluorinated trispyrazole. The electronic response of the material is directly determined by analyte uptake, which provokes a subtle lattice contraction and an observable bathochromic shift in the optical absorption onset. Selectivity for fluorinated absorbates is demonstrated, and toluene is also found to crystallize within the pore. Furthermore, we demonstrate the application of electronic structure calculations to predict a physicochemical response, providing the foundations for the design of electronically tunable porous solids with the chemical properties required for development of novel gas-uptake media. PMID:25706577

  17. Absorbate-induced piezochromism in a porous molecular crystal.

    PubMed

    Hendon, Christopher H; Wittering, Kate E; Chen, Teng-Hao; Kaveevivitchai, Watchareeya; Popov, Ilya; Butler, Keith T; Wilson, Chick C; Cruickshank, Dyanne L; Miljanić, Ognjen Š; Walsh, Aron

    2015-03-11

    Atmospherically stable porous frameworks and materials are interesting for heterogeneous solid-gas applications. One motivation is the direct and selective uptake of pollutant/hazardous gases, where the material produces a measurable response in the presence of the analyte. In this report, we present a combined experimental and theoretical rationalization for the piezochromic response of a robust and porous molecular crystal built from an extensively fluorinated trispyrazole. The electronic response of the material is directly determined by analyte uptake, which provokes a subtle lattice contraction and an observable bathochromic shift in the optical absorption onset. Selectivity for fluorinated absorbates is demonstrated, and toluene is also found to crystallize within the pore. Furthermore, we demonstrate the application of electronic structure calculations to predict a physicochemical response, providing the foundations for the design of electronically tunable porous solids with the chemical properties required for development of novel gas-uptake media.

  18. Excitonic couplings between molecular crystal pairs by a multistate approximation

    SciTech Connect

    Aragó, Juan Troisi, Alessandro

    2015-04-28

    In this paper, we present a diabatization scheme to compute the excitonic couplings between an arbitrary number of states in molecular pairs. The method is based on an algebraic procedure to find the diabatic states with a desired property as close as possible to that of some reference states. In common with other diabatization schemes, this method captures the physics of the important short-range contributions (exchange, overlap, and charge-transfer mediated terms) but it becomes particularly suitable in presence of more than two states of interest. The method is formulated to be usable with any level of electronic structure calculations and to diabatize different types of states by selecting different molecular properties. These features make the diabatization scheme presented here especially appropriate in the context of organic crystals, where several excitons localized on the same molecular pair may be found close in energy. In this paper, the method is validated on the tetracene crystal dimer, a well characterized case where the charge transfer (CT) states are closer in energy to the Frenkel excitons (FE). The test system was studied as a function of an external electric field (to explore the effect of changing the relative energy of the CT excited state) and as a function of different intermolecular distances (to probe the strength of the coupling between FE and CT states). Additionally, we illustrate how the approximation can be used to include the environment polarization effect.

  19. Thwarting Crystallization through Hydrogen Bonding in Triazine Molecular Glasses

    NASA Astrophysics Data System (ADS)

    Laventure, Audrey; Soldera, Armand; Lebel, Olivier; Pellerin, Christian

    2015-03-01

    Using irregular shaped molecules interacting weakly with each other is the most intuitive choice to generate amorphous molecular materials. In contrast, H-bonds are commonly used in crystal engineering to create predictable ordered and well-packed structures. In spite of this fact, Lebel et al. have demonstrated that H-bonds can be used efficiently to thwart crystallization by inducing the self-assembly of aggregates that pack poorly. Since 2006, libraries of triazine derivatives with a variety of different substituents capable of forming molecular glasses have been synthesized and studied. Their outstanding glass-forming ability (with critical cooling rates lower than 0.5 °C/min) and their wide range of Tg (from below ambient temperature up to 160 °C) make them an attractive amorphous model system to deepen our understanding of the relationship between microscopic features and macroscopic behavior of glasses. In this presentation, we will show that variable-temperature infrared spectroscopy is a tool of choice to probe the vitreous state of these compounds. We take advantage of the selectivity of this technique to correlate their molecular features to their thermal properties. Quantitative monitoring of hydrogen bonds during vitrification will be addressed.

  20. Molecular simulation of crystal nucleation in n-octane melts

    NASA Astrophysics Data System (ADS)

    Yi, Peng; Rutledge, Gregory C.

    2009-10-01

    Homogeneous nucleation of the crystal phase in n-octane melts was studied by molecular simulation with a realistic, united-atom model for n-octane. The structure of the crystal phase and the melting point of n-octane were determined through molecular dynamics simulation and found to agree with experimental results. Molecular dynamics simulations were performed to observe the nucleation events at constant pressure and constant temperature corresponding to about 20% supercooling. Umbrella sampling Monte Carlo simulations were used to calculate the nucleation free energy for three temperatures, ranging from 8% to 20% supercooling, and to reveal details of the critical nucleus for the first time. The cylindrical nucleus model was found to provide a better quantitative description of the critical nucleus than the spherical nucleus model. The interfacial free energies of the cylinder model were calculated from the simulation data. As the temperature increased, the interfacial free energy of the side surface remained relatively unchanged, at 7-8 mJ/m2, whereas the interfacial free energy of the end surface decreased significantly from 5.4 mJ/m2 to about 3 mJ/m2. These results, and the methods employed, provide valuable and quantitative information regarding the rate-limiting step during the solidification of chain molecules, with ramifications for both short alkanes and polymers.

  1. Molecular Aspects of Flow-Induced Crystallization of Polymers

    NASA Astrophysics Data System (ADS)

    Kornfield, J.

    Like teeth, bone and sea shells, semicrystalline polymers combine strength with toughness by forming a nano-scale composite with platelet-like crystals stacked with noncrystalline material between them. The morphology and orientation distribution of the nanostructure dictate the material properties. Dynamics of polymer chains in the melt play an important role in controlling the morphology, especially under the influence of flow. Using bimodal isotactic polypropylenes to reveal the effects of small concentrations of very long chains, in collaboration with Mitsubishi Chemical, we show that long chains have a profound effect when they are so long that they can undergo chain stretching, particularly when the long chain concentration is at or above their overlap concentration. When subjected to identical stress at identical subcooling, the blends containing long chains undergo dramatically faster crystallization with very strong orientation. The ``long chains" enhance formatio n of highly oriented crystallization precursors (``shish") on which oriented lamellae (``kebabs") subsequently grow. In collaboration with Sumitomo Chemical and The University of Tokyo, we test the hypothesis that the kebabs are actually composed of long chains using isotopic labelling of selected fractions and small angle neutron scattering (SANS). The results show that long chains in the shish are at the same concentration as they are everywhere else: there is no neutron scattering contrast when the long chains are the deuterium labelled ones! The long chains are essential for the formation of shish and they play their role by ``recruiting" adjacent chains into formation of the shish. Placing molecular defects on the longest chains inhibits their ability to serve this role, providing a molecular tool to independently control the melt elasticity (by choice of the length and concentration of the long chains) and the flow-induced crystallization behavior (by selecting the com onomer content, for

  2. Study on Properties of Energy Spectra of the Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-Feng; Chen, Xiang-Rong

    The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

  3. Nonequilibrium thermodynamics of an interface

    NASA Astrophysics Data System (ADS)

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics.

  4. Nonequilibrium thermodynamics of an interface.

    PubMed

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics.

  5. Nonequilibrium thermodynamics of an interface.

    PubMed

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics. PMID:27300960

  6. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  7. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

    PubMed Central

    2015-01-01

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  8. Molecular interactions and crystal packing in nematogen: Computational thermodynamic approach

    NASA Astrophysics Data System (ADS)

    Lakshmi Praveen, P.; Ojha, Durga P.

    2011-10-01

    A computational thermodynamic approach of molecular interactions in a nematogen p-n-alkyl benzoic acid ( nBAC) molecule with an alkyl group butyl (4BAC) has been carried out with respect to translational and orientational motion. The atomic net charge and dipole moment at each atomic center were evaluated using the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrödinger perturbation theory along with multicentered-multipole expansion method were employed to evaluate long-range intermolecular interactions, while a 6-exp potential function was assumed for short-range interactions. Various possible geometrical arrangements of molecular pairs with regard to different energy components were considered, and the energetically favorable configuration was found to understand the crystal packing picture. Furthermore, these interaction energy values are taken as input to calculate the configurational entropy at room temperature (300 K), nematic-isotropic transition temperature (386 K) and above transition temperature (450 K) during different modes of interactions. An attempt has been made to describe interactions in a nematogen at molecular level, through which one can simplify the system to make the model computationally feasible in understanding the delicate interplay between energy and entropy, that accounts for mesomorphism and there by to analyze the molecular structure of a nematogen.

  9. Alignment of liquid crystals using a molecular layer with patterned molecular density.

    PubMed

    Son, Jong-Ho; Zin, Wang-Cheol; Takezoe, Hideo; Song, Jang-Kun

    2012-11-27

    The surface of self-constructed molecular density modulation (SDM) exhibits a wide range of liquid crystal alignment capabilities including planar, tilted, and homeotropic alignments, disclination-free uniform and heterogeneous alignments, and even spatially varying alignments through the single non-contact process. Alignment defects are eliminated by temporary lowering the frictional energy barrier via the open-boundary elastic stabilization (OES) treatment. PMID:22945601

  10. Molecular dynamics simulations of alkyl substituted nanographene crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, Orestis George; Theodorou, Doros Nicolas

    2015-09-01

    Discotic polyaromatic molecules, similar to nanometric graphene flakes, constitute an interesting class of materials for organic electronic applications. Grafting flexible side chains around the periphery of such molecules enhances their processability and gives rise to diverse behaviours, such as the manifestation of liquid-crystalline character and anisotropic mechanical response. In this work, we examine by means of molecular dynamics simulations the properties of molecular crystals comprised of alkyl-substituted hexa-peri-hexabenzocoronene mesogens. Pristine and mono-substituted systems by hydrogen or iodine atoms are modelled, with variable side chain length. A general structural and mechanical robustness to peripheral substitution is reported, with the mesogens forming tightly packed molecular wires even at elevated temperature and pressure. In their discotic ordering, the molecules present relatively low translational mobility, a beneficial phenomenon for charge transport. A thermotropic dependence of the mechanical response is identified, with the systems behaving differently in their room-temperature crystalline phase and in their liquid-crystalline phase at elevated temperatures. The melting process is also examined, elucidating an initial negative expansion along a high symmetry direction and the existence of a metastable state, before falling into the final liquid-crystalline state. Dedicated to Professor Jean-Pierre Hansen, with deepest appreciation of his outstanding contributions to liquid and soft matter theory.

  11. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  12. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    SciTech Connect

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  13. Monte-Carlo simulations of chemical reactions in molecular crystals

    NASA Astrophysics Data System (ADS)

    Even, J.; Bertault, M.

    1999-01-01

    Chemical reactions in molecular crystals, yielding new entities (dimers, trimers,…, polymers) in the original structure, are simulated for the first time by stochastic Monte Carlo methods. The results are compared with those obtained by deterministic methods. They show that numerical simulation is a tool for understanding the evolution of these mixed systems. They are in kinetic and not in thermodynamic control. Reactive site distributions, x-ray diffuse scattering, and chain length distributions can be simulated. Comparisons are made with deterministic models and experimental results obtained in the case of the solid state dimerization of cinnamic acid in the beta phase and in the case of the solid state polymerization of diacetylenes.

  14. InPBi Single Crystals Grown by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Wang, K.; Gu, Y.; Zhou, H. F.; Zhang, L. Y.; Kang, C. Z.; Wu, M. J.; Pan, W. W.; Lu, P. F.; Gong, Q.; Wang, S. M.

    2014-06-01

    InPBi was predicted to be the most robust infrared optoelectronic material but also the most difficult to synthesize within In-VBi (V = P, As and Sb) 25 years ago. We report the first successful growth of InPBi single crystals with Bi concentration far beyond the doping level by gas source molecular beam epitaxy. The InPBi thin films reveal excellent surface, structural and optical qualities making it a promising new III-V compound family member for heterostructures. The Bi concentration is found to be 2.4 +/- 0.4% with 94 +/- 5% Bi atoms at substitutional sites. Optical absorption indicates a band gap of 1.23 eV at room temperature while photoluminescence shows unexpectedly strong and broad light emission at 1.4-2.7 μm which can't be explained by the existing theory.

  15. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    SciTech Connect

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-06-05

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the <100> direction form intersecting stacking faults by slippage along {l_brace}111{r_brace} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the <111> case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the <110> direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society.

  16. InPBi Single Crystals Grown by Molecular Beam Epitaxy

    PubMed Central

    Wang, K.; Gu, Y.; Zhou, H. F.; Zhang, L. Y.; Kang, C. Z.; Wu, M. J.; Pan, W. W.; Lu, P. F.; Gong, Q.; Wang, S. M.

    2014-01-01

    InPBi was predicted to be the most robust infrared optoelectronic material but also the most difficult to synthesize within In-VBi (V = P, As and Sb) 25 years ago. We report the first successful growth of InPBi single crystals with Bi concentration far beyond the doping level by gas source molecular beam epitaxy. The InPBi thin films reveal excellent surface, structural and optical qualities making it a promising new III–V compound family member for heterostructures. The Bi concentration is found to be 2.4 ± 0.4% with 94 ± 5% Bi atoms at substitutional sites. Optical absorption indicates a band gap of 1.23 eV at room temperature while photoluminescence shows unexpectedly strong and broad light emission at 1.4–2.7 μm which can't be explained by the existing theory. PMID:24965260

  17. Evaluation of molecular mass and tacticity of polyvinyl alcohol by non-equilibrium capillary electrophoresis of equilibrium mixtures of a polymer and a dye.

    PubMed

    Carrasco-Correa, Enrique Javier; Beneito-Cambra, Miriam; Herrero-Martínez, José Manuel; Ramis-Ramos, Guillermo

    2011-04-22

    Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) has been used to characterize polyvinyl alcohol (PVA). Commercial PVA samples with different molecular masses, from M(w)=15 up to 205 kDa, were used. According to the (13)C NMR spectra, the samples also differed in tacticity (stereoregularity). Mixtures of PVA and the anionic azo-dye Congo Red (CR) were injected in the presence of a borate buffer. The electropherograms gave a band and a peak due to the residual PVA-CR complex and the excess dye, respectively, plus a superimposed exponential decay due to the partial dissociation of the complex during migration. The stoichiometry of the PVA-CR complex, q=[monomer]/[dye], reached a maximum, q(sat), which depended on both M(w) and tacticity of PVA. Thus, q(sat) decreased from a molar ratio of ca. 4.9 to 3.6 at increasing M(w) values, this variation also being largely dependent on tacticity. A similar dependence of the electrophoretic mobility of the complex on both M(w) and tacticity was also observed. A possible explanation, based on the formation of a stack of CR ions inside the PVA-CR complex, was proposed and discussed. Finally, at increasing M(w) values, the stability constant of the complex increased slightly, and the pseudo-first order dissociation rate of the complex decreased, this later parameter also showing a dependence on both M(w) and tacticity.

  18. Influence of longitudinal isotope substitution on the thermal conductivity of carbon nanotubes: Results of nonequilibrium molecular dynamics and local density functional calculations

    SciTech Connect

    Leroy, Frédéric Böhm, Michael C.; Schulte, Joachim; Balasubramanian, Ganesh

    2014-04-14

    We report reverse nonequilibrium molecular dynamics calculations of the thermal conductivity of isotope substituted (10,10) carbon nanotubes (CNTs) at 300 K. {sup 12}C and {sup 14}C isotopes both at 50% content were arranged either randomly, in bands running parallel to the main axis of the CNTs or in bands perpendicular to this axis. It is found that the systems with randomly distributed isotopes yield significantly reduced thermal conductivity. In contrast, the systems where the isotopes are organized in patterns parallel to the CNTs axis feature no reduction in thermal conductivity when compared with the pure {sup 14}C system. Moreover, a reduction of approximately 30% is observed in the system with the bands of isotopes running perpendicular to the CNT axis. The computation of phonon dispersion curves in the local density approximation and classical densities of vibrational states reveal that the phonon structure of carbon nanotubes is conserved in the isotope substituted systems with the ordered patterns, yielding high thermal conductivities in spite of the mass heterogeneity. In order to complement our conclusions on the {sup 12}C-{sup 14}C mixtures, we computed the thermal conductivity of systems where the {sup 14}C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

  19. Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Monk, J.; Yang, Y.; Mendelev, M. I.; Asta, M.; Hoyt, J. J.; Sun, D. Y.

    2010-01-01

    The generation and dissipation of latent heat at the moving solid-liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose-Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid-liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a kinetic

  20. Imatinib (Gleevec@) conformations observed in single crystals, protein-Imatinib co-crystals and molecular dynamics: Implications for drug selectivity

    NASA Astrophysics Data System (ADS)

    Golzarroshan, B.; Siddegowda, M. S.; Li, Hong qi; Yathirajan, H. S.; Narayana, B.; Rathore, R. S.

    2012-06-01

    Structure and dynamics of the Leukemia drug, Imatinib, were examined using X-ray crystallography and molecular dynamics studies. Comparison of conformations observed in single crystals with several reported co-crystals of protein-drug complexes suggests existence of two conserved conformations of Imatinib, extended and compact (or folded), corresponding to two binding modes of interaction with the receptor. Furthermore, these conformations are conserved throughout a dynamics simulation. The present study attempts to draw a parallel on conformations and binding patterns of interactions, obtained from small-molecule single-crystal and macromolecule co-crystal studies, and provides structural insights for understanding the high selectivity of this drug molecule.

  1. Nonequilibrium diagnostics of plasma thrusters

    SciTech Connect

    Eddy, T.L.; Grandy, J.D.

    1990-01-01

    This paper describes possible techniques by which the state of plasma thruster operation for space propulsion can be determined from a minimum set of experimental data in the laboratory. The kinetic properties of the nonequilibrium plasma plume usually can not be directly related to the observed radiation; hence, appropriate nonequilibrium diagnostic techniques must be employed. A newly developed multithermal, multichemical equilibrium method is discussed that uses measured line emission intensities and N equations to solve for N unknowns. The effect of arbitrarily changing the number of selected N unknowns and how one determines the optimum (minimum) number to be used for a given composition is also presented. The chemical nonequilibrium aspects and the application to molecular species have not yet been published. The important conclusions are that (1) complete thermodynamic systems in nonequilibrium can be described by relatively few variables if appropriate choices and filtering methods are used, (2) a few radiation measurements can yield valid kinetic properties, and (3) the major question in the relations to be used is in the form of the law of mass action. The results are substantiated in the laboratory by additional alternative methods of measurement of some of the kinetic properties. 13 refs., 1 fig.

  2. Computer simulation of nonequilibrium processes

    SciTech Connect

    Wallace, D.C.

    1985-07-01

    The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed.

  3. Crystallization force--a density functional theory concept for revealing intermolecular interactions and molecular packing in organic crystals.

    PubMed

    Li, Tonglei; Ayers, Paul W; Liu, Shubin; Swadley, Matthew J; Aubrey-Medendorp, Clare

    2009-01-01

    Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short-range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal-growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self-assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, so-called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.

  4. Molecular co-crystals of 2-aminothiazole derivatives.

    PubMed

    Lynch; Nicholls; Smith; Byriel; Kennard

    1999-10-01

    A series of molecular adducts of 2-aminothiazole derivatives - 2-aminothiazole, 2-amino-2-thiazoline and 2-aminobenzothiazole with the carboxylic-acid-substituted heterocyclics indole-2-carboxylic acid, N-methylpyrrole-2-carboxylic acid and thiophene-2-carboxylic acid - have been prepared and characterized using X-ray powder diffraction and in five cases by single-crystal X-ray diffraction methods. These five compounds are the adducts of 2-amino-2-thiazolium with indole-2-carboxylate [(C(3)H(7)N(2)S)(+)(C(9)H(6)NO(2))(-)], and N-methylpyrrole-2-carboxylate [(C(3)H(7)N(2)S)(+)-(C(6)H(6)NO(2))(-)], 2-aminobenzothiazolium with indole-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(9)H(6)NO(2))(-)], N-methylpyrrole-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(6)H(6)NO(2))(-)] and thiophene-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(5)H(3)O(2)S)(-)]. All complexes involve proton transfer, as indicated by IR spectroscopy, while the five crystal structures display similar hydrogen-bonding patterns with the dominant interaction being an R(2)(2)(8) graph set dimer association between carboxylate groups and the amine/heterocyclic nitrogen sites. Futhermore, in each case a subsiduary interaction between an amino proton and a carboxylate oxygen completes a linear hydrogen-bonded chain. In addition to this, the indole-2-carboxylate molecules in the adduct structure with 2-amino-2-thiazolium form associated dimers which add to the hydrogen-bonding network.

  5. Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach.

    PubMed

    Fang, Tao; Jia, Junteng; Li, Shuhua

    2016-05-01

    The generalized energy-based fragmentation (GEBF) approach for molecular crystals with periodic boundary condition (PBC) (denoted as PBC-GEBF) is extended to allow vibrational spectra of molecular crystals to be easily computed at various theory levels. Within the PBC-GEBF approach, the vibrational frequencies of a molecular crystal can be directly evaluated from molecular quantum chemistry calculations on a series of nonperiodic molecular systems. With this approach, the vibrational spectra of molecular crystals can be calculated with much reduced computational costs at various theory levels, as compared to those required by the methods based on periodic electronic structure theory. By testing the performance of the PBC-GEBF method for two molecular crystals (CO2 and imidazole), we demonstrate that the PBC-GEBF approach can reproduce the results of the methods based on periodic electronic structure theory in predicting vibrational spectra of molecular crystals. We apply the PBC-GEBF method at second-order Møller-Plesset perturbation theory (PBC-GEBF-MP2 in short) to investigate the vibrational spectra of the urea and ammonia borane crystals. Our results show that the PBC-GEBF-MP2 method can provide quite accurate descriptions for the observed vibrational spectra of the two systems under study.

  6. Molecular geometry directed Kagomé and honeycomb networks: toward two-dimensional crystal engineering.

    PubMed

    Furukawa, Shuhei; Uji-i, Hiroshi; Tahara, Kazukuni; Ichikawa, Tomoyuki; Sonoda, Motohiro; De Schryver, Frans C; Tobe, Yoshito; De Feyter, Steven

    2006-03-22

    We present here the formation of a molecular Kagomé network within a two-dimensional (2D) crystal on a surface. This system provides a clear example of how, by design, molecular geometry can be expressed at the level of the 2D crystal lattice, leading to the formation of open networks. Key elements to control molecular network formation are core symmetry, location and orientation of interacting and connecting substituents, as well as symmetry matching between the networks and the surface.

  7. Molecular simulation of chevrons in confined smectic liquid crystals

    NASA Astrophysics Data System (ADS)

    Webster, Richard E.; Mottram, Nigel J.; Cleaver, Douglas J.

    2003-08-01

    Chevron structures adopted by confined smectic liquid crystals are investigated via molecular dynamics simulations of the Gay-Berne model. The chevrons are formed by quenching nematic films confined between aligning planar substrates whose easy axes have opposing azimuthal components. When the substrates are perfectly smooth, the chevron formed migrates rapidly towards one of the confining walls to yield a tilted layer structure. However, when substrate roughness is included, by introducing a small-amplitude modulation to the particle-substrate interaction well depth, a symmetric chevron is formed which remains stable over sufficiently long run times for detailed structural information, such as the relevant order parameters and director orientation, to be determined. For both smooth and rough boundaries, the smectic order parameter remains nonzero across the entire chevron, implying that layer identity is maintained across the chevron tip. Also, when the surface-stabilized chevron does eventually revert to a tilted layer structure, it does so via surface slippage, such that layer integrity is maintained throughout the chevron to tilted layer relaxation process.

  8. Supramolecular photochemistry: from molecular crystals to water-soluble capsules.

    PubMed

    Ramamurthy, V; Gupta, Shipra

    2015-01-01

    Photochemical and photophysical behavior of molecules in supramolecular assemblies are different and more selective than in gas and isotropic solution phases. Knowledge of the inherent electronic and steric properties of the reactant is insufficient to predict the excited state behavior of molecules confined in such assemblies. Weak interactions between the medium and the reactant as well as the free space in a reaction cavity would play a significant role in modulating the excited state properties of molecules when they are included within confined spaces. The concepts of 'Molecular Photochemistry' should be modified while applying them to 'Supramolecular Photochemistry'. In this review we show that the topochemical rules established to understand reactions in crystals could be extended to supramolecular assemblies in general. To make the best use of the medium one needs to understand the features of the medium, the nature of interaction between the medium and the molecule and the rules that govern the behavior of a molecule in that medium. This tutorial provides introduction to these aspects of 'Supramolecular Photochemistry'.

  9. Molecular crystals as precursors for poly-nitrogen

    NASA Astrophysics Data System (ADS)

    Borstad, Gustav; Ciezak-Jenkins, Jennifer

    The application of pressure to matter results in dramatic modifications of its properties. The compression of molecular crystals first eliminates ``empty'' space between the molecules. It then alters the electron density distribution, favoring the increase of atomic coordination and the formation of polymers. The polymerization of low-Z compounds into covalently-bonded networks in three dimensions tend to generate materials characterized by superconductivity, super-hardness, and high-energy density.1 Poly-nitrogen (analogous to diamond) has been synthesized under extreme conditions above 100 GPa and 2000 K in diamond anvil cells, but could not be recovered to ambient conditions.2 A useful form of poly-nitrogen would have to be synthesized at low-pressure with enhanced stability at ambient conditions. The changes in the intermolecular and intramolecular interactions with pressure play a crucial role in the synthesizing and stabilizing of the structure as well as in tuning its properties. In this talk, we provide Raman and x-ray diffraction data on nitrogen-containing compound biuret and compare it to work on other possible poly-nitrogen precursors. During this project, coauthor GB was supported in part by an appointment to the Postdoctoral Research Program at the US Army Research Laboratory administered by the Oak Ridge Associated Universities.

  10. Thermodynamic stability and crystallization behavior of molecular complexes with TEP host

    NASA Astrophysics Data System (ADS)

    Fijiwara, Atsushi; Kitamura, Mitsutaka

    2013-06-01

    In the crystallization of molecular complex (co-crystal, clathrate complex), polymorphism in regard to the host structure frequently appears. Previously, we studied the release process of the biocide, CMI (5-chloro-2-methyl-4-isothiazolin-3-one) from the molecular complex with TEP (1,1,2,2-tetrakis(4-hydroxyphenyl)ethane) (TEP·2CMI) in methanol-water mixed solvents. It was clear that the release process of the biocide (CMI) is composed of the transformation from the TEP·2CMI crystal to a more stable molecular complex crystal with solvent. In this work, the crystallization was performed in the methanol solutions including TEP and CMI at constant temperature (298 K and 308 K). It appeared that two kinds of TEP molecular complexes (TEP·2CMI and TEP·2MeOH) crystallize competitively. The crystallization zone of each molecular complex was shown in the map using the coordinates of initial concentrations of TEP and CMI. In the boundary zone both molecular complexes appeared and the transformation from TEP·2CMI to TEP·2MeOH was observed, indicating that the stable form is TEP·2MeOH. Without the boundary zone the corresponding stable form crystallized in each zone. The value of the initial concentration ratio of CMI/TEP for the selective crystallization of TEP·2CMI was higher at 298 K (1.54) than that (1.36) at 308 K. The equilibrium concentrations of TEP and CMI in the presence of two molecular complexes were expressed using the dissociation constants of the molecular complexes and it was indicated that the dissociation of TEP·2CMI highly increases with temperature

  11. Nonequilibrium is different

    NASA Astrophysics Data System (ADS)

    Kirkpatrick, T. R.; Dorfman, J. R.

    2015-08-01

    Nonequilibrium and equilibrium fluid systems differ due to the existence of long-range correlations in nonequilibrium that are not present in equilibrium, except at critical points. Here we examine fluctuations of the temperature, of the pressure tensor, and of the heat current in a fluid maintained in a nonequilibrium stationary state (NESS) with a fixed temperature gradient, a system in which the nonequilibrium correlations are especially long-ranged. For this particular NESS, our results show that (i) the mean-squared fluctuations in nonequilibrium differ markedly in their system-size scaling compared to their equilibrium counterparts, and (ii) there are large, nonlocal correlations of the normal stress in this NESS. These terms provide important corrections to the fluctuating normal stress in linearized Landau-Lifshitz fluctuating hydrodynamics.

  12. Molecular reorientation of a nematic liquid crystal by thermal expansion

    PubMed Central

    Kim, Young-Ki; Senyuk, Bohdan; Lavrentovich, Oleg D.

    2012-01-01

    A unique feature of nematic liquid crystals is orientational order of molecules that can be controlled by electromagnetic fields, surface modifications and pressure gradients. Here we demonstrate a new effect in which the orientation of nematic liquid crystal molecules is altered by thermal expansion. Thermal expansion (or contraction) causes the nematic liquid crystal to flow; the flow imposes a realigning torque on the nematic liquid crystal molecules and the optic axis. The optical and mechanical responses activated by a simple temperature change can be used in sensing, photonics, microfluidic, optofluidic and lab-on-a-chip applications as they do not require externally imposed gradients of temperature, pressure, surface realignment, nor electromagnetic fields. The effect has important ramifications for the current search of the biaxial nematic phase as the optical features of thermally induced structural changes in the uniaxial nematic liquid crystal mimic the features expected of the biaxial nematic liquid crystal. PMID:23072803

  13. Modeling crystal and molecular deformation in regenerated cellulose fibers.

    PubMed

    Eichhorn, Stephen J; Young, Robert J; Davies, Geoffrey R

    2005-01-01

    Experimental deformation micromechanics of regenerated cellulose fibers using Raman spectroscopy have been widely reported. Here we report on computer modeling simulations of Raman band shifts in modes close to the experimentally observed 1095 cm(-1) band, which has previously been shown to shift toward a lower wavenumber upon application of external fiber deformation. A molecular mechanics approach is employed using a previously published model structure of cellulose II. Changing the equilibrium c-spacing of this structure and then performing a minimization routine mimics tensile deformation. Normal-mode analysis is then performed on the minimized structure to predict the Raman-intensive vibrations. By using a dot-product analysis on the predicted eigenvectors it is shown that some Raman active modes close to the 1095 cm(-1) band interchange at certain strain levels. Nevertheless, when this is taken into account it is shown that it is possible to find reasonable agreement between theory and experiment. The effect of the experimentally observed broadening of the Raman bands is discussed in terms of crystalline and amorphous regions of cellulose, and this is compared to the lack of X-ray broadening to explain why discrepancies between theory and experiment are present. A hybrid model structure with a series-parallel arrangement of amorphous and misaligned amorphous-crystalline domains is proposed which is shown to agree with what is observed experimentally. Finally, the theoretical crystal modulus for cellulose II is reported as 98 GPa, which is shown to be in agreement with other studies and with an experimental measurement using synchrotron X-ray diffraction.

  14. The director and molecular dynamics of the field-induced alignment of a Gay-Berne nematic phase: An isothermal-isobaric nonequilibrium molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Luckhurst, Geoffrey R.; Satoh, Katsuhiko

    2010-05-01

    Isothermal-isobaric molecular dynamics simulations have been performed for the generic Gay-Berne (GB) mesogen, GB(4.4, 20.0, 1, 1), to investigate director and molecular rotational motion during the field-induced alignment of a nematic. The alignment process for the director is discussed within the context of a hydrodynamic analysis based on the Ericksen-Leslie theory and this is found to predict the simulated behavior well. The dependence of the relaxation time for the alignment on the field strength is also in good accord with the theory. The rotational viscosity coefficient estimated from the simulation is smaller than that typically observed for real nematics and the possible reasons for this are discussed. However, the simulation results are found to follow not only the theory but also the experiments, at least qualitatively. No significant variation in the local and long-range structure of the nematic phase is found during the field-induced alignment process. In addition, we have explored the molecular dynamics in the nematic phase in the presence of the field using the first- and second-rank time autocorrelation functions. More importantly we are able to show that the director relaxation time is longer than that for molecular rotation. It is also possible to use the two orientational correlation times to explore the relationship between the rotational viscosity coefficient and the rotational diffusion constant. The diffusion constants determined from the orientational correlation times, based on the short-time expansion of the autocorrelation functions, are found to be significantly different. In consequence it is not possible to test, unambiguously, the relationship between the rotational viscosity coefficient and the rotational diffusion constant. However, it would seem that the second-rank rotational correlation time provides the most reliable route to the rotational viscosity coefficient.

  15. Molecular dynamics study of the crystallization of nitromethane from the melt

    NASA Astrophysics Data System (ADS)

    Siavosh-Haghighi, Ali; Sewell, Thomas D.; Thompson, Donald L.

    2010-11-01

    The crystallization of nitromethane, CH3NO2, from the melt on the (100), (010), (001), and (110) crystal surfaces at 170, 180, 190, 200, 210, and 220 K has been investigated using constant-volume and -temperature (NVT) molecular dynamics simulations with a realistic, fully flexible force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The crystallization process and the nature of the solid-liquid interface have been investigated by computing the molecular orientations, density, and radial distribution functions as functions of time and location in the simulation cell. During crystallization the translational motion of the molecules ceases first, after which molecular rotation ceases as the molecules assume proper orientations in the crystal lattice. The methyl groups are hindered rotors in the liquid; hindrance to rotation is reduced upon crystallization. The width of the solid-liquid interface varies between 6 and 13 Å (about two to five molecular layers) depending on which crystal surface is exposed to the melt and which order parameter is used to define the interface. The maximum rate of crystallization varies from 0.08 molecules ns-1 Å-2 for the (010) surface at 190 K to 0.41 molecules ns-1 Å-2 for the (001) surface at 220 K.

  16. Plasmonic Photopatterning of Complex Molecular Orientations in Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Guo, Yubing; Jiang, Miao; Peng, Chenhui; Sun, Kai; Yaroshchuk, Oleg; Lavrentovich, Oleg; Wei, Qi-Huo

    Aligning liquid crystal (LC) molecules in spatially non-uniform patterns are highly demanded for applications such as programmable origami and liquid crystal enabled nonlinear electrokinetics. We developed a high resolution projection photoalignment technique for patterning arbitrary LC alignment fields. The photoalignment is based on carefully engineered metasurfaces, or dubbed as plasmonic metamasks (PMMs). When illuminated by light, the PMMs generate patterns of both light intensity and polarization. By projecting the light transmitted through the PMMs onto liquid crystal cells coated with photosensitive materials, alignment patterns predesigned in polarization patterns of the PMMs can be imposed in liquid crystals. This technique makes the liquid crystal alignment a repeatable and scalable process similar to conventional photolithography, promising various applications. National Science Foundation CMMI-1436565.

  17. Molecular Basis of Urolithiasis: Role of Crystal Retention

    NASA Astrophysics Data System (ADS)

    Koul, Hari K.; Koul, Sweaty

    2008-09-01

    Urolithiasis is a multifactorial disorder, and it is unlikely that a single cause is responsible for entire spectrum of this disorder. Nonetheless, increased concentrations of various urinary constituents (e.g., calcium and/or oxalate) have been associated with a majority of stone formers. Irrespective of the underlying metabolic conditions, crystal precipitation and crystal retention along the urinary tract are two essential pre-requisites for urinary tract stone formation. In this chapter we summarize underlying metabolic abnormalities associated with various subsets of stone formers. We will also present evidence in support of our hypothesis that crystal formation is a normal physiological process of eliminating toxic wastes as solid complexes, and that pathological events begin with crystal retention. In the end we present evidence supporting various mechanisms of crystal retention.

  18. Polymer crystallization under nano-confinement of droplets studied by molecular simulations.

    PubMed

    Hu, Wenbing; Cai, Tao; Ma, Yu; Hobbs, Jamie K; Farrance, O; Reiter, Günter

    2009-01-01

    Fabrication of polymer nano-crystals proceeds usually through hierarchical ordering of the different-scale structures. Nano-scale patterns are produced first, which serve as a spatial template for subsequent polymer crystallization under nano-confinement. We begin with a survey of the effects of nano-confinement on polymer crystallization, mainly on the basis of the knowledge obtained from molecular simulations. After that, we report dynamic Monte Carlo simulations of polymer crystallization confined in nano-droplets. We observed that the shape of droplets on a solid substrate appears as a pancake, and both initiation and development of crystallization are depressed with the decrease of droplet size. Surface-induced crystal nucleation guides the dominant edge-on crystal orientation at high temperatures; however, its contribution to nucleation rates is not much greater than crystal nucleation in the volume of the droplet. At low temperatures, edge-on crystals are frequent at both substrate/polymer and polymer/air interfaces. In conclusion, molecular simulations can shed light on the microscopic mechanisms of polymer crystallization under nano-confinement.

  19. Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Perozzo, Mary A.; Konnert, John H.; Nadarajan, Arunan; Pusey, Marc L.

    1998-01-01

    Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

  20. Study of spectroscopic and thermal characteristics of nonlinear optical molecular crystals based on 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Pavlovetc, I. M.; Fokina, M. I.

    2016-08-01

    The paper presents the results of study of spectroscopic and thermal characteristics of molecular co-crystals: 2-aminopyridine-4-nitrophenol-4-mtrophenolate (2AP4N) and 2,6- diaminopyridine-4-nitrophenol-4nitrophenolate (26DAP4N). Crystals were successfully grown by slow evaporation technique. Optical transparency in the region of 190-1100 was found to be suitable for applications with cut off wavelengths 420 and 430 nm respectively. Thermogravimetric and differential thermal analysis show good quality and thermal stability for studied crystals. Kurtz and Perry powder technique proves that the crystals are acentric and have significant nonlinear optical response.

  1. Crystallization kinetics and molecular mobility of an amorphous active pharmaceutical ingredient: A case study with Biclotymol.

    PubMed

    Schammé, Benjamin; Couvrat, Nicolas; Malpeli, Pascal; Delbreilh, Laurent; Dupray, Valérie; Dargent, Éric; Coquerel, Gérard

    2015-07-25

    The present case study focuses on the crystallization kinetics and molecular mobility of an amorphous mouth and throat drug namely Biclotymol, through differential scanning calorimetry (DSC), temperature resolved X-ray powder diffraction (TR-XRPD) and hot stage microscopy (HSM). Kinetics of crystallization above the glass transition through isothermal and non-isothermal cold crystallization were considered. Avrami model was used for isothermal crystallization process. Non-isothermal cold crystallization was investigated through Augis and Bennett model. Differences between crystallization processes have been ascribed to a site-saturated nucleation mechanism of the metastable form, confirmed by optical microscopy images. Regarding molecular mobility, a feature of molecular dynamics in glass-forming liquids as thermodynamic fragility index m was determined through calorimetric measurements. It turned out to be around m=100, describing Biclotymol as a fragile glass-former for Angell's classification. Relatively long-term stability of amorphous Biclotymol above Tg was analyzed indirectly by calorimetric monitoring to evaluate thermodynamic parameters and crystallization behavior of glassy Biclotymol. Within eight months of storage above Tg (T=Tg+2°C), amorphous Biclotymol does not show a strong inclination to crystallize and forms a relatively stable glass. This case study, involving a multidisciplinary approach, points out the importance of continuing looking for stability predictors.

  2. Exploring Molecular Dimension and Trajectory of Polymer Chains Embedded in Single Crystals

    NASA Astrophysics Data System (ADS)

    Hong, Youlee; Miyoshi, Toshikazu

    2015-03-01

    Semicrystalline polymers are crystallized as folded chains in thin lamellae of ca. 5-20 nm from random coils in the melt and solution states.. Even though there are continuous efforts on understanding of crystallization mechanisms at molecular levels for understanding of crystallization mechanism of polymers at molecular levels, the fundamental questions - when, where, and how do semicrystalline polymers fold during crystallization?- have not been clarified due to experimental limitations. Recently, we developed a novel strategy to access chain trajectory of semi-crystalline polymers using 13C -13C double Quantum (DQ) NMR. In this work, we recently investigated determined molecular dimension as well as chain-trajectory of 13C CH3-labeled isotactic poly(1-butene) (iPB1) in form III chiral single crystals blended with nonlabeled iPB1 crystallized under low supercooling, using solid-state NMR. Comparisons of 13C -13C double quantum (DQ) NMR results at multiple sites with spin dynamics simulation revealed individual chains form the three dimensional nanoclusters via folding. This result supports proves two step process of i) cluster formation by chain-folding the prestage of crystallization. and ii) depositions of the cluster on the growth front of single crystal. National Science Foundation.

  3. High-Resolution and High-Throughput Plasmonic Photopatterning of Complex Molecular Orientations in Liquid Crystals.

    PubMed

    Guo, Yubing; Jiang, Miao; Peng, Chenhui; Sun, Kai; Yaroshchuk, Oleg; Lavrentovich, Oleg; Wei, Qi-Huo

    2016-03-23

    A plasmonic photopatterning technique is proposed and demonstrated for aligning the molecular orientation in liquid crystals (LCs) in patterns with designer complexity. Using plasmonic metamasks in which target molecular directors are encoded, LC alignments of arbitrary planar patterns can be achieved in a repeatable and scalable fashion withunprecedentedly high spatial resolution and high throughput.

  4. Photoinduced shape changes of diarylethene single crystals: correlation between shape changes and molecular packing.

    PubMed

    Kuroki, Lumi; Takami, Shizuka; Yoza, Kenji; Morimoto, Masakazu; Irie, Masahiro

    2010-02-01

    Correlation between the photoinduced shape changes of diarylethene single crystals and their molecular packing in the crystals was studied. Crystals of 1,2-bis(5-ethyl-2-phenyl-4-thiazolyl)perfluorocyclopentene (3a) and 1,2-bis(2-isopropyl-5-phenyl-3-thienyl)perfluorocyclopentene (4a) showed similar photoinduced deformation from square to lozenge as that of 1,2-bis- (2-ethyl-5-phenyl-3-thienyl)perfluorocyclopentene (1a). Although these three diarylethenes have different electronic structures and exhibit different colours upon UV irradiation, the crystallographic structures and molecular packing of the crystals are very similar to each other. The result indicates that the deformation mode is determined by the packing mode of component molecules in the crystal. X-Ray crystallographic analysis of a micrometre-sized crystal 1a (20 x 15 x 8 microm) prepared by sublimation revealed that the small-size crystal, which shows photoinduced deformation, has the same crystal structure as that of the large bulk crystal. PMID:20126798

  5. Molecular dynamics in azobenzene liquid crystal polymer films measured by time-resolved techniques.

    PubMed

    Fujii, T; Kuwahara, S; Katayama, K; Takado, K; Ube, T; Ikeda, T

    2014-06-14

    Photo-induced molecular motion in a liquid crystal polymer film including azobenzene was studied by the heterodyne transient grating method. The film was confined in a liquid crystal cell, where it is a photomobile film under free-standing conditions. By observation of the refractive index change induced by a laser pulse, contraction of the film was observed on the order of several hundreds of nanoseconds, and the subsequent reorientation and molecular rotation dynamics were observed from a few microseconds to a hundred milliseconds. Finally, the cis isomer of azobenzene was thermally returned back to the trans isomer in about ten seconds because the film could not be bent in the liquid crystal cell. Since the contraction, reorientation and molecular rotation took place before the cis to trans back-transformation, these processes correspond to the preliminary molecular motion preceding the macroscopic bending of the film. PMID:24736859

  6. Low-temperature specific heat of molecular glasses and crystals

    NASA Astrophysics Data System (ADS)

    Talón, César; Ramos, Miguel A.; Vieira, Sebastián

    2000-07-01

    We have measured the low-temperature specific heat Cp of several glass-forming alcohols. Special attention has been paid to ethanol, either hydrogenated or deuterated, in its different solid phases (fully ordered crystal, disordered crystal or orientational glass, and true structural glass). New measurements have been carried out on 1- and 2-propanol (for crystal and glass states) and on the glass phase of glycerol. The comparison of the isotopic effects in ethanol, as well as that with two isomers of propanol, provide a unique benchmark to study the relative importance of different kinds of disorder. In this work, the whole set of maxima in Cp/ T3 is discussed in the framework of the scaling procedure of Liu and Löhneysen [Europhys. Lett. 33 (1996) 617].

  7. Tunable molecular distortion in crystals with a supramolecular aggregate

    SciTech Connect

    Falvello, L.R.; Pascual, I.; Palacio, F.

    1996-12-31

    Crystals of trans-[Ni(cyan-N){sub 2}(NH{sub 3}){sub 4}], which possess a stable supramolecular ribbon by cyanurate ligands, undergo a reversible, non-destructive, temperature-induced phase transition. At room temperature, the crystals are orthorhombic, space group Fmmm, with the molecule on a site of D{sub 2h} (mmm) symmetry. At 20 K, the crystals possess the same orthorhombic unit cell, but have space group Cmcm; the molecule has symmetry C{sub 2v} (m2m), and is distorted by bending of the cyanurate rings out of their common plane. At intermediate temperatures, an intermediate distorted structure emerges. Structural characterizations by x-ray or neutron diffraction at five temperatures from 20 to 298 K are presented. Changes in the electronic spectrum of the compound accompany the temperature-dependent distortion of the molecule. Magnetic measurements indicate that the compound orders as an antiferromagnet at about 3 K.

  8. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  9. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  10. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  11. Long-range orientational order, local-field anisotropy, and mean molecular polarizability in liquid crystals

    SciTech Connect

    Aver'yanov, E. M.

    2009-01-15

    The problems on the relation of the mean effective molecular polarizability {gamma}-bar to the long-range orientational order of molecules (the optical anisotropy of the medium) in uniaxial and biaxial liquid crystals, the local anisotropy on mesoscopic scales, and the anisotropy of the Lorentz tensor L and the local-field tensor f are formulated and solved. It is demonstrated that the presence of the long-range orientational order of molecules in liquid crystals imposes limitations from below on the molecular polarizability {gamma}-bar, which differs for uniaxial and biaxial liquid crystals. The relation between the local anisotropy and the molecular polarizability {gamma}-bar is investigated for calamitic and discotic uniaxial liquid crystals consisting of lath- and disk-shaped molecules. These liquid crystals with identical macroscopic symmetry differ in the local anisotropy and the relationships between the components L{sub parallel} < L{sub perpendicular} , f{sub parallel} < f{sub perpendicular} (calamitic) and L{sub parallel} > L{sub perpendicular} , f{sub parallel} > f{sub perpendicular} (discotic) for an electric field oriented parallel and perpendicular to the director. The limitations from below and above on the molecular polarizability {gamma}-bar due to the anisotropy of the tensors L and f are established for liquid crystals of both types. These limitations indicate that the molecular polarizability {gamma}-bar depends on the phase state and the temperature. The factors responsible for the nonphysical consequences of the local-field models based on the approximation {gamma}-bar = const are revealed. The theoretical inferences are confirmed by the experimental data for a number of calamitic nematic liquid crystals with different values of birefringence and the discotic liquid crystal Col{sub ho}.

  12. Molecular motion, dielectric response, and phase transition of charge-transfer crystals: acquired dynamic and dielectric properties of polar molecules in crystals.

    PubMed

    Harada, Jun; Ohtani, Masaki; Takahashi, Yukihiro; Inabe, Tamotsu

    2015-04-01

    Molecules in crystals often suffer from severe limitations on their dynamic processes, especially on those involving large structural changes. Crystalline compounds, therefore, usually fail to realize their potential as dielectric materials even when they have large dipole moments. To enable polar molecules to undergo dynamic processes and to provide their crystals with dielectric properties, weakly bound charge-transfer (CT) complex crystals have been exploited as a molecular architecture where the constituent polar molecules have some freedom of dynamic processes, which contribute to the dielectric properties of the crystals. Several CT crystals of polar tetrabromophthalic anhydride (TBPA) molecules were prepared using TBPA as an electron acceptor and aromatic hydrocarbons, such as coronene and perylene, as electron donors. The crystal structures and dielectric properties of the CT crystals as well as the single-component crystal of TBPA were investigated at various temperatures. Molecular reorientation of TBPA molecules did not occur in the single-component crystal, and the crystal did not show a dielectric response due to orientational polarization. We have found that the CT crystal formation provides a simple and versatile method to develop molecular dielectrics, revealing that the molecular dynamics of the TBPA molecules and the dielectric property of their crystals were greatly changed in CT crystals. The TBPA molecules underwent rapid in-plane reorientations in their CT crystals, which exhibited marked dielectric responses arising from the molecular motion. An order-disorder phase transition was observed for one of the CT crystals, which resulted in an abrupt change in the dielectric constant at the transition temperature.

  13. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    PubMed

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems. PMID:27078486

  14. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    PubMed

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  15. Equilibrium sampling by reweighting nonequilibrium simulation trajectories

    NASA Astrophysics Data System (ADS)

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  16. A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon tetrachloride mixtures III: nonequilibrium hydrogen-bond dynamics and infrared pump-probe spectra.

    PubMed

    Kwac, Kijeong; Geva, Eitan

    2013-06-27

    We present a mixed quantum-classical molecular dynamics study of the nonequilibrium hydrogen-bond dynamics following vibrational energy relaxation of the hydroxyl stretch in a 10 mol % methanol/carbon tetrachloride mixture and pure methanol. The ground and first-excited energy levels and wave functions are identified with the eigenvalues and eigenfunctions of the hydroxyl's adiabatic Hamiltonian and as such depend parametrically on the configuration of the remaining, classically treated, degrees of freedom. The dynamics of the classical degrees of freedom are in turn governed by forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields and nonlinear mapping relations between the hydroxyl transition frequencies and dipole moments and the electric field along the hydroxyl bond are used, which were previously shown to quantitatively reproduce the experimental infrared steady-state absorption spectra and excited state lifetime [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184; 2012, 116, 2856]. The relaxation from the first-excited state to the ground state is treated as a nonadiabatic transition. Within the mixed quantum-classical treatment, relaxation from the excited state to the ground state is accompanied by a momentum-jump in the classical degrees of freedom, which is in turn dictated by the nonadiabatic coupling vector. We find that the momentum jump leads to breaking of hydrogen bonds involving the relaxing hydroxyl, thereby blue-shifting the transition frequency by more than the Stokes shift between the steady-state emission and absorption spectra. The subsequent nonequilibrium relaxation toward equilibrium on the ground state potential energy surface is thereby accompanied by red shifting of the transition frequency. The signature of this nonequilibrium relaxation process on the pump-probe spectrum is analyzed in detail. The calculated pump-probe spectrum is found

  17. Molecular Surface Chemistry by Metal Single Crystals and Nanoparticles from Vacuum to High Pressure.

    SciTech Connect

    Somorjai, Gabor A.; Park, Jeong Y.

    2008-04-05

    Model systems for studying molecular surface chemistry have evolved from single crystal surfaces at low pressure to colloidal nanoparticles at high pressure. Low pressure surface structure studies of platinum single crystals using molecular beam surface scattering and low energy electron diffraction techniques probe the unique activity of defects, steps and kinks at the surface for dissociation reactions (H-H, C-H, C-C, O{double_bond}O bonds). High-pressure investigations of platinum single crystals using sum frequency generation vibrational spectroscopy have revealed the presence and the nature of reaction intermediates. High pressure scanning tunneling microscopy of platinum single crystal surfaces showed adsorbate mobility during a catalytic reaction. Nanoparticle systems are used to determine the role of metal-oxide interfaces, site blocking and the role of surface structures in reactive surface chemistry. The size, shape and composition of nanoparticles play important roles in determining reaction activity and selectivity.

  18. Infrared spectroscopic study of molecular hydrogen bonding in chiral smectic liquid crystals

    PubMed

    Jang; Park; Kim; Glaser; Clark

    2000-10-01

    We report the use of Fourier-transform infrared (IR) spectroscopy to probe intermolecular and intramolecular hydrogen bonding in thermotropic liquid-crystal phases. Infrared spectra of aligned smectic liquid crystal materials vs temperature, and of isotropic liquid-crystal mixtures vs concentration were measured in homologs both with and without hydrogen bonding. Hydrogen bonding significantly changes the direction and magnitude of the vibrational dipole transition moments, causing marked changes in the IR dichroic absorbance profiles of hydrogen-bonded molecular subfragments. A GAUSSIAN94 computation of the directions, magnitudes, and frequencies of the vibrational dipole moments of molecular subfragments shows good agreement with the experimental data. The results show that IR dichroism can be an effective probe of hydrogen bonding in liquid-crystal phases.

  19. Sublimation rate of molecular crystals - role of internal degrees of freedom

    SciTech Connect

    Maiti, A; Zepeda-Ruiz, L A; Gee, R H; Burnham, A

    2007-01-19

    It is a common practice to estimate site desorption rate from crystal surfaces with an Arrhenius expression of the form v{sub eff} exp(-{Delta}E/k{sub B}T), where {Delta}E is an activation barrier to desorb and v{sub eff} is an effective vibrational frequency {approx} 10{sup 12} sec{sup -1}. However, such a formula can lead to several to many orders of magnitude underestimation of sublimation rates in molecular crystals due to internal degrees of freedom. We carry out a quantitative comparison of two energetic molecular crystals with crystals of smaller entities like ice and Argon (solid) and uncover the errors involved as a function of molecule size. In the process, we also develop a formal definition of v{sub eff} and an accurate working expression for equilibrium vapor pressure.

  20. Crystal Properties and Radiation Effects in Solid Molecular Hydrogens

    SciTech Connect

    Kozioiziemski, B

    2000-09-01

    The crystal lattice structure, growth shapes and helium generated by beta-decay of solid deuterium-tritium (D-T) mixtures have been studied. Understanding of these D-T properties is important for predicting and optimizing the target design of the National Ignition Facility (NIF). Raman spectroscopy showed the D-T crystal structure is hexagonal close packed, common to the non-tritiated isotopes. The isotopic mixtures of both tritiated and non-tritiated species broadens the rotational transitions, especially of the lighter species in the mixture. The vibrational frequencies of each isotope is shifted to higher energy in the mixture than the pure components. The J = 1-0 population decreases exponentially with a 1/e time constant which rapidly increases above 10.5 K for both D{sub 2} and T{sub 2} in D-T. The conversion rate is nearly constant from 5 K to 10 K for both D{sub 2} and T{sub 2} at 7.1 hours and 2.1 hours, respectively. The smoothing of D-T layers by beta decay heating is limited by the crystal surface energy. Deuterium and hydrogen-deuteride crystals were grown at a number of temperatures below the triple point to determine the surface energy and roughening transition. Several distinct crystal shapes were observed on a number of different substrates. The a facet roughens between 0.9 T{sub TP} and T{sub TP}, while the c facet persists up to the melting temperature. This is very different from the behavior of the other rare gas crystals which grow completely rounded above 0.8 T{sub TP}. Helium bubbles formed as a product of the beta decay were observed using optical microscopy and the diffusion of smaller bubbles measured with dynamic light scattering. Bubble diffusion coefficients as high as 2.0 x 10{sup -16} m{sup 2}/s were measured for 10-50 nm bubbles. The bubbles move in response to a thermal gradient, with speeds between 1 {micro}m/hour and 100 {micro}m/hour for thermal gradients and temperatures appropriate to NIF targets.

  1. Terahertz and Raman spectra of non-centrosymmetrical organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Trzebiatowska-Gusowska, Monika; Plinski, Edward F.; Baran, Jan; Walczakowski, Michal J.; Jarzab, Przemyslaw P.; Nowak, Kacper; Fuglewicz, Boguslaw; Mikulics, Martin; Palka, Norbert; Szustakowski, Mieczyslaw

    2014-11-01

    The terahertz waves have been applied to the spectroscopy of molecular crystals. The group based on hybrid organic-inorganic crystals like triglycine zinc chloride, triglycine sulphate, triglycine selenate, diglycine hydrobromide, diglycine hydrochloride, diglycine lithium nitrate, glycine lithium nitrate has been considered. The dispersion relation phonon-polariton have been shown between 10 cm-1 and 80 cm-1 for diglycine lithium nitrate, triglycine zinc chloride, and diglycine hydrobromide.

  2. QENS study of molecular motions in partially deuterated liquid crystal 4BT

    NASA Astrophysics Data System (ADS)

    Juszyńska-Gałązka, E.; Zając, W.

    2016-04-01

    Molecular rotational dynamic in the crystalline and smectic E phases of selectively deuterated (in the outer phenyl ring) 4-n-butyl-isothiocyanatobiphenyl was investigated by means of quasielastic neutron scattering. The 120° reorientation of the methyl group in the crystal phase could be identified at 125 K. Additionally, ring flips were seen at 200 K. The structure of crystal and smectic E phases was obtained by X-ray measurements and the data give the identification of type of solid phases.

  3. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    SciTech Connect

    Melnikov, V. V.

    2015-06-15

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H{sub 2} in Si, and the obtained dispersion law is analyzed.

  4. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  5. Computational Protocol for Modeling Thermochromic Molecular Crystals: Salicylidene Aniline As a Case Study.

    PubMed

    Presti, Davide; Labat, Fréderic; Pedone, Alfonso; Frisch, Michael J; Hratchian, Hrant P; Ciofini, Ilaria; Menziani, Maria Cristina; Adamo, Carlo

    2014-12-01

    A computational protocol that combines periodic and QM/QM' calculations has been applied to investigate the structural (geometrical and electronic) and photophysical absorption properties of the salicylidene aniline (SA) thermochromic molecular crystal. The protocol consists of three different steps, namely (i) the description of the molecular crystal using a periodic approach taking into account dispersion interactions, (ii) the identification of reliable finite models (clusters), and (iii) the calculation of vertical transition energies including environmental effects through the use of an electronic embedding model (QM/QM' ONIOM approach). The encouraging results obtained in this work for the β polymorph of SA, both in terms of accuracy and computational cost, open the way to the simulation and the prediction of the photophysical behavior of other molecular crystals, especially those much less well characterized experimentally. PMID:26583240

  6. Molecular mechanism of crystallization impacting calcium phosphate cements

    SciTech Connect

    Giocondi, J L; El-Dasher, B S; Nancollas, G H; Orme, C A

    2009-05-31

    In summary, SPM data has shown that (1) Mg inhibits growth on all steps but relatively high Mg/Ca ratios are needed. Extracting the mechanism of interaction requires more modeling of the kinetic data, but step morphology is consistent with incorporation. (2) Citrate has several effects depending on the citrate/Ca ratio. At the lowest concentrations, citrate increases the step free energy without altering the step kinetics; at higher concentrations, the polar step is slowed. (3) Oxalate also slows the polar step but additionally stabilizes a new facet, with a [100]{sub Cc} step. (4) Etidronate has the greatest kinetic impact of the molecules studied. At 7{micro}M concentrations, the polar step slows by 60% and a new polar step appears. However, at the same time the [10-1]{sub Cc} increases by 67%. It should be noted that all of these molecules complex calcium and can effect kinetics by altering the solution supersaturation or the Ca to HPO{sub 4}{sup 2-} ratio. For the SPM data shown, this effect was corrected for to distinguish the effect of the molecule at the crystal surface from the effect of the molecule on the solution speciation. The goal of this paper is to draw connections between fundamental studies of atomic step motion and potential strategies for materials processing. It is not our intent to promote the utility of SPM for investigating processes in cement dynamics. The conditions are spectacularly different in many ways. The data shown in this paper are fairly close to equilibrium (S=1.6) whereas the nucleation of cements is initiated at supersaturation ratios in the thousands to millions. Of course, after the initial nucleation phase, the growth will occur at more modest supersaturations and as the cement evolves towards equilibrium certainly some of the growth will occur in regimes such as shown here. In addition to the difference in supersaturation, cements tend to have lower additive to calcium ratios. As an example, the additive to Ca ratio is

  7. Molecular structures and crystal packings of 2-styrylquinoline and its derivatives

    SciTech Connect

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2011-07-15

    The crystal and molecular structures of five styrylheterocycles of the quinoline series are studied. All molecules are planar. The double bond in the ethylene fragment is essentially localized. In the molecule of 2-(4-methylstyryl)quinoline, the ethylene fragment is disordered by the bicycle-pedal pattern. In four of the five compounds, the crystal packings do not contain stacking dimers prearranged for the [2+2] photocycloaddition (PCA) reaction. In the crystal of 2-(3-nitrostyryl)quinoline, pairs of crystallographically independent molecules form stacking dimers. In a dimer, the ethylene fragments have a twist orientation, which is incompatible with the PCA reaction. An attempt to initiate a temperature-dependent process of bicyclepedal isomerization in the crystal and, as a consequence, the PCA reaction by means of simultaneous irradiation and heating of a single crystal is unsuccessful.

  8. Induced crystallization of single-chain polyethylene on a graphite surface: molecular dynamics simulation.

    PubMed

    Yang, Hua; Zhao, Xiao Jun; Sun, Miao

    2011-07-01

    Molecular dynamics (MD) simulations have been carried out on the crystallization of single-chain polyethylene (PE) which was adsorbed on a graphite (001) surface on one side and exposed to vacuum on the other at different temperatures. The MD simulation data have been analyzed to provide information about the crystallization process of polymer adsorbed on the solid substrate. The isothermal crystallization of PE proceeds in two steps: (1) adsorption and (2) orientation. The results detail the radial density distribution function, ordered parameters, local bond-orientational order parameters, and the local properties displayed in layers of the polymer parallel to the graphite and vacuum interfaces. It was also shown that the film thickness affected the critical crystallization temperature of the adsorbed polymer on the substrate surface. Furthermore, the influence of the graphite surface area on the crystallization of PE is discussed by comparing the crystallinity evolution of PE on graphite with different coverage.

  9. The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis.

    PubMed

    Devedjiev, Yancho D

    2015-02-01

    Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.

  10. Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

    NASA Astrophysics Data System (ADS)

    Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

    2004-10-01

    Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

  11. A molecular dynamics simulation of solvent effects on the crystal morphology of HMX.

    PubMed

    Duan, Xiaohui; Wei, Chunxue; Liu, Yonggang; Pei, Chonghua

    2010-02-15

    The solvent has a large effect on the crystal morphology of the organic explosive compound octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, C(4)H(8)N(8)O(8)). The attachment energy calculations predict a growth morphology in vacuum dominated by (020), (011), (102 ), (111 ) and (100) crystal forms. Molecular dynamics simulations are performed for these crystal faces of HMX in contact with acetone solvent. A corrected attachment energy model, accounting for the surface chemistry and the associated topography (step structure) of the habit crystal plane, is applied to predict the morphological importance of a crystal surface in solvent. From the solvent-effected attachment energy calculations it follows that the (100) face becomes morphologically more important compared with that in vacuum, while the (020) and (102 ) are not visible at all. This agrees well with the observed experimental HMX morphology grown from the acetone solution.

  12. A mixed quantum-classical molecular dynamics study of anti-tetrol and syn-tetrol dissolved in liquid chloroform II: infrared emission spectra, vibrational excited-state lifetimes, and nonequilibrium hydrogen-bond dynamics.

    PubMed

    Kwac, Kijeong; Geva, Eitan

    2013-11-21

    The effect of vibrational excitation and relaxation of the hydroxyl stretch on the hydrogen-bond structure and dynamics of stereoselectively synthesized syn-tetrol and anti-tetrol dissolved in deuterated chloroform are investigated via a mixed quantum-classical molecular dynamics simulation. Emphasis is placed on the changes in hydrogen-bond structure upon photoexcitation and the nonequilibrium hydrogen-bond dynamics that follows the subsequent relaxation from the excited to the ground vibrational state. The propensity to form hydrogen bonds is shown to increase upon photoexcitation of the hydroxyl stretch, thereby leading to a sizable red-shift of the infrared emission spectra relative to the corresponding absorption spectra. The vibrational excited state lifetimes are calculated within the framework of Fermi's golden rule and the harmonic-Schofield quantum correction factor, and found to be sensitive reporters of the underlying hydrogen-bond structure. The energy released during the relaxation from the excited to the ground state is shown to break hydrogen bonds involving the relaxing hydroxyl. The spectral signature of this nonequilibrium relaxation process is analyzed in detail.

  13. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373

  14. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    PubMed

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide. PMID:27365051

  15. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    PubMed

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

  16. Crystal and molecular structure of perindopril erbumine salt

    NASA Astrophysics Data System (ADS)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  17. Molecular modeling study of chiral drug crystals: lattice energy calculations.

    PubMed

    Li, Z J; Ojala, W H; Grant, D J

    2001-10-01

    The lattice energies of a number of chiral drugs with known crystal structures were calculated using Dreiding II force field. The lattice energies, including van der Waals, Coulombic, and hydrogen-bonding energies, of homochiral and racemic crystals of some ephedrine derivatives and of several other chiral drugs, are compared. The calculated energies are correlated with experimental data to probe the underlying intermolecular forces responsible for the formation of racemic species, racemic conglomerates, or racemic compounds, termed chiral discrimination. Comparison of the calculated energies among ephedrine derivatives reveals that a greater Coulombic energy corresponds to a higher melting temperature, while a greater van der Waals energy corresponds to a larger enthalpy of fusion. For seven pairs of homochiral and racemic compounds, correlation of the differences between the two forms in the calculated energies and experimental enthalpy of fusion suggests that the van der Waals interactions play a key role in the chiral discrimination in the crystalline state. For salts of the chiral drugs, the counter ions diminish chiral discrimination by increasing the Coulombic interactions. This result may explain why salt forms favor the formation of racemic conglomerates, thereby facilitating the resolution of racemates.

  18. A molecular dynamics study of the effect of thermal boundary conductance on thermal transport of ideal crystal of n-alkanes with different number of carbon atoms

    NASA Astrophysics Data System (ADS)

    Rastgarkafshgarkolaei, Rouzbeh; Zeng, Yi; Khodadadi, J. M.

    2016-05-01

    Phase change materials such as n-alkanes that exhibit desirable characteristics such as high latent heat, chemical stability, and negligible supercooling are widely used in thermal energy storage applications. However, n-alkanes have the drawback of low thermal conductivity values. The low thermal conductivity of n-alkanes is linked to formation of randomly oriented nano-domains of molecules in their solid structure that is responsible for excessive phonon scattering at the grain boundaries. Thus, understanding the thermal boundary conductance at the grain boundaries can be crucial for improving the effectiveness of thermal storage systems. The concept of the ideal crystal is proposed in this paper, which describes a simplified model such that all the nano-domains of long-chain n-alkanes are artificially aligned perfectly in one direction. In order to study thermal transport of the ideal crystal of long-chain n-alkanes, four (4) systems (C20H42, C24H50, C26H54, and C30H62) are investigated by the molecular dynamics simulations. Thermal boundary conductance between the layers of ideal crystals is determined using both non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. Both NEMD and EMD simulations exhibit no significant change in thermal conductance with the molecular length. However, the values obtained from the EMD simulations are less than the values from NEMD simulations with the ratio being nearly three (3) in most cases. This difference is due to the nature of EMD simulations where all the phonons are assumed to be in equilibrium at the interface. Thermal conductivity of the n-alkanes in three structures including liquid, solid, and ideal crystal is investigated utilizing NEMD simulations. Our results exhibit a very slight rise in thermal conductivity values as the number of carbon atoms of the chain increases. The key understanding is that thermal transport can be significantly altered by how the molecules and the

  19. Nonequilibrium heat capacity.

    PubMed

    Mandal, Dibyendu

    2013-12-01

    Development of steady state thermodynamics and statistical mechanics depends crucially on our ability to extend the notions of equilibrium thermodynamics to nonequilibrium steady states (NESS). The present paper considers the extension of heat capacity. A modified definition is proposed which continues to maintain the same relation to steady state Shannon entropy as in equilibrium, thus providing a thermodynamically consistent treatment of NESS heat capacity.

  20. Spin-Crossover Molecular Solids Beyond Rigid Crystal Approximation

    NASA Astrophysics Data System (ADS)

    Gudyma, Iurii V.; Ivashko, Victor V.

    2016-04-01

    The qualitative analysis of the spin-crossover molecular solid with distortion effect is presented. A spin-crossover solid with effect of distortion is studied in the framework of the Ising-like model with two-order parameters under statistical approach, where the effect of elastic strain on inter-ion interaction is considered. These considerations lead to examination of the relation between the primary and secondary order parameters during temperature and pressure changes.

  1. Spin-Crossover Molecular Solids Beyond Rigid Crystal Approximation.

    PubMed

    Gudyma, Iurii V; Ivashko, Victor V

    2016-12-01

    The qualitative analysis of the spin-crossover molecular solid with distortion effect is presented. A spin-crossover solid with effect of distortion is studied in the framework of the Ising-like model with two-order parameters under statistical approach, where the effect of elastic strain on inter-ion interaction is considered. These considerations lead to examination of the relation between the primary and secondary order parameters during temperature and pressure changes. PMID:27075338

  2. Molecular field theory for biaxial smectic A liquid crystals.

    PubMed

    To, T B T; Sluckin, T J; Luckhurst, G R

    2013-10-01

    Thermotropic biaxial nematic phases seem to be rare, but biaxial smectic A phases less so. Here we use molecular field theory to study a simple two-parameter model, with one parameter promoting a biaxial phase and the second promoting smecticity. The theory combines the biaxial Maier-Saupe and McMillan models. We use alternatively the Sonnet-Virga-Durand (SVD) and geometric mean approximations (GMA) to characterize molecular biaxiality by a single parameter. For non-zero smecticity and biaxiality, the model always predicts a ground state biaxial smectic A phase. For a low degree of smectic order, the phase diagram is very rich, predicting uniaxial and biaxial nematic and smectic phases, with the addition of a variety of tricritical and tetracritical points. For higher degrees of smecticity, the region of stability of the biaxial nematic phase is restricted and eventually disappears, yielding to the biaxial smectic phase. Phase diagrams from the two alternative approximations for molecular biaxiality are similar, except inasmuch that SVD allows for a first-order isotropic-biaxial nematic transition, whereas GMA predicts a Landau point separating isotropic and biaxial nematic phases. We speculate that the rarity of thermotropic biaxial nematic phases is partly a consequence of the presence of stabler analogous smectic phases.

  3. Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates.

    PubMed

    Liu, Chao-Fei; Fan, Heng; Gou, Shih-Chuan; Liu, Wu-Ming

    2014-02-27

    Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction.

  4. Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates

    PubMed Central

    Liu, Chao-Fei; Fan, Heng; Gou, Shih-Chuan; Liu, Wu-Ming

    2014-01-01

    Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction. PMID:24573303

  5. High-molecular-weight polymers for protein crystallization: poly-gamma-glutamic acid-based precipitants.

    PubMed

    Hu, Ting Chou; Korczyńska, Justyna; Smith, David K; Brzozowski, Andrzej Marek

    2008-09-01

    Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-gamma-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of approximately 400 kDa and PGA-HM (high molecular weight) of >1,000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here.

  6. Raman and infrared spectra of minerals from ab initio molecular dynamics simulations: The spodumene crystal

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo

    2011-05-01

    Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

  7. The calculation of electrostatic interactions and their role in determining the energies and geometries of explosive molecular crystals

    SciTech Connect

    Ritchie, J.P.; Kober, E.M.; Copenhaver, A.S.

    1993-01-01

    Three different procedures were used to calculate electrostatic interactions in explosive molecular crystals. The use of Potential Derived Charges (PDC's) and atom-centered multipole expansions (ACME's) provides reasonable fits of the molecular electrostatic potential. The ability of these approaches to reproduce observed crystal structures was also evaluated.

  8. Molecular-scale soft imprint lithography for alignment layers in liquid crystal devices.

    PubMed

    Lin, Rongsheng; Rogers, John A

    2007-06-01

    We describe molecular-scale soft nanoimprint lithographic replication of rubbed polyimide substrates to form alignment layers for liquid crystal devices. Systematic studies of the surface relief morphology of the polyimide and molded structures in three different polymers illustrate good lithographic fidelity down to relief heights of several nanometers, and with some capabilities at the level of approximately 1 nm. Collective results of experiments with several polymer formulations for molds and molded materials and process conditions indicate that this molecular-scale fidelity in replication can be used to produce surfaces that will effectively align liquid crystal molecules. Good electro-optical responses from liquid crystal light modulators that are formed in this manner suggest utility for fundamental studies and potential practical application.

  9. Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

    NASA Astrophysics Data System (ADS)

    Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

    2016-08-01

    Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ˜100 meV even in the "half-vertical cavity surface emitting lasing" microcavity structure.

  10. Nonequilibrium structure in sequential assembly

    NASA Astrophysics Data System (ADS)

    Popov, Alexander V.; Craven, Galen T.; Hernandez, Rigoberto

    2015-11-01

    The assembly of monomeric constituents into molecular superstructures through sequential-arrival processes has been simulated and theoretically characterized. When the energetic interactions allow for complete overlap of the particles, the model is equivalent to that of the sequential absorption of soft particles on a surface. In the present work, we consider more general cases by including arbitrary aggregating geometries and varying prescriptions of the connectivity network. The resulting theory accounts for the evolution and final-state configurations through a system of equations governing structural generation. We find that particle geometries differ significantly from those in equilibrium. In particular, variations of structural rigidity and morphology tune particle energetics and result in significant variation in the nonequilibrium distributions of the assembly in comparison to the corresponding equilibrium case.

  11. Molecular mechanisms of crystallization impacting calcium phosphate cements

    PubMed Central

    Giocondi, Jennifer L.; El-Dasher, Bassem S.; Nancollas, George H.; Orme, Christine A.

    2010-01-01

    The biomineral calcium hydrogen phosphate dihydrate (CaHPO4·2H2O), known as brushite, is a malleable material that both grows and dissolves faster than most other calcium minerals, including other calcium phosphate phases, calcium carbonates and calcium oxalates. Within the body, this ready formation and dissolution can play a role in certain diseases, such as kidney stone and plaque formation. However, these same properties, along with brushite’s excellent biocompatibility, can be used to great benefit in making resorbable biomedical cements. To optimize cements, additives are commonly used to control crystallization kinetics and phase transformation. This paper describes the use of in situ scanning probe microscopy to investigate the role of several solution parameters and additives in brushite atomic step motion. Surprisingly, this work demonstrates that the activation barrier for phosphate (rather than calcium) incorporation limits growth kinetics and that additives such as magnesium, citrate and bisphosphonates each influence step motion in distinctly different ways. Our findings provide details of how, and where, molecules inhibit or accelerate kinetics. These insights have the potential to aid in designing molecules to target specific steps and to guide synergistic combinations of additives. PMID:20308110

  12. Putting pressure on aromaticity along with in situ experimental electron density of a molecular crystal

    NASA Astrophysics Data System (ADS)

    Casati, Nicola; Kleppe, Annette; Jephcoat, Andrew P.; Macchi, Piero

    2016-03-01

    When pressure is applied, the molecules inside a crystal undergo significant changes of their stereoelectronic properties. The most interesting are those enhancing the reactivity of systems that would be otherwise rather inert at ambient conditions. Before a reaction can occur, however, a molecule must be activated, which means destabilized. In aromatic compounds, molecular stability originates from the resonance between two electronic configurations. Here we show how the resonance energy can be decreased in molecular crystals on application of pressure. The focus is on syn-1,6:8,13-Biscarbonyl[14]annulene, an aromatic compound at ambient conditions that gradually localizes one of the resonant configurations on compression. This phenomenon is evident from the molecular geometries measured at several pressures and from the experimentally determined electron density distribution at 7.7 GPa the observations presented in this work are validated by periodic DFT calculations.

  13. Molecular and crystal structure of a self-assembling pyridinium cationic lipid

    NASA Astrophysics Data System (ADS)

    Balaban, Alexandru T.; Ilies, Marc A.; Eichhöfer, Andreas; Balaban, Teodor Silviu

    2010-12-01

    Molecular insights into cationic lipid assemblies are relatively hard to reveal due to intrinsic mobility of the structural elements, hydration of the polar head and counterion, etc. Using X-ray diffraction of 4,6-dimethyl-2-tetradecyl-1-(2-tetradecanoyloxyethyl)pyridinium hexafluorophosphate ( 1) single crystals we succeeded in visualizing the molecular assembly of this amphiphile, in particular its U-shape structure and the impact of various structural parameters, including the counterion. The two alkyl chains lie parallel in orthogonal planes, and that the pyridinium cationic rings appear closely to the hexafluorophosphate anions. The whole assembly has therefore nonpolar zones alternating with polar cationic-anionic channel-zones. The relevance of this molecular and crystal structure to the gene transfection ability of this cationic lipid is also discussed.

  14. Putting pressure on aromaticity along with in situ experimental electron density of a molecular crystal

    PubMed Central

    Casati, Nicola; Kleppe, Annette; Jephcoat, Andrew P.; Macchi, Piero

    2016-01-01

    When pressure is applied, the molecules inside a crystal undergo significant changes of their stereoelectronic properties. The most interesting are those enhancing the reactivity of systems that would be otherwise rather inert at ambient conditions. Before a reaction can occur, however, a molecule must be activated, which means destabilized. In aromatic compounds, molecular stability originates from the resonance between two electronic configurations. Here we show how the resonance energy can be decreased in molecular crystals on application of pressure. The focus is on syn-1,6:8,13-Biscarbonyl[14]annulene, an aromatic compound at ambient conditions that gradually localizes one of the resonant configurations on compression. This phenomenon is evident from the molecular geometries measured at several pressures and from the experimentally determined electron density distribution at 7.7 GPa; the observations presented in this work are validated by periodic DFT calculations. PMID:26979750

  15. Molecular salts and co-crystals of mirtazapine with promising physicochemical properties.

    PubMed

    Sarkar, Anindita; Rohani, Sohrab

    2015-06-10

    Pharmaceutically suitable non-sublimating salts and molecular salts of anti-depressant drug R/S-mirtazapine with one of several dicarboxilic acids were studied. The salts/salt molecules were characterized by powder X-ray diffraction, differential scanning calorimetry and thermogravimetric analysis and crystal structure of tartarate and oxalate molecular salt were determined by single crystal X-ray diffraction. The salts/salt molecules of mirtazapine do not show any sublimation at elevated temperature whereas sublimation of mirtazapine has been observed at ambient temperature. The aqueous solubility of the mirtazapine molecular salts was significantly improved with a maximum of citrate salt which was about 180 times more than the solubility of the parent mirtazapine at 35 °C.

  16. Effect of annealing on the nonequilibrium carrier lifetime in GaAs grown at low temperatures

    SciTech Connect

    Pastor, A. A.; Prokhorova, U. V.; Serdobintsev, P. Yu.; Chaldyshev, V. V. Yagovkina, M. A.

    2013-08-15

    GaAs samples grown by molecular-beam epitaxy at low (230 Degree-Sign C) temperatures are investigated. One of the samples is subjected to aftergrowth annealing at 600 Degree-Sign C. Using an unconventional pump-probe scheme for measuring the dynamic variation in the light refractive index, the nonequilibrium charge-carrier lifetime (275 {+-} 30 fs before annealing) is determined. Such a short carrier lifetime in the unannealed material is due to the high concentration of point defects, mainly As{sub Ga} antisite defects. According to X-ray diffraction and steady-state optical absorption data, the As{sub Ga} concentration in the samples is 3 Multiplication-Sign 10{sup 19} cm{sup -3}, which corresponds to an arsenic excess of 0.26 at %. Upon annealing at 600 Degree-Sign C, the superstoichiometric As defects self-organize and form As nanoinclusions in the GaAs crystal matrix. It is shown that in this case the nonequilibrium charge-carrier lifetime increases to 452 {+-} 5 fs. This lifetime is apparently ensured by the capture of non-equilibrium charge carriers at metal As nanoinclusions.

  17. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel S.; Bukusoglu, Emre; de Pablo, Juan J.; Abbott, Nicholas L.

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  18. Topological defects in liquid crystals as templates for molecular self-assembly.

    PubMed

    Wang, Xiaoguang; Miller, Daniel S; Bukusoglu, Emre; de Pablo, Juan J; Abbott, Nicholas L

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  19. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    PubMed

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. PMID:27492241

  20. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    PubMed Central

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  1. Study of silicon crystal surface formation based on molecular dynamics simulation results

    NASA Astrophysics Data System (ADS)

    Barinovs, G.; Sabanskis, A.; Muiznieks, A.

    2014-04-01

    The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.

  2. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  3. Unoccupied electronic structure and molecular orientation of rubrene; from evaporated films to single crystals

    NASA Astrophysics Data System (ADS)

    Ueba, T.; Park, J.; Terawaki, R.; Watanabe, Y.; Yamada, T.; Munakata, T.

    2016-07-01

    Two-photon photoemission (2PPE) spectroscopy and ultraviolet photoemission spectroscopy (UPS) have been performed for rubrene single crystals and evaporated thin films on highly oriented pyrolytic graphite (HOPG). The changes in the 2PPE intensity from the single crystals by the polarization of the light and by the angle of the light incident plane against the crystalline axes indicate that the molecular arrangement on the surface is similar to that in the bulk crystal. On the other hand, in the case of evaporated films, the polarization dependence of 2PPE indicates that the tetracene backbone becomes standing upright as the thickness increases. In spite of the alignment of molecules, the broadened 2PPE spectral features for thick films suggest that the films are amorphous and molecules are in largely different environments. The film structures are confirmed by scanning tunneling microscopy (STM). The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) derived levels of the single crystal are shifted by + 0.18 and - 0.20 eV, respectively, from those of the 0.8 ML film. The shifts are attributed to the packing density of molecules. It is shown that the unoccupied electronic structure is more sensitively affected by the film structure than the occupied electronic structure.

  4. Tracking and Motion Analysis of Crack Propagations in Crystals for Molecular Dynamics

    SciTech Connect

    Tsap, L V; Duchaineau, M; Goldgof, D B

    2001-05-14

    This paper presents a quantitative analysis for a discovery in molecular dynamics. Recent simulations have shown that velocities of crack propagations in crystals under certain conditions can become supersonic, which is contrary to classical physics. In this research, they present a framework for tracking and motion analysis of crack propagations in crystals. It includes line segment extraction based on Canny edge maps, feature selection based on physical properties, and subsequent tracking of primary and secondary wavefronts. This tracking is completely automated; it runs in real time on three 834-image sequences using forty 250 MHZ processors. Results supporting physical observations are presented in terms of both feature tracking and velocity analysis.

  5. Molecular and crystal structure of liquid crystalline p-octyloxyphenyl p Prime -pentyloxybenzoate

    SciTech Connect

    Konstantinov, I. I.; Lermontova, E. Kh.; Kuz'mina, L. G.

    2011-01-15

    The crystal and molecular structure of p-octyloxyphenyl p Prime -pentyloxybenzoate C{sub 5}H{sub 11}-O-C{sub 6}H{sub 4}-C(O)-O-C{sub 6}H{sub 4}-O-C{sub 8}H{sub 17}, which forms a nematic mesophase upon melting, was determined by X-ray diffraction. There is one system of weak directional intermolecular C-H Horizontal-Ellipsis {pi} interactions responsible for the formation of the nematic phase in these crystals.

  6. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    SciTech Connect

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  7. Four- and five-component molecular solids: crystal engineering strategies based on structural inequivalence.

    PubMed

    Mir, Niyaz A; Dubey, Ritesh; Desiraju, Gautam R

    2016-03-01

    A synthetic strategy is described for the co-crystallization of four- and five-component molecular crystals, based on the fact that if any particular chemical constituent of a lower cocrystal is found in two different structural environments, these differences may be exploited to increase the number of components in the solid. 2-Methylresorcinol and tetramethylpyrazine are basic template molecules that allow for further supramolecular homologation. Ten stoichiometric quaternary cocrystals and one quintinary cocrystal with some solid solution character are reported. Cocrystals that do not lend themselves to such homologation are termed synthetic dead ends.

  8. Picosecond Transient Photoconductivity in Functionalized Pentacene Molecular Crystals Probed by Terahertz Pulse Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hegmann, F. A.; Tykwinski, R. R.; Lui, K. P.; Bullock, J. E.; Anthony, J. E.

    2002-11-01

    We have measured transient photoconductivity in functionalized pentacene molecular crystals using ultrafast optical pump-terahertz probe techniques. The single crystal samples were excited using 800nm, 100fs pulses, and the change in transmission of time-delayed, subpicosecond terahertz pulses was used to probe the photoconducting state over a temperature range from 10 to 300K. A subpicosecond rise in photoconductivity is observed, suggesting that mobile carriers are a primary photoexcitation. At times longer than 4ps, a power-law decay is observed consistent with dispersive transport.

  9. Phenomenological model of spin crossover in molecular crystals as derived from atom-atom potentials.

    PubMed

    Sinitskiy, Anton V; Tchougréeff, Andrei L; Dronskowski, Richard

    2011-08-01

    The method of atom-atom potentials, previously applied to the analysis of pure molecular crystals formed by either low-spin (LS) or high-spin (HS) forms (spin isomers) of Fe(II) coordination compounds (Sinitskiy et al., Phys. Chem. Chem. Phys., 2009, 11, 10983), is used to estimate the lattice enthalpies of mixed crystals containing different fractions of the spin isomers. The crystals under study were formed by LS and HS isomers of Fe(phen)(2)(NCS)(2) (phen = 1,10-phenanthroline), Fe(btz)(2)(NCS)(2) (btz = 5,5',6,6'-tetrahydro-4H,4'H-2,2'-bi-1,3-thiazine), and Fe(bpz)(2)(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2'-bipyridine). For the first time the phenomenological parameters Γ pertinent to the Slichter-Drickamer model (SDM) of several materials were independently derived from the microscopic model of the crystals with use of atom-atom potentials of intermolecular interaction. The accuracy of the SDM was checked against the numerical data on the enthalpies of mixed crystals. Fair semiquantitative agreement with the experimental dependence of the HS fraction on temperature was achieved with use of these values. Prediction of trends in Γ values as a function of chemical composition and geometry of the crystals is possible with the proposed approach, which opens a way to rational design of spin crossover materials with desired properties.

  10. Understanding molecular crystals with dispersion-inclusive density functional theory: pairwise corrections and beyond.

    PubMed

    Kronik, Leeor; Tkatchenko, Alexandre

    2014-11-18

    CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids. PMID:24901508

  11. Molecular dynamics study of the isothermal crystallization mechanism of polyethylene chain: the combined effects of chain length and temperature.

    PubMed

    Gao, Rui; He, Xuelian; Zhang, Haiyang; Shao, Yunqi; Liu, Zhen; Liu, Boping

    2016-03-01

    A molecular level understanding of the polyethylene (PE) crystallization process was elucidated by molecular dynamics simulation of three states, with varying chain length and temperature. The process can be classified into the following three states: (1) nucleation controlled state, (2) competitive state of crystal growth process and new nuclei formation, and (3) crystal growth controlled state, which could be quantified by the evolution of nuclei number. With increasing chain length, two phenomena occur: the single crystallization mechanism changes from state (1) to (3), and the crystal size increases while the b/a axial ratio in the lateral surface decreases. These changes can be explained from a thermodynamic point of view, in that the van der Waals (vdW) interaction per CH2 unit is strengthened and more nucleation sites are generated for longer chain. Size effect (meaning different surface fractions when the chain collapses into a globule) was an important factor determining vdW energy per unit and the crystallization states of a single PE chain. On the other hand, the crystallization states were independent of chain length for short chains systems with the same size effect. In both conditions, a long chain generates multi-crystal domains, and a short chain prefers a single crystal domain. Our results not only provide molecular level evidence for crystallization states but also clarify the influence of chain length on the crystallization process.

  12. The Role of Anharmonicity and Nuclear Quantum Effects in the Pyridine Molecular Crystal: An ab initio Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto

    Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

  13. PREFACE: International Symposium on Non-Equilibrium Soft Matter 2010 International Symposium on Non-Equilibrium Soft Matter 2010

    NASA Astrophysics Data System (ADS)

    Kawakatsu, T.; Matsuyama, A.; Ohta, T.; Tanaka, H.; Tanaka, S.

    2011-07-01

    Soft matter is a rapidly growing interdisciplinary research field covering a range of subject areas including physics, chemistry, biology, mathematics and engineering. Some of the important universal features of these materials are their mesoscopic structures and their dynamics. Due to the existence of such large-scale structures, which nevertheless exhibit interactions of the order of the thermal energy, soft matter can readily be taken out of equilibrium by imposing a weak external field such as an electric field, a mechanical stress or a shear flow. The importance of the coexistence of microscopic molecular dynamics and the mesoscopic/macroscopic structures and flows requires us to develop hierarchical approaches to understand the nonlinear and nonequilibrium phenomena, which is one of the central issues of current soft matter research. This special section presents selected contributions from the 'International Symposium on Non-Equilibrium Soft Matter 2010' held from 17-20 August 2010 in Nara, Japan, which aimed to describe recent advances in soft matter research focusing especially on its nonequilibrium aspects. The topics discussed cover statics and dynamics of a wide variety of materials ranging from traditional soft matter like polymers, gels, emulsions, liquid crystals and colloids to biomaterials such as biopolymers and biomembranes. Among these studies, we highlighted the physics of biomembranes and vesicles, which has attracted great attention during the last decade; we organized a special session for this active field. The work presented in this issue deals with (1) structure formation in biomembranes and vesicles, (2) rheology of polymers and gels, (3) mesophases in block copolymers, (4) mesoscopic structures in liquid crystals and ionic liquids, and (5) nonequilibrium dynamics. This symposium was organized as part of a research project supported by the Grant-in-Aid for the priority area 'Soft Matter Physics' (2006-2010) from the Ministry of Education

  14. Nonequilibrium interfaces in colloidal fluids

    NASA Astrophysics Data System (ADS)

    Bier, Markus; Arnold, Daniel

    2013-12-01

    The time-dependent structure, interfacial tension, and evaporation of an oversaturated colloid-rich (liquid) phase in contact with an undersaturated colloid-poor (vapor) phase of a colloidal dispersion is investigated theoretically during the early-stage relaxation, where the interface is relaxing towards a local equilibrium state while the bulk phases are still out of equilibrium. Since systems of this type exhibit a clear separation of colloidal and solvent relaxation time scales with typical times of interfacial tension measurements in between, they can be expected to be suitable for analogous experimental studies, too. The major finding is that, irrespective of how much the bulk phases differ from two-phase coexistence, the interfacial structure and the interfacial tension approach those at two-phase coexistence during the early-stage relaxation process. This is a surprising observation since it implies that the relaxation towards global equilibrium of the interface is not following but preceding that of the bulk phases. Scaling forms for the local chemical potential, the flux, and the dissipation rate exhibit qualitatively different leading order contributions depending on whether an equilibrium or a nonequilibrium system is considered. The degree of nonquilibrium between the bulk phases is found to not influence the qualitative relaxation behavior (i.e., the values of power-law exponents), but to determine the quantitative deviation of the observed quantities from their values at two-phase coexistence. Whereas the underlying dynamics differs between colloidal and molecular fluids, the behavior of quantities such as the interfacial tension approaching the equilibrium values during the early-stage relaxation process, during which nonequilibrium conditions of the bulk phases are not changed, can be expected to occur for both types of systems.

  15. Non-equilibrium control of complex solids by nonlinear phononics

    NASA Astrophysics Data System (ADS)

    Mankowsky, Roman; Först, Michael; Cavalleri, Andrea

    2016-06-01

    We review some recent advances in the use of optical fields at terahertz frequencies to drive the lattice of complex materials. We will focus on the control of low energy collective properties of solids, which emerge on average when a high frequency vibration is driven and a new crystal structure induced. We first discuss the fundamentals of these lattice rearrangements, based on how anharmonic mode coupling transforms an oscillatory motion into a quasi-static deformation of the crystal structure. We then discuss experiments, in which selectively changing a bond angle turns an insulator into a metal, accompanied by changes in charge, orbital and magnetic order. We then address the case of light induced non-equilibrium superconductivity, a mysterious phenomenon observed in some cuprates and molecular materials when certain lattice vibrations are driven. Finally, we show that the dynamics of electronic and magnetic phase transitions in complex-oxide heterostructures follow distinctly new physical pathways in case of the resonant excitation of a substrate vibrational mode.

  16. Electron-beam nanopatterning and spectral modulation of organic molecular light-emitting single crystals.

    PubMed

    Persano, Luana; Camposeo, Andrea; Pisignano, Dario; Burini, Andrea; Spearman, Peter; Tavazzi, Silvia

    2014-02-18

    The nanopatterning of light-emitting molecular crystals with semiconducting properties can be crucial for the development of future optoelectronic and nanoelectronic devices based on organic materials. In this respect, electron-beam writing is a powerful tool to realize patterns at the nanoscale, but it is still rarely applied to active organic materials. Here, sub-100-nm-scale nanopatterning is performed on the surface of quaterthiophene monocrystals by direct maskless electron-beam writing. Gratings are produced on organic crystals with periods ranging from 80 nm to 1 μm and single-line lateral dimensions ranging from 20 to 500 nm, with electron-beam exposure doses between 100 and 1500 μC/cm(2). The morphological and texturing properties of the pattern are discussed, together with the interaction mechanisms between the electron beam and the crystal. The resulting modulation of the light emission is consistent with Bragg scattering from the patterned periodic features.

  17. Improved Re-Crystallization of p+ Poly-Si Gates with Molecular Ion Implantation

    NASA Astrophysics Data System (ADS)

    Lee, Jin-Ku; Ju, Min-Ae; Oh, Jae-Geun; Hwang, Sun-Hwan; Jeon, Seung-Joon; Ku, Ja-Chun; Park, Sungki; Lee, Kyung-Won; Kim, Steve; Ra, Geum-Joo; Reece, Ron; Rubin, Leonard M.; Krull, W. A.; Cho, H. T.

    2008-11-01

    Implantation of B18H22 molecules at 80 keV and doses up to 4×1016 cm-2 were evaluated for the application of p-type counterdoping of in situ n-type doped polysilicon gates. Compared to conventional B implants, molecular implantation provides greatly improved throughput without the risk of energy contamination. Implants at these high doses resulted in poor re-crystallization of the polysilicon layer due to the formation of excessive cluster-type defects. Subjecting the polysilicon to either UV-curing or low temperature soak annealing prior to dopant activation was not effective in improving the re-crystallization process. However, breaking the dose into two portions at two different energies was shown to significantly improve re-crystallization of the polysilicon layer. Improved dopant activation was confirmed by a >90% reduction in ring oscillator delay time on a 60 nm PMOSFET.

  18. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

    2015-03-01

    Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

  19. Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study

    PubMed Central

    Zhou, Li-li; Liu, Rang-su; Tian, Ze-an; Liu, Hai-rong; Hou, Zhao-yang; Peng, Ping

    2016-01-01

    The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90–150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule. PMID:27526660

  20. Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study.

    PubMed

    Zhou, Li-Li; Liu, Rang-Su; Tian, Ze-An; Liu, Hai-Rong; Hou, Zhao-Yang; Peng, Ping

    2016-01-01

    The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90-150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule. PMID:27526660

  1. Molecular rotation-vibration dynamics of low-symmetric hydrate crystal in the terahertz region.

    PubMed

    Fu, Xiaojian; Wu, Hongya; Xi, Xiaoqing; Zhou, Ji

    2014-01-16

    The rotational and vibrational dynamics of molecules in copper sulfate pentahydrate crystal are investigated with terahertz dielectric spectra. It is shown that the relaxation-like dielectric dispersion in the low frequency region is related to the reorientation of water molecules under the driving of terahertz electric field, whereas the resonant dispersion can be ascribed to lattice vibration. It is also found that, due to the hydrogen-bond effect, the vibrational mode at about 1.83 THz along [-111] direction softens with decreasing temperature, that is, the crystal expands in this direction when cooled. On the contrary, the mode hardens in the direction perpendicular to [-111] during the cooling process. This contributes to the further understanding of the molecular structure and bonding features of hydrate crystals. PMID:24359294

  2. The Crystal and Molecular Structure of Acetatochlorobis(4-methylpyridine)oxovanadium (IV)

    NASA Technical Reports Server (NTRS)

    Schupp, John D.; Hepp, Aloysius F.; Duraj, Stan A.; Richman, Robert M.; Fanwick, Phillip E.; Hakimzadeh, Roshanak (Technical Monitor)

    2001-01-01

    The crystal and molecular structure of the title compound, VOCl(O2CCH3)(4-CH3C5H4N)2, has been determined by single-crystal x-ray diffraction. The material crystallizes in the space group P 1(bar) (#2) with a = 7.822(2), b = 8.023(l), c = 14.841(2) Angstroms, alpha = 99.73(l), beta = 91.41(l), and gamma = 117.13(l). The coordination geometry around the vanadium is a highly distorted octahedron. The molecule is remarkable for being a monomeric oxovanadium (IV) carboxylate. A generalized synthetic strategy is proposed for the preparation of oxovanadium (IV) monomers.

  3. Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Zhou, Li-Li; Liu, Rang-Su; Tian, Ze-An; Liu, Hai-Rong; Hou, Zhao-Yang; Peng, Ping

    2016-08-01

    The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90–150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule.

  4. General theory of electronic transport in molecular crystals. I. Local linear electron-phonon coupling

    NASA Astrophysics Data System (ADS)

    Silbey, R.; Munn, R. W.

    1980-02-01

    An improved general theory of electronic transport in molecular crystals with local linear electron-phonon coupling is presented. It is valid for arbitrary electronic and phonon bandwidths and for arbitrary electron-phonon coupling strength, yielding small-polaron theory for narrow electronic bands and strong coupling, and semiconductor theory for wide electronic bands and weak coupling. Detailed results are derived for electronic excitations fully clothed with phonons and having a bandwidth no larger than the phonon frequency; the electronic and phonon densities of states are taken as Gaussian for simplicity. The dependence of the diffusion coefficient on temperature and on the other parameters is analyzed thoroughly. The calculated behavior provides a rational interpretation of observed trends in the magnitude and temperature dependence of charge-carrier drift mobilities in molecular crystals.

  5. Improving the Description of Nonmagnetic and Magnetic Molecular Crystals via the van der Waals Density Functional

    NASA Astrophysics Data System (ADS)

    Obata, Masao; Nakamura, Makoto; Hamada, Ikutaro; Oda, Tatsuki

    2015-02-01

    We have derived and implemented a stress tensor formulation for the van der Waals density functional (vdW-DF) with spin-polarization-dependent gradient correction (GC) recently proposed by the authors [J. Phys. Soc. Jpn. 82, 093701 (2013)] and applied it to nonmagnetic and magnetic molecular crystals under ambient condition. We found that the cell parameters of the molecular crystals obtained with vdW-DF show an overall improvement compared with those obtained using local density and generalized gradient approximations. In particular, the original vdW-DF with GC gives the equilibrium structural parameters of solid oxygen in the α-phase, which are in good agreement with the experiment.

  6. The effects of Raman scattering accompanied by the soliton excitation occurring in molecular crystals

    NASA Astrophysics Data System (ADS)

    Pang, X. F.

    2001-06-01

    A theoretical research is made for the effects of Raman scattering caused by the soliton excitation occurring in the organic molecular crystals, e.g., acetanilide, on the basis of vibration model of amide-I. The energy gap between the soliton state and the vibron state have been found by partial diagonalized method in second quantized representation, which is 18.1-33 cm -1. This result is approximately consistent with the red shift value obtained from the experiments, 16 cm -1. The differential cross-section of the Raman scattering, arising from the soliton excitation, has also been obtained. Finally, we derive some properties of the Raman scattering in such a case. This result establishes spectral signatures of the soliton in the molecular crystals, which may be observed in the experiment.

  7. Light quasiparticles dominate electronic transport in molecular crystal field-effect transistors

    SciTech Connect

    Li, Z. Q.; Podzorov, V.; Sai, N.; Martin, Michael C.; Gershenson, M. E.; Di Ventra, M.; Basov, D. N.

    2007-03-01

    We report on an infrared spectroscopy study of mobile holes in the accumulation layer of organic field-effect transistors based on rubrene single crystals. Our data indicate that both transport and infrared properties of these transistors at room temperature are governed by light quasiparticles in molecular orbital bands with the effective masses m[small star, filled]comparable to free electron mass. Furthermore, the m[small star, filled]values inferred from our experiments are in agreement with those determined from band structure calculations. These findings reveal no evidence for prominent polaronic effects, which is at variance with the common beliefs of polaron formation in molecular solids.

  8. A molecular-field approximation for quantum crystals. Ph.D. Thesis; [considering ground state properties

    NASA Technical Reports Server (NTRS)

    Danilowicz, R.

    1973-01-01

    Ground-state properties of quantum crystals have received considerable attention from both theorists and experimentalists. The theoretical results have varied widely with the Monte Carlo calculations being the most successful. The molecular field approximation yields ground-state properties which agree closely with the Monte Carlo results. This approach evaluates the dynamical behavior of each pair of molecules in the molecular field of the other N-2 molecules. In addition to predicting ground-state properties that agree well with experiment, this approach yields data on the relative importance of interactions of different nearest neighbor pairs.

  9. An Analysis of the NEXAFS Spectra of a molecular crystal: alpha-Glycine

    SciTech Connect

    Schwartz, Craig P.; Saykally, Richard J.; Prendergast, David

    2010-06-18

    The nitrogen K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectrum of alpha-crystalline glycine has been calculated for temperatures ranging from 0 K to 450 K. Significant temperature dependent spectral changes are predicted. The calculated room temperature spectrum is in good agreement with experiment. At high temperatures, molecular motions strongly influence the spectrum, as any unique spectrum from an individual instantaneous configuration does not resemble the experimental result or the average calculated spectrum; complex coupled motions in this prototypical molecular crystal underlie the observed spectral changes.

  10. Vapor deposition of a smectic liquid crystal: highly anisotropic, homogeneous glasses with tunable molecular orientation.

    PubMed

    Gómez, Jaritza; Jiang, Jing; Gujral, Ankit; Huang, Chengbin; Yu, Lian; Ediger, M D

    2016-03-21

    Physical vapor deposition (PVD) has been used to prepare glasses of itraconazole, a smectic A liquid crystal. Glasses were deposited onto subtrates at a range of temperatures (Tsubstrate) near the glass transition temperature (Tg), with Tsubstrate/Tg ranging from 0.70 to 1.02. Infrared spectroscopy and spectroscopic ellipsometry were used to characterize the molecular orientation using the orientational order parameter, Sz, and the birefringence. We find that the molecules in glasses deposited at Tsubstrate = Tg are nearly perpendicular to the substrate (Sz = +0.66) while at lower Tsubstrate molecules are nearly parallel to the substrate (Sz = -0.45). The molecular orientation depends on the temperature of the substrate during preparation, allowing layered samples with differing orientations to be readily prepared. In addition, these vapor-deposited glasses are macroscopically homogeneous and molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. Vapor deposition of liquid crystals is likely a general approach for the preparation of highly anisotropic glasses with tunable molecular orientation for use in organic electronics and optoelectronics.

  11. Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

    PubMed

    Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

    2016-06-22

    The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

  12. Examination of surface nucleation during the growth of long alkane crystals by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Bourque, Alexander; Rutledge, Gregory

    2015-03-01

    Crystal growth from the melt of n-pentacontane (C50) was studied by molecular dynamics simulation using a validated united atom model. By quenching below the melting temperature of C50 (370 K), propagation of the crystal growth front into the C50 melt from a crystalline polyethylene surface was observed. By tracking the location of the midpoint in the orientational order parameter profile between the crystal and melt, crystal growth rates between 0.015-0.040 m/s were observed, for quench depths of 10 to 70 K below the melting point. In this work, surface nucleation is identified with the formation of 2D clusters of crystalline sites within layers parallel to the propagating growth front, by analogy to the formation of 3D clusters in primary, homogeneous nucleation. These surface nucleation events were tracked over several layers and numerous simulations, and a mean first passage time analysis was employed to estimate critical nucleus sizes, induction times and rates for surface nucleation. Based on new insights provided by the detailed molecular trajectories obtained from simulation, the classical theory proposed by Lauritzen and Hoffman is re-examined.

  13. Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

  14. Statistical physics of shear flow: a non-equilibrium problem

    NASA Astrophysics Data System (ADS)

    Evans, R. M. L.

    2010-09-01

    Complex fluids are easily and reproducibly driven into non-equilibrium steady states by the action of shear flow. The statistics of the microstructure of non-equilibrium fluids is important to the material properties of every complex fluid that flows, e.g. axle grease on a rotating bearing; blood circulating in capillaries; molten plastic flowing into a mould; the non-equilibrium onion phase of amphiphiles used for drug delivery; the list is endless. Such states are as diverse and interesting as equilibrium states, but are not governed by the same statistics as equilibrium materials. I review some recently discovered principles governing the probabilities of various types of molecular re-arrangements taking place within a sheared fluid. As well as providing new foundations for the study of non-equilibrium matter, the principles are applied to some simple models of particles interacting under flow, showing that the theory exhibits physically convincing behaviour.

  15. Sucrose crystal growth in the presence of dextran of different molecular weights

    NASA Astrophysics Data System (ADS)

    Khaddour, Issam; Ferreira, António; Bento, Luís; Rocha, Fernando

    2012-09-01

    The effects of variable concentrations of different molecular weight fractions of dextran on the interfacial free energies and the kinetic coefficients of the overall linear growth rates of the sucrose crystal were evaluated at 40 and 50 °C. Dextrans-reducing effects on the interfacial free energy increased the overall linear growth rates of sucrose at 40 °C. Further, dextrans-reducing effects of the growth kinetic coefficients resulted in lower growth rates of the sucrose crystals at 50 °C. Impurity effectiveness factor, differential heat of adsorption and Langmuir isotherm constant were determined, for the used dextrans, at 50 °C and relative supersaturation of 0.161. The dextran of molecular fraction of 2000 kilo Daltons (kDa) showed considerably high effectiveness factor in comparison with the dextrans of molecular fractions of 70 and 250 kDa. Role of dextran in retarding the advancement of the growth steps in the vicinity of its incorporation on the face (100) of the sucrose crystal is pointed out using AFM technique.

  16. Peculiarities of exciton polariton dispersion for ternary molecular crystal with isotopic replacement defects.

    NASA Astrophysics Data System (ADS)

    Rumyantsev, Vladimir V.; Fedorov, Stanislav A.

    2002-03-01

    The peculiarities of exciton polariton spectrum caused of isotopic replacement defects in ternary molecular crystal have been studied. In the examined case configuration dependence of molecular currents, energies and intermolecular resonance interaction matrix W is weak as well as W-components are small. It enabled to describe main exciton spectrum peculiarities in approach similar to orientated gas model [1] and to obtain polariton dispersion low in analytical form. Three specific dispersion curves having two “the bottle throat” and reflecting isotopic replacement effect is added to the pair of typical polariton curves for perfect crystal. The values of “the bottle throats” of that curves has been evaluated. Non-collinearity of the molecule dipole moments in crystalline matrix and the moments of isotopic replacement admixture determine it. 1.Rumyantsev V.V., Fedorov S.A. Polariton propagation in mixed molecular crystals.Fizika i Tekhnika Vysokikh Davlenii. 2001, v.11, N.4 (special issue).-P.112-117.

  17. Role of supramolecular synthons in the formation of the supramolecular architecture of molecular crystals revisited from an energetic viewpoint.

    PubMed

    Shishkin, Oleg V; Zubatyuk, Roman I; Shishkina, Svitlana V; Dyakonenko, Viktoriya V; Medviediev, Volodymyr V

    2014-04-14

    Analysis of the strengths and directionality of intermolecular interactions in the crystals containing only one type of supramolecular synthon allows the suggestion of a general classification of molecular crystals depending on type of their basic structural motifs. All crystals may be divided on four classes namely (I) crystals with isotropic packing of the building units; (II) columnar crystals where the basic structural motif (BSM) is a chain/column; (III) layered crystals with layers as the BSM; (IV) columnar-layered crystals containing chains/columns as the primary basic structural motif and layers as the secondary BSM. Taking into account the participation of different supramolecular synthons in the formation of different levels of the organization of molecular crystals, they may be considered as basic (responsible for the formation of molecular complexes as building units of crystals), primary, secondary and auxiliary, which are involved in the agglomeration of molecules in primary or secondary basic structural motifs or in the packing of these motifs, respectively. The ranking of supramolecular synthons depends on values of energies of intermolecular interactions and it is individual for each crystal.

  18. Molecular theory of smectic ordering in liquid crystals with nanoscale segregation of different molecular fragments

    NASA Astrophysics Data System (ADS)

    Gorkunov, M. V.; Osipov, M. A.; Kapernaum, N.; Nonnenmacher, D.; Giesselmann, F.

    2011-11-01

    A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure.

  19. INTRODUCTION: Nonequilibrium Processes in Plasmas

    NASA Astrophysics Data System (ADS)

    Petrović, Zoran; Marić, Dragana; Malović, Gordana

    2009-07-01

    lead to new fundamental understanding is illustrated well in the paper by Uwe Czarnetzki which describes a new method for separate control of flux and energy of ions reaching the surface of electrodes. Deborah O'Connell from Belfast has shown space and phase resolved mode transitions in rf inductively coupled plasmas obtained by optical emission measurements. At the same time an application of a similar rf discharge for the treatment of paper was presented by Irina Filatova from Belarus. Many applications of non-equilibrium plasmas depend on the development of plasma sources operating at atmospheric pressure and one such source that promises to be prominent in medicine is described by Timo Gans. In a similar way, practical considerations require studies of the injection of liquids into plasmas and progress on the development of one such source is described by Mathew Goeckner and his colleagues from Dallas. From the Institute Jožef Štefan in Slovenia and the group of Miran Mozetič we have a detailed review of their work on functionalization of organic materials by oxygen plasmas. Even higher density plasmas, where the collective phenomena dominate, show different degrees of non-equilibrium and one example presented here by Zoltan Donko deals with two dimensional plasma dust crystals and liquids, while the lecture by Jovo Vranješ from Belgium deals with the treatment of collisions in multicomponent plasmas. Finally we have papers on the transport of pollutants. The association of the two fields started initially through joint interest in some of the methods for removal of NOx and SOx, from electrostatic precipitation of industrial dust to dielectric barrier discharges. The joint work continued on the application of flowing afterglow plasma combined with a hollow cathode discharge in order to achieve a proton transfer mass analysis of organic volatile compounds and also on the possibilities of applying similar methods for solving transport equations. In this volume we

  20. Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential.

    PubMed

    Zhou, Xiaowang; Ward, Donald K; Wong, Bryan M; Doty, F Patrick; Zimmerman, Jonathan A

    2012-08-23

    Cd(1-x)Zn(x)Te (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals.

  1. Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata

    SciTech Connect

    Gavira, José A.; Jesus, Walleska de; Camara-Artigas, Ana; López-Garriga, Juan; García-Ruiz, Juan M.

    2006-03-01

    The haemoglobin II from the clam L. pectinata has been crystallized using counter-diffusion in single capillary in the presence of agarose to improve crystal quality. Initial phases have been obtained by molecular replacement. Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 73.92, c = 152.35 Å, and diffracted X-rays to a resolution of better than 2.0 Å. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (V{sub M}) of 3.15 Å{sup 3} Da{sup −1} and a solvent content of 61% by volume.

  2. Nonequilibrium Interlayer Transport in Pulsed Laser Deposition

    SciTech Connect

    Tischler, Jonathan Zachary; Eres, Gyula; Larson, Ben C; Rouleau, Christopher M; Zschack, P.; Lowndes, Douglas H

    2006-01-01

    We use time-resolved surface x-ray diffraction measurements with microsecond range resolution to study the growth kinetics of pulsed laser deposited SrTiO3. Time-dependent surface coverages corresponding to single laser shots were determined directly from crystal truncation rod intensity transients. Analysis of surface coverage evolution shows that extremely fast nonequilibrium interlayer transport, which occurs concurrently with the arrival of the laser plume, dominates the deposition process. A much smaller fraction of material, which is governed by the dwell time between successive laser shots, is transferred by slow, thermally driven interlayer transport processes.

  3. Nonequilibrium superconducting detectors

    NASA Astrophysics Data System (ADS)

    Cristiano, R.; Ejrnaes, M.; Esposito, E.; Lisitskyi, M. P.; Nappi, C.; Pagano, S.; Perez de Lara, D.

    2006-03-01

    Nonequilibrium superconducting detectors exploit the early stages of the energy down cascade which occur after the absorption of radiation. They operate on a short temporal scale ranging from few microseconds down to tens of picoseconds. In such a way they provide fast counting capability, high time discrimination and also, for some devices, energy sensitivity. Nonequilibrium superconducting detectors are developed for their use both in basic science and in practical applications for detection of single photons or single ionized macromolecules. In this paper we consider two devices: distributed readout imaging detectors (DROIDs) based on superconducting tunnel junctions (STJs), which are typically used for high-speed energy spectroscopy applications, and hot-electron superconductive detectors (HESDs), which are typically used as fast counters and time discriminators. Implementation of the DROID geometry to use a single superconductor is discussed. Progress in the fabrication technology of NbN nanostructured HESDs is presented. The two detectors share the high sensitivity that makes them able to efficiently detect even single photons down to infrared energy.

  4. Dynamic behavior of molecular switches in crystal under pressure and its reflection on tactile sensing.

    PubMed

    Wang, Yi; Tan, Xiao; Zhang, Yu-Mo; Zhu, Shaoyin; Zhang, Ivan; Yu, Binhong; Wang, Kai; Yang, Bing; Li, Minjie; Zou, Bo; Zhang, Sean Xiao-An

    2015-01-21

    Molecular switches have attracted increasing interest in the past decades, due to their broad applications in data storage, optical gating, smart windows, and so on. However, up till now, most of the molecular switches are operated in solutions or polymer blends with the stimuli of light, heat, and electric fields. Herein, we demonstrate the first pressure-controllable molecular switch of a benzo[1,3]oxazine OX-1 in crystal. Distinct from the light-triggered tautomerization between two optical states, applying hydrostatic pressure on the OX-1 crystal results in large-scale and continuous states across the whole visible light range (from ∼430 to ∼700 nm), which has not been achieved with other stimuli. Based on detailed and systematic control experiments and theoretical calculation, the preliminary requirements and mechanism of pressure-dependent tautomerization are fully discussed. The contributions of molecular tautomerization to the large-scale optical modulation are also stressed. Finally, the importance of studying pressure-responsive materials on understanding tactile sensing is also discussed and a possible mechanotransduction mode is proposed. PMID:25533888

  5. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt.

    PubMed

    He, Xiaoxia; Shen, Yan; Hung, Francisco R; Santiso, Erik E

    2015-09-28

    The homogeneous nucleation of crystals of the ionic liquid [dmim(+)][Cl(-)] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10(10) cm(-3) s(-1) was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores. PMID:26429023

  6. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt.

    PubMed

    He, Xiaoxia; Shen, Yan; Hung, Francisco R; Santiso, Erik E

    2015-09-28

    The homogeneous nucleation of crystals of the ionic liquid [dmim(+)][Cl(-)] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10(10) cm(-3) s(-1) was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

  7. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

    SciTech Connect

    He, Xiaoxia; Shen, Yan; Hung, Francisco R.; Santiso, Erik E.

    2015-09-28

    The homogeneous nucleation of crystals of the ionic liquid [dmim{sup +}][Cl{sup −}] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10{sup 10} cm{sup −3} s{sup −1} was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

  8. The Role of High Molecular Weight Chains in Flow-Induced Crystallization Precursor Structures

    SciTech Connect

    Yang,L.; Somani, R.; Scis, I.; Hsiao, B.; Kolb, R.; Lohse, D.

    2006-01-01

    Flow-induced crystallization in a bimodal polyethylene blend was investigated by means of in situ shear-WAXD (wide-angle x-ray diffraction) and shear-SAXS (small-angle x-ray scattering) techniques. The blend contained a low molecular weight (M{sub w} = 50 000 g mol{sup -1} and polydispersity = 2) polyethylene copolymer matrix (MB-50k) with 2 mol% of hexene, and a nearly monodisperse high molecular weight (M{sub w} = 161 000 g mol{sup -1} and polydispersity = 1.1) hydrogenated polybutadiene component (MD-161k), which has the microstructure of an ethylene-butene copolymer with 4 mol% butene. At the experimental temperatures of 112 and 115 C, MB-50k exhibited faster crystallization kinetics and higher crystallinity due to higher chain mobility and higher ethylene content than those of the MB-50k/MD-161k blend. However, both WAXD and SAXS results indicated that the high molecular weight component (MD-161k) is responsible for the formation of more highly oriented crystals, which we relate to a shear-induced precursor scaffold. Values of the lamellar long period in all experimental runs were found to slightly decrease in the beginning of crystallization and then reached a plateau value. Vonk's method for single lamella scattering was employed to estimate the lamellar thickness in the MB-50k/MD-161k blend at high temperature (115 C), where the lamellar thickness was also found to decrease in the beginning and remained about constant afterward. Twisted lamellar structures were observed in all formed kebabs.

  9. The role of high molecular weight chains in flow-induced crystallization precursor structures

    NASA Astrophysics Data System (ADS)

    Yang, Ling; Somani, Rajesh H.; Sics, Igors; Hsiao, Benjamin S.; Kolb, Rainer; Lohse, David

    2006-09-01

    Flow-induced crystallization in a bimodal polyethylene blend was investigated by means of in situ shear-WAXD (wide-angle x-ray diffraction) and shear-SAXS (small-angle x-ray scattering) techniques. The blend contained a low molecular weight (Mw = 50 000 g mol-1 and polydispersity = 2) polyethylene copolymer matrix (MB-50k) with 2 mol% of hexene, and a nearly monodisperse high molecular weight (Mw = 161 000 g mol-1 and polydispersity = 1.1) hydrogenated polybutadiene component (MD-161k), which has the microstructure of an ethylene-butene copolymer with 4 mol% butene. At the experimental temperatures of 112 and 115 °C, MB-50k exhibited faster crystallization kinetics and higher crystallinity due to higher chain mobility and higher ethylene content than those of the MB-50k/MD-161k blend. However, both WAXD and SAXS results indicated that the high molecular weight component (MD-161k) is responsible for the formation of more highly oriented crystals, which we relate to a shear-induced precursor scaffold. Values of the lamellar long period in all experimental runs were found to slightly decrease in the beginning of crystallization and then reached a plateau value. Vonk's method for single lamella scattering was employed to estimate the lamellar thickness in the MB-50k/MD-161k blend at high temperature (115 °C), where the lamellar thickness was also found to decrease in the beginning and remained about constant afterward. Twisted lamellar structures were observed in all formed kebabs.

  10. Probing structure and phase-transitions in molecular crystals by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Franz, Morten; Fischer, Bernd M.; Walther, Markus

    2011-12-01

    Since the introduction of ultra-fast laser techniques for the generation and detection of broadband terahertz pulses, terahertz time-domain spectroscopy has become a versatile tool for vibrational spectroscopy of molecular systems in the far-infrared. Due to their highly collective and delocalized character vibrational modes in this part of the spectrum are highly sensitive to molecular structure and arrangement within a molecular crystal. Here we utilize this sensitivity to differentiate between the enantiopure amino acid L-cysteine and its racemic crystalline DL-form. Using terahertz time-domain spectroscopy we are able to observe temperature induced solid-state phase transitions in polycrystalline DL-cysteine, as well as in polycrystalline benzoic acid. The dynamics of the transitions is studied by tracing the temperature dependency of spectral features that are assigned to certain conformational phases.

  11. Molecular theory of ferroelectric ordering in enantiomeric mixtures of smectic-C* liquid crystals.

    PubMed

    Osipov, M A; Guillon, D

    1999-12-01

    A molecular theory of ferroelectric ordering in smectic-C* liquid crystals composed of left and right enantiomers is developed taking into account the effects of chiral discrimination. The recently observed nonlinear dependence of the spontaneous polarization on the enantiomeric excess is explained in the framework of a molecular model that takes into consideration the strong electrostatic interaction between effective atomic charges in the chiral centers of the two enantiomers. This nonlinear dependence is determined by a difference of interaction energies between the pairs of chiral molecules with equal and opposite handedness, respectively. A relation between the molecular structure of different ferroelectric smectics C* and the dependence of the polarization on the enantiomeric excess is discussed in detail.

  12. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel; Bukusoglu, Emre; de Pablo, Juan; Abbott, Nicholas

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals that nanoscopic environments defined by LC defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic o-rings synthesized from Saturn-ring disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates.

  13. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  14. Supercell convergence of charge-transfer energies in pentacene molecular crystals from constrained DFT

    NASA Astrophysics Data System (ADS)

    Turban, David H. P.; Teobaldi, Gilberto; O'Regan, David D.; Hine, Nicholas D. M.

    2016-04-01

    Singlet fission (SF) is a multiexciton generation process that could be harnessed to improve the efficiency of photovoltaic devices. Experimentally, systems derived from the pentacene molecule have been shown to exhibit ultrafast SF with high yields. Charge-transfer (CT) configurations are likely to play an important role as intermediates in the SF process in these systems. In molecular crystals, electrostatic screening effects and band formation can be significant in lowering the energy of CT states, enhancing their potential to effectively participate in SF. In order to simulate these, it desirable to adopt a computational approach which is acceptably accurate, relatively inexpensive, and which scales well to larger systems, thus enabling the study of screening effects. We propose an electrostatically corrected constrained density functional theory (cDFT) approach as a low-cost solution to the calculation of CT energies in molecular crystals such as pentacene. Here we consider an implementation in the context of the onetep linear-scaling DFT code, but our electrostatic correction method is in principle applicable in combination with any constrained DFT implementation, also outside the linear-scaling framework. Our newly developed method allows us to estimate CT energies in the infinite crystal limit, and with these to validate the accuracy of the cluster approximation.

  15. Liquid crystal polymer networks: preparation, properties, and applications of films with patterned molecular alignment.

    PubMed

    Liu, Danqing; Broer, Dirk J

    2014-11-18

    Monolithically ordered liquid crystal polymer networks are formed by the photoinitiated polymerization of multifunctional liquid crystal monomers. This paper describes the relevant principles and methods, the basic structure-property relationships in terms of mesogenic properties of the monomers, and the mechanical and optical properties of the polymers. Strategies are discussed to control the molecular orientation by various means and in all three dimensions. The versatility of the process is demonstrated by two examples of films with a patterned molecular order. It is shown that patterned retarders can be made by a two-step polymerization process which is successfully employed in a transflective display principle. A transflective display is a liquid crystal display that operates in both a reflective mode using ambient light and a transmissive mode with light coming from a backlight system. Furthermore, a method is discussed to create a patterned film in a single polymerization process. This film has alternating planar chiral nematic areas next to perpendicularly oriented (so-called homeotropic) areas. When applied as a coating to a substrate, the film changes its surface texture. During exposure to UV light, it switches from a flat to a corrugated state. PMID:24707811

  16. Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  17. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  18. Liquid crystal polymer networks: preparation, properties, and applications of films with patterned molecular alignment.

    PubMed

    Liu, Danqing; Broer, Dirk J

    2014-11-18

    Monolithically ordered liquid crystal polymer networks are formed by the photoinitiated polymerization of multifunctional liquid crystal monomers. This paper describes the relevant principles and methods, the basic structure-property relationships in terms of mesogenic properties of the monomers, and the mechanical and optical properties of the polymers. Strategies are discussed to control the molecular orientation by various means and in all three dimensions. The versatility of the process is demonstrated by two examples of films with a patterned molecular order. It is shown that patterned retarders can be made by a two-step polymerization process which is successfully employed in a transflective display principle. A transflective display is a liquid crystal display that operates in both a reflective mode using ambient light and a transmissive mode with light coming from a backlight system. Furthermore, a method is discussed to create a patterned film in a single polymerization process. This film has alternating planar chiral nematic areas next to perpendicularly oriented (so-called homeotropic) areas. When applied as a coating to a substrate, the film changes its surface texture. During exposure to UV light, it switches from a flat to a corrugated state.

  19. Purification, characterization, and crystallization of single molecular species of beta-conglycinin from soybean seeds.

    PubMed

    Morita, S; Fukase, M; Yamaguchi, M; Fukuda, Y; Morita, Y

    1996-05-01

    Four major molecular species of beta-conglycinin, alpha 3, alpha 2 beta, alpha beta 2, and beta 3, were isolated and purified from seeds of an alpha' subunit-deficient strain of soybeans (Glycine max). All components were found to be homogeneous by high pressure liquid chromatography, SDS-polyacrylamide gel electrophoresis, and amino acid and amino terminal sequence analyses. The amino acid compositions of the alpha 3 and beta 3 components agreed fairly well with the compositions deduced from the cDNA sequences, and all of the components were highly glycosylated. The alpha 3 and beta 3 components were compared regarding their secondary structures. The secondary structure of the alpha 3 component deduced from CD measurements showed a higher alpha-helix content than that of the beta 3 component. The beta 3 component was crystallized by decreasing the ionic strength from 0.5 to 0.14 in phosphate buffer, pH 7.3, and the crystals grew to a size (1.0 mm x 0.2 mm x 0.2 mm) suitable for X-ray crystallographic analysis. A preliminary X-ray analysis showed that the crystal belonged to an orthorhombic crystal system having the space group P2(1)2(1)2(1) and unit cell dimensions of a = 185.1 A, b = 107.9 A, and c = 97.6 A.

  20. Molecular and crystal structure of n-hexyloxybenzoic anhydride at low and room temperatures

    SciTech Connect

    Konstantinov, I. I.; Churakov, A. V.; Kuz'mina, L. G.

    2010-09-15

    The crystal and molecular structures of n-hexyloxybenzoic anhydride, C{sub 6}H{sub 13}-O-C{sub 6}H{sub 4}-C(O)-O-C(O)-C{sub 6}H{sub 4}-C{sub 6}H{sub 13}, at low (120 K) and room (296 K) temperatures have been investigated. The molecule has an asymmetric bent structure. The dihedral angle between the benzene ring planes is 48.5 deg. The aliphatic chain on one side of the molecule has a transoid orientation with respect to the 'internal' C4 atom of the closest benzene ring, whereas the aliphatic chain on the other side has a cissoid orientation with respect to the analogous C(4A) atom. The crystal packing does not exhibit any pronounced separation of the crystal space into closely packed aromatic or loosely packed aliphatic regions. No weak directional interactions are observed in the packing; this fact explains the absence of liquid-crystal properties for this compound.

  1. Self-assembling of molecular nanowires for enhancing the conducting properties of discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Park, Ji Hyun; Kim, Kyung Ho; Takanishi, Yoichi; Yamamoto, Jun; Park, Yung Woo; Kim, Youn Sang; Scalia, Giusy

    2015-08-01

    The self-organization of discotic liquid crystal molecules in columns has enormous interest for soft nanoelectronic applications. A great advantage of discotic liquid crystal is that defects can be self-annealed in contrast to typical organic materials. Through the overlap of molecular orbitals, the aromatic cores assemble into long range ordered one-dimensional structures. Very thin structured films can be obtained by spin-coating from solution and the resulting morphologies are strongly dependent on the interaction between discotics and solvent molecules. Toluene produces films formed by very long nanowires, spontaneously aligned along a common direction and over fairly large areas. These nanostructured films are a result of the interplay between liquid crystal self-organization and solvent driven assembly. The ordered nanowire structures exhibit improvement in the electrical properties compared to misaligned structures and even to pristine HAT5, deposited without the aid of solvent. In this study we show that the toluene-based deposition of discotic liquid crystals is advantageous because it allows a uniform coverage of the substrate, unlike pristine HAT5 but also thanks to the type of induced structures exhibiting one order of magnitude higher conductivity, in the aligned nanowire films, compared to bare HAT5 ones.

  2. Comparison of the crystal structure and molecular models of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide (CMPO)

    SciTech Connect

    Rogers, R.D.; Rollins, A.N.; Gatrone, R.C.; Horwitz, E.P.

    1994-06-01

    The compound crystallizes in the space group P2{sub 1}/c with a=13. 446(6), b=22.280(7) {Angstrom}, b=92.07(4){degrees}, and D{sub calc}=1.05 g/cm{sup 3} for Z=8 (@20{degrees}C). Molecular mechanics, molecular dynamics, and MNDO calculations were also performed on CMPO utilizing the SYBYL{sup 2} suite of programs. Results from these calculations are compared to the crystal structure and to similar calculations performed on CMPO using ALCHEMY. The calculations agree fairly well with the crystal structure.

  3. Photoinduced reversible switching of porosity in molecular crystals based on star-shaped azobenzene tetramers.

    PubMed

    Baroncini, Massimo; d'Agostino, Simone; Bergamini, Giacomo; Ceroni, Paola; Comotti, Angiolina; Sozzani, Piero; Bassanetti, Irene; Grepioni, Fabrizia; Hernandez, Taylor M; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-08-01

    The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of great interest for separation, catalysis, optoelectronics, holography, mechanical actuation and solar energy conversion. Here, we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, the porosity of which can be tuned by changing the peripheral substituents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties such as birefringence as well as the capture of CO2 from the gas phase. The linear design, structural versatility and synthetic accessibility make this new family of materials potentially interesting for technological applications.

  4. High breakdown single-crystal GaN p-n diodes by molecular beam epitaxy

    SciTech Connect

    Qi, Meng; Zhao, Yuning; Yan, Xiaodong; Li, Guowang; Verma, Jai; Fay, Patrick; Nomoto, Kazuki; Zhu, Mingda; Hu, Zongyang; Protasenko, Vladimir; Song, Bo; Xing, Huili Grace; Jena, Debdeep; Bader, Samuel

    2015-12-07

    Molecular beam epitaxy grown GaN p-n vertical diodes are demonstrated on single-crystal GaN substrates. A low leakage current <3 nA/cm{sup 2} is obtained with reverse bias voltage up to −20 V. With a 400 nm thick n-drift region, an on-resistance of 0.23 mΩ cm{sup 2} is achieved, with a breakdown voltage corresponding to a peak electric field of ∼3.1 MV/cm in GaN. Single-crystal GaN substrates with very low dislocation densities enable the low leakage current and the high breakdown field in the diodes, showing significant potential for MBE growth to attain near-intrinsic performance when the density of dislocations is low.

  5. High breakdown single-crystal GaN p-n diodes by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Qi, Meng; Nomoto, Kazuki; Zhu, Mingda; Hu, Zongyang; Zhao, Yuning; Protasenko, Vladimir; Song, Bo; Yan, Xiaodong; Li, Guowang; Verma, Jai; Bader, Samuel; Fay, Patrick; Xing, Huili Grace; Jena, Debdeep

    2015-12-01

    Molecular beam epitaxy grown GaN p-n vertical diodes are demonstrated on single-crystal GaN substrates. A low leakage current <3 nA/cm2 is obtained with reverse bias voltage up to -20 V. With a 400 nm thick n-drift region, an on-resistance of 0.23 mΩ cm2 is achieved, with a breakdown voltage corresponding to a peak electric field of ˜3.1 MV/cm in GaN. Single-crystal GaN substrates with very low dislocation densities enable the low leakage current and the high breakdown field in the diodes, showing significant potential for MBE growth to attain near-intrinsic performance when the density of dislocations is low.

  6. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

  7. Critical CuI buffer layer surface density for organic molecular crystal orientation change

    SciTech Connect

    Ahn, Kwangseok; Kim, Jong Beom; Lee, Dong Ryeol; Kim, Hyo Jung; Lee, Hyun Hwi

    2015-01-21

    We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 −2) by a CuI buffer layer with a very low surface density, so low that a large proportion of the substrate surface is bare.

  8. Molecular dynamics studies of sticking and reflection of low-energy deuterium on single crystal tungsten

    NASA Astrophysics Data System (ADS)

    Maya, P. N.

    2016-11-01

    Molecular dynamics simulations have been performed to study deuterium sticking and reflection properties of single crystal tungsten surfaces using two different Tersoff-type tungsten-hydrogen potentials. Single crystal tungsten surfaces of (001) and (110) orientations were bombarded with deuterium atoms up to 100 eV energy at 300 K sample temperature. The potentials show differences in the nature of sticking as well as in the sticking coefficient. In order to understand the variation in the observed sticking coefficient, detailed potential energy analysis has been carried out using both the potentials. The analysis is able to explain the nature of the sticking for various surfaces as well as the observed minima in sticking coefficient in both the potentials. The variation in the sticking and reflection coefficients with energy can be explained from the local variation of the repulsive and attractive potential energy in the near-surface region which are considerably different in both the potentials.

  9. On the molecular and crystal structure of cyclo( L-methionyl- L-methionyl)

    NASA Astrophysics Data System (ADS)

    Valle, G.; Guantieri, V.; Tamburro, A. M.

    1990-04-01

    The crystal and molecular structure of a methionyl containing diketopiperazine, cyclo ( L-methionyl- L-methionyl), is reported. The molecule crystallizes in the space group P1 with a = 13.469(2), b=5.304(1), c=4.885(1) Å; α=105.8(1)°, β=99.7(1)°, γ=79.4(1)°; V=327.54 Å 3; Z = 1. The diketopiperazine ring adopts a twist boat conformation (fold angle β= +30°). The packing of the molecules is characterized by hydrogen-bonded ribbons. Circular dichroism measurements gave evidence of a concentration-dependent conformational transition between two conformers having opposite directions of ring folding.

  10. Effect of rubbing on the molecular orientation within polyimide orienting layers of liquid-crystal displays

    NASA Astrophysics Data System (ADS)

    van Aerle, N. A. J. M.; Barmentlo, M.; Hollering, R. W. J.

    1993-09-01

    The influence of various rubbing parameters on the molecular reorientation of thin polyimide orienting layers, used to align liquid-crystal (LC) molecules within liquid-crystal displays, has been studied. For this purpose the optical phase retardation in the polymer layer, explicitly induced during the rubbing treatment, was determined. The observed rubbing-induced phase retardation can directly be related to a molecular orientation within the polymer orienting layer, as could be shown by infrared dichroism studies. Furthermore, it is found that the top of the polymer layer, directly contacting the rubbing cloth during the actual rubbing process, is almost instantaneously oriented to a certain maximum value as soon as the rubbing is started. Additional or stronger rubbing has no detectable influence on the orientation within the top layer. Increasing the rubbing density or the rubbing pressure only results in an increase of the penetration depth of the rubbing process, i.e., molecular reorientation occurs deeper within the layer. Experiments show that the penetration depth can be varied from less than 10 nm to more than 60 nm by variation in rubbing conditions. These findings are supported by surface second-harmonic-generation studies of LC monolayers deposited onto rubbed orienting layers and by infrared dichroism studies.

  11. Molecular imprinted photonic crystal hydrogels for the rapid and label-free detection of imidacloprid.

    PubMed

    Wang, Xuan; Mu, Zhongde; Liu, Ran; Pu, Yuepu; Yin, Lihong

    2013-12-15

    A novel sensor for the rapid and label-free detection of imidacloprid was developed based on the combination of a colloidal crystal templating method and a molecular imprinting technique. The molecular imprinted photonic hydrogel film was prepared with methacrylic acid as monomers, ethylene glycol dimethylacrylate as cross-linkers and imidacloprid as imprinting template molecules. When the colloidal crystal template and the molecularly imprinted template was removed, the resulted MIPH film possessed a highly ordered three-dimensional macroporous structure with nanocavities. The response of the MIPH film to imidacloprid in aqueous solution can be detected through a readable Bragg diffraction red shift. When the concentration of imidacloprid increased from 10(-13) to 10(-7) g/mL, the Bragg diffraction peak shifted from 551 to 589 nm, while there were no obvious peak shifts for thiamethoxam and acetamiprid. This sensor which comprises of no label techniques and expensive instruments has potential application for the detection of trace imidacloprid. PMID:23993570

  12. Predicting crystal structure and habit of organic micro-crystals by experimentally assisted molecular modelling (EAMM). The case of n-octylamino-NBD

    NASA Astrophysics Data System (ADS)

    Pèpe, Gérard; Fery-Forgues, Suzanne; Jouanna, Paul

    2011-10-01

    Experimentally Assisted Molecular Modelling (EAMM) is an original approach for predicting the structure of organic micro-crystals and deducing their habit in the presence of various solvents and additives. It is applied here in the case of n-octylamino-nitrobenzoxadiazole ( nOA-NBD), a fluorescent compound. This general approach is first of all described and validated by its blind application to three known and closely-related crystals. Then, the whole process is applied to predict the molecular crystal generated by n-octylamino-NBD, including the molecule conformation, its structure (cell parameters, molecular packing, X-ray powder diagrams) and its theoretical plus actual habits in the presence of a solvent ( p-xylene) and two additives (acetic acid and n-dodecane). The conformation of the predicted molecule is validated by comparison with two similar molecules embedded in observable crystals. Then, the choice between two proposed structures (with the same energy and two equiprobable packings) is based on the comparison between experimental and re-computed X-ray powder diffraction diagrams, and also on the interpretation of an actual TEM image in the light of the proposed cell parameters. This choice is confirmed by the comparison between the vapour-grown face development (proposed by the BFDH or the attachment energy models) and the actual face development in a pure solvent. Finally, the actual habit deduced from comparing the crystal attachment energy with the adsorption energy of solvent or additive molecules is validated by SEM images of NBD micro-crystals in presence of the solvent alone or in presence of both additives. In conclusion, the EAMM approach appears to be a decisive tool for quickly simulating structural and habit properties of the molecular crystals, accessible or not by experimentation. Thus, a numerical selection of molecules becomes possible in view of deriving organic materials with predetermined properties, such as the fluorescence

  13. Intermediate state during the crystal transition in aspartame, studied with thermal analysis, solid-state NMR, and molecular dynamics simulation.

    PubMed

    Ebisawa, K; Nagashima, N; Fukuhara, K; Kumon, S; Kishimoto, S; Suzuki, E; Yoneda, S; Umeyama, H

    2000-05-01

    Aspartame (L-alpha-aspartyl-L-phenylalanine methyl ester) is a dipeptide sweetener about 200 times as sweet as sugar. It exists in crystal forms such as IA, IB, IIA, and IIB, which differ in crystal structure and in the degree of hydration. Among these, IIA is the most stable crystal form, and its crystal structure has been well determined (Hatada et al., J. Am. Chem. Soc., 107, 4279-4282 (1985)). To elucidate the structural factors of thermal stability in the IIA form of aspartame and to examine the physical process in the crystal transformation between the IIA and IIB forms, we performed a thermal analysis and solid-state NMR measurements. We found that a quasi-stable intermediate state exists in the transformation, and it has the same crystal lattice as the usual IIA form, despite the dehydration from 1/2 mol to 1/3 mol per 1 mol of aspartame. The results of the energy component analysis and the molecular dynamics simulation suggest that the entropic effect promotes the generation of the intermediate state, which is presumably caused by the evaporation of the water of crystallization and the increase of molecular motion in aspartame. Thus, the thermal stability of the IIA form is attributable to a structural property, i.e., the crystal lattice itself is retained during the above dehydration. Moreover, the molecular dynamics simulations suggest that the aspartame molecules have two kinds of conformational flexibility in the intermediate state. PMID:10823710

  14. Intermediate state during the crystal transition in aspartame, studied with thermal analysis, solid-state NMR, and molecular dynamics simulation.

    PubMed

    Ebisawa, K; Nagashima, N; Fukuhara, K; Kumon, S; Kishimoto, S; Suzuki, E; Yoneda, S; Umeyama, H

    2000-05-01

    Aspartame (L-alpha-aspartyl-L-phenylalanine methyl ester) is a dipeptide sweetener about 200 times as sweet as sugar. It exists in crystal forms such as IA, IB, IIA, and IIB, which differ in crystal structure and in the degree of hydration. Among these, IIA is the most stable crystal form, and its crystal structure has been well determined (Hatada et al., J. Am. Chem. Soc., 107, 4279-4282 (1985)). To elucidate the structural factors of thermal stability in the IIA form of aspartame and to examine the physical process in the crystal transformation between the IIA and IIB forms, we performed a thermal analysis and solid-state NMR measurements. We found that a quasi-stable intermediate state exists in the transformation, and it has the same crystal lattice as the usual IIA form, despite the dehydration from 1/2 mol to 1/3 mol per 1 mol of aspartame. The results of the energy component analysis and the molecular dynamics simulation suggest that the entropic effect promotes the generation of the intermediate state, which is presumably caused by the evaporation of the water of crystallization and the increase of molecular motion in aspartame. Thus, the thermal stability of the IIA form is attributable to a structural property, i.e., the crystal lattice itself is retained during the above dehydration. Moreover, the molecular dynamics simulations suggest that the aspartame molecules have two kinds of conformational flexibility in the intermediate state.

  15. Molecular characterization and genetic diversity of insecticidal crystal protein genes in native Bacillus thuringiensis isolates.

    PubMed

    Mahadeva Swamy, H M; Asokan, R; Mahmood, Riaz; Nagesha, S N

    2013-04-01

    The Western Ghats of Karnataka natural ecosystem are among the most diverse and is one of the eight hottest hotspots of biological diversity in the world, that runs along the western part of India through four states including Karnataka. Bacillus thuringiensis (Bt) strains were isolated from soils of Western Ghats of Karnataka and characterized by molecular and analytical methods as a result of which 28 new Bt-like isolates were identified. Bt strains were isolated from soil samples using sodium acetate selection method. The morphology of crystals was studied using light and phase contrast microscopy. Isolates were further characterized for insecticidal cry gene by PCR, composition of toxins in bacterial crystals by SDS-PAGE cloning, sequencing and evaluation of toxicity was done. As a result 28 new Bt-like isolates were identified. Majority of the isolates showed the presence of a 55 kDa protein bands on SDS-PAGE while the rest showed 130, 73, 34, and 25 kDa bands. PCR analysis revealed predominance of Coleopteran-active cry genes in these isolates. The variations in the nucleotide sequences, crystal morphology, and mass of crystal protein(s) purified from the Bt isolates revealed genetic and molecular diversity. Three strains containing Coleopteran-active cry genes showed higher activity against larvae Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) than B. thuringiensis subsp. Morrisoni. Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production.

  16. Detection of Non-Equilibrium Fluctuations in Active Gels

    NASA Astrophysics Data System (ADS)

    Bacanu, Alexandru; Broedersz, Chase; Gladrow, Jannes; Mackintosh, Fred; Schmidt, Christoph; Fakhri, Nikta

    Active force generation at the molecular scale in cells can result in stochastic non-equilibrium dynamics on mesoscpopic scales. Molecular motors such as myosin can drive steady-state stress fluctuations in cytoskeletal networks. Here, we present a non-invasive technique to probe non-equilibrium fluctuations in an active gel using single-walled carbon nanotubes (SWNTs). SWNTs are semiflexible polymers with intrinsic fluorescence in the near infrared. Both thermal and active motor-induced forces in the network induce transverse fluctuations of SWNTs. We demonstrate that active driven shape fluctuations of the SWNTs exhibit dynamics that reflect the non-equilibrium activity, in particular the emergence of correlations between the bending modes. We discuss the observation of breaking of detailed balance in this configurational space of the SWNT probes. Supported by National Defense Science and Engineering Graduate Student Fellowship (NDSEG).

  17. Effects of High Molecular Weight Species on Shear-Induced Orientation and Crystallization of Isotactic Polypropylene

    SciTech Connect

    Somani,R.; Yang, L.; Hsiao, B.

    2006-01-01

    In situ rheo-SAXS (small-angle X-ray scattering) and rheo-WAXD (wide-angle X-ray diffraction) techniques were used to investigate the role of high molecular weight species on the evolution of oriented microstructure in isotactic polypropylene (iPP) melt under shear flow. The two iPP samples, designated as PP-A and PP-B, respectively, had the same number-average (M{sub n}) but different weight-average (M{sub w}) and Z-average (M{sub z}) molecular weights. Molecular weight distribution (MWD) of PP-A and PP-B was such that for MW<10{sup 5} the MWD curves overlapped; whereas in the high MW tail region, the amount of high molecular weight species was higher in PP-B than PP-A. Both samples were subjected to an identical shear condition (rate=60 s{sup -1}, duration=5 s, T=155 degC). In situ 2D SAXS and WAXD images allowed the tracking of shear-induced oriented structures in the melt. It was found that the shish structures evolved much earlier, and the degree of crystal orientation and oriented crystal fractions were higher in PP-B than PP-A. Moreover, PP-B exhibited faster crystallization kinetics than PP-A. These results, along with the predictions of double reptation models of chain motion and experimental studies of chain conformation dynamics in dilute solutions under flow, suggest the following: When a polymer melt that consists of entangled chains of different lengths is deformed, the chain segments aligned with the flow eigenvector can undergo the abrupt coil-stretch-like transition, while other segments would remain in the coiled state. Since, flow-induced orientation decays much more slowly for long chains than for short chains, oriented high molecular weight species play a prominent role in formation of the stretched sections, where shish originates. Our experimental results are strong evidence of the hypothesis that even a small increase in the concentration of high molecular weight species causes a significant increase in the formation, stability and

  18. Topological defects in liquid crystals as templates for molecular self-assembly.

    PubMed

    Wang, Xiaoguang; Miller, Daniel S; Bukusoglu, Emre; de Pablo, Juan J; Abbott, Nicholas L

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly. PMID:26390324

  19. A simple theory of molecular organization in fullerene-containing liquid crystals

    NASA Astrophysics Data System (ADS)

    Peroukidis, S. D.; Vanakaras, A. G.; Photinos, D. J.

    2005-10-01

    Systematic efforts to synthesize fullerene-containing liquid crystals have produced a variety of successful model compounds. We present a simple molecular theory, based on the interconverting shape approach [Vanakaras and Photinos, J. Mater. Chem. 15, 2002 (2005)], that relates the self-organization observed in these systems to their molecular structure. The interactions are modeled by dividing each molecule into a number of submolecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and nonmesogenic linkage units. The blocks are constrained to move on a cubic three-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch monoadducts of C60, twin dendromesogenic branch monoadducts, and conical (badminton shuttlecock) multiadducts of C60. The dependence of the phase diagrams on the interaction parameters is explored. In spite of its many simplifications and the minimal molecular modeling used (three types of chemically distinct submolecular blocks with only repulsive interactions), the theory accounts remarkably well for the phase behavior of these systems.

  20. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  1. Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen.

    PubMed

    Pandian, Ramasamy P; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M; Hammel, P Chris; Manoharan, Periakaruppan T; Kuppusamy, Periannan

    2009-01-01

    The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å(2) in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å(2)) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO(2) with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy.

  2. Experiments with phase transitions at very high pressure. [compressed solidifed gases, semiconductors, superconductors, and molecular crystals

    NASA Technical Reports Server (NTRS)

    Spain, I. L.

    1983-01-01

    Diamond cells were constructed for use to 1 Mbar. A refrigerator for cooling diamond cells was adapted for studies between 15 and 300 K. A cryostat for superconductivity studies between 1.5 to 300 K was constructed. Optical equipment was constructed for fluorescence, transmission, and reflectance studies. X-ray equipment was adapted for use with diamond cells. Experimental techniques were developed for X-ray diffraction studies using synchrotron radiation. AC susceptibility techniques were developed for detecting superconducting transitions. The following materials were studied: compressed solidified gases (Xe, Ar), semiconductors (Ge, Si, GaAs), superconductors (Nb3Ge, Nb3Si, Nb3As, CuCl), molecular crystals (I).

  3. Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-Feng; Zhang, Huai-Wu

    We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

  4. Surface energetics of freely suspended fluid molecular monolayer and multilayer smectic liquid crystal films

    PubMed Central

    Nguyen, Zoom Hoang; Park, Cheol Soo; Pang, Jinzhong; Clark, Noel A.

    2012-01-01

    A study of the surface energetics of the thinnest substrate-free liquid films, fluid molecular monolayer and multilayer smectic liquid crystal films suspended in air, is reported. In films having monolayer and multilayer domains, the monolayer areas contract, contrary to predictions from the van der Waals disjoining pressure of thin uniform slabs. This discrepancy is accounted for by modeling the environmental asymmetry of the surface layers in multilayer films, leading to the possibility that preferential end-for-end polar ordering of the rod shaped molecules can reduce the surface energy of multilayers relative to that of the monolayer, which is inherently symmetric. PMID:22826264

  5. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

    PubMed

    Huang, Yanhua; Zong, Wenjun

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature. PMID:25426007

  6. Vacuum Ultraviolet Radiation Desorption of Molecular Contaminants Deposited on Quartz Crystal Microbalances

    NASA Technical Reports Server (NTRS)

    Albyn, Keith; Burns, Dewitt

    2006-01-01

    Recent quartz crystal microbalance measurements made in the Marshall Space Flight Center, Photo-Deposition Facility, for several materials, recorded a significant loss of deposited contaminants when the deposition surface of the microbalance was illuminated by a deuterium lamp. These measurements differ from observations made by other investigators in which the rate of deposition increased significantly when the deposition surface was illuminated with vacuum ultraviolet radiation. These observations suggest that the accelerated deposition of molecular contaminants on optically sensitive surfaces is dependant upon the contaminant being deposited and must be addressed during the materials selection process by common material screening techniques.

  7. Molecular dynamics calculation of elastic constants in Gay-Berne nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Allen, Michael P.; Warren, Mark A.; Wilson, Mark R.; Sauron, Alain; Smith, William

    1996-08-01

    In this paper we present a molecular dynamics calculation of the Frank elastic constants of a nematic liquid crystal. We study two well-known variants of the Gay-Berne potential, and determine the elastic constants by measuring orientational fluctuations as a function of wave vector, using reasonably large system sizes in the range 1000-8000 molecules. For some of the simulations, a set of Lagrangian constraints was applied in order to keep the director fixed along one of the box axes, facilitating the measurement of fluctuations in components of the reciprocal-space order tensor Q̂(k) in the director frame.

  8. Molecular beam epitaxy growth and optical properties of single crystal Zn3N2 films

    NASA Astrophysics Data System (ADS)

    Wu, Peng; Tiedje, T.; Alimohammadi, H.; Bahrami-Yekta, V.; Masnadi-Shirazi, M.; Wang, Cong

    2016-10-01

    Single crystal Zn3N2 films with (100) orientation have been grown by plasma-assisted molecular beam epitaxy on MgO and A-plane sapphire substrates with in situ optical reflectance monitoring of the growth. The optical bandgap was found to be 1.25-1.28 eV and an electron Hall mobility as high as 395 cm2 V-1 s-1 was measured. The films were n-type with carrier concentrations in the 1018-1019 cm-3 range.

  9. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals

    PubMed Central

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature. PMID:25426007

  10. Tuning 'de Vries-like' properties in binary mixtures of liquid crystals with different molecular lengths.

    PubMed

    Song, Qingxiang; Bogner, Andreas; Giesselmann, Frank; Lemieux, Robert P

    2013-09-25

    Smectic liquid crystals with 'de Vries-like' properties are characterized by a maximum layer contraction of ≤1% upon transition from the orthogonal SmA phase to the tilted SmC phase. We show that binary mixtures of 'de Vries-like' and conventional SmC mesogens with a molecular length ratio of 1.34 undergo a SmA-SmC phase transition with a maximum layer contraction ranging from 1.0 to 1.9% depending on the mixture composition.

  11. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

    PubMed

    Huang, Yanhua; Zong, Wenjun

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature.

  12. Molecular flexibility and orientational statistics of liquid crystals: Raman study of 7-CB and 8-OCB

    NASA Astrophysics Data System (ADS)

    Prasad, S. N.; Venugopalan, S.

    1981-09-01

    The Raman depolarization ratios of the -C≡N vibrational band of 7-CB and 8-OCB have been measured in the aligned liquid crystal and isotropic phases. The temperature dependence of the absolute orientational order parameters and have been evaluated for the mesophases of both compounds. A comparison of their values in the nematic phase with those determined by Miyano for 5-CB suggests that molecular flexibility is an importnant factor that serves to lower well below the predictions of mean field theories.

  13. DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography.

    PubMed

    Batyuk, Alexander; Wu, Yufan; Honegger, Annemarie; Heberling, Matthew M; Plückthun, Andreas

    2016-04-24

    DARPin libraries, based on a Designed Ankyrin Repeat Protein consensus framework, are a rich source of binding partners for a wide variety of proteins. Their modular structure, stability, ease of in vitro selection and high production yields make DARPins an ideal starting point for further engineering. The X-ray structures of around 30 different DARPin complexes demonstrate their ability to facilitate crystallization of their target proteins by restricting flexibility and preventing undesired interactions of the target molecule. However, their small size (18 kDa), very hydrophilic surface and repetitive structure can limit the DARPins' ability to provide essential crystal contacts and their usefulness as a search model for addressing the crystallographic phase problem in molecular replacement. To optimize DARPins for their application as crystallization chaperones, rigid domain-domain fusions of the DARPins to larger proteins, proven to yield high-resolution crystal structures, were generated. These fusions were designed in such a way that they affect only one of the terminal capping repeats of the DARPin and do not interfere with residues involved in target binding, allowing to exchange at will the binding specificities of the DARPin in the fusion construct. As a proof of principle, we designed rigid fusions of a stabilized version of Escherichia coli TEM-1 β-lactamase to the C-terminal capping repeat of various DARPins in six different relative domain orientations. Five crystal structures representing four different fusion constructs, alone or in complex with the cognate target, show the predicted relative domain orientations and prove the validity of the concept. PMID:26975886

  14. DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography.

    PubMed

    Batyuk, Alexander; Wu, Yufan; Honegger, Annemarie; Heberling, Matthew M; Plückthun, Andreas

    2016-04-24

    DARPin libraries, based on a Designed Ankyrin Repeat Protein consensus framework, are a rich source of binding partners for a wide variety of proteins. Their modular structure, stability, ease of in vitro selection and high production yields make DARPins an ideal starting point for further engineering. The X-ray structures of around 30 different DARPin complexes demonstrate their ability to facilitate crystallization of their target proteins by restricting flexibility and preventing undesired interactions of the target molecule. However, their small size (18 kDa), very hydrophilic surface and repetitive structure can limit the DARPins' ability to provide essential crystal contacts and their usefulness as a search model for addressing the crystallographic phase problem in molecular replacement. To optimize DARPins for their application as crystallization chaperones, rigid domain-domain fusions of the DARPins to larger proteins, proven to yield high-resolution crystal structures, were generated. These fusions were designed in such a way that they affect only one of the terminal capping repeats of the DARPin and do not interfere with residues involved in target binding, allowing to exchange at will the binding specificities of the DARPin in the fusion construct. As a proof of principle, we designed rigid fusions of a stabilized version of Escherichia coli TEM-1 β-lactamase to the C-terminal capping repeat of various DARPins in six different relative domain orientations. Five crystal structures representing four different fusion constructs, alone or in complex with the cognate target, show the predicted relative domain orientations and prove the validity of the concept.

  15. Elastic anisotropy of shocked aluminum single crystals: Use of molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zimmerman, J. A.; Winey, J. M.; Gupta, Y. M.

    2011-05-01

    Molecular dynamics (MD) calculations were used to examine shock wave propagation along [100], [111], and [110] directions in aluminum single crystals. Four different embedded-atom method (EAM) potentials were used to obtain wave profiles in ideal (defect-free) crystals shocked to peak longitudinal stresses approaching 13 GPa. Due to the lack of defects in the simulated crystals, the peak stresses considered, and the short time scales examined, inelastic deformation was not observed in the MD simulations. Time-averaged and spatially averaged continuum variables were determined from the MD simulations to compare results from different potentials and to provide a direct comparison with results from nonlinear elastic continuum calculations that incorporated elastic constants up to fourth order. These comparisons provide a basis for selecting the optimal potential from among the four potentials examined. MD results for shocks along the [100] direction show significant differences for stresses and densities determined from simulations using different EAM potentials. In contrast, the continuum variables for shocks along the [111] and [110] directions show smaller differences for three of the four potentials examined. Comparisons with the continuum calculations show that the potential developed recently by Winey, Kubota, and Gupta [Modell. Simul. Mater. Sci. Eng.0965-039310.1088/0965-0393/17/5/055004 17, 055004 (2009)] provides the best overall agreement between the MD simulations and the continuum calculations. As such, this potential is recommended for MD simulations of shock wave propagation in aluminum single crystals. Extending the current findings to elastic-plastic deformation would be desirable. More generally, our work demonstrates that MD simulations of elastic shock waves in defect-free single crystals, in combination with nonlinear elastic continuum calculations, constitute an important step in establishing the applicability of classical MD potentials for

  16. PREFACE: International Symposium on Non-Equilibrium Soft Matter 2010 International Symposium on Non-Equilibrium Soft Matter 2010

    NASA Astrophysics Data System (ADS)

    Kawakatsu, T.; Matsuyama, A.; Ohta, T.; Tanaka, H.; Tanaka, S.

    2011-07-01

    Soft matter is a rapidly growing interdisciplinary research field covering a range of subject areas including physics, chemistry, biology, mathematics and engineering. Some of the important universal features of these materials are their mesoscopic structures and their dynamics. Due to the existence of such large-scale structures, which nevertheless exhibit interactions of the order of the thermal energy, soft matter can readily be taken out of equilibrium by imposing a weak external field such as an electric field, a mechanical stress or a shear flow. The importance of the coexistence of microscopic molecular dynamics and the mesoscopic/macroscopic structures and flows requires us to develop hierarchical approaches to understand the nonlinear and nonequilibrium phenomena, which is one of the central issues of current soft matter research. This special section presents selected contributions from the 'International Symposium on Non-Equilibrium Soft Matter 2010' held from 17-20 August 2010 in Nara, Japan, which aimed to describe recent advances in soft matter research focusing especially on its nonequilibrium aspects. The topics discussed cover statics and dynamics of a wide variety of materials ranging from traditional soft matter like polymers, gels, emulsions, liquid crystals and colloids to biomaterials such as biopolymers and biomembranes. Among these studies, we highlighted the physics of biomembranes and vesicles, which has attracted great attention during the last decade; we organized a special session for this active field. The work presented in this issue deals with (1) structure formation in biomembranes and vesicles, (2) rheology of polymers and gels, (3) mesophases in block copolymers, (4) mesoscopic structures in liquid crystals and ionic liquids, and (5) nonequilibrium dynamics. This symposium was organized as part of a research project supported by the Grant-in-Aid for the priority area 'Soft Matter Physics' (2006-2010) from the Ministry of Education

  17. Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer

    SciTech Connect

    Vogeley, Lutz; Luecke, Hartmut

    2006-04-01

    Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2{sub 1}2{sub 1}2{sub 1} diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2{sub 1}2{sub 1}2{sub 1}). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2 and P2{sub 1}2{sub 1}2{sub 1}, which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form.

  18. Synthesis, crystal structure, and in vitro and in silico molecular docking of novel acyl thiourea derivatives

    NASA Astrophysics Data System (ADS)

    Haribabu, Jebiti; Subhashree, Govindarajulu Rangabashyam; Saranya, Sivaraj; Gomathi, Kannayiram; Karvembu, Ramasamy; Gayathri, Dasararaju

    2015-08-01

    In the present study, a series of six biologically active substituted acyl thiourea compounds (1-6) has been synthesized from cyclohexanecarbonyl isothiocyanate and various primary amines (2-methyl aniline, aniline, 4-methoxy aniline, 4-ethoxy aniline, benzyl amine and 2-methoxy aniline). The synthesized compounds were characterized by elemental analyses, UV-Visible, FT-IR, 1H & 13C NMR and mass spectroscopic techniques. Three dimensional molecular structure of two compounds (1 and 5) was determined by single crystal X-ray crystallography. All the synthesized compounds show good anti-oxidant and anti-haemolytic activities. In silico molecular docking studies were performed to screen against DprE1 and HSP90 enzymes targeting tuberculosis and cancer respectively.

  19. Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Busselez, Rémi; Cerclier, Carole V.; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

    2014-10-01

    A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.

  20. Crystal field and molecular orbital theory of MBm centres in glasses

    NASA Astrophysics Data System (ADS)

    Kustov, E. F.; Bulatov, L. I.; Dvoyrin, V. V.; Mashinsky, V. M.; Dianov, E. M.

    2010-01-01

    The spectral phenomena in optical fibres with bismuth-doped aluminosilicate glass core are explicated on the basis of a molecular orbital theory and of a Schrödinger equation solution, taking into account the exchange, spin-orbit and crystal field interactions of s, p and d electrons of M atoms (M signifies Bi, Sb, Pb, Sn, In, Te, etc) with ligand orbits of environmental B atoms (B signifies O, S, Se, etc). Energy level diagrams and selection rules of transitions between molecular orbital states of s and p electrons of MBm molecule permit us to determine the energies of the main spectral transitions of absorption and luminescent spectra and their correspondence with experimental spectra of different types of optical fibres is obtained.

  1. Molecular simulation study of polar order in orthogonal bent-core smectic liquid crystals.

    PubMed

    Peroukidis, Stavros D; Vanakaras, Alexandros G; Photinos, Demetri J

    2015-06-01

    We explore the phase behavior and structure of orthogonal smectic liquid crystals consisting of bent-core molecules (BCMs) by means of Monte Carlo molecular simulations. A simple athermal molecular model is introduced that describes the basic features of the BCMs. Phase transitions between uniaxial and biaxial (antiferroelectric) orthogonal smectics are obtained. The results indicate the presence of local in-plane polar correlations in the uniaxial smectic phase. The macroscopic uniaxial-biaxial transformation is rationalized in terms of local polar correlations giving rise to polar domains. The size of these polar domains grows larger under the action of an external vector field and their internal ordering is enhanced, leading to field-induced biaxial order-disorder transitions.

  2. Electronic excitation transport in photosynthesis and crystal and molecular structures of porphyrin compounds

    SciTech Connect

    Yang, Shumei.

    1991-04-22

    The excitation energy transfer in three photosynthetic organism samples, Bacteriochlorophyll a-protein from Prosthecochloris aestuarii, and enriched photosystem I particles from spinach chloroplasts, have been investigated by pump-probe ultrafast spectroscopy. The isotropic photobleaching profiles were best described by two exponential decay components in one Bchl a-protein complex, and three exponential decay components in another. The experimental results from the three samples show that nonrandom chromophore orientations exist and Sauer's pebble mosaic'' model is an appropriate one for excitation transfer in these samples. The polarized pump-probe transients have been analyzed in terms of an exciton hopping model that incorporates the known geometry of the Bchl a-protein. The crystal and molecular structures of four metalloporphyrins have been determined by X-ray diffraction and molecular mechanics. 207 refs., 44 figs., 15 tabs.

  3. Topological defects around a spherical nanoparticle in nematic liquid crystal: coarse-grained molecular dynamics simulations.

    PubMed

    Ilnytskyi, Jaroslav M; Trokhymchuk, Andrij; Schoen, Martin

    2014-09-21

    We consider the applicability of coarse-grained molecular dynamics for the simulation of defects in a nematic liquid crystal around a colloidal particle. Two types of colloids are considered, a soft colloid resembling a liquid crystal dendrimer or a similar macromolecule. In addition, a decorated colloid is used which could represent a gold nanoparticle with mesogen-modified surface. For both models we consider homeotropic and tangential anchoring. Precise control of the easy axis on the colloid's surface enables us to focus on specific planar arrangements in the case of a decorated colloid. The nematic phase is modelled explicitly via soft spherocylinders interacting through a potential, suggested by Lintuvuori and Wilson [J. Chem. Phys. 128, 044906 (2008)]. Properties of the nematic phase are studied by computing the Frank elastic constants. In addition, estimates for the nematic-isotropic transition and the coherence length allow us to establish a relation between energy and length scales with respect to experimental systems. Both models exhibit similar defect topologies, namely, that of a Saturn ring and a boojum-type of defect for homeotropic and tangential surface anchoring, respectively. In the decorated colloid model we tune the anchoring strength through the density of the mesogenic shell on the surface. We also found the biaxial boojum defect for the special case of longitudinal planar anchoring. The study demonstrates the potential of coarse-grained simulation methods for studying defects in liquid crystals. PMID:25240368

  4. Liquid Crystal Phases of Molecular Bananas: Polarity and Chirality as Broken Symmetries

    NASA Astrophysics Data System (ADS)

    Clark, Noel

    2006-03-01

    The study of the interplay of chirality and polarity has been a particularly rich theme of soft matter science since Meyer's seminal discovery that tilted smectics of chiral molecules are macroscopically polar. This event, and the subsequent realization of polar domains and high-speed electro-optic switching in chiral smectics, engaged the liquid crystal community in a worldwide pursuit of novel smectics for applications, featured by the synthesis of more than 50,000 new liquid crystal compounds, and by a consequent broad diversification of the palette of liquid crystal phases and possibilities for supermolecular ordering. A current important activity in this scenario is the study of polar order in synthetically achiral molecules, for example, in molecular bananas, which, as their shape suggests, might be expected to organize in a polar way. Indeed they do, but beyond this, almost everything learned about them has been surprising, including their persistent tendency to exhibit chirality as a spontaneously broken symmetry. I will discuss some of these new phases and phenomena, including the discovery of fluid conglomerates (Pasteur's experiment in a fluid), triclinic fluid order, chiral twist grain boundary phases of achiral molecules, chirality flipping and field-induced deracemization, ferroelectric and antiferroelectric phases with supermolecular- scale polarization modulation, and chiral thermotropic sponge phases.

  5. Accelerating MP2C dispersion corrections for dimers and molecular crystals

    NASA Astrophysics Data System (ADS)

    Huang, Yuanhang; Shao, Yihan; Beran, Gregory J. O.

    2013-06-01

    The MP2C dispersion correction of Pitonak and Hesselmann [J. Chem. Theory Comput. 6, 168 (2010)], 10.1021/ct9005882 substantially improves the performance of second-order Møller-Plesset perturbation theory for non-covalent interactions, albeit with non-trivial computational cost. Here, the MP2C correction is computed in a monomer-centered basis instead of a dimer-centered one. When applied to a single dimer MP2 calculation, this change accelerates the MP2C dispersion correction several-fold while introducing only trivial new errors. More significantly, in the context of fragment-based molecular crystal studies, combination of the new monomer basis algorithm and the periodic symmetry of the crystal reduces the cost of computing the dispersion correction by two orders of magnitude. This speed-up reduces the MP2C dispersion correction calculation from a significant computational expense to a negligible one in crystals like aspirin or oxalyl dihydrazide, without compromising accuracy.

  6. Self-assembled molecular wires of discotic liquid crystal formed with the crucial contribution of solvents

    NASA Astrophysics Data System (ADS)

    Park, Ji Hyun; Kim, Kyung Ho; Sosa Vargas, Lydia; Takanishi, Yoichi; Kim, Youn Sang; Yamamoto, Jun; Shimizu, Yo; Park, Yung Woo; Lagerwall, Jan Pf; Scalia, Giusy

    The self-organization of discotic liquid crystal molecules allows the spontaneous formation of well-aligned and tens of micrometer long molecular wires. In this work, we present a study based on hexapentyloxytriphenylene (HAT5) to investigate the molecular wire formation mechanism induced by solvents with selected characteristics, including chemical structure, boiling point, vapor pressure, and surface tension. The aromaticity in solvents such as toluene and benzene promotes the assembly into very long and thin wires entering into the structures, while chain-like solvents promotes more disordered structures. This finding allows a guided formation of different nanostructures from the same type of molecules just by choosing the type of solvent according to the need. Raman spectroscopy supports the idea of an active role of aromatic solvents entering into the molecular structure between discotic molecules with good quality intermolecular order. Highly aligned molecular wires bridging electrodes on SiO2 substrate show a clearly higher electrical conductivity compared to disorganized aggregates and bare HAT5. DLS and X-ray scattering were also used to investigate films and solutions. We finally discuss possible mechanisms behind the hierarchical assembly of the nanowires. NRF.

  7. Non-Equilibrium Water-Glassy Polymer Dynamics

    NASA Astrophysics Data System (ADS)

    Davis, Eric; Minelli, Matteo; Baschetti, Marco; Sarti, Giulio; Elabd, Yossef

    2012-02-01

    For many applications (e.g., medical implants, packaging), an accurate assessment and fundamental understanding of the dynamics of water-glassy polymer interactions is of great interest. In this study, sorption and diffusion of pure water in several glassy polymers films, such as poly(styrene) (PS), poly(methyl methacrylate) (PMMA), poly(lactide) (PLA), were measured over a wide range of vapor activities and temperatures using several experimental techniques, including quartz spring microbalance (QSM), quartz crystal microbalance (QCM), and time-resolved Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy. Non-Fickian behavior (diffusion-relaxation phenomena) was observed by all three techniques, while FTIR-ATR spectroscopy also provides information about the distribution of the states of water and water transport mechanisms on a molecular-level. Specifically, the states of water are significantly different in PS compared to PMMA and PLA. Additionally, a purely predictive non-equilibrium lattice fluid (NELF) model was applied to predict the sorption isotherms of water in these glassy polymers.

  8. Single Crystal Diffractometry and Solid State Modelling in the Analysis of Molecular Interactions.

    NASA Astrophysics Data System (ADS)

    Bracke, Ben Rachel Frans

    Central in this thesis is the analysis of intermolecular interactions which are essential in chemical, physical and biological processes. The geometry changes of a molecule that goes from the gas phase to its solid state, are indicative for the packing influence. The experimental geometries in this thesis are obtained from single crystal diffractometry by means of X-ray and neutron scattering. The basic principles used to infer the molecular structure from a set of X-ray data are summarised in chapter 1. The application of standard X-ray procedures is illustrated in chapter 2. The theoretical analysis is centred around ab initio modelling and is explained in chapter 3. To simulate the solid state an external Coulomb field of point charges is used to represent the coordinating neighbours of a particular molecule. This crystal field is used as a perturbation to modify the wave function of the target molecule. Some spectroscopic properties are also obtained from ab initio results and can be verified from IR/Raman. In Chapter 4, 5 and 6 discusses the consequence of packing on the geometry and spectroscopy of 2,3-diketopiperazine, oxalyldihydrazide, cyanoacetohydrazide and carbonohydrazide. It is well reproduced by crystal field perturbed ab initio calculations. All solid state calculations on these molecules converged to the a solid state geometry matching the experimentally observed structure, which is clearly different from the minimum energy form of the isolated entity. The influence of packing on the electron density distribution of oxalyldihydrazide is dealt with in chapters 7 to 11. The combination of X-ray and neutron diffraction at 103 K results in a structure that reveals an anharmonic potential which is confirmed from crystal field calculations. A X-(X,N) multipole refinement with an R = 1.2% shows a deformation density in which the lone pairs of the oxygen atom are rotated out of the molecular plane as a consequence of intermolecular hydrogen bonds. The

  9. How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures?

    PubMed

    Heit, Yonaton N; Beran, Gregory J O

    2016-08-01

    Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Möller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs. PMID:27484373

  10. Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method

    SciTech Connect

    Gerts, Egor D. Komolkin, Andrei V.; Burmistrov, Vladimir A.; Alexandriysky, Victor V.; Dvinskikh, Sergey V.

    2014-08-21

    Fully-atomistic molecular dynamics simulations were carried out on two similar cyanobiphenyl nematogens, HO-6OCB and 7OCB, in order to study effects of hydrogen bonds on local structure of liquid crystals. Comparable length of these two molecules provides more evident results on the effects of hydrogen bonding. The analysis of radial and cylindrical distribution functions clearly shows the differences in local structure of two mesogens. The simulations showed that anti-parallel alignment is preferable for the HO-6OCB. Hydrogen bonds between OH-groups are observed for 51% of HO-6OCB molecules, while hydrogen bonding between CN- and OH-groups occurs only for 16% of molecules. The lifetimes of H-bonds differ due to different mobility of molecular fragments (50 ps for N⋅⋅⋅H–O and 41 ps for O⋅⋅⋅H–O). Although the standard Optimized Potentials for Liquid Simulations - All-Atom force field cannot reproduce some experimental parameters quantitatively (order parameters are overestimated, diffusion coefficients are not reproduced well), the comparison of relative simulated results for the pair of mesogens is nevertheless consistent with the same relative experimental parameters. Thus, the comparative study of simulated and experimental results for the pair of similar liquid crystals still can be assumed plausible.

  11. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

    PubMed

    Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

    2015-02-01

    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.

  12. Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

    SciTech Connect

    Nguyen, Trung D; Carrillo, Jan-Michael Y; Brown, W Michael; Matheson, Michael A

    2014-01-01

    The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented largescale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.

  13. Understanding Molecular Epitaxial Mechanism of the γ-form Crystal and Chain Tilt in the α-form Single Crystal of Isotactic Polypropylene

    NASA Astrophysics Data System (ADS)

    Cao, Yan; van Horn, Ryan; Zhang, Guoliang; Sun, Hao-Jan; Jeong, Kwang-Un; Auriemma, Finizia; de Rosa, Claudio; Lotz, Bernard; Cheng, Stephen

    2012-02-01

    We attempt to investigate how the epitaxial domination of the crystal morphologies takes place in the γ-form of the chain-folded crystals using high molecular weight isotactic polypropylene (i-PP) samples with a controlled number of stereodefects. Two different morphologies were identified via transmission electron and atomic force microscopies (TEM and AFM). One is needle-like and the other is ``flat''. Based on the tilted selected area electron diffraction (SAED) results from TEM, the microscopic formation mechanism of the ``needle'' and ``flat'' morphology was discussed and it revealed that in the ``flat'' γ-form crystal, the initial α-form single crystal had to have a stem orientation tilted away from the thin film normal within the ac-plane around the b-axis. Elongated α2-form lath-like single crystals were grown from thin film melt at Tx = 145 ^oC -155 ^oC using commercial sample. SAED experimental results show that the stems in these lath-like single crystals were tilted at an unusual 17^o angle around the b-axis. This 17^o-stem tilt in the α2-form single crystals favors the (102) fold surface and appears to depend upon both conformational and chain folding constraints.

  14. Nonequilibrium thermodynamics of nucleation

    SciTech Connect

    Schweizer, M.; Sagis, L. M. C.

    2014-12-14

    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent literature results obtained by more microscopic considerations for the suppression of the nucleation rate due to nonisothermal effects.

  15. PREFACE: Progress in Nonequilibrium Green's Functions IV

    NASA Astrophysics Data System (ADS)

    Bonitz, Michael; Balzer, Karsten

    2010-04-01

    This is the fourth volume1 of articles on the theory of Nonequilibrium Green's functions (NEGF) and their modern application in various fields such as plasma physics, semiconductor physics, molecular electronics and high energy physics. It contains 23 articles written by experts in many-body theory and quantum transport who summarize recent progress in their respective area of research. The articles are based on talks given at the interdisciplinary conference Progress in Nonequilibrium Green's functions IV which was held 17-21 August 2009 at the University of Glasgow, Scotland. This conference continues the tradition of the previous meetings which started in 1999 and which aimed at an informal exchange across field boundaries. The previous meetings and the earlier proceedings proved to be very stimulating not only for young researchers but also for experienced scientists, and we are convinced that this fourth volume will be as successful as the previous ones. As before, this volume includes only extended review-type papers which are written in a way that they are understandable to a broad interdisciplinary audience. All papers published in this volume of Journal of Physics: Conference Series have been peer reviewed through processes administrated by the Editors assuring highest scientific standards. In the review process some papers were substantially revised and improved and some were rejected. This conference would not have been possible without the remarkable work of the local organizing team around John Barker and Scott Roy and the generous financial support from the University of Glasgow and the Deutsche Forschungsgemeinschaft via SFB-Transregio 24. Michael Bonitz and Karsten Balzer Kiel, February 2010 1 The first two volumes are Progress in Nonequilibrium Green's functions, M Bonitz (ed) and Progress in Nonequilibrium Green's functions II, M Bonitz and D Semkat (eds), which were published by World Scientific (Singapore), in 2000 and 2003, respectively (ISBN

  16. Comparison of the crystal structure and molecular models of N,N-dissobutyl-2-(octylphenylphosphinyl)acetamide(CMPO).

    SciTech Connect

    Rogers, R. D.; Rollins, A. N.; Gatrone, R. C.; Horwitz, E. P.; Chemistry; Northern Illinois Univ.

    1995-01-01

    The crystal structure of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide, or CMPO was recently determined. The compound crystallizes in the space group P2{sub 1}/c with a=13.446(6),b=22.280(7),c=17.217(7) Angstroms, {beta}=92.07(4) degrees, and D{sub calc}=1.05 g/cm3 for Z=8 @20 C. Molecular mechanics, molecular dynamics, and MNDO calculations were also performed on CMPO utilizing the SYBYL suite of programs. The results from these calculations are compared to the crystal structure and to similar calculations performed on CMPO using ALCHEMY. In general, the results from the calculations agree fairly well with the parameters from the crystal structure.

  17. Time Dependent Hartree Fock Equation: Gateway to Nonequilibrium Plasmas

    SciTech Connect

    James W. Dufty

    2007-04-28

    This is the Final Technical Report for DE-FG02-2ER54677 award “Time Dependent Hartree Fock Equation - Gateway to Nonequilibrium Plasmas”. Research has focused on the nonequilibrium dynamics of electrons in the presence of ions, both via basic quantum theory and via semi-classical molecular dynamics (MD) simulation. In addition, fundamental notions of dissipative dynamics have been explored for models of grains and dust, and for scalar fields (temperature) in turbulent edge plasmas. The specific topics addressed were Quantum Kinetic Theory for Metallic Clusters, Semi-classical MD Simulation of Plasmas , and Effects of Dissipative Dynamics.

  18. Effective interactions in molecular dynamics simulations of lysozyme solutions

    NASA Astrophysics Data System (ADS)

    Pellicane, Giuseppe; Sarkisov, Lev

    2014-09-01

    In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces.

  19. Crucial role of molecular planarity on the second order nonlinear optical property of pyridine based chalcone single crystals

    NASA Astrophysics Data System (ADS)

    Menezes, Anthoni Praveen; Jayarama, A.; Ng, Seik Weng

    2015-05-01

    An efficient nonlinear optical material 2E-3-(4-bromophenyl)-1-(pyridin-3-yl) prop-2-en-1-one (BPP) was synthesized and single crystals were grown using slow evaporation solution growth technique at room temperature. Grown crystal had prismatic morphology and its structure was confirmed by various spectroscopic studies, elemental analysis, and single crystal X-ray diffraction (XRD) technique. The single crystal XRD of the crystal showed that BPP crystallizes in monoclinic system with noncentrosymmetric space group P21 and the cell parameters are a = 5.6428(7) Å, b = 3.8637(6) Å, c = 26.411(2) Å, β = 97.568(11) deg and v = 575.82(12) Å3. The UV-Visible spectrum reveals that the crystal is optically transparent and has high optical energy band gap of 3.1 eV. The powder second harmonic generation efficiency (SHG) of BPP is 6.8 times that of KDP. From thermal analysis it is found that the crystal melts at 139 °C and decomposes at 264 °C. High optical transparency down to blue region, higher powder SHG efficiency and better thermal stability than that of urea makes this chalcone derivative a promising candidate for SHG applications. Furthermore, effect of molecular planarity on SHG efficiency and role of pyridine ring adjacent to carbonyl group in forming noncentrosymmetric crystal systems of chalcone family is also discussed.

  20. In command of non-equilibrium.

    PubMed

    Roduner, Emil; Radhakrishnan, Shankara Gayathri

    2016-05-21

    The second law of thermodynamics is well known for determining the direction of spontaneous processes in the laboratory, life and the universe. It is therefore often called the arrow of time. Less often discussed but just as important is the effect of kinetic barriers which intercept equilibration and preserve highly ordered, high energy non-equilibrium states. Examples of such states are many modern materials produced intentionally for technological applications. Furthermore, all living organisms fuelled directly by photosynthesis and those fuelled indirectly by living on high energy nutrition represent preserved non-equilibrium states. The formation of these states represents the local reversal of the arrow of time which only seemingly violates the second law. It has been known since the seminal work of Prigogine that the stabilisation of these states inevitably requires the dissipation of energy in the form of waste heat. It is this feature of waste heat dissipation following the input of energy that drives all processes occurring at a non-zero rate. Photosynthesis, replication of living organisms, self-assembly, crystal shape engineering and distillation have this principle in common with the well-known Carnot cycle in the heat engine. Drawing on this analogy, we subsume these essential and often sophisticated driven processes under the term machinery of life. PMID:27146424

  1. Graphene Nanocomposites with High Molecular Weight Poly(ε-caprolactone) Grafts: Controlled Synthesis and Accelerated Crystallization

    DOE PAGESBeta

    Mondal, Titash; Ashkar, Rana; Butler, Paul; Bhowmick, Anil K.; Krishnamoorti, Ramanan

    2016-02-08

    Grafting of high molecular weight polymers to graphitic nanoplatelets is a critical step toward the development of high performance graphene nanocomposites. However, designing such a grafting route has remained a major impediment. Herein, we report a "grafting to" synthetic pathway by which high molecular weight polymer, poly(e-caprolactone) (PCL), is tethered, at high grafting density, to highly anisotropic graphitic nanoplatelets. The efficacy of this tethering route and the resultant structural arrangements within the composite are confirmed by neutron and X-ray scattering measurements in the melt and solution phase. In the semicrystalline state, Xray analysis indicates that chain tethering onto the graphiticmore » nanoplatelets results in conformational changes of the polymer chains, which enhance the nucleation process and aid formation of PCL crystallites. This is corroborated by the superior thermal properties of the composite, manifested in accelerated crystallization kinetics and a significant increase in the thermal degradation temperature. Lastly, in principle, this synthesis route can be extended to a variety of high molecular weight polymers, which can open new avenues to solution-based processing of graphitic nanomaterials and the fabrication of complex 3D patterned graphitic nanocomposites.« less

  2. Thermodynamic scaling of dynamic properties of liquid crystals: Verifying the scaling parameters using a molecular model

    NASA Astrophysics Data System (ADS)

    Satoh, Katsuhiko

    2013-08-01

    The thermodynamic scaling of molecular dynamic properties of rotation and thermodynamic parameters in a nematic phase was investigated by a molecular dynamic simulation using the Gay-Berne potential. A master curve for the relaxation time of flip-flop motion was obtained using thermodynamic scaling, and the dynamic property could be solely expressed as a function of TV^{γ _τ }, where T and V are the temperature and volume, respectively. The scaling parameter γτ was in excellent agreement with the thermodynamic parameter Γ, which is the logarithm of the slope of a line plotted for the temperature and volume at constant P2. This line was fairly linear, and as good as the line for p-azoxyanisole or using the highly ordered small cluster model. The equivalence relation between Γ and γτ was compared with results obtained from the highly ordered small cluster model. The possibility of adapting the molecular model for the thermodynamic scaling of other dynamic rotational properties was also explored. The rotational diffusion constant and rotational viscosity coefficients, which were calculated using established theoretical and experimental expressions, were rescaled onto master curves with the same scaling parameters. The simulation illustrates the universal nature of the equivalence relation for liquid crystals.

  3. Thermal behavior of disordered phase of caffeine molecular crystal: Insights from Monte Carlo simulation studies

    NASA Astrophysics Data System (ADS)

    Murugan, N. Arul; Sayeed, Ahmed

    2009-05-01

    We have studied the thermal behavior of orientationally disordered phase of caffeine molecular crystal using variable shape variable size Monte Carlo simulations in isothermal-isobaric ensemble. We have investigated the structure, especially the nature of orientational disorder of caffeine molecules as a function of temperature in the range of 400-550 K. Experimentally this system is known to undergo a phase transition at 426 K (considered to be an orientational order-disorder transition) and melt at 512 K. Our simulations reproduce these two transitions in excellent agreement with experiment. We find that the in-plane reorientational motion of molecules is restricted to small angles below 425 K, and above this temperature, molecules undergo essentially free rotations in molecular plane, and we find the melting to occur between 525 and 550 K. In the high temperature disordered phase, the disorder is mostly attributable to the in-plane orientational motion of the molecules. The potential energy profile for the in-plane reorientational rotation has six wells as a consequence of specific packing of molecules in the ab crystallographic plane. Also we find considerable out-of-plane reorientational disorder for the molecules in the high temperature disordered phase. We have also studied the structure and orientational disorder of the system that is quenched from 450 to 300 K. We find that in the quenched phase, the molecular orientational arrangement remains partially frozen.

  4. Relationship between molecular association and re-entrant phenomena in polar calamitic liquid crystals.

    PubMed

    Mandle, Richard J; Cowling, Stephen J; Sage, Ian; Colclough, M Eamon; Goodby, John W

    2015-02-19

    The relationship between molecular association and re-entrant phase behavior in polar calamitic liquid crystals has been explored in two families of materials: the 4'-alkoxy-4-cyanobiphenyls (6OCB and 8OCB) and the 4'-alkoxy-4-nitrobiphenyls. Although re-entrant nematic phase behavior has previously been observed in the phase diagram of 6OCB/8OCB, this is not observed in mixtures of the analogous nitro materials. As there is no stabilization of the smectic A phase in mixture studies, it was conjectured that the degree of association for the nitro systems is greater than that for the cyano analogues. This hypothesis was tested by using measured dielectric anisotropies and computed molecular properties to obtain a value of the Kirkwood factor, g, which describes the degree of association of dipoles in a liquid. These computed values of g confirm that the degree of association for nitro materials is greater than that for cyano and offer a useful method for quantifying molecular association in systems exhibiting a re-entrant polymorphism.

  5. Relaxational dynamics in the glassy, supercooled liquid, and orientationally disordered crystal phases of a polymorphic molecular material

    NASA Astrophysics Data System (ADS)

    Jiménez-Ruiz, M.; González, M. A.; Bermejo, F. J.; Miller, M. A.; Birge, Norman O.; Cendoya, I.; Alegría, A.

    1999-04-01

    The relaxational dynamics of the ambient pressure phases of ethyl alcohol are studied by means of measurements of frequency dependent dielectric susceptibility. A comparison of the α relaxation in the supercooled liquid and in the rotator phase crystal indicates that the molecular rotational degrees of freedom are the dominant contribution to structural relaxation at temperatures near the glass transition, the flow processes having lesser importance. Below the glass transition a secondary β relaxation is resolved for the orientational and structural glasses. Computer molecular-dynamics results suggest that localized molecular librations, strongly coupled to the low-frequency internal molecular motions, are responsible for this secondary relaxation.

  6. From the molecular structure to spectroscopic and material properties: computational investigation of a bent-core nematic liquid crystal.

    PubMed

    Greco, Cristina; Marini, Alberto; Frezza, Elisa; Ferrarini, Alberta

    2014-05-19

    We present a computational investigation of the nematic phase of the bent-core liquid crystal A131. We use an integrated approach that bridges density functional theory calculations of molecular geometry and torsional potentials to elastic properties through the molecular conformational and orientational distribution function. This unique capability to simultaneously access different length scales enables us to consistently describe molecular and material properties. We can reassign (13)C NMR chemical shifts and analyze the dependence of phase properties on molecular shape. Focusing on the elastic constants we can draw some general conclusions on the unconventional behavior of bent-core nematics and highlight the crucial role of a properly-bent shape.

  7. Nonequilibrium chemical and radiation coupling phenomena in AOTV flowfields

    NASA Technical Reports Server (NTRS)

    Carlson, Leland A.; Gally, Thomas A.

    1991-01-01

    A flowfield model for the nonequilibrium stagnation region of high altitude entry vehicles which includes nonequilibrium chemistry, multitemperature, viscous, conduction, and diffusion effects is presented. It contains coupled nongray nonequilibrium radiative transfer for atoms and molecules and local thermodynamic nonequilibrium phenomena. Comparison with Fire 2 flight data verifies that the model is reasonably accurate; and it has been applied to two AFE trajectory points, a high speed return from Mars, a series of points at 80 km for 12 to 16 km/sec, and three altitudes at 16 km/sec. Based on these results shock slip is significant, radiation cooling/coupling is minor at AFE conditions but important by 14 km/sec and dominant at 16 km/sec, radiation for the AFE is small but important and primarily molecular, above 12 km/sec atomic radiation is a significant or dominant portion of the total heating, and local thermodynamic nonequilibrium is important and should be included in all models.

  8. Nonequilibrium fluctuation-dissipation inequality and nonequilibrium uncertainty principle.

    PubMed

    Fleming, C H; Hu, B L; Roura, Albert

    2013-07-01

    The fluctuation-dissipation relation is usually formulated for a system interacting with a heat bath at finite temperature, and often in the context of linear response theory, where only small deviations from the mean are considered. We show that for an open quantum system interacting with a nonequilibrium environment, where temperature is no longer a valid notion, a fluctuation-dissipation inequality exists. Instead of being proportional, quantum fluctuations are bounded below by quantum dissipation, whereas classically the fluctuations vanish at zero temperature. The lower bound of this inequality is exactly satisfied by (zero-temperature) quantum noise and is in accord with the Heisenberg uncertainty principle, in both its microscopic origins and its influence upon systems. Moreover, it is shown that there is a coupling-dependent nonequilibrium fluctuation-dissipation relation that determines the nonequilibrium uncertainty relation of linear systems in the weak-damping limit.

  9. Constant molecular rotation at the smectic-A to smectic-C* transition in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Kremer, F.; Vallerien, S. U.; Kapitza, H.; Zentel, R.; Fischer, E. W.

    1990-09-01

    We present dielectric measurements extended over the frequency range from 106 to 109 Hz on a pure ferroelectric liquid crystal. In clear contrast to the generally attributed origin of the ferroelectricity in liquid crystals arising from a slowing down of the molecular rotation around the long molecular axis, we find by direct observation the corresponding dielectric relaxation unchanged at the smectic-A to smectic-C* transition. This result requires a new interpretation of a recently published degenerate four-wave-mixing experiment by Lalanne et al. [Phys. Rev. Lett. 62, 3046 (1989)].

  10. Accommodative Behavior of Non-porous Molecular crystal at Solid-Gas and Solid-Liquid Interface

    NASA Astrophysics Data System (ADS)

    Mande, Hemant M.; Ghalsasi, Prasanna S.

    2015-09-01

    Molecular crystals demonstrate drastically different behavior in solid and liquid state, mainly due to their difference in structural frameworks. Therefore, designing of unique structured molecular compound which can work at both these interfaces has been a challenge. Here, we present remarkable ‘molecular’ property by non-porous molecular solid crystal, dinuclear copper complex (C6H5CH(X)NH2)2CuCl2, to reversibly ‘adsorb’ HCl gas at solid-gas interface as well as ‘accommodate’ azide anion at solid-liquid interface with crystal to crystal transformation. The latter process is driven by molecular recognition, self-assembly, and anchimeric assistance. The observed transformations are feasible due to breathing of inner and outer coordination sphere around metal center resulting in change in metal polyhedra for ‘accommodating’ guest molecule. These transformations cause changes in optical, magnetic, and/or ferroelectric property offering diversity in ‘sensing’ application. With the proposed underlying principles in these exceptional reversible and cyclic transformations, we prepared a series of compounds, can facilitate designing of novel multifunctional molecular materials.

  11. Accommodative Behavior of Non-porous Molecular crystal at Solid-Gas and Solid-Liquid Interface

    PubMed Central

    Mande, Hemant M.; Ghalsasi, Prasanna S.

    2015-01-01

    Molecular crystals demonstrate drastically different behavior in solid and liquid state, mainly due to their difference in structural frameworks. Therefore, designing of unique structured molecular compound which can work at both these interfaces has been a challenge. Here, we present remarkable ‘molecular’ property by non-porous molecular solid crystal, dinuclear copper complex (C6H5CH(X)NH2)2CuCl2, to reversibly ‘adsorb’ HCl gas at solid-gas interface as well as ‘accommodate’ azide anion at solid-liquid interface with crystal to crystal transformation. The latter process is driven by molecular recognition, self-assembly, and anchimeric assistance. The observed transformations are feasible due to breathing of inner and outer coordination sphere around metal center resulting in change in metal polyhedra for ‘accommodating’ guest molecule. These transformations cause changes in optical, magnetic, and/or ferroelectric property offering diversity in ‘sensing’ application. With the proposed underlying principles in these exceptional reversible and cyclic transformations, we prepared a series of compounds, can facilitate designing of novel multifunctional molecular materials. PMID:26411980

  12. Single crystal EPR measurements of the Fe8 and Mn_12 molecular magnetic clusters

    NASA Astrophysics Data System (ADS)

    Achey, Randall; Dalal, Naresh; Maccagnano, Sara; Negusse, Ezana; Lussier, Alex; Hill, Stephen

    2001-03-01

    We report high sensitivity, high field/frequency (up to 9 tesla/210 GHz) EPR measurements for oriented single crystals of the Fe8 and Mn_12 molecular magnetic clusters. Extrapolating the frequency dependence of transitions to zero-field allows us to directly, and accurately (to within 0.5%), determine the zero-field splittings, which are in reasonable agreement with other studies. Subsequent analysis of EPR spectra for field parallel and perpendicular to the easy axis enables us to independently deduce g-values and the spin Hamiltonian parameters up to fourth order. Analysis of individual resonances, which we can assign to known transitions, reveals a pronounced MS dependence of the resonance line widths. Furthermore, the line positions exhibit complex (again MS dependent) temperature dependences which cannot be reconciled with the standard spin Hamiltonian.

  13. Atomic resolution ADF-STEM imaging of organic molecular crystal of halogenated copper phthalocyanine.

    PubMed

    Haruta, Mitsutaka; Yoshida, Kaname; Kurata, Hiroki; Isoda, Seiji

    2008-05-01

    Annular dark-field (ADF) scanning transmission electron microscopy (STEM) measurements are demonstrated for the first time to be applicable for acquiring Z-contrast images of organic molecules at atomic resolution. High-angle ADF imaging by STEM is a new technique that provides incoherent high-resolution Z-contrast images for organic molecules. In the present study, low-angle ADF-STEM is successfully employed to image the molecular crystal structure of hexadecachloro-Cu-phthalocyanine (Cl16-CuPc), an organic molecule. The structures of CuPc derivatives (polyhalogenated CuPc with Br and Cl) are determined quantitatively using the same technique to determine the occupancy of halogens at each chemical site. By comparing the image contrasts of atomic columns, the occupancy of Br is found to be ca. 56% at the inner position, slightly higher than that for random substitution and in good agreement with previous TEM results.

  14. Excellently guarded materials against UV and oxygen in the surfactant molecular complex crystal matrix

    NASA Astrophysics Data System (ADS)

    Ichikawa, Haruyo; Iimura, Nahoko; Hirata, Hirotaka

    2000-07-01

    Crystalline surfactant molecular complexes (SCMs) generated between quaternary ammonium cationic surfactants such as CTAB and various additives disclose their excellent protective properties from UV light and oxygen to complex additive materials, which are occluded in the complex crystal matrix. The effects of UV and oxygen were followed by the absorption decay of additive chromophores in comparing that of naked additive specimens with that of those in the complexed state. From the decay profiles, the rate constants and the half-life times were estimated under the assumptions in which the photo and oxidation processes were dominated in accordance with the first-ordered reaction. The results afford us promising prospects in extending the shelf-life of every material, above all medicinal drug, with the consequence that these obtained values evidently demonstrate the remarkably suppressed rate and extremely elongated half-life times.

  15. Optical Kerr effect in nematic liquid crystals: a molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Kiyohara, Kenji; Ohta, Koji; Shimizu, Yo

    Molecular dynamics simulations of the Gay-Berne model have been undertaken and optical response properties calculated for the isotropic and nematic phases. The components of the optical response were calculated for the coordinate system with respect to the director. Furthermore, the response for the components was separated into the orientational and collision induced contributions in order to analyse the mechanism of the optical response. It was observed, in particular, that one of the depolarized components of the response function does not vanish after long times for the nematic phase, unlike in the isotropic phase. This means that the orientation of the director can be permanently changed by instant irradiation with polarized light. The results give a microscopic picture of the optical Kerr effect in nematic liquid crystals.

  16. Crystal Structures of Human and Staphylococcus aureus Pyruvate Carboxylase and Molecular Insights into the Carboxyltransfer Reaction

    SciTech Connect

    Xiang,S.; Tong, L.

    2008-01-01

    Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-Angstroms resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.

  17. High-resolution crystal structure reveals molecular details of target recognition by bacitracin

    PubMed Central

    Economou, Nicoleta J.; Cocklin, Simon; Loll, Patrick J.

    2013-01-01

    Bacitracin is a metalloantibiotic agent that is widely used as a medicine and feed additive. It interferes with bacterial cell-wall biosynthesis by binding undecaprenyl-pyrophosphate, a lipid carrier that serves as a critical intermediate in cell wall production. Despite bacitracin’s broad use, the molecular details of its target recognition have not been elucidated. Here we report a crystal structure for the ternary complex of bacitracin A, zinc, and a geranyl-pyrophosphate ligand at a resolution of 1.1 Å. The antibiotic forms a compact structure that completely envelopes the ligand’s pyrophosphate group, together with flanking zinc and sodium ions. The complex adopts a highly amphipathic conformation that offers clues to antibiotic function in the context of bacterial membranes. Bacitracin’s efficient sequestration of its target represents a previously unseen mode for the recognition of lipid pyrophosphates, and suggests new directions for the design of next-generation antimicrobial agents. PMID:23940351

  18. Elastic response of shocked aluminum single crystals: a continuum analysis of molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zimmerman, J. A.; Winey, J. M.; Gupta, Y. M.

    2011-06-01

    Molecular dynamics (MD) simulations were used to examine elastic shock wave propagation in aluminum single crystals along [100], [110] and [111] directions using four different embedded-atom method potentials. Continuum variables extracted from MD results show that stresses, densities, and temperatures for [100] shock propagation are significantly different for the various potentials, while the results for [110] and [111] propagation are similar for three of the four potentials. Overall, the recent potential by Winey, Kubota and Gupta [MSMSE 17, 055004 (2009)] provides the best agreement with nonlinear elastic calculations that include elastic constants up to fourth order. Our MD-continuum approach provides a key step in establishing the applicability of classical MD potentials for dynamic compression. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  19. Isotope effects in lithium hydride and lithium deuteride crystals by molecular dynamics simulations.

    PubMed

    Dammak, Hichem; Antoshchenkova, Ekaterina; Hayoun, Marc; Finocchi, Fabio

    2012-10-31

    Molecular dynamics (MD) simulations have been carried out to study isotope effects in lithium hydride and lithium deuteride crystals. Quantum effects on nuclear motion have been included through a quantum thermal bath (QTB). The interatomic forces were described either within the density functional theory (DFT) in the generalized gradient approximation (GGA) or by the phenomenological approach using the shell model. For both models, the isotopic shift in the lattice parameter can be successfully predicted by QTB-MD simulations. The slope of the experimental isotopic shift in pressure is satisfactorily reproduced by QTB-MD within DFT-GGA, in contrast to both density functional perturbation theory and QTB-MD with the shell model. We have analyzed the reasons for these discrepancies through the vibrational densities of states and the isotopic shifts in bulk modulus. The results illustrate the importance of anharmonic contributions to vibrations and to the isotopic pressure shift between LiH and LiD.

  20. Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

    SciTech Connect

    Wang, Linjun E-mail: oleg.prezhdo@rochester.edu; Chen, Liping; Prezhdo, Oleg V. E-mail: oleg.prezhdo@rochester.edu; Akimov, Alexey V.

    2013-11-07

    The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

  1. Deformation and fracture of LLM-105 molecular crystals studied by nanoindentation

    NASA Astrophysics Data System (ADS)

    Kucheyev, S. O.; Gash, A. E.; Lorenz, T.

    2014-04-01

    Mechanical deformation of crystalline high explosives plays an important role in both the fabrication of polymer-bonded explosives and controlling their sensitivity to mechanically-induced decomposition. Here, we study the deformation behavior of (010)-oriented LLM-105 and β-HMX molecular crystals by nanoindentation with pyramidal (Berkovich) and spherical (19 μm-diameter) indenters. Results reveal indentation elastic moduli of 21 and 18 GPa and Berkovich hardness of 0.73 and 0.65 GPa for LLM-105 and HMX, respectively. For LLM-105 (but not for HMX), indentation stress remains essentially unchanged for spherical indentation strains of ˜10-25%, suggesting that inelastic deformation above a certain strain proceeds via flow at constant stress. Both materials exhibit highly anisotropic surface fracture patterns after Berkovich and spherical indentation, consistent with fracture along (011) cleavage planes. No deformation-induced material decomposition is observed in either material for the indentation conditions used.

  2. Liquid crystals and their interactions with colloidal particles and phospholipid membranes: Molecular simulation studies

    NASA Astrophysics Data System (ADS)

    Kim, Evelina B.

    Experimentally, liquid crystals (LC) can be used as the basis for optical biomolecular sensors that rely on LC ordering. Recently, the use of LC as a reporting medium has been extended to investigations of molecular scale processes at lipid laden aqueous-LC interfaces and at biological cell membranes. In this thesis, we present two related studies where liquid crystals are modelled at different length scales. We examine (a) the behavior of nanoscopic colloidal particles in LC systems, using Monte Carlo (MC) molecular simulations and a mesoscopic dynamic field theory (DyFT); and (b) specific interactions of two types of mesogens with a model phospholipid bilayer, using atomistic molecular dynamics (MD) at the A-nm scale. In (a), we consider colloidal particles suspended in a LC, confined between two walls. We calculate the colloid-substrate and colloid-colloid potentials of mean force (PMF). For the MC simulations, we developed a new technique (ExEDOS or Expanded Ensemble Density Of States) that ensures good sampling of phase space without prior knowledge of the energy landscape of the system. Both results, simulation and DyFT, indicate a repulsive force acting between a colloid and a wall. In contrast, both techniques indicate an overall colloid-colloid attraction and predict a new topology of the disclination lines that arises when the particles approach each other. In (b), we find that mesogens (pentylcyanobiphenyl [5CB] or difluorophenyl-pentylbicyclohexyl [5CF]) preferentially partition from the aqueous phase into a dipalmitoylphosphatidylcholine (DPPC) bilayer. We find highly favorable free energy differences for partitioning (-18kBT for 5CB, -26k BT for 5CF). We also simulated fully hydrated bilayers with embedded 5CB or 5CF at concentrations used in recent experiments (6 mol% and 20 mol%). The presence of mesogens in the bilayer enhances the order of lipid acyl tails and changes the spatial and orientational arrangement of lipid headgroup atoms. A stronger

  3. Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal

    NASA Astrophysics Data System (ADS)

    Wang, Feng-he; Wang, Feng-yun; Gong, Xue-dong

    2012-10-01

    Four acrylamide polymer flocculants, anionic polyacrylamide P(AA-co-AM), cationic polyacrylamide P(DMB-co-AM), nonionic polyacrylamide P(AM), and hydrophobical polyacrylamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants with the (012) surface of alumina crystal (Al2O3) have been simulated by molecular dynamics method. All the polymers can bind tightly with Al2O3 crystal, the interaction between the O of polymers and Al of the (012) surface of Al2O3 is significantly strong. The order of binding energy is as follows: P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), implying a better flocculation performance of P(DMB-co-AM) than the others. Analysis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the Al atoms of Al2O3. The polymers' structures deform when they combine with Al2O3 crystal, but the deformation energies are low and far less than non-bonding energies. Flocculation experiments in suspension medium of 1%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM). The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), which is in excellent agreement with the simulation results of binding energy.

  4. CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals

    NASA Astrophysics Data System (ADS)

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-01

    A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol-1 on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.

  5. Reactive molecular dynamics simulations of shock through a single crystal of pentaerythritol tetranitrate.

    PubMed

    Budzien, Joanne; Thompson, Aidan P; Zybin, Sergey V

    2009-10-01

    Large-scale molecular dynamics simulations and the reactive force field ReaxFF were used to study shock-induced initiation in crystalline pentaerythritol tetranitrate (PETN). In the calculations, a PETN single crystal was impacted against a wall, driving a shockwave back through the crystal in the [100] direction. Two impact speeds (4 and 3 km/s) were used to compare strong and moderate shock behavior. The primary difference between the two shock strengths is the time required to exhibit the same qualitative behaviors with the lower impact speed lagging behind the faster impact speed. For both systems, the shock velocity exhibits an initial deceleration due to onset of endothermic reactions followed by acceleration due to the onset of exothermic reactions. At long times, the shock velocity reaches a steady value. After the initial deceleration period, peaks are observed in the profiles of the density and axial stress with the strongly shocked system having sharp peaks while the weakly shocked system developed broad peaks due to the slower shock velocity acceleration. The dominant initiation reactions in both systems lead to the formation of NO(2) with lesser quantities of NO(3) and formaldehyde also produced.

  6. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

    2015-02-01

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  7. Coarse-Grained Molecular Monte Carlo Simulations of Liquid Crystal-Nanoparticle Mixtures

    NASA Astrophysics Data System (ADS)

    Neufeld, Ryan; Kimaev, Grigoriy; Fu, Fred; Abukhdeir, Nasser M.

    Coarse-grained intermolecular potentials have proven capable of capturing essential details of interactions between complex molecules, while substantially reducing the number of degrees of freedom of the system under study. In the domain of liquid crystals, the Gay-Berne (GB) potential has been successfully used to model the behavior of rod-like and disk-like mesogens. However, only ellipsoid-like interaction potentials can be described with GB, making it a poor fit for many real-world mesogens. In this work, the results of Monte Carlo simulations of liquid crystal domains using the Zewdie-Corner (ZC) potential are presented. The ZC potential is constructed from an orthogonal series of basis functions, allowing for potentials of essentially arbitrary shapes to be modeled. We also present simulations of mixtures of liquid crystalline mesogens with nanoparticles. Experimentally these mixtures have been observed to exhibit microphase separation and formation of long-range networks under some conditions. This highlights the need for a coarse-grained approach which can capture salient details on the molecular scale while simulating sufficiently large domains to observe these phenomena. We compare the phase behavior of our simulations with that of a recently presented continuum theory. This work was made possible by the Natural Sciences and Engineering Research Council of Canada and Compute Ontario.

  8. CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals.

    PubMed

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-14

    A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems. PMID:26874495

  9. Investigation of hydrogen bonds properties in the terephthalic acid crystal, using molecular dynamics method.

    PubMed

    Wierzbicka, Ewa; Boczar, Marek; Wójcik, Marek J

    2014-09-15

    The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.

  10. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

    PubMed Central

    Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

    2013-01-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

  11. Photoinduced reversible switching of porosity in molecular crystals based on star-shaped azobenzene tetramers.

    PubMed

    Baroncini, Massimo; d'Agostino, Simone; Bergamini, Giacomo; Ceroni, Paola; Comotti, Angiolina; Sozzani, Piero; Bassanetti, Irene; Grepioni, Fabrizia; Hernandez, Taylor M; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-08-01

    The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of great interest for separation, catalysis, optoelectronics, holography, mechanical actuation and solar energy conversion. Here, we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, the porosity of which can be tuned by changing the peripheral substituents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties such as birefringence as well as the capture of CO2 from the gas phase. The linear design, structural versatility and synthetic accessibility make this new family of materials potentially interesting for technological applications. PMID:26201739

  12. Phonon dispersion in acene molecular crystals using van der Waals density functionals

    NASA Astrophysics Data System (ADS)

    Brown-Altvater, Florian; Rangel, Tonatiuh; Neaton, Jeffrey B.

    Much progress has been made of late in understanding the fundamental processes in optoelectronic materials. An ongoing challenge is the accurate inclusion of nuclear motion and to go beyond the Born-Oppenheimer approximation. Especially in materials like molecular crystals, where van der Waals (vdW) forces dominate the cohesive energy and the electronic structure is very sensitive to intermolecular geometry, phonons can be an important facilitator and dissipation mechanism. Thus there is a need to assess and understand the efficacy of existing approaches for phonon dispersions in vdW-bound solids. In this work we use a vdW density functional to calculate the phonon dispersion of members of the acene family. We establish the accuracy of the method using naphthalene, obtaining excellent agreement with experimental results, and in a further step, we explore the strength of the electron-phonon coupling across the Brillouin zone. Taken all together, our calculations illustrate the potential for quantitative prediction of vibrational properties of weakly-bound organic crystals over the entire Brillouin zone from first principles.

  13. Director alignment relative to the temperature gradient in nematic liquid crystals studied by molecular dynamics simulation.

    PubMed

    Sarman, Sten; Laaksonen, Aatto

    2014-07-28

    The director alignment relative to the temperature gradient in nematic liquid crystal model systems consisting of soft oblate or prolate ellipsoids of revolution has been studied by molecular dynamics simulation. The temperature gradient is maintained by thermostating different parts of the system at different temperatures by using a Gaussian thermostat. It is found that the director of the prolate ellipsoids aligns perpendicularly to the temperature gradient whereas the director of the oblate ellipsoids aligns parallel to this gradient. When the director is oriented in between the parallel and perpendicular orientations a torque is exerted forcing the director to the parallel or perpendicular orientation. Because of symmetry restrictions there is no linear dependence of the torque being a pseudovector on the temperature gradient being a polar vector in an axially symmetric system such as a nematic liquid crystal. The lowest possible order of this dependence is quadratic. Thus the torque is very weak when the temperature gradient is small, which may explain why this orientation phenomenon is hard to observe experimentally. In both cases the director attains the orientation that minimises the irreversible entropy production.

  14. Nonequilibrium Growth Processes

    NASA Astrophysics Data System (ADS)

    Ramanlal, Pradipkumar

    A number of issues in nonequilibrium aggregation and pattern formation are addressed. Using analytical, numerical, and computer simulation methods, an attempt is made to infer or conclude on a number of aspects of compact, fractal and dendritic growth. Using the ballistic aggregation model, we develop a mean-field continuum theory that successfully predicts the morphology of thin films formed by vapor deposition and aggregation on a seed. In addition, by relating the evolution of the surface of ballistic deposits to a problem of spin dynamics, we develop a theory for the roughness of the interface, showing it to be a self-affine fractal, and at the same time having a bounded interface length. We also develop a deterministic continuum model for the fractal growth of diffusion-limited aggregation (DLA), related to the problem of two-dimensional viscous fluid flow in a hele-shaw cell. With the introduction of a real-space renormalization scheme we solve the equations numerically to produce fractal growth and patterns reminiscent of real fluid flow experiments. In addition, we show the fractal patterns to have the same metric properties of DLA, with a prediction for the asymptotic value for the fractal dimension; D = 1.65. An important consequence of these results is that DLA is sufficiently unstable and sensitive to initial conditions to produce fractal growth in the absence of external noise present in computer simulation results. Further, we examine the effect of an underlying lattice on the growth process in both the discrete and continuum deterministic formulations of DLA. In both cases, the lattice anisotropy destroys the fractal characteristics and this is confirmed by studying large on-lattice DLA simulations. And finally, we infer a relationship between the lattice anisotropy and the phenomenological formulations of the interfacial anisotropy, and examine the nature of the transition between fractal and dendritic growth as a function of the interfacial

  15. Direct Numerical Simulation Study of Thermochemical Nonequilibrium Effect on Mixing and Combustion

    NASA Astrophysics Data System (ADS)

    Fievet, Romain; Voelkel, Stephen; Koo, Heeseok; Raman, Venkat; Varghese, Philip

    2014-11-01

    Nonequilibrium of internal states of molecules is an important physical phenomenon that could affect flow behavior in supersonic flows. Translational nonequilibrium, where molecular velocities do not conform to the Maxwell distribution could impact dissipation processes in turbulence. Similarly, vibrational and/or rotational nonequilibrium will lead to marked changes in mixing and combustion. In this study, these nonequilibrium effects are explored using direct numerical simulation of a supersonic hydrogen jet issuing into a coflow of air. Nonequilibrium reaction rates derived using detailed computational chemistry methods are used in the flow simulations. It is shown that underpopulation of vibrational states leads to significant change in flame stabilization. Hence, the processing of the incoming air by the bow shocks formed ahead of a scramjet could lead to significant ignition delay.

  16. Crystal growth and melting in NiZr alloy: Linking phase-field modeling to molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Guerdane, M.; Wendler, F.; Danilov, D.; Teichler, H.; Nestler, B.

    2010-06-01

    We compare results from molecular dynamics simulations with those from phase-field modeling concerning the solidification and melting kinetics of a planar [NicZr1-c]liquid-Zrcrystal interface. Our study is an illustration that both approaches may predict the same quantitative physical description when the key parameters calculated within the atomistic molecular dynamics approach are used to construct the mesoscopic phase-field model. We show in this way that a thermodynamic consistent phase-field model can be applied down to the range of atomic structure. At the same time, molecular dynamics simulation seems to be capable to treat correctly relaxation dynamics, driven by thermodynamic forces, in a nonequilibrium state of solidification and melting. We discuss, in particular, how the free energy from atomistic calculations is used to design the phase dependent free-energy density in the phase-field model. Bridging the gap between both simulation approaches contributes to a better understanding of the thermodynamic and kinetic processes underlying the solidification and melting processes in alloys out of chemical equilibrium. The effective thermodynamic enhancement of the diffusivity through the strong negative enthalpy of mixing in the NiZr solution is discussed.

  17. Role of the Strength of Drug-Polymer Interactions on the Molecular Mobility and Crystallization Inhibition in Ketoconazole Solid Dispersions.

    PubMed

    Mistry, Pinal; Mohapatra, Sarat; Gopinath, Tata; Vogt, Frederick G; Suryanarayanan, Raj

    2015-09-01

    The effects of specific drug-polymer interactions (ionic or hydrogen-bonding) on the molecular mobility of model amorphous solid dispersions (ASDs) were investigated. ASDs of ketoconazole (KTZ), a weakly basic drug, with each of poly(acrylic acid) (PAA), poly(2-hydroxyethyl methacrylate) (PHEMA), and polyvinylpyrrolidone (PVP) were prepared. Drug-polymer interactions in the ASDs were evaluated by infrared and solid-state NMR, the molecular mobility quantified by dielectric spectroscopy, and crystallization onset monitored by differential scanning calorimetry (DSC) and variable temperature X-ray diffractometry (VTXRD). KTZ likely exhibited ionic interactions with PAA, hydrogen-bonding with PHEMA, and weaker dipole-dipole interactions with PVP. On the basis of dielectric spectroscopy, the α-relaxation times of the ASDs followed the order: PAA > PHEMA > PVP. In addition, the presence of ionic interactions also translated to a dramatic and disproportionate decrease in mobility as a function of polymer concentration. On the basis of both DSC and VTXRD, an increase in strength of interaction translated to higher crystallization onset temperature and a decrease in extent of crystallization. Stronger drug-polymer interactions, by reducing the molecular mobility, can potentially delay the crystallization onset temperature as well as crystallization extent.

  18. Studying the Impact of Modified Saccharides on the Molecular Dynamics and Crystallization Tendencies of Model API Nifedipine.

    PubMed

    Kaminska, E; Tarnacka, M; Wlodarczyk, P; Jurkiewicz, K; Kolodziejczyk, K; Dulski, M; Haznar-Garbacz, D; Hawelek, L; Kaminski, K; Wlodarczyk, A; Paluch, M

    2015-08-01

    Molecular dynamics of pure nifedipine and its solid dispersions with modified carbohydrates as well as the crystallization kinetics of active pharmaceutical ingredient (API) above and below the glass transition temperature were studied in detail by means of broadband dielectric spectroscopy (BDS), differential scanning calorimetry (DSC), and X-ray diffraction method. It was found that the activation barrier of crystallization increases in molecular dispersions composed of acetylated disaccharides, whereas it slightly decreases in those consisting of modified monocarbohydrates for the experiments carried out above the glass transition temperature. As shown by molecular dynamics simulations it can be related to the strength, character, and structure of intermolecular interactions between API and saccharides, which vary dependently on the excipient. Long-term physical stability studies showed that, in solid dispersions consisting of acetylated maltose and acetylated sucrose, the crystallization of nifedipine is dramatically slowed down, although it is still observable for a low concentration of excipients. With increasing content of modified carbohydrates, the crystallization of API becomes completely suppressed. This is most likely due to additional barriers relating to the intermolecular interactions and diffusion of nifedipine that must be overcome to trigger the crystallization process.

  19. The Strength of Single Crystal Copper under Uniaxial Shock Compression at Mbar pressures

    SciTech Connect

    Murphy, W; Higginbotham, A; Kimminau, G; Barbrel, B; Bringa, E; Hawreliak, J; Koenig, M; McBarron, W; Meyers, M; Nagler, B; Ozaki, N; Park, N; Remington, B; Rothman, S; Vinko, S M; Whitcher, T; Wark, J

    2009-05-21

    In situ x-ray diffraction has been used to measure the shear strain (and thus strength) of single crystal copper shocked to Mbar pressures along the [001] and [111] axes. These direct shear strain measurements indicate shear strengths at these ultra-high strain rates (of order 10{sup 9} s{sup -1}) of a few GPa, which are both broadly in agreement with the extrapolation of lower strain-rate data and with non-equilibrium molecular dynamics simulations.

  20. Fracture of molecular glasses under tension and fracture-induced crystallization

    NASA Astrophysics Data System (ADS)

    Chen, Yinshan; Powell, Travis; Yu, Lian

    Molecular glasses are formed and fractured by cooling a liquid on a less thermally expansive substrate. In-plane tension is created by the mismatch of thermal expansion coefficients and accumulates to cause catastrophic network fracture. This simple experiment allowed the measurement of fracture toughness and the heat of fracture of molecular glasses for the first time. For the systems studied (o - terphenyl, indomethacin, and sucrose benzoate), the fracture condition is well described by recent theories and a material-specific energy release rate (fracture toughness) approximately 1 J/m2. The heat of fracture was found to be anomalously high relative to the value expected for the energy release rate and the surface area created. The large release of heat is caused by the reduction of heat capacity for a glass film constrained on a rigid substrate. Rapid crystal growth was observed along fracture surfaces. (Ref.: Powell, C. T.; Chen, Y.; Yu, L. J. Non-Crystalline Solids 2015, 429, 122-128)

  1. Modeling emission features of salicylidene aniline molecular crystals: A QM/QM' approach.

    PubMed

    Presti, Davide; Labat, Frédéric; Pedone, Alfonso; Frisch, Michael J; Hratchian, Hrant P; Ciofini, Ilaria; Cristina Menziani, Maria; Adamo, Carlo

    2016-04-01

    A new computational protocol relying on the use of electrostatic embedding, derived from QM/QM' ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals is here applied to the β-form of salicylidene aniline (SA). The first singlet excited states (S1 ) of the SA cis-keto and trans-keto conformers, surrounded by a cluster of other molecules representing the crystalline structure, were optimized by using a QM/QM' ONIOM approach with and without electronic embedding. The model system consisting of the central salicylidene aniline molecule was treated at the DFT level by using either the B3LYP, PBE0, or the CAM-B3LYP functional, whereas the real system was treated at the HF level. The CAM-B3LYP/HF level of theory provides emission energies in good agreement with experiment with differences of -20/-32 nm (cis-keto form) and -8/-14 nm (trans-keto form), respectively, whereas notably larger differences are obtained using global hybrids. Though such differences on the optical properties arise from the density functional choice, the contribution of the electronic embedding is rather independent of the functional used. This plays in favor of a more general applicability of the present protocol to other crystalline molecular systems. PMID:26919703

  2. Visual detection of 2,4,6-trinitrotolune by molecularly imprinted colloidal array photonic crystal.

    PubMed

    Lu, Wei; Asher, Sanford A; Meng, Zihui; Yan, Zequn; Xue, Min; Qiu, Lili; Yi, Da

    2016-10-01

    We developed a photonic crystal (PhC) sensor for the quantification of 2,4,6-trinitrotoluene (TNT) in solution. Monodisperse (210nm in diameter) molecularly imprinted colloidal particles (MICs) for TNT were prepared by the emulsion polymerization of methyl methacrylate and acrylamide in the presence of TNT as a template. The MICs were then self-assembled into close-packed opal PhC films. The adsorption capacity of the MICs for TNT was 64mg TNT/g. The diffraction from the PhC depended on the TNT concentration in a methanol/water (3/2, v/v) potassium dihydrogen phosphate buffer solution (pH=7.0, 30mM). The limit of detection (LOD) of the sensor was 1.03μg. The color of the molecularly imprinted colloidal array (MICA) changed from green to red with an 84nm diffraction red shift when the TNT concentration increased to 20mM. The sensor response time was 3min. The PhC sensor was selective for TNT compared to similar compounds such as 2,4,6-trinitrophenol, 2,4-dinitrotoluene, 2,6-dinitrotoluene, 2-nitromesitylene, 4-nitrotoluene, 2-nitrotoluene, 1,3-dinitrobenzene, methylbenzene, 4-nitrophenol, 2-nitroaniline, 3-aminophenol and 3-nitroaniline. The sensor showed high stability with little response change after three years storage. This sensor technology might be useful for the visual determination of TNT. PMID:27214001

  3. Thermally controlled optical shutter in an inter-molecular hydrogen bonded liquid crystal

    NASA Astrophysics Data System (ADS)

    Vijayakumar, V. N.; Madhu Mohan, M. L. N.

    2011-11-01

    Novel homologs series of supra-molecular liquid crystals have been isolated. Hydrogen bond is formed between mandelic acid (MD) and various homologs of p- n-alkyloxy benzoic acids (nOBA) and has been confirmed by FTIR studies. Optical polarizing microscopic observations show that all these materials exhibit rich liquid crystallinity with various mesophases. Phase transition temperatures and enthalpy values are experimentally evaluated by DSC studies and the phase diagram of homologous series has been constructed. An interesting feature is the observation of thermally controlled reversible optical shuttering action in one of the homolog, wherein with the increment of temperature the homeotropic texture changes to homogenous texture of smectic F. Thus, this optical shuttering phenomenon is reversible. Optical tilt angle data of two homologs have been fitted to power law equation and it is found that the mean field theory prediction is valid. The light intensity profile in homeotropic region of smectic F in one complex has been experimentally analyzed and a steep sudden decrement of the intensity of light manifesting the distortion of the molecular alignment is experimentally found.

  4. High Resolution Imaging of Defect Structures in Polymer and Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Martin, David

    2003-03-01

    We have been developing techniques for the low dose High Resolution Electron Microscopy (HREM) imaging of defect structures in polymer and organic molecular crystals. We have examined a variety of technologically important materials systems including rigid-rod polymers, poly(imides), poly(diacetylenes), poly(bisthiazoles), poly(bisoxazoles), and aromatic polyamides such as poly(paraphenylene terephthalamide) (PPTA or Kevlar(R)) and poly(metaphenylene diisophthalamide) (MPDI or Nomex(R)). These studies have made it possible for us to image the molecular reorganization in the vicinity of dislocations, surfaces, and grain boundaries. We have also learned about the micromechanisms of lattice bending and twisting. Most recently we have been examining the microstructure of pentacene, a highly-crystalline conjugated organic small molecule that is of interest for making flexible electronic devices such as thin-film transistors. We have also been examing the utility of low voltage techniques using a table-top sized electron microscope that operates near 5 kV.

  5. In situ analysis of melt-drawing behavior of ultrahigh molecular weight polyethylene films with different molecular weights: roles of entanglements on oriented crystallization.

    PubMed

    Kato, Satomi; Tanaka, Hidekazu; Yamanobe, Takeshi; Uehara, Hiroki

    2015-04-16

    Ultrahigh molecular weight polyethylene (UHMW-PE) films having different molecular weights (MWs) were melt-drawn at 150 °C. The stress-strain curve for higher-MW film exhibits higher stress on the characteristic plateau region and a subsequent steeper increase of stress due to strain hardening. Structural changes during such melt-drawing were analyzed using in situ wide-angle X-ray diffraction measurements. Hexagonal crystallization occurs at the beginning of the plateau region, independent of the sample MW. Once this hexagonal reflection intensity is saturated, it remains constant even at the later stage of draw. In contrast, orthorhombic reflection intensities gradually increase with increasing draw strain. Both of these oriented crystallizations into plateau hexagonal and increasing orthorhombic forms are accelerated with increasing MW. Correspondingly, the higher amount of extended chain crystals (ECCs) was confirmed from morphological observation for the resultant melt-drawn films of the higher-MW sample. Deep entanglements can effectively transmit the applied stress; thus, the oriented amorphous melts induce rapid hexagonal crystallization with disentangling shallow entanglements, which subsequently transforms into orthorhombic form. Such hexagonal crystallization plays the role of a thermodynamic pathway for growing such ECCs, where the stable orthorhombic form gradually accumulates with increasing draw strain.

  6. In situ analysis of melt-drawing behavior of ultrahigh molecular weight polyethylene films with different molecular weights: roles of entanglements on oriented crystallization.

    PubMed

    Kato, Satomi; Tanaka, Hidekazu; Yamanobe, Takeshi; Uehara, Hiroki

    2015-04-16

    Ultrahigh molecular weight polyethylene (UHMW-PE) films having different molecular weights (MWs) were melt-drawn at 150 °C. The stress-strain curve for higher-MW film exhibits higher stress on the characteristic plateau region and a subsequent steeper increase of stress due to strain hardening. Structural changes during such melt-drawing were analyzed using in situ wide-angle X-ray diffraction measurements. Hexagonal crystallization occurs at the beginning of the plateau region, independent of the sample MW. Once this hexagonal reflection intensity is saturated, it remains constant even at the later stage of draw. In contrast, orthorhombic reflection intensities gradually increase with increasing draw strain. Both of these oriented crystallizations into plateau hexagonal and increasing orthorhombic forms are accelerated with increasing MW. Correspondingly, the higher amount of extended chain crystals (ECCs) was confirmed from morphological observation for the resultant melt-drawn films of the higher-MW sample. Deep entanglements can effectively transmit the applied stress; thus, the oriented amorphous melts induce rapid hexagonal crystallization with disentangling shallow entanglements, which subsequently transforms into orthorhombic form. Such hexagonal crystallization plays the role of a thermodynamic pathway for growing such ECCs, where the stable orthorhombic form gradually accumulates with increasing draw strain. PMID:25785561

  7. Open problems in non-equilibrium physics

    SciTech Connect

    Kusnezov, D.

    1997-09-22

    The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions.

  8. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

    NASA Astrophysics Data System (ADS)

    Lee, Hsing; Darden, Thomas; Pedersen, Lee

    1995-09-01

    Long molecular dynamics (MD) simulations for two crystal RNA dinucleotides ApU (2.0 ns) and GpC (1.5 ns) were performed, starting from the crystallographic positions of all heavy atoms in the crystals. By employing the particle-mesh-Ewald algorithm [Darden et al., J. Chem. Phys. 98 (1993) 10089] to accommodate the long-range Coulomb interactions, highly accurate MD structures were obtained for both crystals. The instantaneous root-mean-square positional deviations of the heavy atoms equilibrate at approximately 0.4 Å for both systems, while the experimental and calculated temperature factors are comparable in size. These results describe the first successful crystal MD simulation of RNA molecules.

  9. Molecular dynamics simulation of the dissolution process of a cellulose triacetate-II nano-sized crystal in DMSO.

    PubMed

    Hayakawa, Daichi; Ueda, Kazuyoshi; Yamane, Chihiro; Miyamoto, Hitomi; Horii, Fumitaka

    2011-12-27

    An understanding of the dissolution process of cellulose derivatives is important not only for basic research but also for industrial purposes. We investigated the dissolution process of cellulose triacetate II (CTA II) nano-sized crystal in DMSO solvent using molecular dynamics simulations. The nano-sized crystal consists of 18 CTA chains. During the 9 ns simulation, it was observed that one chain (C01) located at the corner of the lozenge crystal was solvated by the DMSO molecules and moved away from the remaining cluster into the DMSO solvent. The analysis showed that the breakage of the interaction between the H1, H3, and H5 hydrogens of the pyranose ring and the acetyl carbonyl oxygen in the C01 and C02 adjacent chains would be crucial for the dissolution of CTA. The DMSO molecules solvating around these atoms would prevent the re-crystallization of the CTA molecules and facilitate further dissolution. PMID:22063502

  10. Local structure and molecular motions in imidazolium hydrogen malonate crystal as studied by 2H and 13C NMR

    NASA Astrophysics Data System (ADS)

    Mizuno, M.; Chizuwa, M.; Umiyama, T.; Kumagai, Y.; Miyatou, T.; Ohashi, R.; Ida, T.; Tansho, M.; Shimizu, T.

    2015-04-01

    The local structure and molecular motion of the imidazolium hydrogen malonate crystal were investigated using solid-state 2H and 13C NMR. The imidazolium ion undergoes isotropic rotation, which is correlated with a defect in the crystal, as observed by 2H NMR broadline spectra above 263 K. A 180∘ flip of the imidazolium ion in the regular site was observed from 2H NMR quadrupole Carr-Purcell-Meiboom-Gill (QCPMG) spectra. The Grotthuss mechanism was accompanied by a 180∘ flip of the imidazolium ion in regular sites. Moreover, the proton transfer associated with the imidazolium ion of the defective crystal is important for proton conductivity of the imidazolium hydrogen malonate crystal.

  11. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin.

    PubMed

    Jagadeesan, G; Malathy, P; Gunasekaran, K; Harikrishna Etti, S; Aravindhan, S

    2014-11-01

    Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3₁21, with unit-cell parameters a=b=55.64, c=153.38 Å, β=120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit. PMID:25372822

  12. Computer simulation of nonequilibrium processes

    SciTech Connect

    Hoover, W.G.; Moran, B.; Holian, B.L.; Posch, H.A.; Bestiale, S.

    1987-01-01

    Recent atomistic simulations of irreversible macroscopic hydrodynamic flows are illustrated. An extension of Nose's reversible atomistic mechanics makes it possible to simulate such non-equilibrium systems with completely reversible equations of motion. The new techniques show that macroscopic irreversibility is a natural inevitable consequence of time-reversible Lyapunov-unstable microscopic equations of motion.

  13. A molecular dynamics study of the growth rate of SiC crystal and its dependence on the temperature

    NASA Astrophysics Data System (ADS)

    Zhou, Naigen; Zhang, Chi; Zeng, Xiang; Yuan, Jiren; Zhou, Lang

    2016-07-01

    Molecular dynamics simulations of crystal growth of SiC in the reduced temperature range of 0.51-1.02 have been carried out. In particular, the relationship between the growth rate and the reduced temperature has been investigated by the simulations. The results show that the growth rate increases first with the temperature and then decreases dramatically after passing through a maximum. Calculations of the growth rate according to the Wilson-Frenkel model have been applied to the present system, with the required parameters of the activation energy for atomic diffusion and the free energy changes calculated by molecular dynamics simulations. The temperature dependence of the growth rate, calculated by molecular dynamics, agrees with the prediction of Wilson-Frenkel model, indicating that the crystal growth of SiC is a kind of diffusion limited growth.

  14. Optical and resonant X-ray diffraction studies of molecular arrangements in several liquid crystals

    NASA Astrophysics Data System (ADS)

    Wang, Suntao

    Using optical and x-ray techniques, we have studied several selected liquid crystal compounds formed by three types of molecules: rod-like; hockey-stick-shaped and bent-core-shaped molecules. This thesis describes four research projects. The first one is a study of the molecular arrangements in freestanding films of three chiral compounds showing no-layer-shrinkage behavior above their bulk SmA-SmC* transition temperatures. Upon cooling under a proper electric field, novel nonplanar-anticlinic-synclinic and nonplanar-synclinic transitions have been observed in two compounds. Increasing electric field can induce a rare transition from a synclinic to an anticlinic structure. Results from both x-ray diffraction and optical studies indicate that different molecular packing arrangements exist within the Sm A phase window. The second project is to investigate three achiral meta-substituted three-ring compounds. These compounds exhibit two different tilted smectic phases, Sm C1 and SmC2. A recent paper has reported that mirror symmetry is broken in one of these compounds. However, no mirror symmetry breaking has been observed in our studies of the same compound. Our studies of another two compounds confirmed previous results that the Sm C1 and SmC2 phases are Sm C and SmCA, respectively. Thirdly, we confirmed the SM C*FI2 -SmC* phase sequence reversal in one liquid crystal compound and specially prepared binary mixtures. This phase sequence reversal was predicted by a recent phenomenological model. Moreover, the temperature range for the SM C*FI2 phase increases significantly in the mixture suggesting that such a phase sequence may exist in other compounds. The last project is to study the B2 phase formed by bent-core molecules using polarization-analyzed resonant x-ray diffraction. The B2 phase has three possible arrangements which show a two-layer unit cell. We analyzed the polarization of the resonant peaks at different Bragg orders. By comparing a theoretical

  15. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

    SciTech Connect

    Jagadeesan, G.; Malathy, P.; Gunasekaran, K.; Harikrishna Etti, S.; Aravindhan, S.

    2014-10-25

    The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

  16. Stagnation Point Nonequilibrium Radiative Heating and the Influence of Energy Exchange Models

    NASA Technical Reports Server (NTRS)

    Hartung, Lin C.; Mitcheltree, Robert A.; Gnoffo, Peter A.

    1991-01-01

    A nonequilibrium radiative heating prediction method has been used to evaluate several energy exchange models used in nonequilibrium computational fluid dynamics methods. The radiative heating measurements from the FIRE II flight experiment supply an experimental benchmark against which different formulations for these exchange models can be judged. The models which predict the lowest radiative heating are found to give the best agreement with the flight data. Examination of the spectral distribution of radiation indicates that despite close agreement of the total radiation, many of the models examined predict excessive molecular radiation. It is suggested that a study of the nonequilibrium chemical kinetics may lead to a correction for this problem.

  17. Discriminatory Proofreading Regimes in Nonequilibrium Systems

    NASA Astrophysics Data System (ADS)

    Murugan, Arvind; Huse, David A.; Leibler, Stanislas

    2014-04-01

    We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in nonequilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change in its energy. In biological contexts, higher sensitivity corresponds to stronger discrimination between molecular substrates with different energetics competing in the same reaction. We study this discriminatory ability in systems with discrete states that are connected by a general network of transitions. We find multiple regimes of different discriminatory ability when the energy of a given state of the network is varied. Interestingly, the occupancy of the state can even increase with its energy, corresponding to an "antiproofreading" regime. The number and properties of such discriminatory regimes are limited by the topology of the network. Finally, we find that discriminatory regimes can be changed without modifying any "hard-wired" structural aspects of the system but rather by simply changing external chemical potentials.

  18. An integral equation and simulation study of hydrogen inclusions in a molecular crystal of short-capped nanotubes

    NASA Astrophysics Data System (ADS)

    Lomba, Enrique; Bores, Cecilia; Notario, Rafael; Sánchez-Gil, V.

    2016-09-01

    In this work we have assessed the ability of a recently proposed three-dimensional integral equation approach to describe the explicit spatial distribution of molecular hydrogen confined in a crystal formed by short-capped nanotubes of C50 H10. To that aim we have resorted to extensive molecular simulation calculations whose results have been compared with our three-dimensional integral equation approximation. We have first tested the ability of a single C50 H10 nanocage for the encapsulation of H2 by means of molecular dynamics simulations, in particular using targeted molecular dynamics to estimate the binding Gibbs energy of a host hydrogen molecule inside the nanocage. Then, we have investigated the adsorption isotherm of the nanocage crystal using grand canonical Monte Carlo simulations in order to evaluate the maximum load of molecular hydrogen. For a packing close to the maximum load explicit hydrogen density maps and density profiles have been determined using molecular dynamics simulations and the three-dimensional Ornstein–Zernike equation with a hypernetted chain closure. In these conditions of extremely tight confinement the theoretical approach has shown to be able to reproduce the three-dimensional structure of the adsorbed fluid with accuracy down to the finest details.

  19. An integral equation and simulation study of hydrogen inclusions in a molecular crystal of short-capped nanotubes.

    PubMed

    Lomba, Enrique; Bores, Cecilia; Notario, Rafael; Sánchez-Gil, V

    2016-09-01

    In this work we have assessed the ability of a recently proposed three-dimensional integral equation approach to describe the explicit spatial distribution of molecular hydrogen confined in a crystal formed by short-capped nanotubes of C50 H10. To that aim we have resorted to extensive molecular simulation calculations whose results have been compared with our three-dimensional integral equation approximation. We have first tested the ability of a single C50 H10 nanocage for the encapsulation of H2 by means of molecular dynamics simulations, in particular using targeted molecular dynamics to estimate the binding Gibbs energy of a host hydrogen molecule inside the nanocage. Then, we have investigated the adsorption isotherm of the nanocage crystal using grand canonical Monte Carlo simulations in order to evaluate the maximum load of molecular hydrogen. For a packing close to the maximum load explicit hydrogen density maps and density profiles have been determined using molecular dynamics simulations and the three-dimensional Ornstein-Zernike equation with a hypernetted chain closure. In these conditions of extremely tight confinement the theoretical approach has shown to be able to reproduce the three-dimensional structure of the adsorbed fluid with accuracy down to the finest details. PMID:27367179

  20. An integral equation and simulation study of hydrogen inclusions in a molecular crystal of short-capped nanotubes

    NASA Astrophysics Data System (ADS)

    Lomba, Enrique; Bores, Cecilia; Notario, Rafael; Sánchez-Gil, V.

    2016-09-01

    In this work we have assessed the ability of a recently proposed three-dimensional integral equation approach to describe the explicit spatial distribution of molecular hydrogen confined in a crystal formed by short-capped nanotubes of C50 H10. To that aim we have resorted to extensive molecular simulation calculations whose results have been compared with our three-dimensional integral equation approximation. We have first tested the ability of a single C50 H10 nanocage for the encapsulation of H2 by means of molecular dynamics simulations, in particular using targeted molecular dynamics to estimate the binding Gibbs energy of a host hydrogen molecule inside the nanocage. Then, we have investigated the adsorption isotherm of the nanocage crystal using grand canonical Monte Carlo simulations in order to evaluate the maximum load of molecular hydrogen. For a packing close to the maximum load explicit hydrogen density maps and density profiles have been determined using molecular dynamics simulations and the three-dimensional Ornstein-Zernike equation with a hypernetted chain closure. In these conditions of extremely tight confinement the theoretical approach has shown to be able to reproduce the three-dimensional structure of the adsorbed fluid with accuracy down to the finest details.

  1. ATOMIC AND MOLECULAR PHYSICS: High-Temperature Raman Investigation on Phase Transition of LBO Crystal

    NASA Astrophysics Data System (ADS)

    Zhang, Xia; Wan, Song-Ming; Yin, Shao-Tang; You, Jing-Lin

    2009-11-01

    The high-temperature Raman spectroscopy technique is applied to investigate the phase transition of LiB3O5 crystal. The result shows that the crystal is stable in the range of 293-893 K. When the temperature increases up to above 1107K, the phase transition occurs. In the liquid phase, Li2B4O7 crystal precipitates out. Up to 1173K, the Li2B4O7 crystal disappears in the melt.

  2. Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

    ERIC Educational Resources Information Center

    Bindel, Thomas H.

    2008-01-01

    A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

  3. Crystal and molecular structure of aspartame X HCl X 2H2O.

    PubMed

    Görbitz, C H

    1987-02-01

    The crystal and molecular structure of the hydrochloride salt of the peptide sweetener aspartame (alpha-L-Asp-L-Phe methyl ester) has been determined at 120 K using 3877 reflections with I greater than 2.5 sigma I. Space group P2(1)2(1)2(1), cell dimensions a = 6.768(1), b = 9.796(1) and c = 26.520(3) A; final R factor 0.033. While the N-terminal L-Asp group in the structure of aspartame itself forms a six-membered ring with an intramolecular hydrogen bond between the carboxylate and the protonated amino terminus, the corresponding group in the hydrochloride adopts a completely different conformation with a weak intramolecular hydrogen bond between the carboxyl group and the N atom of the L-Phe residue. The L-Phe methyl ester moiety is rather similar in the two structures. Of the many possible conformations of aspartame, only one may be expected to function as a substrate at the receptor site for sweet taste, and a proposal is made for this active conformation. PMID:3604519

  4. Light-triggered crystallization of a molecular host-guest complex.

    PubMed

    Clever, Guido H; Tashiro, Shohei; Shionoya, Mitsuhiko

    2010-07-28

    The control of structural changes in supramolecular assemblies is a key point in the development of molecular machines. The reversible photoisomerization of organic compounds such as azobenzene using light as an external input is especially suited because no waste products are generated. Based on our previous studies on the quantitative encapsulation of suitably sized bis-sulfonate guests by a self-assembled, metal-organic cage consisting of four rigid, bent bis-monodentate pyridyl ligands and two Pd(II) ions, we show here how the light-switchable guest cis-4,4'-azobenzene bis-sulfonate can be expelled from its 1:1 host-guest complex triggered by its photoisomerization to the trans-isomer. Using a highly soluble, PEGylated cage derivative, the full reversibility of this light-driven encapsulation/release process is demonstrated. In contrast, a sample of the less soluble, unsubstituted cages including 1 equiv of the cis-guest was shown to result in immediate crystallization upon photoisomerization of the guest. X-ray structure analysis confirmed the guest molecules having left the cavity of the host and on the contrary joining the cages into a polymeric material by binding to their Pd(II) centers from outside.

  5. Strong and Anomalous Thermal Expansion Precedes the Thermosalient Effect in Dynamic Molecular Crystals.

    PubMed

    Panda, Manas K; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče

    2016-01-01

    The ability of thermosalient solids, organic analogues of inorganic martensites, to move by rapid mechanical reconfiguration or ballistic event remains visually appealing and potentially useful, yet mechanistically elusive phenomenon. Here, with a material that undergoes both thermosalient and non-thermosalient phase transitions, we demonstrate that the thermosalient effect is preceded by anomalous thermal expansion of the unit cell. The crystal explosion occurs as sudden release of the latent strain accumulated during the anisotropic, exceedingly strong expansion of the unit cell with αa = 225.9 × 10(-6) K(-1), αb = 238.8 × 10(-6) K(-1) and αc = -290.0 × 10(-6) K(-1), the latter being the largest negative thermal expansivity observed for an organic compound thus far. The results point out to the occurence of the thermosalient effect in phase transitions as means to identify new molecular materials with strong positive and/or negative thermal expansion which prior to this work could only be discovered serendipitously. PMID:27403616

  6. Vibrational spectra and anharmonic effects in crystals studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Dolgusheva, E. B.; Trubitsin, V. Yu.

    2012-12-01

    Using the molecular-dynamics method with pair and many-body potentials of interatomic interaction we study the role of the lattice vibrations and anharmonicity in structural stability and structural transformations in both bulk crystals (periodic boundary conditions) and nanoparticles (free boundary conditions) in a wide range of temperatures and pressures. In particular, the structural stability and lattice dynamics of the high-temperature bcc phase in zirconium and iron are studied under various thermodynamical conditions (P-const, V-const). The dispersion curves of the vibrational spectrum of Zr are calculated at high temperature and pressure. The anharmonic corrections (frequency shift and phonon damping) are estimated for different volumes. It is shown that the lattice vibrations in bcc Zr, remaining strongly anharmonic in a wide interval of volumes and temperatures, determine the peculiarities of the zirconium P-T phase diagram. The effect of the cluster size on physical properties of bcc Zr and Fe nanoparticles is studied. It is found that in bcc Zr nanocrystals the temperature and mechanism of the structural bcc → hcp transition depend substantially on the particle size and shape. The effect of lattice vibrations on the mechanism of structural bcc → hcp transformation and the local lattice distortions is discussed.

  7. Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum

    SciTech Connect

    Luo, Hai-Bin; Zheng, Heping; Zimmerman, Matthew D.; Chruszcz, Maksymilian; Skarina, Tatiana; Egorova, Olga; Savchenko, Alexei; Edwards, Aled M.; Minor, Wladek

    2010-05-12

    A crystal structure of the putative N-carbamoylsarcosine amidase (CSHase) Ta0454 from Thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35 {angstrom}. CSHases are involved in the degradation of creatinine. Ta0454 shares a similar fold and a highly conserved C-D-K catalytic triad (Cys123, Asp9, and Lys90) with the structures of three cysteine hydrolases (PDB codes 1NBA, 1IM5, and 2H0R). Molecular dynamics (MD) simulations of Ta0454/N-carbamoylsarcosine and Ta0454/pyrazinamide complexes were performed to determine the structural basis of the substrate binding pattern for each ligand. Based on the MD-simulated trajectories, the MM/PBSA method predicts binding free energies of -24.5 and -17.1 kcal/mol for the two systems, respectively. The predicted binding free energies suggest that Ta0454 is selective for N-carbamoylsarcosine over pyrazinamide, and zinc ions play an important role in the favorable substrate bound states.

  8. Possible superfluidity of molecular hydrogen in a two-dimensional crystal phase of sodium

    NASA Astrophysics Data System (ADS)

    Cazorla, Claudio; Boronat, Jordi

    2013-12-01

    We theoretically investigate the ground-state properties of a molecular para-hydrogen (p-H2) film in which crystallization is energetically frustrated by embedding sodium (Na) atoms periodically distributed in a triangular lattice. In order to fully deal with the quantum nature of p-H2 molecules, we employ the diffusion Monte Carlo method and realistic semiempirical pairwise potentials describing the interactions between H2-H2 and Na-H2 species. In particular, we calculate the energetic, structural, and superfluid properties of two-dimensional Na-H2 systems within a narrow density interval around equilibrium at zero temperature. In contrast to previous computational studies considering other alkali metal species such as rubidium and potassium, we find that the p-H2 ground state is a liquid with a significantly large superfluid fraction of ρs/ρ=0.29(2). The appearance of p-H2 superfluid response is due to the fact that the interactions between Na atoms and H2 molecules are less attractive than between H2 molecules. This induces a considerable reduction of the hydrogen density which favors the stabilization of the liquid phase.

  9. Sensing picornaviruses using molecular imprinting techniques on a quartz crystal microbalance.

    PubMed

    Jenik, Michael; Schirhagl, Romana; Schirk, Christian; Hayden, Oliver; Lieberzeit, Peter; Blaas, Dieter; Paul, Guntram; Dickert, Franz L

    2009-07-01

    Molecular imprinting techniques were adapted to design a sensor for the human rhinovirus (HRV) and the foot-and-mouth disease virus (FMDV), which are two representatives of picornaviruses. Stamp imprinting procedures lead to patterned polyurethane layers that depict the geometrical features of the template virus, as confirmed by AFM for HRV. Quartz crystal microbalance (QCM) measurements show that the resulting layers incorporate the template viruses reversibly and lead to mass effects that are almost an order of magnitude higher than those of nonspecific adsorption. Thus, for example, the sensor yields a net frequency effect of -300 Hz when applying a virus suspension with a concentration of approximately 100 microg/mL with an excellent signal-to-noise ratio. The cavities are not only selective to shape but also to surface chemistry: different HRV serotypes (HRV1A, HRV2, HRV14, and HRV16, respectively) can be distinguished with the sensor materials by a selectivity factor of 3, regardless of the group (major/minor) to which they belong. The same selectivity factor can be observed between HRV and FMDV. Hence, imprinting leads to an "artificial antibody" toward viruses, which does not only recognize their receptor binding sites, but rather detects the whole virus as an entity. Brunauer-Emmett-Teller (BET) studies allow simulation of the sensor characteristics and reveal the number of favorable binding sites in the coatings. PMID:19469532

  10. Strong and Anomalous Thermal Expansion Precedes the Thermosalient Effect in Dynamic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Panda, Manas K.; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče

    2016-07-01

    The ability of thermosalient solids, organic analogues of inorganic martensites, to move by rapid mechanical reconfiguration or ballistic event remains visually appealing and potentially useful, yet mechanistically elusive phenomenon. Here, with a material that undergoes both thermosalient and non-thermosalient phase transitions, we demonstrate that the thermosalient effect is preceded by anomalous thermal expansion of the unit cell. The crystal explosion occurs as sudden release of the latent strain accumulated during the anisotropic, exceedingly strong expansion of the unit cell with αa = 225.9 × 10‑6 K‑1, αb = 238.8 × 10‑6 K‑1 and αc = ‑290.0 × 10‑6 K‑1, the latter being the largest negative thermal expansivity observed for an organic compound thus far. The results point out to the occurence of the thermosalient effect in phase transitions as means to identify new molecular materials with strong positive and/or negative thermal expansion which prior to this work could only be discovered serendipitously.

  11. Liquid crystals with patterned molecular orientation as an electrolytic active medium.

    PubMed

    Peng, Chenhui; Guo, Yubing; Conklin, Christopher; Viñals, Jorge; Shiyanovskii, Sergij V; Wei, Qi-Huo; Lavrentovich, Oleg D

    2015-11-01

    Transport of fluids and particles at the microscale is an important theme in both fundamental and applied science. One of the most successful approaches is to use an electric field, which requires the system to carry or induce electric charges. We describe a versatile approach to generate electrokinetic flows by using a liquid crystal (LC) with surface-patterned molecular orientation as an electrolyte. The surface patterning is produced by photoalignment. In the presence of an electric field, the spatially varying orientation induces space charges that trigger flows of the LC. The active patterned LC electrolyte converts the electric energy into the LC flows and transport of embedded particles of any type (fluid, solid, gaseous) along a predesigned trajectory, posing no limitation on the electric nature (charge, polarizability) of these particles and interfaces. The patterned LC electrolyte exhibits a quadratic field dependence of the flow velocities; it induces persistent vortices of controllable rotation speed and direction that are quintessential for micro- and nanoscale mixing applications. PMID:26651712

  12. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-01

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  13. Influence of different polymers on the crystallization tendency of molecularly dispersed amorphous felodipine.

    PubMed

    Konno, Hajime; Taylor, Lynne S

    2006-12-01

    The ability of various polymers to inhibit the crystallization of amorphous felodipine was studied in amorphous molecular dispersions. Spin-coated films of felodipine with poly(vinylpyrrolidone) (PVP), hydroxypropylmethylcellulose acetate succinate (HPMCAS), and hydroxypropylmethylcellulose (HPMC) were prepared and used for measurement of the nucleation rate and to probe drug-polymer intermolecular interactions. Bulk solid dispersions were prepared by a solvent evaporation method and characterized using thermal analysis. It was found that each polymer was able to significantly decrease the nucleation rate of amorphous felodipine even at low concentrations (3-25% w/w). Each polymer was found to affect the nucleation rate to a similar extent at an equivalent weight fraction. For HPMC and HPMCAS, thermal analysis indicated that the glass transition temperature (T(g)) of the solid dispersions were not significantly different from that of felodipine alone, whereas an increase in T(g) was observed for the PVP containing solid dispersions. Infrared spectroscopic studies indicated that hydrogen bonding interactions were formed between felodipine and each of the polymers. These interactions were stronger between felodipine and PVP than for the other polymers. It was speculated that, at the concentrations employed, the polymers reduce the nucleation rate through increasing the kinetic barrier to nucleation.

  14. Macroscopic birefringence in liquid crystals from novel cyanobacterial polysaccharide with an extremely high molecular weight

    NASA Astrophysics Data System (ADS)

    Okajima-Kaneko, Maiko; Hayasaka-Kaneko, Daisaku; Miyazato, Shinji; Kaneko, Tatsuo

    2007-05-01

    We report an efficient method for extraction of anionic polysaccharides (PS) from cyanobacteria, Aphanothece sacrum; we used a hot alkaline solution (0.01 N NaOH) as an elution solvent in the first step of the extraction and isopropanol as a precipitation solvent in the last step. Thin fibers of PS were obtained at a high yield (50-80 % to the weight of the raw cyanobacterial sample). The spectroscopy and elemental analyses indicated the PS contains fucose, uronic acids (14.2 % by a carbazole-sulfuric acid method), a sugar unit containing amides. The solution of PS with a concentration of 1 wt% showed a very high viscosity (80 000cps) implying a high molecular weight, and a strong macroscopic birefringence with a texture typical of nematic liquid crystals was confirmed by crossed-polarizing microscopy (more than 0.5 wt%). The PS from A. sacrum may form a special structure rigid-rod enough to show LC phase and macroscopic birefringence.

  15. Strong and Anomalous Thermal Expansion Precedes the Thermosalient Effect in Dynamic Molecular Crystals

    PubMed Central

    Panda, Manas K.; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče

    2016-01-01

    The ability of thermosalient solids, organic analogues of inorganic martensites, to move by rapid mechanical reconfiguration or ballistic event remains visually appealing and potentially useful, yet mechanistically elusive phenomenon. Here, with a material that undergoes both thermosalient and non-thermosalient phase transitions, we demonstrate that the thermosalient effect is preceded by anomalous thermal expansion of the unit cell. The crystal explosion occurs as sudden release of the latent strain accumulated during the anisotropic, exceedingly strong expansion of the unit cell with αa = 225.9 × 10−6 K−1, αb = 238.8 × 10−6 K−1 and αc = −290.0 × 10−6 K−1, the latter being the largest negative thermal expansivity observed for an organic compound thus far. The results point out to the occurence of the thermosalient effect in phase transitions as means to identify new molecular materials with strong positive and/or negative thermal expansion which prior to this work could only be discovered serendipitously. PMID:27403616

  16. Crystal structure and molecular dynamics studies of human purine nucleoside phosphorylase complexed with 7-deazaguanine.

    PubMed

    Caceres, Rafael Andrade; Timmers, Luis Fernando Saraiva Macedo; Pauli, Ivani; Gava, Lisandra Marques; Ducati, Rodrigo Gay; Basso, Luiz Augusto; Santos, Diógenes Santiago; de Azevedo, Walter Filgueira

    2010-03-01

    In humans, purine nucleoside phosphorylase (HsPNP) is responsible for degradation of deoxyguanosine, and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. HsPNP is a target for inhibitor development aiming at T-cell immune response modulation. Here we report the crystal structure of HsPNP in complex with 7-deazaguanine (HsPNP:7DG) at 2.75 A. Molecular dynamics simulations were employed to assess the structural features of HsPNP in both free form and in complex with 7DG. Our results show that some regions, responsible for entrance and exit of substrate, present a conformational variability, which is dissected by dynamics simulation analysis. Enzymatic assays were also carried out and revealed that 7-deazaguanine presents a lower inhibitory activity against HsPNP (K(i)=200 microM). The present structure may be employed in both structure-based design of PNP inhibitors and in development of specific empirical scoring functions.

  17. Mol-ecular and crystal structure of gossypol tetra-methyl ether with an unknown solvate.

    PubMed

    Honkeldieva, Muhabbat; Talipov, Samat; Mardanov, Rustam; Ibragimov, Bakhtiyar

    2015-02-01

    The title compound, C34H38O8 (systematic name: 5,5'-diisopropyl-2,2',3,3'-tetra-meth-oxy-7,7'-dimethyl-2H,2'H-8,8'-bi-[naphtho-[1,8-bc]furan]-4,4'-diol), has been obtained from a gossypol solution in a mixture of dimethyl sulfate and methanol. The mol-ecule is situated on a twofold rotation axis, so the asymmetric unit contains one half-mol-ecule. In the mol-ecule, the hy-droxy groups are involved in intra-molecular O-H⋯O hydrogen bonds, and the two naphthyl fragments are inclined each to other by 83.8 (1)°. In the crystal, weak C-H⋯O and C-H⋯π inter-actions consolidate the packing, which exhibits channels with an approximate diameter of 6 Å extending along the c-axis direction. These channels are filled with highly disordered solvent mol-ecules, so their estimated scattering contribution was subtracted from the observed diffraction data using the SQUEEZE option in PLATON [Spek, A. L. (2015). Acta Cryst. C71, 9-18]. PMID:25878814

  18. Molecular disorder and translation/rotation coupling in the plastic crystal phase of hybrid perovskites

    NASA Astrophysics Data System (ADS)

    Even, J.; Carignano, M.; Katan, C.

    2016-03-01

    The complexity of hybrid organic perovskites calls for an innovative theoretical view that combines usually disconnected concepts in order to achieve a comprehensive picture: (i) the intended applications of this class of materials are currently in the realm of conventional semiconductors, which reveal the key desired properties for the design of efficient devices. (ii) The reorientational dynamics of the organic component resembles that observed in plastic crystals, therefore requiring a stochastic treatment that can be done in terms of pseudospins and rotator functions. (iii) The overall structural similarity with all inorganic perovskites suggests the use of the high temperature pseudo cubic phase as the reference platform on which further refinements can be built. In this paper we combine the existing knowledge on these three fields to define a general scenario based on which we can continue the quest towards a fundamental understanding of hybrid organic perovskites. With the introduction of group theory as the main tool to rationalize the different ideas and with the help of molecular dynamics simulations, several experimentally observed properties are naturally explained with possible suggestions for future work.

  19. Crystal and molecular structure of aspartame X HCl X 2H2O.

    PubMed

    Görbitz, C H

    1987-02-01

    The crystal and molecular structure of the hydrochloride salt of the peptide sweetener aspartame (alpha-L-Asp-L-Phe methyl ester) has been determined at 120 K using 3877 reflections with I greater than 2.5 sigma I. Space group P2(1)2(1)2(1), cell dimensions a = 6.768(1), b = 9.796(1) and c = 26.520(3) A; final R factor 0.033. While the N-terminal L-Asp group in the structure of aspartame itself forms a six-membered ring with an intramolecular hydrogen bond between the carboxylate and the protonated amino terminus, the corresponding group in the hydrochloride adopts a completely different conformation with a weak intramolecular hydrogen bond between the carboxyl group and the N atom of the L-Phe residue. The L-Phe methyl ester moiety is rather similar in the two structures. Of the many possible conformations of aspartame, only one may be expected to function as a substrate at the receptor site for sweet taste, and a proposal is made for this active conformation.

  20. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer.

    PubMed Central

    Tu, K; Tobias, D J; Klein, M L

    1995-01-01

    We report a constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal (L alpha) phase bilayer of dipalmitoylphosphatidylcholine at 50 degrees C and 28 water molecules/lipid. We have shown that the bilayer is stable throughout the 1550-ps simulation and have demonstrated convergence of the system dimensions. Several important aspects of the bilayer structure have been investigated and compared favorably with experimental results. For example, the average positions of specific carbon atoms along the bilayer normal agree well with neutron diffraction data, and the electron density profile is in accord with x-ray diffraction results. The hydrocarbon chain deuterium order parameters agree reasonably well with NMR results for the middles of the chains, but the simulation predicts too much order at the chain ends. In spite of the deviations in the order parameters, the hydrocarbon chain packing density appears to be essentially correct, inasmuch as the area/lipid and bilayer thickness are in agreement with the most refined experimental estimates. The deuterium order parameters for the glycerol and choline groups, as well as the phosphorus chemical shift anisotropy, are in qualitative agreement with those extracted from NMR measurements. PMID:8599662

  1. Nonequilibrium mesoscopic transport: a genealogy

    NASA Astrophysics Data System (ADS)

    Das, Mukunda P.; Green, Frederick

    2012-05-01

    Models of nonequilibrium quantum transport underpin all modern electronic devices, from the largest scales to the smallest. Past simplifications such as coarse graining and bulk self-averaging served well to understand electronic materials. Such particular notions become inapplicable at mesoscopic dimensions, edging towards the truly quantum regime. Nevertheless a unifying thread continues to run through transport physics, animating the design of small-scale electronic technology: microscopic conservation and nonequilibrium dissipation. These fundamentals are inherent in quantum transport and gain even greater and more explicit experimental meaning in the passage to atomic-sized devices. We review their genesis, their theoretical context, and their governing role in the electronic response of meso- and nanoscopic systems.

  2. Crystal Growth Inhibitors for the Prevention of L-Cystine Kidney Stones Through Molecular Design

    SciTech Connect

    Rimer, Jeffrey D.; An, Zhihua; Zhu, Zina; Lee, Michael H.; Goldfarb, David S.; Wesson, Jeffrey A.; Ward, Michael D.

    2010-11-12

    Crystallization of L-cystine is a critical step in the pathogenesis of cystine kidney stones. Treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) dramatically reduce the growth velocity of the six symmetry-equivalent {l_brace}100{r_brace} steps because of specific binding at the crystal surface, which frustrates the attachment of L-cystine molecules. L-CDME and L-CME produce L-cystine crystals with different habits that reveal distinct binding modes at the crystal surfaces. The AFM observations are mirrored by reduced crystal yield and crystal size in the presence of L-CDME and L-CME, collectively suggesting a new pathway to the prevention of L-cystine stones by rational design of crystal growth inhibitors.

  3. The Molecular Volcano Revisited: Determination of Crack Propagation and Distribution During the Crystallization of Nanoscale Amorphous Solid Water Films.

    PubMed

    May, R Alan; Smith, R Scott; Kay, Bruce D

    2012-02-01

    Temperature programmed desorption (TPD) is utilized to determine the length distribution of cracks formed through amorphous solid water (ASW) during crystallization. This distribution is determined by monitoring how the thickness of an ASW overlayer alters desorption of an underlayer of O2. As deposited, ASW prevents desorption of O2. During crystallization, cracks form through the ASW and open a path to vacuum, which allows O2 to escape in a rapid episodic release known as the "molecular volcano". Sufficiently thick ASW overlayers further trap O2 resulting in a second, higher temperature, O2 desorption peak. The evolution of this trapping peak with overlayer thickness is the basis for determining the length distribution of crystallization-induced cracks spanning the ASW. Reflection absorption infrared spectroscopy (RAIRS) and TPD of multicomponent parfait structures of ASW, O2, and Kr indicate that a preponderance of these cracks propagate down from the outer surface of the ASW. PMID:26285846

  4. Towards more accurate molecular dynamics calculation of thermal conductivity: Case study of GaN bulk crystals

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Aubry, S.; Jones, R. E.; Greenstein, A.; Schelling, P. K.

    2009-03-01

    Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative thermal conductivity, have been found. Using GaN as an example case and the direct nonequilibrium method, extensive molecular dynamics simulations and Monte Carlo analysis of the results have been carried out to quantify the uncertainty level of the molecular dynamics methods and to identify the conditions that can yield sufficiently accurate calculations of thermal conductivity. We found that the errors of the calculations are mainly due to the statistical thermal fluctuations. Extrapolating results to the limit of an infinite-size system tend to magnify the errors and occasionally lead to unphysical results. The error in bulk estimates can be reduced by performing longer time averages using properly selected systems over a range of sample lengths. If the errors in the conductivity estimates associated with each of the sample lengths are kept below a certain threshold, the likelihood of obtaining unphysical bulk values becomes insignificant. Using a Monte Carlo approach developed here, we have determined the probability distributions for the bulk thermal conductivities obtained using the direct method. We also have observed a nonlinear effect that can become a source of significant errors. For the extremely accurate results presented here, we predict a [0001] GaN thermal conductivity of 185W/Km at 300 K, 102W/Km at 500 K, and 74W/Km at 800 K. Using the insights obtained in the work, we have achieved a corresponding error level (standard deviation) for the bulk (infinite sample length) GaN thermal conductivity of less than 10W/Km , 5W/Km , and 15W/Km at 300 K, 500 K, and 800 K, respectively.

  5. Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups

    NASA Astrophysics Data System (ADS)

    Gorkunov, M. V.; Osipov, M. A.; Kocot, A.; Vij, J. K.

    2010-06-01

    Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry.

  6. Collapse of homeotropic liquid-crystal alignment by increased molecular packing on comb-like polymer surfaces.

    PubMed

    Sohn, Eun-Ho; Kang, Hyo; Kim, Dong-Gyun; Song, Kigook; Lee, Jong-Chan

    2012-06-01

    We report an unusual alignment behavior of liquid crystals (LCs) on well-ordered comb-like poly(oxyethylene) surfaces. The homeotropic LC alignments that are observed on as-coated surfaces of the polymers are transformed to the random planar type after annealing treatment, even though the molecular structure of the polymer surface becomes more ordered and the surface energy decreases. Studies of the surface properties, such as molecular structure, morphology, and wettability, reveal that such an unexpected alteration of the LC alignment originates from the density of the alkyl side chains being enhanced by localized packing. PMID:22511283

  7. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

    NASA Astrophysics Data System (ADS)

    Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

    2016-09-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

  8. Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

    PubMed

    Mörschel, Philipp; Schmidt, Martin U

    2015-01-01

    A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

  9. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol.

    PubMed

    Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

    2016-09-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction. PMID:27661700

  10. Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

    PubMed

    Mörschel, Philipp; Schmidt, Martin U

    2015-01-01

    A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies. PMID:25537386

  11. Hydrophilic-Hydrophobic Patterned Molecularly Imprinted Photonic Crystal Sensors for High-Sensitive Colorimetric Detection of Tetracycline.

    PubMed

    Hou, Jue; Zhang, Huacheng; Yang, Qiang; Li, Mingzhu; Jiang, Lei; Song, Yanlin

    2015-06-01

    A hydrophilic-hydrophobic patterned molecularly imprinted (MIP) photonic crystal (PC) sensor is fabricated for highly sensitive tetracycline detection. The relationship between the tetracycline concentration, its corresponding color of the sensor, and the diameter of MIP-PC dot is found using a fan-shaped color card. This work provides a new strategy to design the sensors with tunable detection ranges for practical applications.

  12. Application of the short and long consecutive pairs model to the triplet-doublet interaction in molecular crystals

    NASA Astrophysics Data System (ADS)

    Barhoumi, T.; Monge, J. L.; Bouchriha, H.

    2010-10-01

    We have adapted the model of two consecutive pairs to the study of the triplet-doublet (T-D) interaction in molecular crystals. We have applied this model to the modulation of the photoconductivity in crystalline anthracene by a static magnetic field (MFE) and a microwave field (PDMR). We were able to reproduce, for the first time, quite perfectly two types of experiments with the same set of kinetic constants.

  13. Hydrophilic-Hydrophobic Patterned Molecularly Imprinted Photonic Crystal Sensors for High-Sensitive Colorimetric Detection of Tetracycline.

    PubMed

    Hou, Jue; Zhang, Huacheng; Yang, Qiang; Li, Mingzhu; Jiang, Lei; Song, Yanlin

    2015-06-01

    A hydrophilic-hydrophobic patterned molecularly imprinted (MIP) photonic crystal (PC) sensor is fabricated for highly sensitive tetracycline detection. The relationship between the tetracycline concentration, its corresponding color of the sensor, and the diameter of MIP-PC dot is found using a fan-shaped color card. This work provides a new strategy to design the sensors with tunable detection ranges for practical applications. PMID:25649896

  14. Crystal and molecular structures of 3-amino-4-hydroxy benzenesulfonamide and its hydrochloride: Quantum-chemical study of their tautomerism

    SciTech Connect

    Kovalchukova, O. V. Strashnova, S. B.; Romashkina, E. P.; Strashnov, P. V.; Zaitsev, B. E.; Sergienko, V. S.

    2013-03-15

    3-amino-4-hydroxy benzenesulfonamide and its hydrochloride have been isolated in the crystalline state. Their crystal and molecular structures are determined by X-ray diffraction. The equilibrium between neutral tautomeric forms of the 3-amino-4-hydroxy benzenesulfonamide molecule is studied within the approximation of density functional theory (B3LYP/aug-cc-pVDZ). The constants of acid-base equilibrium of 3-amino-4-hydroxy benzenesulfonamide are deter-mined using spectrophotometry.

  15. Steady-State Density Functional Theory for Non-equilibrium Quantum Systems

    NASA Astrophysics Data System (ADS)

    Shuanglong, Liu

    Recently, electron transport properties of molecular junctions under finite bias voltages have attracted a lot of attention because of the potential application of molecular electronic devices. When a molecular junction is under zero bias voltage at zero temperature, it is in equilibrium ground state and all its properties can be solved by ground-state density functional theory (GS-DFT) where ground-state electron density determines everything. Under finite bias voltage, the molecular junction is in non-equilibrium steady state. According to Hershfield's non-equilibrium statistics, a system in non-equilibrium steady state corresponds to an effective equilibrium system. This correspondence provides the basis for the steady-state density functional theory (SS-DFT) which will be developed in this thesis. (Abstract shortened by UMI.).

  16. Influence of nonequilibrium radiation and shape change on aerothermal environment of a Jovian entry body

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Subramanian, S. V.

    1981-01-01

    The influence of nonequilibrium radiative energy transfer and the effect of probe configuration changes on the flow phenomena around a Jovian entry body are investigated. The radiating shock layer flow is assumed to be axisymmetric, viscous, laminar and in chemical equilibrium. The radiative transfer equations are derived under nonequilibrium conditions which include multilevel energy transitions. The equilibrium radiative transfer analysis is performed with an existing nongray radiation model which accounts for molecular band, atomic line, and continuum transitions. The nonequilibrium results are obtained with and without ablation injection in the shock layer. The nonequilibrium results are found to be greatly influenced by the temperature distribution in the shock layer. In the absence of ablative products, the convective and radiative heating to the entry body are reduced under nonequilibrium conditions. The influence of nonequilibrium is found to be greater at higher entry altitudes. With coupled ablation and carbon phenolic injection, 16 chemical species are used in the ablation layer for radiation absorption. Equilibrium and nonequilibrium results are compared under peak heating conditions.

  17. Predictive Calculation of the Crystallization Tendency of Model Pharmaceuticals in the Supercooled State from Molecular Dynamics Simulations.

    PubMed

    Gerges, J; Affouard, F

    2015-08-20

    Molecular dynamics (MD) simulations were used to perform a comparative study of the crystallization tendency from the melt of two model pharmaceutical compounds: felodipine and nifedipine. Two crystalline polymorphs of nifedipine (N(α), N(β)) and felodipine (FI, FII) have been studied. Calculations were performed on liquid and crystal systems separately in order to determine their main physical properties (diffusivity, density, and enthalpy). A fair agreement was found between the simulation and the known experimental data confirming the ability of the force field GAFF to reproduce accurately the experimental data for both compounds. Simulations of the crystal-liquid interface enabled the determination of the melting temperature and the interfacial free energy of the different polymorphs. Guided by the classical nucleation theory (CNT) predictions and different growth mechanism models (normal, two-dimensional, and screw dislocation), the nucleation and growth rates have been determined. The present investigation particularly raises the very important role of the solid-liquid interfacial free energy and its interplay with the driving force during the crystallization. The origin of the higher crystallization tendency of nifedipine with respect to felodipine is discussed from the present computed kinetic and thermodynamical factors.

  18. Crystal engineering rescues a solution organic synthesis in a cocrystallization that confirms the configuration of a molecular ladder

    PubMed Central

    Atkinson, Manza B. J.; Mariappan, S. V. Santhana; Bučar, Dejan-Krešimir; Baltrusaitis, Jonas; Friščić, Tomislav; Sinada, Naif G.; MacGillivray, Leonard R.

    2011-01-01

    Treatment of an achiral molecular ladder of C2h symmetry composed of five edge-sharing cyclobutane rings, or a [5]-ladderane, with acid results in cis- to trans-isomerization of end pyridyl groups. Solution NMR spectroscopy and quantum chemical calculations support the isomerization to generate two diastereomers. The NMR data, however, could not lead to unambiguous configurational assignments of the two isomers. Single-crystal X-ray diffraction was employed to determine each configuration. One isomer readily crystallized as a pure form and X-ray diffraction revealed the molecule as being achiral based on Ci symmetry. The second isomer resisted crystallization under a variety of conditions. Consequently, a strategy based on a cocrystallization was developed to generate single crystals of the second isomer. Cocrystallization of the isomer with a carboxylic acid readily afforded single crystals that confirmed a chiral ladderane based on C2 symmetry. The chiral ladderane and acid self-assembled to generate a five-component hydrogen-bonded complex that packs to form large solvent-filled homochiral channels of nanometer-scale dimensions. Whereas cocrystallizations are frequently applied to structure determinations of proteins, our study represents the first application of a cocrystallization to confirm the relative configuration of a small-molecule diastereomer generated in a solution-phase organic synthesis. PMID:21690362

  19. Molecular adsorption on ZnO(1010) single-crystal surfaces: morphology and charge transfer.

    PubMed

    Chen, Jixin; Ruther, Rose E; Tan, Yizheng; Bishop, Lee M; Hamers, Robert J

    2012-07-17

    While ZnO has excellent electrical properties, it has not been widely used for dye-sensitized solar cells, in part because ZnO is chemically less stable than widely used TiO(2). The functional groups typically used for surface passivation and for attaching dye molecules either bind weakly or etch the ZnO surface. We have compared the formation of molecular layers from alkane molecules with terminal carboxylic acid, alcohol, amine, phosphonic acid, or thiol functional groups on single-crystal zinc oxide (1010) surfaces. Atomic force microscopy (AFM) images show that alkyl carboxylic acids etch the surface whereas alkyl amine and alkyl alcohols bind only weakly on the ZnO(1010) surface. Phosphonic acid-terminated molecules were found to bind to the surface in a heterogeneous manner, forming clusters of molecules. Alkanethiols were found to bind to the surface, forming highly uniform monolayers with some etching detected after long immersion times in an alkanethiol solution. Monolayers of hexadecylphosphonic acid and octadecanethiol were further analyzed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and electrochemical measurements. AFM scratching shows that thiols were bound strongly to the ZnO surface, suggesting the formation of strong Zn-S covalent bonds. Surprisingly, the tridentate phosphonic acids adhered much more weakly than the monodentate thiol. The influence of organic grafting on the charge transfer to ZnO was studied by time-resolved surface photovoltage measurements and electrochemical impedance measurements. Our results show that the grafting of thiols to ZnO leads to robust surfaces and reduces the surface band bending due to midgap surface states.

  20. [Protein conformational dynamics of crambin in crystal, solution and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    Atomic displacement parameters--B factors of the eight crambin crystal structures obtained at 0.54-1.5 angstroms resolution and temperatures of 100-293K have been analyzed. The comparable contributions to the B factor values are the intramolecular motions which are modeled by the harmonic vibration calculations and derived from the molecular dynamics simulation (MD) as well as rigid body changes in the position of a protein molecule as a whole. In solution for the average NMR structure of crambin the amplitudes of the backbone atomic fluctuations of the most residues of the segments with the regular backbone conformations are close to the amplitudes of the small scale harmonic vibrations. For the same residues the probability of the medium scale fluctuations fixed by the hydrogen exchange method is very low. The restricted conformational mobility of those segments is coupled with the depressed amplitudes of the fluctuation changes of the tertiary structure registered by the residue accessibility changes in an ensemble of NMR structures that forms the average NMR structure of crambin. The amplitudes of temperature fluctuations of backbone atoms and the tertiary structure raise in the segment with the irregular conformations, turn and loops. In the same segments the amplitudes of the calculated harmonic vibrations also increase, but to a lesser extent and especially in the interhelical loop with the most strong and complicated fluctuation changes of the backbone conformation. In solution for the NMR structure in this loop the conformational transitions occur between the conformational substates separated by the energy barriers, but they are not observed even in the long 100 ns trajectories from the MD simulation of crambin. These strong local fluctuation changes of the structure may play a key role in the protein functioning and modern performance improvements in the MD simulation techniques are oriented to increase the probability of protein appearance in the

  1. Dopaminergic receptor-ligand binding assays based on molecularly imprinted polymers on quartz crystal microbalance sensors.

    PubMed

    Naklua, Wanpen; Suedee, Roongnapa; Lieberzeit, Peter A

    2016-07-15

    Molecularly imprinted polymers (MIPs) have been successfully applied as selective materials for assessing the binding activity of agonist and antagonist of dopamine D1 receptor (D1R) by using quartz crystal microbalance (QCM). In this study, D1R derived from rat hypothalamus was used as a template and thus self-organized on stamps. Those were pressed into an oligomer film consisting of acrylic acid: N-vinylpyrrolidone: N,N'-(1,2-dihydroxyethylene) bis-acrylamide in a ratio of 2:3:12 spin coated onto a dual electrode QCM. Such we obtained one D1R-MIP-QCM electrode, whereas the other electrode carried the non-imprinted control polymer (NIP) that had remained untreated. Successful imprinting of D1R was confirmed by AFM. The polymer can re-incorporate D1R leading to frequency responses of 100-1200Hz in a concentration range of 5.9-47.2µM. In a further step such frequency changes proved inherently useful for examining the binding properties of test ligands to D1R. The resulting mass-sensitive measurements revealed Kd of dopamine∙HCl, haloperidol, and (+)-SCH23390 at 0.874, 25.6, and 0.004nM, respectively. These results correlate well with the values determined in radio ligand binding assays. Our experiments revealed that D1R-MIP sensors are useful for estimating the strength of ligand binding to the active single site. Therefore, we have developed a biomimetic surface imprinting strategy for QCM studies of D1R-ligand binding and presented a new method to ligand binding assay for D1R. PMID:26926593

  2. Nonequilibrium chemistry boundary layer integral matrix procedure

    NASA Technical Reports Server (NTRS)

    Tong, H.; Buckingham, A. C.; Morse, H. L.

    1973-01-01

    The development of an analytic procedure for the calculation of nonequilibrium boundary layer flows over surfaces of arbitrary catalycities is described. An existing equilibrium boundary layer integral matrix code was extended to include nonequilibrium chemistry while retaining all of the general boundary condition features built into the original code. For particular application to the pitch-plane of shuttle type vehicles, an approximate procedure was developed to estimate the nonequilibrium and nonisentropic state at the edge of the boundary layer.

  3. Effects of molecular architecture on crystallization behavior of poly(lactic acid) and random ethylene-vinyl acetate copolymers

    NASA Astrophysics Data System (ADS)

    Kalish, Jeffrey P.

    2011-07-01

    faster crystallization kinetics and a higher degree of crystallinity. The observed increase in degree of crystallinity was directly related to the chain configuration. Compositional mapping using Raman spectroscopy provided evidence for oligomer nucleation. The cocrystallization kinetics and morphology of EVA and n-alkane blends was found to depend on the chain length of oligomer. In both systems studied, crystallization kinetics determines the morphologies formed, which are undoubtedly related to the details of molecular architecture.

  4. Dynamical characterization of inactivation path in voltage-gated Na(+) ion channel by non-equilibrium response spectroscopy.

    PubMed

    Pal, Krishnendu; Gangopadhyay, Gautam

    2016-11-01

    Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena.

  5. Nonequilibrium volumetric response of shocked polymers

    SciTech Connect

    Clements, B E

    2009-01-01

    Polymers are well known for their non-equilibrium deviatoric behavior. However, investigations involving both high rate shock experiments and equilibrium measured thermodynamic quantities remind us that the volumetric behavior also exhibits a non-equilibrium response. Experiments supporting the notion of a non-equilibrium volumetric behavior will be summarized. Following that discussion, a continuum-level theory is proposed that will account for both the equilibrium and non-equilibrium response. Upon finding agreement with experiment, the theory is used to study the relaxation of a shocked polymer back towards its shocked equilibrium state.

  6. Thermal resistance at an interface between a crystal and its melt

    NASA Astrophysics Data System (ADS)

    Liang, Zhi; Evans, William J.; Keblinski, Pawel

    2014-07-01

    Non-equilibrium molecular dynamics simulations are used to determine interfacial thermal resistance (Kapitza resistance) between a crystal and its melt for three materials including Ar, H2O, and C8H18 (octane). The simulation results show that the Kapitza resistance at a crystal-melt interface is very small and thus has a negligible effect on thermal transport across the crystal-melt interface. The underlying origins of this behavior are the very good vibrational property match between the two materials forming the interface and good interfacial bonding. The result also indicates that the commonly-used assumption that temperature profile is continuous at the crystal-melt interface is valid even in the case of very rapid crystal melting or growth.

  7. Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals.

    PubMed

    Jiang, Jianwen; Babarao, Ravichandar; Hu, Zhongqiao

    2011-07-01

    Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.

  8. Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

    NASA Astrophysics Data System (ADS)

    Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

    2007-01-01

    The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

  9. Nonequilibrium transport in superconducting filaments

    NASA Technical Reports Server (NTRS)

    Arutyunov, K. YU.; Danilova, N. P.; Nikolaeva, A. A.

    1995-01-01

    The step-like current-voltage characteristics of highly homogeneous single-crystalline tin and indium thin filaments has been measured. The length of the samples L approximately 1 cm was much greater than the nonequilibrium quasiparticle relaxation length Lambda. It was found that the activation of a successive i-th voltage step occurs at current significantly greater than the one derived with the assumption that the phase slip centers are weakly interacting on a scale L much greater than Lambda. The observation of 'subharmonic' fine structure on the voltage-current characteristics of tin filaments confirms the hypothesis of the long-range phase slip centers interaction.

  10. The Avogadro Challenge ---Nanodynamics Study on Nonequilibrium Problems---

    NASA Astrophysics Data System (ADS)

    Yukawa, S.; Ito, N.

    Computer performance is now reaching to realize 1 mol operations, that is, 6 × 10(23) arithmetic operations. Such Avogadro-scale computer will open a new era of sciences and technologies via renovations of fields in material sciences, which had been assuming that the Avogadro number be a synonym of infinity. Since the first milestone was placed by B. J. Alder half-a-century ago, a road to thermal equilibrium properties was well paved and linear transport phenomena have also been tamed with nonequilibrium simulations. Now the front lines confront nonlinear nonequilibrium problems. As an example, molecular-dynamics simulation of a shock tube which is an analogue of volcanic eruption is given.

  11. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy

    PubMed Central

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C.; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A.

    2016-01-01

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance. PMID:27619423

  12. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C.; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A.

    2016-09-01

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance.

  13. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy.

    PubMed

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A

    2016-09-13

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance.

  14. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy.

    PubMed

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A

    2016-01-01

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance. PMID:27619423

  15. Mimicking Nonequilibrium Steady States with Time-Periodic Driving

    NASA Astrophysics Data System (ADS)

    Raz, O.; Subaşı, Y.; Jarzynski, C.

    2016-04-01

    Under static conditions, a system satisfying detailed balance generically relaxes to an equilibrium state in which there are no currents. To generate persistent currents, either detailed balance must be broken or the system must be driven in a time-dependent manner. A stationary system that violates detailed balance evolves to a nonequilibrium steady state (NESS) characterized by fixed currents. Conversely, a system that satisfies instantaneous detailed balance but is driven by the time-periodic variation of external parameters—also known as a stochastic pump (SP)—reaches a periodic state with nonvanishing currents. In both cases, these currents are maintained at the cost of entropy production. Are these two paradigmatic scenarios effectively equivalent? For discrete-state systems, we establish a mapping between nonequilibrium stationary states and stochastic pumps. Given a NESS characterized by a particular set of stationary probabilities, currents, and entropy production rates, we show how to construct a SP with exactly the same (time-averaged) values. The mapping works in the opposite direction as well. These results establish a proof of principle: They show that stochastic pumps are able to mimic the behavior of nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics. Nonequilibrium steady states and stochastic pumps are often used to model, respectively, biomolecular motors driven by chemical reactions and artificial molecular machines steered by the variation of external, macroscopic parameters. Our results loosely suggest that anything a biomolecular machine can do, an artificial molecular machine can do equally well. We illustrate this principle by showing that kinetic proofreading, a NESS mechanism that explains the low error rates in biochemical reactions, can be effectively mimicked by a constrained periodic driving.

  16. INTRODUCTION: Nonequilibrium Processes in Plasmas

    NASA Astrophysics Data System (ADS)

    Petrović, Zoran; Marić, Dragana; Malović, Gordana

    2009-07-01

    This book aims to give a cross section from a wide range of phenomena that, to different degrees, fall under the heading of non-equilibrium phenomenology. The selection is, of course, biased by the interests of the members of the scientific committee and of the FP6 Project 026328 IPB-CNP Reinforcing Experimental Centre for Non-equilibrium Studies with Application in Nano-technologies, Etching of Integrated Circuits and Environmental Research. Some of the papers included here are texts based on selected lectures presented at the Second International Workshop on Non-equilibrium Processes in Plasmas and Environmental Science. However, this volume is not just the proceedings of that conference as it contains a number of papers from authors that did not attend the conference. The goal was to put together a volume that would cover the interests of the project and support further work. It is published in the Institute of Physics journal Journal of Physics: Conference Series to ensure a wide accessibility of the articles. The texts presented here range from in-depth reviews of the current status and past achievements to progress reports of currently developed experimental devices and recently obtained still unpublished results. All papers have been refereed twice, first when speakers were selected based on their reputation and recently published results, and second after the paper was submitted both by the editorial board and individual assigned referees according to the standards of the conference and of the journal. Nevertheless, we still leave the responsibility (and honours) for the contents of the papers to the authors. The papers in this book are review articles that give a summary of the already published work or present the work in progress that will be published in full at a later date (or both). In the introduction to the first volume, in order to show how far reaching, ubiquitous and important non-equilibrium phenomena are, we claimed that ever since the early

  17. Non-equilibrium phase transitions

    SciTech Connect

    Mottola, E.; Cooper, F.M.; Bishop, A.R.; Habib, S.; Kluger, Y.; Jensen, N.G.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Non-equilibrium phase transitions play a central role in a very broad range of scientific areas, ranging from nuclear, particle, and astrophysics to condensed matter physics and the material and biological sciences. The aim of this project was to explore the path to a deeper and more fundamental understanding of the common physical principles underlying the complex real time dynamics of phase transitions. The main emphasis was on the development of general theoretical tools to deal with non-equilibrium processes, and of numerical methods robust enough to capture the time-evolving structures that occur in actual experimental situations. Specific applications to Laboratory multidivisional efforts in relativistic heavy-ion physics (transition to a new phase of nuclear matter consisting of a quark-gluon plasma) and layered high-temperature superconductors (critical currents and flux flow at the National High Magnetic Field Laboratory) were undertaken.

  18. Thermodynamics of Stability of Nonequilibrium Steady States.

    ERIC Educational Resources Information Center

    Rastogi, R. P.; Shabd, Ram

    1983-01-01

    Presented is a concise and critical account of developments in nonequilibrium thermodynamics. The criterion for stability of nonequilibrium steady states is critically examined for consecutive and monomolecular triangular reactions, autocatalytic reactions, auto-inhibited reactions, and the Lotka-Volterra model. (JN)

  19. Oriented single-crystal-like molecular arrangement of optically nonlinear 2-methyl-4-nitroaniline in electrospun nanofibers.

    PubMed

    Isakov, Dmitry V; de Matos Gomes, Etelvina; Vieira, Luis G; Dekola, Tatsiana; Belsley, Michael S; Almeida, Bernardo G

    2011-01-25

    In-plane aligned nanofibers of organic 2-methyl-4-nitroaniline (MNA) were produced by the electrospinning technique using a 1:1 weight ratio with poly(l-lactic acid). The fibers are capable of enormous efficient optical second harmonic generation as strong as pure MNA crystals in powder form. Structural, spectroscopic, and second harmonic generation polarimetry studies show that the MNA crystallizes within the fibers in an orientation in which the aromatic rings of MNA are predominantly orientated edge-on with respect to the plane of the fiber array and with their dipole moments aligned with the fiber axis. The results show that the electrospinning technique is an effective method to fabricate all-organic molecular functional devices based on polymer nanofibers with guest molecules possessing strong nonlinear optical and/or polar properties.

  20. GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Tseng, H. Y.; Yang, W. C.; Lee, P. Y.; Lin, C. W.; Cheng, Kai-Yuan; Hsieh, K. C.; Cheng, K. Y.; Hsu, C.-H.

    2016-08-01

    GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.