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Sample records for initio molecular-dynamics study

  1. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

  2. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  3. Ethanol decomposition on transition metal nanoparticles during carbon nanotube growth: ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu

    2015-03-01

    The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.

  4. An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction

    NASA Astrophysics Data System (ADS)

    Yu, Hua-Gen

    2011-08-01

    We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.

  5. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dixit, Mudit; Major, Dan Thomas; Pal, Sourav

    2016-05-01

    Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.

  6. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    NASA Astrophysics Data System (ADS)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  7. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    SciTech Connect

    Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  8. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

    2016-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

  9. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    PubMed

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range. PMID:25524926

  10. Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

    DOE PAGESBeta

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.; Li, Sean

    2015-02-09

    In this study, the response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser,more » electron and ion irradiations.« less

  11. Polymerization transition in liquid AsS under pressure: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Shimojo, Fuyuki

    2011-12-01

    We study the pressure dependence of the structural and electronic properties of liquid AsS by ab initio molecular dynamics simulations. We confirm that liquid AsS consists of As4S4 molecules at ambient pressure, as in the crystalline state. With increasing pressure, a structural transition from molecular to polymeric liquid occurs near 2 GPa, which is eventually followed by metallization. The pressure dependence of the density and diffusion coefficients changes qualitatively with this transition. We find that, during metallization in the polymeric phase at higher pressures, the remnants of covalent interactions between atoms play an important role in the dynamics, i.e., the As-S bond length becomes longer with increasing pressure and the diffusion coefficients have a local maximum near 5 GPa. When the pressure approaches about 15 GPa, the covalent nature of the liquid becomes quite weak. These results explain recent experiments on the pressure dependence of the viscosity.

  12. Ring closure in dioxin formation process: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Farajian, Amir A.; Mikami, Masuhiro; Ordejón, Pablo; Tanabe, Kazutoshi

    2001-10-01

    The four possible mechanisms of ring closure in dioxin formation from chlorophenols are studied using ab initio molecular dynamics, within generalized gradient approximation. Free energy barriers, derived as the potential of mean constraint force, directly lead to a static approximation for the transition rates. We show, however, that the static approximation overestimates the actual rates by 33%-345%, depending on the intermediate/temperature. Comparing our results with the available experimental data, we conclude that, contrary to what is widely assumed, the pathways starting from two chlorophenols are not among the most dominant pathways in the formation of highly toxic dioxins, at least in the gas phase. This signifies the role of catalysts and/or other precursors.

  13. Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian

    2016-01-01

    High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5-60 GPa and temperature range of 250-400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation.

  14. Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate

    PubMed Central

    Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian

    2016-01-01

    High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation. PMID:26754622

  15. Combined ab initio molecular dynamics and experimental studies of carbon atom addition to benzene.

    PubMed

    McKee, Michael L; Reisenauer, Hans Peter; Schreiner, Peter R

    2014-04-17

    Car-Parrinello molecular dynamics was used to explore the reactions between triplet and singlet carbon atoms with benzene. The computations reveal that, in the singlet C atom reaction, products are very exothermic where nearly every collision yields a product that is determined by the initial encounter geometry. The singlet C atom reaction does not follow the minimum energy path because the bimolecular reaction is controlled by dynamics (i.e., initial orientation of encounter). On the other hand, in a 10 K solid Ar matrix, ground state C((3)P) atoms do tend to follow RRKM kinetics. Thus, ab initio molecular dynamics (AIMD) results indicate that a significant fraction of C-H insertion occurs to form phenylcarbene whereas, in marked contrast to previous theoretical and experimental conclusions, the Ar matrix isolation studies indicate a large fraction of direct cycloheptatetraene formation, without the intermediacy of phenylcarbene. The AIMD calculations are more consistent with vaporized carbon atom experiments where labeling studies indicate the initial formation of phenylcarbene. This underlines that the availability of thermodynamic sinks can completely alter the observed reaction dynamics. PMID:24661002

  16. Two Dimensional Epitaxial Water Adlayer on Mica with Graphene Coating: An ab Initio Molecular Dynamics Study.

    PubMed

    Li, Hui; Zeng, Xiao Cheng

    2012-09-11

    Motivated by a recent atomic-force-microscopy (AFM) study of water adlayers on mica by Heath and co-workers (Graphene Visualizes the First Water Adlayers on Mica at Ambient Conditions. Science2010, 329, 1188), we performed an ab initio molecular dynamics study of structural and dynamic properties of monolayer, bilayer, and trilayer water adlayers on the muscovite mica (001) surface with and without a graphene coating. We find that in the first epitaxial water adlayer, water molecules that form strong hydrogen bonds with the oxygen on the mica surface show little motions, thereby solid-like, while those "bridging" water molecules on top of the first water adlayer exhibit "itinerant" behavior, thereby liquid-like. Overall, the Born-Oppenheim molecular dynamics (BOMD) simulations (based on the BLYP-D functional) show that the first water adlayer on mica exhibits a unique hybrid solid-liquid-like behavior with a very low diffusion coefficient at ambient conditions. In particular, no dangling hydrogen bonds are found in the first water adlayer on mica. Moreover, the bilayer and trilayer water adlayers show slightly higher structural stability than the first water adlayer. A graphene coating on the water adlayer further enhances stability of the water adlayers. Most importantly, the bilayer water adlayer on mica with the graphene coating becomes fully solid-like, the structure of which is the same as the bilayer slice of ice-Ih with a thickness of 7.4 Å, consistent with the AFM measurement. PMID:26605715

  17. Proton transport in triflic acid pentahydrate studied via ab initio path integral molecular dynamics.

    PubMed

    Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E

    2011-06-16

    Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the

  18. Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field.

    PubMed

    Cassone, Giuseppe; Creazzo, Fabrizio; Giaquinta, Paolo V; Saija, Franz; Marco Saitta, A

    2016-08-17

    We report on an ab initio molecular dynamics study of an aqueous NaCl solution under the effect of static electric fields. We found that at low-to-moderate field intensity regimes chlorine ions have a greater mobility than sodium ions which, being a sort of "structure makers", are able to drag their own coordination shells. However, for field strengths exceeding 0.15 V Å(-1) the mobility of sodium ions overcomes that of chlorine ions as both types of ions do actually escape from their respective hydration cages. The presence of charged particles lowers the water dissociation threshold (i.e., the minimum field strength which induces a transfer of protons) from 0.35 V Å(-1) to 0.25 V Å(-1); moreover, a protonic current was also recorded at the estimated dissociation threshold of the solution. The behaviour of the current-voltage diagram of the protonic response to the external electric field is Ohmic as in pure water, with a resulting protonic conductivity of about 2.5 S cm(-1). This value is approximately one third of that estimated in pure water (7.8 S cm(-1)), which shows that the partial breaking of hydrogen bonds induced by the solvated ions hinders the migration of protonic defects. Finally, the conductivity of Na(+) and Cl(-) ions (0.2 S cm(-1)) is in fair agreement with the available experimental data for a solution molarity of 1.7 M. PMID:27494789

  19. Ab initio molecular dynamics study of polarization effects on ionic hydration in aqueous AlCl3 solution

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2003-12-01

    The solvation shell structure and dynamics of Al3+ and Cl- in an aqueous solution of 0.8 M AlCl3 are studied under ambient conditions by using an ab initio molecular dynamics method. The solvation structures obtained from our ab initio simulations are in good agreement with the experimental ones for both Al3+ and Cl-. A detailed analysis of intramolecular geometry of hydration waters and dipole moments of the ingredients shows that the polarization has substantial effects on the structures and dynamics of both the cation and anion hydration shells. Implications for metal hydrolysis of Al3+ will also be given.

  20. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  1. Silicate-Metal Partitioning of Trace Elements: An Exploratory Ab Initio Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Künzel, D.; Jahn, S.

    2014-12-01

    Partition coefficients of trace elements are very important for the reconstruction of Earth formation and evolution processes. As such processes typically take place at extreme conditions of pressure and temperature, it is still challenging to obtain experimental data. However, recent developments in super-computing facilities and in computational methods have made it possible to obtain supplementing information on melts and element partitioning from ab initio atomistic calculations. The model system used in this pilot study consists of two different melts: a simple Fe-Ni alloy representing the metal and a silicate phase with a varying ratio of Fe and Mg ((Fe,Mg)2SiO4). Traces of Ni or Cr are added to each system. Molecular dynamics simulations based on density functional theory are initially run at 2500 K and ambient pressure, using the CPMD and CP2K software packages. Conditions are chosen so that the results can be compared to available experimental data in order to assess the feasibility of the approach and the quality of its results. However, preliminary results at increased pressure and temperature conditions that are more relevant for core formation will be presented as well. The results of the calculations include information on the melt structure, such as coordination environment, nearest neighbor distance and x-ray diffraction structure factors. The calculations at ambient pressure show that the behavior of Ni atoms in the silicate melt shows similarities to Mg and differs clearly from Fe. First results with a Cr trace show that it resembles Fe rather than Ni. Furthermore, thermodynamic integration is able to provide thermodynamic information about the exchange of trace elements between both phases. It is possible to obtain the energy difference connected to this exchange, which can then be used to estimate partition factors. First results on the Ni partitioning will be presented.

  2. Ab initio molecular dynamics study of the interlayer and micropore structure of aqueous montmorillonite clays

    NASA Astrophysics Data System (ADS)

    Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.

    2015-11-01

    Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.

  3. Threshold displacement energy in GaN; Ab initio molecular dynamics study

    SciTech Connect

    Xiao, H. Y.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.

    2009-06-25

    Large-scale ab initio molecular dynamics method has been used to determine the threshold displacement energies, Ed, along five specific directions and to determine the defect configurations created during low energy events. The Ed shows a significant dependence on direction. The minimum Ed is determined to be 39 eV along the <-1010> direction for a gallium atom and 17.0 eV along the <-1010> direction for a nitrogen atom, which are in reasonable agreement with the experimental measurements. The average Ed values determined are 73.2 and 32.4 eV for gallium and nitrogen atoms, respectively. The N defects created at low energy events along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed in GaN.

  4. Adsorption-Induced Surface Stresses of the Water/Quartz Interface: Ab Initio Molecular Dynamics Study.

    PubMed

    Gor, Gennady Y; Bernstein, Noam

    2016-05-31

    Adsorption-induced deformation is expansion or contraction of a solid due to adsorption on its surface. This phenomenon is important for a wide range of applications, from chemomechanical sensors to methane recovery from geological formations. The strain of the solid is driven by the change of the surface stress due to adsorption. Using ab initio molecular dynamics, we calculate the surface stresses for the dry α-quartz surfaces, and investigate how these stresses change when the surfaces are exposed to water. We find that the nonhydroxylated surface shows small and approximately isotropic changes in stress, while the hydroxylated surface, which interacts more strongly with the polar water molecules, shows larger and qualitatively anisotropic (opposite sign in xx and yy) surface stress changes. All of these changes are several times larger than the surface tension of water itself. The anisotropy and possibility of positive surface stress change can explain experimentally observed surface area contraction due to adsorption. PMID:27159032

  5. Ionic conductivity in Gd-doped CeO2: Ab initio color-diffusion nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nilsson, Johan O.; Vekilova, Olga Yu.; Hellman, Olle; Klarbring, Johan; Simak, Sergei I.; Skorodumova, Natalia V.

    2016-01-01

    A first-principles nonequilibrium molecular dynamics (NEMD) study employing the color-diffusion algorithm has been conducted to obtain the bulk ionic conductivity and the diffusion constant of gadolinium-doped cerium oxide (GDC) in the 850-1150 K temperature range. Being a slow process, ionic diffusion in solids usually requires simulation times that are prohibitively long for ab initio equilibrium molecular dynamics. The use of the color-diffusion algorithm allowed us to substantially speed up the oxygen-ion diffusion. The key parameters of the method, such as field direction and strength as well as color-charge distribution, have been investigated and their optimized values for the considered system have been determined. The calculated ionic conductivity and diffusion constants are in good agreement with available experimental data.

  6. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    SciTech Connect

    Miller, J.; Miaskiewicz, K.; Osman, R.

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  7. An ab initio molecular dynamics study on hydrogen bonds between water molecules

    NASA Astrophysics Data System (ADS)

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-01

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dHṡṡṡH between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rOṡṡṡH between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dHṡṡṡH and rOṡṡṡH are small (e.g., dHṡṡṡH < 2.0 Å and rOṡṡṡH < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They

  8. Icosahedral short-range order in amorphous Cu80Si20 by ab initio molecular dynamics simulation study

    SciTech Connect

    Wu, S.; Kramer, Matthew J.; Fang, Xiaowei; Wang, Shy-Guey; Wang, Cai-Zhuang; Ho, Kai-Ming; Ding, Z.J.; Chen, L.Y.

    2012-04-26

    Short-range order in liquid and amorphous structures of Cu80Si20 is studied by ab initio molecular dynamics simulations. We performed the simulations at 1140 and 300 K respectively to investigate the local structure change from liquid to amorphous. The result of structure factor in comparison with experimental data indicates that our simulation of amorphous Cu80Si20 is reliable. By using the bond-angle distribution function, Honeycutt–Andersen index, Voronoi tessellation method, and the atomistic cluster alignment method, the icosahedral short-range order in the system is revealed. Strong Cu–Si interaction was also observed.

  9. How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study

    PubMed Central

    2015-01-01

    Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the covalent inhibition mechanism between AChE and the nerve toxin soman and determined its free energy profile for the first time. Our results indicate that phosphonylation of the catalytic serine by soman employs an addition–elimination mechanism, which is highly associative and stepwise: in the initial addition step, which is also rate-limiting, His440 acts as a general base to facilitate the nucleophilic attack of Ser200 on the soman’s phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate; in the subsequent elimination step, Try121 of the catalytic gorge stabilizes the leaving fluorine atom prior to its dissociation from the active site. Together with our previous characterization of the aging mechanism of soman inhibited AChE, our simulations have revealed detailed molecular mechanistic insights into the damaging function of the nerve agent soman. PMID:24786171

  10. Ab initio molecular dynamics simulation study of dissociative electron attachment to dialanine conformers.

    PubMed

    Feng, Wen-Ling; Tian, Shan Xi

    2015-03-12

    Dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in the gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupies the virtual molecular orbital π*, which is followed by the different dissociation processes. The electron attachments to conformers 1 and 2 having the stronger N-H···N and O-H···O intramolecular hydrogen bonds do not lead to fragmentations, but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process and demonstrate a promising way toward understanding of the radiation damages of complicated biological system. PMID:25679256

  11. Ab Initio ONIOM-Molecular Dynamics (MD) Study on the Deamination Reaction by Cytidine Deaminase

    SciTech Connect

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2007-08-23

    We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determing step is the release of the NH3 molecule. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.

  12. Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

    SciTech Connect

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.; Li, Sean

    2015-02-09

    In this study, the response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

  13. High adsorption capacity of heavy metals on two-dimensional MXenes: an ab initio study with molecular dynamics simulation.

    PubMed

    Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming

    2016-01-01

    Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974

  14. Selective Tuning of a Particular Chemical Reaction on Surfaces through Electrical Resonance: An ab Initio Molecular Dynamics Study.

    PubMed

    Yousaf, Masood; Shin, Dongbin; Ruoff, Rodney; Park, Noejung

    2015-12-17

    We used ab initio molecular dynamics (AIMD) to investigate the effect of a monochromatic oscillating electric field in resonance with a particular molecular vibration on surfaces. As a case study, AIMD simulations were carried out for hydroxyl functional groups on graphene. When the frequency of the applied field matches with the C-OH vibration frequency, the amplitude is monotonically amplified, leading to a complete desorption from the surface, overcoming the substantial barrier. This suggests the possibility of activating a particular bond without damaging the remaining surface. We extended this work to the case of the amination of sp(2)-bonded carbon surfaces and discussed the general perspective that, in general, an unfavorable chemical process can be activated by applying an external electric field with an appropriate resonance frequency. PMID:26634785

  15. Experimental and ab initio molecular dynamics simulation studies of liquid Al[subscript 60]Cu[subscript 40] alloy

    SciTech Connect

    Wang, S.Y.; Kramer, M.J.; Xu, M.; Wu, S.; Hao, S.G.; Sordelet, D.J.; Ho, K.M.; Wang, C.Z.

    2009-06-12

    X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al{sub 60}Cu{sub 40} have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.

  16. Ab initio molecular dynamics study of the properties of cerium in liquid sodium at 1000 K temperature

    NASA Astrophysics Data System (ADS)

    Samin, Adib; Li, Xiang; Zhang, Jinsuo; Mariani, R. D.; Unal, Cetin

    2015-12-01

    For liquid-sodium-cooled fast nuclear reactor systems, it is crucial to understand the behavior of lanthanides and other potential fission products in liquid sodium or other liquid metal solutions such as liquid cesium-sodium. In this study, we focus on lanthanide behavior in liquid sodium. Using ab initio molecular dynamics, we found that the solubility of cerium in liquid sodium at 1000 K was less than 0.78 at. %, and the diffusion coefficient of cerium in liquid sodium was calculated to be 5.57 × 10-9 m2/s. Furthermore, it was found that cerium in small amounts may significantly alter the heat capacity of the liquid sodium system. Our results are consistent with the experimental results for similar materials under similar conditions.

  17. Ab initio molecular dynamics study of the properties of cerium in liquid sodium at 1000 K temperature

    SciTech Connect

    Samin, Adib; Li, Xiang; Zhang, Jinsuo; Mariani, R. D.; Unal, Cetin

    2015-12-21

    For liquid-sodium-cooled fast nuclear reactor systems, it is crucial to understand the behavior of lanthanides and other potential fission products in liquid sodium or other liquid metal solutions such as liquid cesium-sodium. In this study, we focus on lanthanide behavior in liquid sodium. Using ab initio molecular dynamics, we found that the solubility of cerium in liquid sodium at 1000 K was less than 0.78 at. %, and the diffusion coefficient of cerium in liquid sodium was calculated to be 5.57 × 10{sup −9} m{sup 2}/s. Furthermore, it was found that cerium in small amounts may significantly alter the heat capacity of the liquid sodium system. Our results are consistent with the experimental results for similar materials under similar conditions.

  18. The structural phase transition of ZnSe under hydrostatic and nonhydrostatic compressions: an ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Durandurdu, Murat

    2009-03-01

    Ab initio constant pressure molecular dynamics simulations within a generalized gradient approximation (GGA) are carried out to study the structural phase transformation of ZnSe under hydrostatic and nonhydrostatic conditions. ZnSe undergoes a first-order phase transition from the zinc-blende structure to a rocksalt structure having practically identical transformation mechanisms under hydrostatic and nonhydrostatic compressions. This phase transformation is also analyzed using the enthalpy calculations. Our transition parameters and bulk properties are comparable with experimental and theoretical data. Furthermore, the influence of pressure on the electronic structure of ZnSe is investigated. It is found that the band gap energy increases nonlinearly under both hydrostatic and nonhydrostatic conditions and the effect of stress deviations on the band gap energy is small. The computed pressure coefficients and deformation potential of the band gap are in good agreement with experiments.

  19. Ab initio molecular dynamics study of the static, dynamic, and electronic properties of liquid mercury at room temperature.

    PubMed

    Calderín, L; González, L E; González, D J

    2009-05-21

    We report a study on several static, dynamic, and electronic properties of liquid Hg at room temperature. We have performed ab initio molecular dynamics simulations using Kohn-Sham density functional theory combined with a nonlocal ultrasoft pseudopotential. The calculated static structure shows good agreement with the available experimental data. We present results for the single-particle dynamics, and recent experimental data are analyzed. The calculated dynamic structure factors S(q,omega) fairly agree with their experimental counterparts as measured by inelastic x-ray (and neutron) scattering experiments. The dispersion relation exhibits a positive dispersion, which however is not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit provides a good estimate of the experimental sound velocity. We have also analyzed the dynamical processes behind the S(q,omega) in terms of a model including a relaxation mechanism with both fast and slow characteristic time scales. PMID:19466841

  20. Effects of boron-nitride substrates on Stone-Wales defect formation in graphene: An ab initio molecular dynamics study

    SciTech Connect

    Jin, K.; Xiao, H. Y.; Zhang, Y.; Weber, W. J.

    2014-05-19

    Ab initio molecular dynamics simulations are performed to investigate the effects of a boron nitride (BN) substrate on Stone-Wales (SW) defect formation and recovery in graphene. It is found that SW defects can be created by an off-plane recoil atom that interacts with the BN substrate. A mechanism with complete bond breakage for formation of SW defects in suspended graphene is also revealed for recoils at large displacement angles. In addition, further irradiation can result in recovery of the SW defects through a bond rotation mechanism in both graphene and graphene/BN, and the substrate has little effect on the recovery process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.

  1. Movement of Ng2 molecules confined in a C60 cage: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Khatua, Munmun; Pan, Sudip; Chattaraj, Pratim K.

    2014-08-01

    An ab initio molecular dynamics study on Ng2@C60 (Ng = Hesbnd Kr) systems is performed to analyze the movement of Ng2 molecules inside a C60 cage. Within 500 fs time window, the He2 undergoes precession encompassing translation, vibration and rotation readily whereas other Ng2 molecules show usual vibration but the degrees of translation and rotation decrease with an increase in size of the Ng atoms. Increase in interaction between the Ng centers and cage carbons and an increased distortion of cage in moving from He to Kr seem to be responsible for this. During the movement, the Ng2 units behave as single entity. To check the kinetic stability of these systems through ab initio molecular dynamics study since they are thermodynamically unstable. Frenking et al. [40] argued about the free precession of the Ng2 units inside the cage on the basis of the very small energy differences between differently oriented Ng2 units. We need to check whether these Ng2 units really precess inside the C60 cage at room temperature and if yes then by what extent, up to 500 fs time scale. To check whether these weakly interacting He2 and Ne2 systems can be termed as molecules we would like to analyze the Ngsbnd Ng bond distance values at different time steps. In order to check the applicability of maximum hardness principle and minimum electrophilicity principle during time evolution of these endohedrally trapped systems the variation of hardness and electrophilicity with time during simulation and their correlation with the change in energy of the systems are studied.

  2. Methodological approach to study energetic and structural properties of nanostructured cadmium sulfide by using ab-initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Burresi, E.; Celino, M.

    2012-05-01

    A single wurtzite phase of cadmium sulfide cluster is investigated by ab-initio molecular dynamics simulations at different temperatures, ranging from 100 K to 600 K. In this study we propose a possible procedure to characterize the CdS quantum dots system by means of molecular dynamics calculations using a standard Car-Parrinello scheme. In order to ensure the accuracy of the numerical approach, preliminary calculations to test pseudopotentials, cutoff and box size on both single atoms systems and Cd-Cd, S-S, Cd-S dimers have been performed. Calculated binding energies and bond lengths are obtained in good agreement with experimental data. Subsequently, an uncapped CdS cluster with size below 2 nm, 48 atoms of cadmium and 48 atoms of sulfur, in a wurtzite geometry was structurally optimized to minimize internal stresses. The CdS cluster has been carefully characterized structurally at several temperatures up to T = 600 K. At the temperature of 340 K atomic diffusion on the surface allows the onset of a new stable atomic configuration.

  3. Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2013-05-28

    The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations. PMID:23742495

  4. Ab initio molecular dynamics study of high-pressure melting of beryllium oxide

    PubMed Central

    Li, Dafang; Zhang, Ping; Yan, Jun

    2014-01-01

    We investigate, through first-principles molecular dynamics simulations, the high-pressure melting of BeO in the range 0 ≤ p ≤ 100 GPa. The wurtzite (WZ), zinc blend (ZB), and rocksalt (RS) phases of BeO are considered. It is shown that below 40 GPa, the melting temperature for the WZ phase is higher than that for the ZB and RS phases. When the pressure is beyond 66 GPa, the melting temperature for the RS phase is the highest one, in consistent with the previously reported phase diagram calculated within the quasiharmonic approximation. We find that in the medium pressure range between 40 to 66 GPa, the ZB melting data are very close to those of RS, which results from the fact that the ZB structure first transforms to RS phase before melting. The ZB-RS-liquid phase transitions have been observed directly during the molecular dynamics runs and confirmed using the pair correlation functions analysis. In addition, we propose the melting curve of BeO in the form Tm = 2696.05 (1 + P/24.67)0.42, the zero-pressure value of 2696.05 K falling into the experimental data range of 2693 ~ 2853 K. PMID:24759594

  5. Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

    SciTech Connect

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-17

    Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

  6. Ab initio molecular dynamics: concepts, recent developments, and future trends.

    PubMed

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E

    2005-05-10

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  7. Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections

    NASA Astrophysics Data System (ADS)

    Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.

    2012-07-01

    It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)], 10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.

  8. Oxidation of ligand-protected aluminum clusters: an ab initio molecular dynamics study.

    PubMed

    Alnemrat, Sufian; Hooper, Joseph P

    2014-03-14

    We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material. PMID:24628175

  9. Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

    SciTech Connect

    Alnemrat, Sufian; Hooper, Joseph P.

    2014-03-14

    We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O{sub 2} molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O{sub 2} diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material.

  10. Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Alnemrat, Sufian; Hooper, Joseph P.

    2014-03-01

    We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material.

  11. Vibrational lifetimes of hydrogen on lead films: An ab initio molecular dynamics with electronic friction (AIMDEF) study

    SciTech Connect

    Saalfrank, Peter; Juaristi, J. I.

    2014-12-21

    Using density functional theory and Ab Initio Molecular Dynamics with Electronic Friction (AIMDEF), we study the adsorption and dissipative vibrational dynamics of hydrogen atoms chemisorbed on free-standing lead films of increasing thickness. Lead films are known for their oscillatory behaviour of certain properties with increasing thickness, e.g., energy and electron spillout change in discontinuous manner, due to quantum size effects [G. Materzanini, P. Saalfrank, and P. J. D. Lindan, Phys. Rev. B 63, 235405 (2001)]. Here, we demonstrate that oscillatory features arise also for hydrogen when chemisorbed on lead films. Besides stationary properties of the adsorbate, we concentrate on finite vibrational lifetimes of H-surface vibrations. As shown by AIMDEF, the damping via vibration-electron hole pair coupling dominates clearly over the vibration-phonon channel, in particular for high-frequency modes. Vibrational relaxation times are a characteristic function of layer thickness due to the oscillating behaviour of the embedding surface electronic density. Implications derived from AIMDEF for frictional many-atom dynamics, and physisorbed species will also be given.

  12. Ab initio molecular dynamics studies of the structure and dynamics of molten SexTe1-x alloys

    NASA Astrophysics Data System (ADS)

    Lomba, E.; Katcho, N. A.; Otero-Díaz, L. C.

    2005-10-01

    We calculate the microscopic structure and dynamics of molten SexTe1-x alloys ( x=0.3 , 0.5, 0.7) at 748 K by means of ab initio molecular dynamics. We present results for the static and dynamic structure factors, diffusion coefficients, and frequency spectra, in addition to the electronic density of states. Both the results for the structural and dynamic properties are in relatively good agreement with the available experimental data, despite the known shortcomings of ab initio techniques for the limiting case x=0 . The results also indicate that, as expected, the increase in the number of Te atoms augments the metallic character of the sample in close connection with a corresponding disruption of the Se chain network that dominates the structure of the condensed phases of pure selenium.

  13. Coordination properties of a metal chelator clioquinol to Zn(2+) studied by static DFT and ab initio molecular dynamics.

    PubMed

    Rodríguez-Santiago, Luis; Alí-Torres, Jorge; Vidossich, Pietro; Sodupe, Mariona

    2015-05-28

    Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(ii) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)2, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)2(H2O) and hexa Zn(CQ)2(H2O)2 coordinated complexes. The possible reasons for these discrepant results are discussed. PMID:25939963

  14. Structure and dynamics of high-pressure Na close to the melting line: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Marqués, M.; González, D. J.; González, L. E.

    2016-07-01

    The melting curve of sodium for a pressure range up to 100 GPa has been evaluated by the orbital free ab initio molecular dynamics method. This method uses the electronic density as the basic variable combined with an approximate electronic kinetic energy functional and a local ionic pseudopotential and makes it possible to perform simulations with a large number of particles and for long simulation times. The calculated melting curve shows a maximum melting temperature at a pressure around 30 GPa followed by a steep decrease up to 100 GPa. For various pressures and temperatures we have evaluated several static properties, including average and local structure, electronic properties, like the electron localization function (ELF), and dynamic properties, both single-particle and collective ones, from which some transport coefficients are deduced. Despite the accurate reproduction of the available experimental data, we do not observe any indication of an early transition from a bcc-like to an fcc-like liquid, as suggested previously by other authors, but rather pressure-induced change in the variation of icosahedral-like order and bcc-like order, with no sign of fcc-like structures in the whole liquid range studied. We also consider the evolution of the ELF within this type of local arrangement upon pressurization. In the dynamic realm, we find an enlarged wave-vector region where atomic collisions play an important role in the dynamic properties of the system as pressure is increased and temperature decreased along the melting line, leading to a peculiar behavior of the dynamic properties.

  15. On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

    PubMed

    Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

    2014-07-14

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results. PMID:25028021

  16. On the room-temperature phase diagram of high pressure hydrogen: An ab initio molecular dynamics perspective and a diffusion Monte Carlo study

    SciTech Connect

    Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

    2014-07-14

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

  17. Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study.

    PubMed

    Kolb, Brian; Guo, Hua

    2016-07-01

    Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment. PMID:27394092

  18. Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kolb, Brian; Guo, Hua

    2016-07-01

    Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.

  19. Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

    SciTech Connect

    Jakse, N.; Pasturel, A.

    2014-12-21

    In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

  20. Characterization of amorphous In{sub 2}O{sub 3}: An ab initio molecular dynamics study

    SciTech Connect

    Aliano, Antonio; Catellani, Alessandra; Cicero, Giancarlo

    2011-11-21

    In this work, we report on the structural and electronic properties of amorphous In{sub 2}O{sub 3} obtained with ab initio molecular dynamics. Our results show crystal-like short range InO{sub 6} polyhedra having average In-O distance consistent with x-ray spectroscopy data. Structural disorder yields band tailing and localized states, which are responsible of a strong reduction of the electronic gap. Most importantly, the appearance of a peculiar O-O bond imparts n-type character to the amorphous compound and provides contribution for interpreting spectroscopic measurements on indium based oxidized systems. Our findings portray characteristic features to attribute transparent semiconductive properties to amorphous In{sub 2}O{sub 3}.

  1. Ab initio molecular dynamics studies on effect of Zr on oxidation resistance of TiAlN coatings

    NASA Astrophysics Data System (ADS)

    Pi, Jingwu; Kong, Yi; Chen, Li; Du, Yong

    2016-08-01

    It was demonstrated experimentally that doping Zr into TiAlN coatings at room temperature will detriment its oxidation resistance. On the other hand, there are evidences that doping Zr into TiAlN at high temperature will improve coating's oxidation resistance. In the present work, we address the effect of Zr on the oxidation resistance of TiAlN by means of ab initio molecular dynamics simulations. The TiAlN and TiAlZrN (1 Zr atom replacing 1 Ti atom) surfaces covered with 4 oxygen atoms at 300 K and 1123 K were simulated. Based on the analysis of the atomic motion, bond formation after relaxation, and the charge density difference maps we find that at 300 K, the addition of Zr induces escape of Ti atoms from the surface, resulting in formation of surface vacancies and subsequently TiO2. Comparison of metal-oxygen dimers in the vacuum and above the TiAlZrN surface further shows that the addition of Zr in the TiAlN surface will change the lowest bonding energy sequence from Zrsbnd O < Tisbnd O < Alsbnd O in the vacuum to Tisbnd O < Zrsbnd O < Alsbnd O above the TiAlZrN surface. From Molecular Dynamics simulations at 1123 K, it is find that no Ti vacancies were generated in the surface. Moreover, less charge is transferred from metal to N atoms and the bond lengths between Ti and O atoms become shorter at 1123 K as compared with 300 K, suggesting that the addition of Zr atom promotes the interaction of Ti and O at TiAlZrN surface at 1123 K, leading to a more stable surface. Our simulation explains why Zr-doping at 1123 K increases TiAlN coating's oxidation resistance while at 300 K reduces its oxidation resistance.

  2. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

    PubMed

    Czeleń, Przemysław; Czyżnikowska, Żaneta

    2016-06-01

    In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component. PMID:27154340

  3. Study on Exploration of Azeotropic Point of Pb-Sb Alloys by Vacuum Distillation and Ab Initio Molecular Dynamic Simulation

    NASA Astrophysics Data System (ADS)

    Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian

    2016-07-01

    The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.

  4. Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study.

    PubMed

    Pepin, Robert; Petrone, Alessio; Laszlo, Kenneth J; Bush, Matthew F; Li, Xiaosong; Tureček, František

    2016-07-21

    Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections. PMID:27389035

  5. The amorphous silica-liquid water interface studied by ab initio molecular dynamics (AIMD): local organization in global disorder.

    PubMed

    Cimas, Álvaro; Tielens, Frederik; Sulpizi, Marialore; Gaigeot, Marie-Pierre; Costa, Dominique

    2014-06-18

    The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface. PMID:24863440

  6. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  7. Origin of the reverse optical-contrast change of Ga-Sb phase-change materials—An ab initio molecular-dynamics study

    SciTech Connect

    Dixon, J. A.; Elliott, S. R.

    2014-04-07

    A large number of phase-change materials (PCMs) have been developed experimentally; however, only Ge{sub 2}Sb{sub 2}Te{sub 5}-based PCMs have been significantly explored using ab initio molecular-dynamics (AIMD) simulations. We present an AIMD study of the full melt/quench/anneal PC cycle for Ga-Sb materials, namely, the stoichiometric composition, GaSb, and the near-eutectic alloy, Ga{sub 16}Sb{sub 84}. The calculated electronic densities of states and optical reflectivities are compared between the amorphous and crystalline phases for both compositions, and it is shown that the contrasting opto-electronic properties of each crystalline material can be attributed to different structural transformations of Ga and Sb on crystallization from the amorphous state.

  8. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

    SciTech Connect

    Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

    2013-07-07

    Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

  9. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  10. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  11. Thulium(III) and ytterbium(III) in aqueous solution ab initio quantum mechanical charge field molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Passler, Peter P.; Rode, Bernd M.

    2015-10-01

    Hydration properties of trivalent thulium and ytterbium ions in aqueous solution are investigated via quantum mechanical charge field molecular dynamics (QMCF-MD) simulations. The QMCF-MD formalism is a special type of QM/MM simulation, where the chemically most relevant part of the system - in this case the ion with its first and second hydration shells - is treated by quantum mechanics. The mean ionsbnd O distances and the average coordination numbers of the first hydration shells are compared with experimental EXAFS data. Mean ligand residence times, vibrational frequencies and force constants were evaluated to characterise the dynamics of the systems.

  12. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  13. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics.

    PubMed

    Campetella, M; Bovi, D; Caminiti, R; Guidoni, L; Bencivenni, L; Gontrani, L

    2016-07-14

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm(-1)), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm(-1) where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment. PMID:27421420

  14. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.

    2016-07-01

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  15. Ab initio and molecular dynamics studies of crystalline TNAD (trans-1,4,5,8-tetranitro-1,4,5,8-tetraazadecalin).

    PubMed

    Qiu, Ling; Xiao, He-Ming; Zhu, Wei-Hua; Xiao, Ji-Jun; Zhu, Wei

    2006-06-01

    The structural and electronic properties of the energetic crystal TNAD (trans-1,4,5,8-tetranitro-1,4,5,8- tetraazadecalin) have been studied using plane-wave ab initio calculations based on the density function theory method with the ultrasoft pseudopotentials. It is found that the predicted crystal structure is in good agreement with experimental data and there are strong inter- and intramolecular interactions in bulk TNAD. Band structure calculations indicate that TNAD is an insulator with the band gap of ca. 3.3 eV. The hydrostatic compression effect on TNAD has been studied in the pressure range of 0-600 GPa. The results show that a pressure less than 10 GPa does not significantly change the geometric parameters, charge distributions, and electronic bands. When the pressure is over 10 GPa, increasing the pressure determines significant changes of the geometrical and electronic structures and large broadening of the electronic bands together with a sharp decrease of the band gap. Isothermal-isobaric molecular dynamics simulations at atmospheric pressure were further performed on the TNAD crystal in the temperature range 5-500 K. Average equilibrium lattice parameters and elastic properties as functions of temperature were determined. The thermal expansion coefficients calculated for the crystal indicate anisotropic behavior with the largest expansion along the b axis. PMID:16771311

  16. Hydrogen evolution from formic acid in an ionic liquid solvent: a mechanistic study by ab initio molecular dynamics.

    PubMed

    Bhargava, B L; Yasaka, Yoshiro; Klein, Michael L

    2011-12-01

    The reversible decomposition of formic acid (HCOOH ⇌ CO(2) + H(2)) has been attracting attention for its potential utility in hydrogen storage and production. It is therefore of interest to explore the influence of solvents on the decomposition reaction. To this end, Born-Oppenheimer (BO) molecular dynamics (MD) calculations have been performed to explore the mechanism involved in hydrogen (H(2)) evolution from formic acid decomposition in an ionic liquid solvent. Specifically, for a solvent consisting of 1,3-dimethylimidazolium cations and formate anions, evolution of hydrogen (H(2)) and carbon dioxide (CO(2)) was observed within a few picoseconds when BO-MD trajectories were carried out at an elevated temperature of 3000 K. The observed dehydrogenation involved a reaction between a formic acid solute and a nearby solvent formate anion. The observed mechanism contrasts with the unimolecular mechanism proposed in the gas phase. Specifically, in the ionic liquid, the reaction is initiated from a C-H bond dissociation of a formate anion to produce a short-lived hydride anion, which subsequently captures the acidic proton of a nearby formic acid molecule. The present BO-MD computations suggest that the high reducing ability of formic acid in the ionic liquid is due in part to its acid-dissociated form: the formate anion, which is encouraged to dissociate into a hydride anion and CO(2) by the strong electrostatic field of the ionic liquid solvent. PMID:21774513

  17. Spatial distribution of rare-earth ions and GaS4 tetrahedra in chalcogenide glasses studied via laser spectroscopy and ab initio molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lee, T. H.; Simdyankin, S. I.; Hegedus, J.; Heo, J.; Elliott, S. R.

    2010-03-01

    The spatial distribution of Nd3+ ions and GaS4 tetrahedral units in Nd-doped Ge-As-Ga-S glasses has been studied by laser spectroscopy and ab initio molecular dynamics (MD) simulations. A sharp increase in Nd3+ fluorescence intensities and lifetimes was observed with increasing Ga content, and attributed to the formation of tightly bound Nd3+ clusters in Ga-free glasses and the subsequent dissolution of such clusters upon Ga doping. A large modification in Nd3+ sites was also identified from low-temperature site-selective excitation spectra, suggesting preferential spatial correlations between Nd3+ and GaS4 tetrahedra even at low Ga-doping levels. MD simulations of these materials in the liquid state showed a tendency for Ga cluster formation as well as spatial correlations between Nd and Ga atoms consistent with the experimental results. On the basis of this result, a comprehensive structural model for Nd- and Ga-doped sulfide glasses is proposed.

  18. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  19. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  20. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573

  1. Pressure-induced phase transitions and structural properties of CoF2: An ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya

    2016-04-01

    The crystal structure of CoF2 was studied theoretically using first-principles density functional theory (DFT) methods within the generalized gradient approximation (GGA) and local density approximation (LDA) under rapid hydrostatic pressure up to 144 GPa. CoF2 undergoes a structural phase transformation from the rutile-type tetragonal parent phase with space group P42/mnm to the CaCl2-type orthorhombic parent phase with space group Pnnm at 64 GPa with GGA and at 96 GPa with LDA methods. Another phase transformation occurs from the CaCl2-type structure to monoclinic parent phase with space group P21/c at 96 GPa with a GGA method. These phase transitions are also studied by enthalpy and total energy calculations. According to these calculations, we obtained the first phase transformation at about 6.5 GPa both GGA and LDA methods and the later phase transformation at about 45 GPa with the GGA method.

  2. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

    SciTech Connect

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2008-02-01

    We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.

  3. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  4. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2⇌ CH + H on Ni(111) as a case study.

    PubMed

    Sun, Geng; Jiang, Hong

    2015-12-21

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH2⇌CH+H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of

  5. N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

    2015-03-01

    We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

  6. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2(+)) Cation.

    PubMed

    Dietrick, Scott M; Iyengar, Srinivasan S

    2012-12-11

    A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted. PMID:26593181

  7. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  8. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGESBeta

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-22

    Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less

  9. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  10. Mechanism of dissolution of a lithium salt in an electrolytic solvent in a lithium ion secondary battery: a direct ab initio molecular dynamics (AIMD) study.

    PubMed

    Tachikawa, Hiroto

    2014-06-01

    The mechanism of dissolution of the Li(+) ion in an electrolytic solvent is investigated by the direct ab initio molecular dynamics (AIMD) method. Lithium fluoroborate (Li(+)BF4(-)) and ethylene carbonate (EC) are examined as the origin of the Li(+) ion and the solvent molecule, respectively. This salt is widely utilized as the electrolyte in the lithium ion secondary battery. The binding of EC to the Li(+) moiety of the Li(+)BF4(-) salt is exothermic, and the binding energies at the CAM-B3LYP/6-311++G(d,p) level for n=1, 2, 3, and 4, where n is the number of EC molecules binding to the Li(+) ion, (EC)n(Li(+)BF4(-)), are calculated to be 91.5, 89.8, 87.2, and 84.0 kcal mol(-1) (per EC molecule), respectively. The intermolecular distances between Li(+) and the F atom of BF4(-) are elongated: 1.773 Å (n=0), 1.820 Å (n=1), 1.974 Å (n=2), 1.942 Å (n=3), and 4.156 Å (n=4). The atomic bond populations between Li(+) and the F atom for n=0, 1, 2, 3, and 4 are 0.202, 0.186, 0.150, 0.038, and 0.0, respectively. These results indicate that the interaction of Li(+) with BF4(-) becomes weaker as the number of EC molecules is increased. The direct AIMD calculation for n=4 shows that EC reacts spontaneously with (EC)3(Li(+)BF4(-)) and the Li(+) ion is stripped from the salt. The following substitution reaction takes place: EC+(EC)3(Li(+)BF4(-))→(EC)4Li(+)-(BF4(-)). The reaction mechanism is discussed on the basis of the theoretical results. PMID:24616076

  11. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  12. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  13. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-01

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed. PMID:23298049

  14. Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane.

    PubMed

    Devanathan, Ram; Idupulapati, Nagesh; Baer, Marcel D; Mundy, Christopher J; Dupuis, Michel

    2013-12-27

    We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H2O/SO3(-) corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3(-)-H3O(+) contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10(-5) cm(2)/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations. PMID:24320080

  15. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    DOE PAGESBeta

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

  16. The Aqueous Ca2+ System, in Comparison with Zn2+, Fe3+, and Al3+: An Ab Initio Molecular Dynamics Study

    SciTech Connect

    Bogatko, Stuart A.; Cauet, Emilie L.; Bylaska, Eric J.; Schenter, Gregory K.; Fulton, John L.; Weare, John H.

    2013-02-21

    Results of Ab Initio Molecular Dynamics (AIMD) simulations of a Ca2+ ion in an aqueous environment (64 waters, 38ps=5ps equilibration + 33ps data collection, 300K) are reported. The 1st hydration shell contains 6-7 waters with d(OH) = 0.97Å (identical to our bulk water estimate) and average tilt angle, I = 32º. The 1st maximum in the radial distribution function occurs at GCaO(r) = 2.45Å. Our results compare well with published experimental structural data from X-Ray Absorption (XAFS) and Neutron Diffraction. We also generate simulated XAFS spectra using a 1st principles MD-XAFS procedure and show quantitative agreement with experimental XAFS data from a 0.2m Ca(ClO4)2 aqueous solution. The Ca2+ 1st shell water dipole moment of 3.1D is identical to our bulk water estimate (3.1D). The structured 2nd hydration shell, composed of ~16.5 waters, has a maximum at GCaO(r) =4.6Å. The average 2nd shell dipole moment = 2.9D, is suppressed relative to bulk water values. Detailed H-bond analysis demonstrates the waters in this shell predominately coordinate 1st shell waters with a trigonally structured H-bond network. Two exchanges between the 1st hydration shell and the bulk were observed. These were consistent with a dissociative and dissociative interchange Eigen-Wilkins ligand exchange mechanism. Many transfers between the 2nd shell and bulk are detected for Ca2+ allowing an estimation of the 2nd shell mean residence time (MRT) of 4.6ps. Comparison of the Ca2+ hydration shell structure and dynamics with those of the recently reported Zn2+, Fe3+ and Al3+ cation species show that the 1st and 2nd hydration shell parameters, d(M-OI) distance, CNII, H-bond d(OI-OII) distance and %Tetrahedral structure are correlated with cation charge density, the ratio of cation charge (Z) and size (Rion). However, important exceptions are d(M-OII) and the 2nd shell Mean Residence Time (MRT). These differences are explained in terms of the 1st shell structure parameters (d(M-OI) distance

  17. Molecular Dynamics Study of Potassium Azide (KN_3)

    NASA Astrophysics Data System (ADS)

    Ossowski, M.; Hardy, J. R.

    1998-03-01

    An ab initio model developed for intermolecular and intramolecular potentials in ionic molecular solids(H. M. Lu and J. R. Hardy, Phys. Rev. B, 42, 8339 (1990)) is employed to study the phase diagram of potassium azide (KN_3). We performed first-principles static structural relaxation, supercell molecular dynamics, lattice- dynamical studies and predict the existence of a high temperature rotationally disordered phase in KN_3. A selected work on other members of the alkali azide family will also be discussed.

  18. Ab initio molecular dynamics simulation of pressure-induced zinc blende to rocksalt phase transition in SiC

    SciTech Connect

    Xiao, Haiyan J.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.

    2009-06-17

    The high-pressure induced phase transformation from the zinc blende to rocksalt structure in SiC has been studied by ab initio molecular dynamics. The simulations show that SiC passes through tetragonal and then monoclinic intermediate states before finally forming the rock salt structure at 160 GPa. The mechanism for this phase transformation agrees well with recent ab initio MD simulations, in which the applied pressure was as high as ~600 GPa, but in the present study the transformation occurs at much lower pressure. It is found that the phase transition has to overcome an energy barrier of 0.44 eV/pair.

  19. Investigation of the liquid Pb/Si(001) interface from ab initio molecular-dynamics calculations

    NASA Astrophysics Data System (ADS)

    Gonzalez, D. J.; Souto, J.; Alemany, M. M. G.; Longo, R. C.; Gallego, L. J.; Gonzalez, L. E.

    2013-03-01

    The structure of liquid Pb on an ideal Si(001) surface was studied experimentally a decade ago by means of x-ray diffraction and the results were interpreted in terms of the presence of fivefold symmetry Pb structures captured transiently by the potential created by the unreconstructed Si(001) surface. We critically analyze this interpretation in the light of the results obtained in an extensive ab initio molecular dynamics study of a system comprising 314 Pb atoms and 175 Si atoms setup in 7 (001) ideal layers (a total number of 1956 valence electrons) in a slab geometry. The structure found for the first Pb layer is very different from that of bulk Pb, mostly consisting in one-dimensional lines. However, we do observe the possibility of forming transient structures, in particular icosahedral caps. Supported by FIS2008-02490/FIS, FIS2008-04894/FIS, GR120, INCITE09E2R206033ES and INCITE08PXIB206107PR.

  20. Hydrogen Recombination and Dimer Formation on Graphite from Ab Initio Molecular Dynamics Simulations.

    PubMed

    Casolo, S; Tantardini, G F; Martinazzo, R

    2016-07-14

    We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques. PMID:26905385

  1. Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.

    PubMed

    Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R

    2015-07-01

    We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching. PMID:26040531

  2. Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

  3. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations.

    PubMed

    Brandt, Erik G; Agosta, Lorenzo; Lyubartsev, Alexander P

    2016-07-21

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. PMID:27341183

  4. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics

    PubMed Central

    2012-01-01

    In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra. PMID:22904696

  5. An ab initio Molecular Dynamics study of the solvated OHCl- complex. Implications for the atmospheric oxidation of (Cl-)aq to (Cl2)g

    SciTech Connect

    D'Auria, R; Kuo, I W; Tobias, D J

    2007-07-26

    We have studied the OHCl{sup -} complex in a six water cluster and in bulk liquid water by means of generalized gradient-corrected BLYP density functional theory based Born-Oppenheimer molecular dynamics. Self-interaction corrected results, that predict an H-bonded OH...Cl{sup -} complex, are compared to the uncorrected ones, that predict a bonded (HO-Cl){sup -}. A second order Moeller-Plesset potential energy landscape of the gas-phase complex in its ground state was computed to determine which of the two configurations represents the true nature of the bond. Since no evidence of a local minimum was found in the vicinity of the geometry corresponding to the (HO-Cl){sup -} we conclude that the complex is held together by a H-bond like interaction in both an asymmetric solvation environment, as represented by the cluster, and in a symmetric solvation environment, as represented by the bulk system. In the limits of the present results we postulate that the mechanism that governs the atmospheric oxidation of (Cl{sup -}){sub int} to (Cl{sub 2}){sub gas} on the surface of marine aerosols [Knipping et al. 2000] is initiated by the formation of an H-bonded OH...Cl{sup -} complex. Furthermore, since no evidence of charge transfer mechanism from Cl{sup -} to OH was found, in the liquid as well as in the cluster environments, a likely second step toward the oxidation of Cl{sup -} should consist in the reaction of the complex with a second Cl{sup -} that would result in the formation of the species Cl{sup -2} and OH{sup -}. (Cl{sub 2}){sub g} could then be formed upon charge exchange reaction with an impinging OH molecule.

  6. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    PubMed

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  7. Spectroscopic properties with a combined approach of ab initio molecular dynamics and wavelet analysis

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Francesco; Cardini, Gianni; Righini, Roberto; Schettino, Vincenzo

    2011-05-01

    In order to extract spectroscopic information from trajectories obtained by classical or ab initio molecular dynamics simulations, usually Fourier transforms are employed. In recent years wavelet transforms have been shown to be a valid alternative tool to analyze time-series, due to their capability of localizing a signal both in time and frequency. In this article wavelet transforms are applied for the analysis of Car-Parrinello molecular dynamics simulations to the purpose of time-correlating structural and spectroscopic properties of methyl acetate dissolved in water and methanol. The results demonstrate the possibility of obtaining information that may be of valuable help in the interpretation of time-resolved spectroscopic data.

  8. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.

    2016-07-01

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and

  9. An ab initio molecular dynamics study of the liquid-vapor interface of an aqueous NaCl solution: inhomogeneous density, polarity, hydrogen bonds, and frequency fluctuations of interfacial molecules.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-11-21

    We have presented a first principles simulation study of the structural and dynamical properties of a liquid-vapor interfacial system of a concentrated (5.3 M) aqueous NaCl solution. We have used ab initio molecular dynamics to examine the structural and dynamical properties of the bulk and interfacial regions. The structural aspects of the system that have been considered here include the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions in the bulk and interfacial regions. It is found that the sodium ions are mostly located in the interior, while the chloride anions occupy a significant portion of the interface of the slab. The water dipoles at the interface prefer to orient parallel to the surface. The dynamical aspects of the interfaces are investigated in terms of diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion. The results of the interfacial dynamics are compared with those of the corresponding bulk region. It is observed that the interfacial molecules exhibit faster diffusion and orientational relaxation with respect to the bulk. However, the interfacial molecules are found to have longer hydrogen bond lifetimes than those of the bulk. We have also investigated the correlations of hydrogen bond relaxation with the vibrational frequency fluctuations of interfacial water molecules. PMID:25416903

  10. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor.

    PubMed

    Papoian, Garegin A; DeGrado, William F; Klein, Michael L

    2003-01-15

    We present three theoretical models of various degree of completeness to explore the chemical phase space available to the Glu4His2Zn2 cofactor found in the four-helix bundle of de novo designed metalloprotein Duo Ferro 1. We have found that the planewave DFT geometry optimization of 94-atom Model I, which contains both the protein scaffold constraints as well as the second shell hydrogen bonding network, reproduces the crystal structure bonding with remarkable accuracy (0.34 A). Surprisingly, the geometry optimization of 66-atom Model II (lacking the second shell hydrogen bonding) and 48-atom Model III (being also free of the protein scaffold constraints) still result in the fidelity with the crystallographic structure (RMSDs 0.29 and 0.34 A, respectively). To examine whether these structures are close to the global minimum as well as to investigate various conformational transitions to which the di-Zn cofactor may be susceptible to, we have carried out a 10 ps Car-Parrinello Molecular Dynamics (CPMD) simulation of Model III. We suggest that weak hydrogen bonds between imidazole hydrogens and carboxylate oxygens modulate the dynamical behavior of the system. One part of the molecule was found to be rigid due to the particular H(imidazole)-O(carboxylate) interaction restricting both the motion of the imidazole ring as well as the terminal carboxylate conformational mobility. The second half of the system was very flexible demonstrating a coupling of a transient formation of H(imidazole)-O(carboxylate) bonds with the spinning of the imidazole ring and syn-anti isomerization of the terminal carboxylate group. In addition, two low-energy snapshots from the 10 ps CPMD run were quenched, and their geometries were optimized, leading to two new isomers 48 kJ/mol lower in energy than the one associated with the crystal structure. We suggest that periodic quenching of the CPMD simulation snapshots of a minimalist model may be used as an efficient method to generate a large

  11. An ab initio molecular dynamics analysis of lignin as a potential antioxidant for hydrocarbons.

    PubMed

    Pan, Tongyan; Cheng, Cheng

    2015-11-01

    Lignins are complex phenolic polymers with limited industrial uses. To identify new applications of lignins, this study aims to evaluate the conifer alcohol lignin as a potential antioxidant for hydrocarbons, using the petroleum asphalt as an example. Using the ab initio molecular dynamics (AIMD) method, the evaluation is accomplished by tracking the generation of critical species in a lignin-asphalt mixture under a simulated oxidative condition. The generation of new species was detected using nuclear magnetic resonance and four analytical methods including density of states analysis, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses, bonding and energy level analysis, and electrostatic potential energy analysis. Results of the analyses show that the chemical radicals of carbon, nitrogen and sulfur generated in the oxidation process could enhance the agglomeration and/or decomposition tendency of asphalt. The effectiveness of lignins as an antioxidant depends on their chemical compositions. Lignins with a HOMO-LUMO gap larger than the HOMO-LUMO gap of the hydrocarbon system to be protected, such as the conifer alcohol lignin to protect petroleum asphalt as was studied in this work, do not demonstrate beneficial anti-oxidation capacity. Lignins, however, may be effective oxidants for hydrocarbon systems with a larger HOMO-LUMO gap. In addition, lignins may contain more polar sites than the hydrocarbons to be protected; thus the lignins' hydrophobicity and compatibility with the host hydrocarbons need to be well evaluated. The developed AIMD model provides a useful tool for developing antioxidants for generic hydrocarbons. PMID:26562413

  12. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    NASA Astrophysics Data System (ADS)

    Lespade, Laure

    2016-08-01

    Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  13. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  14. Quantum yields and reaction times of photochromic diarylethenes: nonadiabatic ab initio molecular dynamics for normal- and inverse-type.

    PubMed

    Wiebeler, Christian; Schumacher, Stefan

    2014-09-11

    Photochromism is a light-induced molecular process that is likely to find its way into future optoelectronic devices. In further optimization of photochromic materials, light-induced conversion efficiencies as well as reaction times can usually only be determined once a new molecule was synthesized. Here we use nonadiabatic ab initio molecular dynamics to study the electrocyclic reaction of diarylethenes, comparing normal- and inverse-type systems. Our study highlights that reaction quantum yields can be successfully predicted in accord with experimental findings. In particular, we find that inverse-type diarylethenes show a significantly higher reaction quantum yield and cycloreversion on times typically as short as 100 fs. PMID:25140609

  15. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

    PubMed

    Zhou, Y; Wang, S; Li, Y; Zhang, Y

    2016-01-01

    There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636

  16. Molecular dynamics modeling using ab initio interatomic potentials for thermal properties of Ni-rich alloys

    SciTech Connect

    Mei, J.; Cooper, B.R.; Hao, Y.G.; Scoy, F.L. Van

    1994-12-31

    Molecular dynamics simulations have been performed to study thermal expansions of Ni-rich (fcc structure) Ni/Cr alloys (which serve as the basis for practical superalloy systems). This has been done using ab initio interatomic potentials with no experimental input. The coefficient of thermal expansion (CTE) as a function of temperature has been calculated. By admixing Re and Me atoms into fee Ni and the fee alloy system Ni/Cr, additive effects on the thermal expansion have been predicted. While addition of Cr lowers the CTE of Ni, and moderate addition of Mo lowers the CTE of Ni over a wide temperature range, moderate addition of Re raises the CTE of both Ni and Ni/Cr alloys over a significant temperature range. An explanation for the contrasting effect of additive Re on the CTE, based on a one-dimensional atomic chain model, is that the trade-off, between atomic volume effects increasing the CTE over that of pure Ni and pair-potential effects (exemplified by the Grueneisen parameter) decreasing the CTE from that of pure nickel, changes for Re compared to Cr and Mo.

  17. Ab initio molecular dynamics simulations of threshold displacement energies in SrTiO3

    SciTech Connect

    Liu, Bin; Xiao, Haiyan; Zhang, Yanwen; Aidhy, Dilpuneet S; Weber, William J

    2013-01-01

    Ab initio molecular dynamics simulations have been carried out to study low-energy recoil events in SrTiO3. The threshold displacement energies are shown to be strongly dependent on both the orientation and the corresponding atomic arrangement. The minimum threshold displacement energies are 13 eV for an O recoil along the <100> O-O chain, 25 eV for a Sr recoil along the <100> Sr-Sr chain and 38 eV for a Ti recoil along the <110> Ti-Ti chain. The weighted average threshold displacement energies along the primary crystallographic directions are 35.7, 53.5 and > 64.9 eV for O, Sr and Ti, respectively. The interstitial configurations produced by the recoil events are <100> and <111> split-interstitials for O and Sr, respectively, together with a Ti interstitial occupying a distorted bridge position between two Sr sites. It is found that the recoil events in SrTiO3 are partial- charge transfer assisted processes, and the partial- charge transfer plays an important role in these recoil events.

  18. Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations

    SciTech Connect

    Chen Shilu; Fang Weihai

    2009-08-07

    In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.

  19. Ab Initio Molecular Dynamics Simulations and GIPAW NMR Calculations of a Lithium Borate Glass Melt.

    PubMed

    Ohkubo, Takahiro; Tsuchida, Eiji; Takahashi, Takafumi; Iwadate, Yasuhiko

    2016-04-14

    The atomic structure of a molten 0.3Li2O-0.7B2O3 glass at 1250 K was investigated using ab initio molecular dynamics (AIMD) simulations. The gauge including projector augmented wave (GIPAW) method was then employed for computing the chemical shift and quadrupolar coupling constant of (11)B, (17)O, and (7)Li from 764 AIMD derived structures. The chemical shift and quadrupolar coupling constant distributions were directly estimated from the dynamical structure of the molten glass. (11)B NMR parameters of well-known structural units such as the three-coordinated ring, nonring, and four-coordinated tetrahedron were found to be in good agreement with the experimental results. In this study, more detailed classification of B units was presented based on the number of O species bonded to the B atoms. This highlights the limitations of (11)B NMR sensitivity for resolving (11)B local environment using the experimentally obtained spectra only. The (17)O NMR parameter distributions can theoretically resolve the bridging and nonbridging O atoms with different structural units such as nonring, single boroxol ring, and double boroxol ring. Slight but clear differences in the number of bridging O atoms surrounding Li that have not been reported experimentally were observed in the theoretically obtained (7)Li NMR parameters. PMID:27010637

  20. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  1. Vibrational dynamics of zero-field-splitting hamiltonian in gadolinium-based MRI contrast agents from ab initio molecular dynamics.

    PubMed

    Lasoroski, Aurélie; Vuilleumier, Rodolphe; Pollet, Rodolphe

    2014-07-01

    The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution. PMID:25005282

  2. Vibrational dynamics of zero-field-splitting hamiltonian in gadolinium-based MRI contrast agents from ab initio molecular dynamics

    SciTech Connect

    Lasoroski, Aurélie; Vuilleumier, Rodolphe; Pollet, Rodolphe

    2014-07-07

    The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution.

  3. Classical Magnetic Dipole Moments for the Simulation of Vibrational Circular Dichroism by ab Initio Molecular Dynamics.

    PubMed

    Thomas, Martin; Kirchner, Barbara

    2016-02-01

    We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method. PMID:26771403

  4. Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kim, Hyoungchul; Kim, Moo Hwan; Kaviany, Massoud

    2014-03-01

    We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000 K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500 K.

  5. Lattice thermal conductivity of UO{sub 2} using ab-initio and classical molecular dynamics

    SciTech Connect

    Kim, Hyoungchul; Kim, Moo Hwan; Kaviany, Massoud

    2014-03-28

    We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000 K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500 K.

  6. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  7. Molecular dynamics studies of polyurethane nanocomposite hydrogels

    NASA Astrophysics Data System (ADS)

    Strankowska, J.; Piszczyk, Ł.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.

    2013-10-01

    Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.

  8. Temperature dependent mechanical properties of Mo-Si-B compounds via ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Dharmawardhana, C. C.; Sakidja, R.; Aryal, S.; Ching, W. Y.

    2013-07-01

    A new method was proposed to obtain high temperature mechanical properties with a combination of ab initio molecular dynamics and stress-strain analyses. It was applied to compounds in the Mo-Si-B ternary system, namely, T1 (Mo5Si3) and T2 (Mo5SiB2) phases. The calculated coefficient of thermal expansion, thermal expansion anisotropy, and elastic constants agree well with those from the available experiments. The method enables us to theoretically access these properties up to 2000 K.

  9. Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

    NASA Astrophysics Data System (ADS)

    Venâncio, Mateus F.; Rocha, Willian R.

    2015-10-01

    Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.

  10. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    SciTech Connect

    Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  11. Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces.

    PubMed

    Herron, Jeffrey A; Morikawa, Yoshitada; Mavrikakis, Manos

    2016-08-23

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation. PMID:27503889

  12. Ab initio molecular dynamics with noisy forces: Validating the quantum Monte Carlo approach with benchmark calculations of molecular vibrational properties

    SciTech Connect

    Luo, Ye Sorella, Sandro; Zen, Andrea

    2014-11-21

    We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.

  13. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu{sub 60}Ti{sub 20}Zr{sub 20} alloy

    SciTech Connect

    Amokrane, S.; Ayadim, A.; Levrel, L.

    2015-11-21

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  14. Study of the effects of metalloid elements (P, C, B) on Fe-based amorphous alloys by ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbiao; Li, Qiang; Duan, Haiming

    2015-03-01

    In order to understand the effects of the metalloid elements M (M: P, C, B) on the atomic structure, glass formation ability (GFA) and magnetic properties of Fe-based amorphous alloys, Fe80P13C7, Fe80P14B6 and Fe80B14C6 amorphous alloys are chosen to study through first-principle simulations in the present work. The atomic structure characteristic of the three amorphous alloys is investigated through the pair distribution functions (PDFs) and Voronoi Polyhedra (VPs) analyses. The PDFs and VPs analyses suggest that the GFA of the three alloys dropped in the order of Fe80P13C7, Fe80P14B6, and Fe80B14C6, which is well consistent with the experimental results. The density of state (DOS) of the three amorphous alloys is calculated to investigate their magnetic properties. Based on the DOS analysis, the average magnetic moment of Fe atom in Fe80P13C7 and Fe80P14B6 amorphous alloys can be estimated to be 1.71 μB and 1.70 μB, respectively, which are in acceptable agreement with the experimental results. However, the calculated average magnetic moment of Fe atom in Fe80B14C6 amorphous alloy is about 1.62 μB, which is far less than the experimental result.

  15. Study of the effects of metalloid elements (P, C, B) on Fe-based amorphous alloys by ab initio molecular dynamics simulations

    SciTech Connect

    Zhang, Wenbiao; Li, Qiang E-mail: dhm@xju.edu.cn; Duan, Haiming E-mail: dhm@xju.edu.cn

    2015-03-14

    In order to understand the effects of the metalloid elements M (M: P, C, B) on the atomic structure, glass formation ability (GFA) and magnetic properties of Fe-based amorphous alloys, Fe{sub 80}P{sub 13}C{sub 7}, Fe{sub 80}P{sub 14}B{sub 6} and Fe{sub 80}B{sub 14}C{sub 6} amorphous alloys are chosen to study through first-principle simulations in the present work. The atomic structure characteristic of the three amorphous alloys is investigated through the pair distribution functions (PDFs) and Voronoi Polyhedra (VPs) analyses. The PDFs and VPs analyses suggest that the GFA of the three alloys dropped in the order of Fe{sub 80}P{sub 13}C{sub 7}, Fe{sub 80}P{sub 14}B{sub 6}, and Fe{sub 80}B{sub 14}C{sub 6}, which is well consistent with the experimental results. The density of state (DOS) of the three amorphous alloys is calculated to investigate their magnetic properties. Based on the DOS analysis, the average magnetic moment of Fe atom in Fe{sub 80}P{sub 13}C{sub 7} and Fe{sub 80}P{sub 14}B{sub 6} amorphous alloys can be estimated to be 1.71 μ{sub B} and 1.70 μ{sub B}, respectively, which are in acceptable agreement with the experimental results. However, the calculated average magnetic moment of Fe atom in Fe{sub 80}B{sub 14}C{sub 6} amorphous alloy is about 1.62 μ{sub B}, which is far less than the experimental result.

  16. Structure and dynamics of high-spin Ru 2+ in aqueous solution: Ab initio QM/MM molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Kritayakornupong, Chinapong; Hannongbua, Supot

    2007-01-01

    The structural and dynamical properties of high-spin Ru 2+ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru 2+. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru 2+ and the 6-31G ∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru 2+-O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru 2+ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.

  17. The hydriding resistance of plutonium oxides and mononitride: A view from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Liu, Haifeng; Song, Haifeng

    2015-06-01

    Based on the non-local van der Waals density functional (vdW-DF)+ U scheme, we carry out the ab initio molecular dynamics study of the interaction dynamics for H2 molecules impingement against Pu-oxides and mononitride surfaces. We show that except for the weak physisorption, both PuO2 and PuN surfaces are so difficult of access that almost all of H2 molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H2 on PuO2 surfaces is found to be exothermic, the collision-induced dissociation barriers of H2 are very high (up to 2.2 eV). However, PuO2 overlayer on Pu-metal can be reduced to α-Pu2O3 drived by oxygen-lean conditions, and H2 can penetrate and diffuse in α-Pu2O3 easily. As a result, α-Pu2O3 can promote the hydriding process of Pu. Unlike PuO2, PuN is found to be one kind of stable and uniform passivation layer against Pu-hydriding. Specifically, the incorporation of PuN and H-atom is proven to be thermodynamically unstable. Overall, our current study reveals the mechanical and chemical resistances of Pu-oxide and Pu-nitride to hydrogen corrosion, which have strong implications to the understanding of the surface corrosion and passivation of Pu metal. This work was supported by the FDST of CAEP under Grant No. 9090707.

  18. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  19. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  20. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  1. The different roles of Pu-oxide overlayers in the hydrogenation of Pu-metal: an ab initio molecular dynamics study based on van der Waals density functional (vdW-DF)+U.

    PubMed

    Sun, Bo; Liu, Haifeng; Song, Haifeng; Zhang, Guangcai; Zheng, Hui; Zhao, Xian-Geng; Zhang, Ping

    2014-04-28

    Based on the non-local van der Waals density functional (vdW-DF)+U scheme, we carry out the ab initio molecular dynamics (AIMD) study of the interaction dynamics for H2 impingement against the stoichiometric PuO2(111), the reduced PuO2(111), and the stoichiometric α-Pu2O3(111) surfaces. The hydrogen molecular physisorption states, which cannot be captured by pure DFT+U method, are obtained by employing the vdW-DF+U scheme. We show that except for the weak physisorption, PuO 2(111) surfaces are so difficult of access that almost all of the H2 molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H2 on PuO2(111) surfaces is found to be very exothermic, the collision-induced dissociation barriers of H2 are calculated to be as high as 3.2 eV and 2.0 eV for stoichiometric and reduced PuO2 surfaces, respectively. Unlike PuO2, our AIMD study directly reveals that the hydrogen molecules can penetrate into α-Pu2O3(111) surface and diffuse easily due to the 25% native O vacancies located along the ⟨111⟩ diagonals of α-Pu2O3 matrix. By examining the temperature effect and the internal vibrational excitations of H2, we provide a detailed insight into the interaction dynamics of H2 in α-Pu2O3. The optimum pathways for hydrogen penetration and diffusion, the corresponding energy barriers (1.0 eV and 0.53 eV, respectively) and rate constants are systematically calculated. Overall, our study fairly reveals the different interaction mechanisms between H2 and Pu-oxide surfaces, which have strong implications to the interpretation of experimental observations. PMID:24784301

  2. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2 ⇌ CH + H on Ni(111) as a case study

    NASA Astrophysics Data System (ADS)

    Sun, Geng; Jiang, Hong

    2015-12-01

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH 2 ⇌ CH + H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for

  3. Haber Process Made Efficient by Hydroxylated Graphene: Ab Initio Thermochemistry and Reactive Molecular Dynamics.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-07-01

    The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry. PMID:27340901

  4. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  5. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations.

    PubMed

    Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F

    2016-04-13

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616

  6. Aqueous solutions: state of the art in ab initio molecular dynamics.

    PubMed

    Hassanali, Ali A; Cuny, Jérôme; Verdolino, Vincenzo; Parrinello, Michele

    2014-03-13

    The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects. PMID:24516179

  7. Dielectrophoresis of nanocolloids: a molecular dynamics study.

    PubMed

    Salonen, E; Terama, E; Vattulainen, I; Karttunen, M

    2005-10-01

    Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature. PMID:16195818

  8. An analysis of hydrated proton diffusion in ab initio molecular dynamics.

    PubMed

    Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A

    2015-01-01

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore

  9. An analysis of hydrated proton diffusion in ab initio molecular dynamics

    SciTech Connect

    Tse, Ying-Lung Steve; Voth, Gregory A.; Knight, Chris

    2015-01-07

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions

  10. An analysis of hydrated proton diffusion in ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A.

    2015-01-01

    A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ˜2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore

  11. Ab initio molecular dynamics determination of competitive O₂ vs. N₂ adsorption at open metal sites of M₂(dobdc).

    PubMed

    Parkes, Marie V; Greathouse, Jeffery A; Hart, David B; Gallis, Dorina F Sava; Nenoff, Tina M

    2016-04-28

    The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF. PMID:27063148

  12. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    PubMed

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics. PMID:27280740

  13. Ab initio molecular dynamics of Al irradiation-induced processes during Al{sub 2}O{sub 3} growth

    SciTech Connect

    Music, Denis; Nahif, Farwah; Friederichsen, Niklas; Schneider, Jochen M.; Sarakinos, Kostas

    2011-03-14

    Al bombardment induced structural changes in {alpha}-Al{sub 2}O{sub 3} (R-3c) and {gamma}-Al{sub 2}O{sub 3} (Fd-3m) were studied using ab initio molecular dynamics. Diffusion and irradiation damage occur for both polymorphs in the kinetic energy range from 3.5 to 40 eV. However, for {gamma}-Al{sub 2}O{sub 3}(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to {alpha}-Al{sub 2}O{sub 3}. Consequently, fast diffusion along {gamma}-Al{sub 2}O{sub 3}(001) gives rise to preferential {alpha}-Al{sub 2}O{sub 3}(0001) growth, which is consistent with published structure evolution experiments.

  14. Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

    NASA Astrophysics Data System (ADS)

    Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2014-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  15. Ab initio molecular dynamics simulations of the static, dynamic and electronic properties of liquid lead using real-space pseudopotentials

    SciTech Connect

    Alemany, Manuel M. G.; Longo, Roberto; Gallego, Luis; Gonzales, D. J.; Gonzales, L. E.; Tiago, Murilo L; Chelikowsky, James

    2007-01-01

    We performed a comprehensive study of the static, dynamic and electronic properties of liquid Pb at T = 650 kelvins, density 0.0309 angstroms^{-3} by means of 216-particle ab initio molecular dynamics simulations based on a real-space implementation of pseudopotentials constructed within density-functional theory. The predicted results and available experimental data are very in good agreement, which confirms the adequacy of this technique to achieve a reliable description of the behavior of liquid metals, including their dynamic properties. Although some of the computed properties of liquid Pb are similar to those of simple liquid metals, others differ markedly. Our results show that an appropriate description of liquid Pb requires the inclusion of relativistic effects in the determination of the pseudopotentials of Pb.

  16. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    SciTech Connect

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.

  17. Molecular dynamics studies of aromatic hydrocarbon liquids

    SciTech Connect

    McLaughlin, E.; Gupta, S.

    1990-01-01

    This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.

  18. A molecular dynamics study of dielectric friction

    SciTech Connect

    Kurnikova, M.G.; Waldeck, D.H.; Coalson, R.D.

    1996-07-01

    A molecular dynamics study of the friction experienced by the dye molecule resorufamine rotating in a polar solvent is performed. The validity of simple continuum theories of dielectric friction is tested. It is found that the Alavi{endash}Waldeck theory gives reasonable results for the zero frequency dielectric friction coefficient while the Nee{endash}Zwanzig theory requires an unphysically small cavity radius. A procedure for evaluating the time dependent friction kernel from torques and angular velocities, which enables the contributions to the friction from the van der Waals and Coulomb forces to be evaluated separately, is suggested. This study of a realistic system shows that electrostatic interactions can enhance friction by at least two physical mechanisms. First is a contribution to the friction which arises solely from retardation of the solvent reaction field. Second is a contribution arising from local structural changes of the solvent which are driven by the electrostatic field, i.e., a change in the local viscosity. {copyright} {ital 1996 American Institute of Physics.}

  19. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

    PubMed

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost. PMID:26851913

  20. Ground state structures and excited state dynamics of pyrrole-water complexes: Ab initio excited state molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kumar, Anupriya; Kołaski, Maciej; Kim, Kwang S.

    2008-01-01

    Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted π-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34a.u.) around ˜100fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the π H-bonded water molecule and then the charge transfer takes place from this water molecule to the σ H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53a.u.) around ˜100fs.

  1. Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2014-03-01

    The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.

  2. Ab Initio Molecular Dynamics of Dimerization and Clustering in Alkali Metal Vapors.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-06-30

    Alkali metals are known to form dimers, trimers, and tetramers in their vapors. The mechanism and regularities of this phenomenon characterize the chemical behavior of the first group elements. We report ab initio molecular dynamics (AIMD) simulations of the alkali metal vapors and characterize their structural properties, including radial distribution functions and atomic cluster size distributions. AIMD confirms formation of Men, where n ranges from 2 to 4. High pressure sharply favors larger structures, whereas high temperature decreases their fraction. Heavier alkali metals maintain somewhat larger fractions of Me2, Me3, and Me4, relative to isolated atoms. A single atom is the most frequently observed structure in vapors, irrespective of the element and temperature. Due to technical difficulties of working with high temperatures and pressures in experiments, AIMD is the most affordable method of research. It provides valuable understanding of the chemical behavior of Li, Na, K, Rb, and Cs, which can lead to development of new chemical reactions involving these metals. PMID:27294399

  3. Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations.

    PubMed

    He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng

    2016-04-26

    Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation. PMID:27071120

  4. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  5. Thermal transpiration: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    T, Joe Francis; Sathian, Sarith P.

    2014-12-01

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  6. Thermal transpiration: A molecular dynamics study

    SciTech Connect

    T, Joe Francis; Sathian, Sarith P.

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  7. Molecular dynamics studies on nanoscale gas transport

    NASA Astrophysics Data System (ADS)

    Barisik, Murat

    Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the

  8. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi

    Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence

  9. Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

    PubMed

    Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

    2016-07-15

    The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. PMID:27232117

  10. Molecular dynamics study of cyclohexane interconversion

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Chandler, David

    1990-12-01

    Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.

  11. Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.

    NASA Astrophysics Data System (ADS)

    Fidelis, Krzysztof Andrzej

    1990-08-01

    The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.

  12. A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

    PubMed

    Fonner, John M; Schmidt, Christine E; Ren, Pengyu

    2010-10-01

    Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521

  13. A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole

    PubMed Central

    Fonner, John M.; Schmidt, Christine E.; Ren, Pengyu

    2010-01-01

    Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521

  14. Structural and electronic properties of organo-halide hybrid perovskites from ab initio molecular dynamics.

    PubMed

    Quarti, Claudio; Mosconi, Edoardo; De Angelis, Filippo

    2015-04-14

    The last two years have seen the unprecedentedly rapid emergence of a new class of solar cells, based on hybrid organic-inorganic halide perovskites. The success of this class of materials is due to their outstanding photoelectrochemical properties coupled to their low cost, mainly solution-based, fabrication techniques. Solution processed materials are however often characterized by an inherent flexible structure, which is hardly mapped into a single local minimum energy structure. In this perspective, we report on the interplay between structural and electronic properties of hybrid lead iodide perovskites investigated using ab initio molecular dynamics (AIMD) simulations, which allow the dynamical simulation of disordered systems at finite temperature. We compare the prototypical MAPbI3 (MA = methylammonium) perovskite in its cubic and tetragonal structure with the trigonal phase of FAPbI3 (FA = formamidinium), investigating different starting arrangements of the organic cations. Despite the relatively short time scale amenable to AIMD, typically a few tens of ps, this analysis demonstrates the sizable structural flexibility of this class of materials, showing that the instantaneous structure could significantly differ from the time and thermal averaged structure. We also highlight the importance of the organic-inorganic interactions in determining the fluxional properties of this class of materials. A peculiar spatial localization of the valence and conduction band edges is also found, with a dynamics in the range of 0.1 ps, which is associated with the positional dynamics of the organic cations within the cubo-octahedral perovskite cage. This asymmetry in the spatial localization of the band edges is expected to ease exciton dissociation and assist the initial stages of charge separation, possibly constituting one of the key factors for the impressive photovoltaic performances of hybrid lead-iodide perovskites. PMID:25766785

  15. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    SciTech Connect

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  16. Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-01

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.

  17. Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

    SciTech Connect

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-07

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.

  18. Finite-temperature elastic constants of paramagnetic materials within the disordered local moment picture from ab initio molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.

    2016-08-01

    We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.

  19. Dissociative chemisorption of methane on metal surfaces: tests of dynamical assumptions using quantum models and ab initio molecular dynamics.

    PubMed

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-01

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined. PMID:25106565

  20. Efficient and accurate determination of lattice-vacancy diffusion coefficients via non equilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sangiovanni, D. G.; Hellman, O.; Alling, B.; Abrikosov, I. A.

    2016-03-01

    We revisit the color-diffusion algorithm [Aeberhard et al., Phys. Rev. Lett. 108, 095901 (2012), 10.1103/PhysRevLett.108.095901] in non equilibrium ab initio molecular dynamics (NE-AIMD) and propose a simple efficient approach for the estimation of monovacancy jump rates in crystalline solids at temperatures well below melting. Color-diffusion applied to monovacancy migration entails that one lattice atom (colored atom) is accelerated toward the neighboring defect site by an external constant force F. Considering bcc molybdenum between 1000 and 2800 K as a model system, NE-AIMD results show that the colored-atom jump rate kNE increases exponentially with the force intensity F , up to F values far beyond the linear-fitting regime employed previously. Using a simple model, we derive an analytical expression which reproduces the observed kNE(F ) dependence on F . Equilibrium rates extrapolated by NE-AIMD results are in excellent agreement with those of unconstrained dynamics. The gain in computational efficiency achieved with our approach increases rapidly with decreasing temperatures and reaches a factor of 4 orders of magnitude at the lowest temperature considered in the present study.

  1. Ab initio molecular dynamics simulations of the static, dynamic and electronic properties of the liquid Bi-Pb alloy

    NASA Astrophysics Data System (ADS)

    Souto, J.; Alemany, M. M. G.; Gallego, L. J.; Gonzalez, L. E.; Gonzalez, D. J.

    2013-03-01

    We perform an ab initio molecular dynamics study of the static, dynamic and electronic properties of the liquid Bi-Pb alloy at three concentrations, including the eutectic one. This alloy is of particular technological interest for its possible use as coolant in fast reactors. Our predictions are in good agreement with the available experimental data. In particular, the computed total static structure factors reproduce accurately the neutron diffraction results, and the predicted adiabatic sound velocity and shear viscosity compare well with the experimental values. The partial dynamic structure factors exhibit clear side peaks indicative of propagating density fluctuations, and the longitudinal and transverse dispersion relations show several branches.The electronic density of states show that the liquid Bi-Pb alloy is a good metal, but with strong deviations from the free-electron parabolic curve. Supported by FIS2008-02490/FIS, FIS2008-04894/FIS, VA068A06, GR120, INCITE09E2R206033ES and INCITE08PXIB206107PR

  2. Ab initio molecular dynamics simulations of organic electrolytes, electrodes, and lithium ion transport for Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Kent, P. R. C.; Ganesh, P.; Jiang, De-En; Borodin, O.

    2012-02-01

    Optimizing the choice of electrolyte in lithium ion batteries and an understanding of the solid-electrolyte interphase (SEI) is required to optimize the balance between high-energy storage, high rate capability, and lifetime. We perform accurate ab initio molecular-dynamics simulations of common cyclic carbonates and LiPF6 to build solvation models which explain available Neutron and NMR spectroscopies. Our results corroborate why ethylene carbonate is a preferred choice for battery applications over propylene carbonate and how mixtures with dimethyl carbonate improve Li-ion diffusion. We study the role of functionalization of graphite-anode edges on the reducibility of the electrolyte and the ease of Li-ion intercalation at the initial stages of SEI formation. We find that oxygen terminated edges readily act as strong reductive sites, while hydrogen terminated edges are less reactive and allow faster Li diffusion. Orientational ordering of the solvent molecules precedes reduction at the interphase. Inorganic reductive components are seen to readily migrate to the anode edges, leading to increased surface passivation of the anode. We are currently quantifying Li-intercalation barriers across realistic SEI models, and progress along these lines will be presented.

  3. Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo

    SciTech Connect

    Liu, Bin; Yuan, Fenglin; Jin, Ke; Zhang, Yanwen; Weber, William J.

    2015-10-06

    Low-energy recoil events in pure Ni and the equiatomic NiCo alloy are studied using ab initio molecular dynamics simulations. We found that the threshold displacement energies are strongly dependent on orientation and weakly dependent on composition. The minimum threshold displacement energies are along the [1 1 0] direction in both pure Ni and the NiCo alloy. Compared to pure Ni, the threshold displacement energies increase slightly in the NiCo alloy due to stronger bonds in the alloy, irrespective of the element type of the PKA. A single Ni interstitial occupying the center of a tetrahedron formed by four Ni atoms and a <1 0 0> split interstitial is produced in pure Ni by the recoils, while only the <1 0 0> split interstitial is formed in the NiCo alloy. Compared to the replacement sequences in pure Ni, anti-site defect sequences are observed in the alloy, which have high efficiency for both producing defects and transporting energy outside of the cascade core. These results provide insights into energy transfer processes occurring in equiatomic alloys under irradiation.

  4. Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo

    DOE PAGESBeta

    Liu, Bin; Yuan, Fenglin; Jin, Ke; Zhang, Yanwen; Weber, William J.

    2015-10-06

    Low-energy recoil events in pure Ni and the equiatomic NiCo alloy are studied using ab initio molecular dynamics simulations. We found that the threshold displacement energies are strongly dependent on orientation and weakly dependent on composition. The minimum threshold displacement energies are along the [1 1 0] direction in both pure Ni and the NiCo alloy. Compared to pure Ni, the threshold displacement energies increase slightly in the NiCo alloy due to stronger bonds in the alloy, irrespective of the element type of the PKA. A single Ni interstitial occupying the center of a tetrahedron formed by four Ni atomsmore » and a <1 0 0> split interstitial is produced in pure Ni by the recoils, while only the <1 0 0> split interstitial is formed in the NiCo alloy. Compared to the replacement sequences in pure Ni, anti-site defect sequences are observed in the alloy, which have high efficiency for both producing defects and transporting energy outside of the cascade core. These results provide insights into energy transfer processes occurring in equiatomic alloys under irradiation.« less

  5. On the structure of crystalline and molten cryolite: Insights from the ab initio molecular dynamics in NpT ensemble.

    PubMed

    Bučko, Tomáš; Šimko, František

    2016-02-14

    Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F(-) ions observed in X-ray diffraction experiments. The isolated AlF6(3-), AlF5(2-), AlF4(-), as well as the bridged Al2Fm(6-m) ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5(2-) has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn(3-n) species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment. PMID:26874492

  6. Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations

    SciTech Connect

    Leung, Kevin; Nenoff, Tina M.

    2012-08-21

    We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.

  7. On the structure of crystalline and molten cryolite: Insights from the ab initio molecular dynamics in NpT ensemble

    NASA Astrophysics Data System (ADS)

    Bučko, Tomáš; Šimko, František

    2016-02-01

    Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F- ions observed in X-ray diffraction experiments. The isolated AlF63-, AlF52-, AlF4-, as well as the bridged Al 2 Fm 6 - m ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5 2 - has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn 3 - n species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment.

  8. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics

    SciTech Connect

    Plašienka, Dušan Martoňák, Roman; Cifra, Peter

    2015-04-21

    We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.

  9. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics.

    PubMed

    Plašienka, Dušan; Cifra, Peter; Martoňák, Roman

    2015-04-21

    We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram. PMID:25903892

  10. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations.

    PubMed

    Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-08-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface. PMID:26174102

  11. Ab initio molecular dynamics simulations of low energy recoil events in ceramics

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Weber, William J.

    2011-07-15

    The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In 3C-SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

  12. Ab initio molecular dynamics simulations of low energy recoil events in ceramics

    SciTech Connect

    Gao, Fei; Xiao, Haiyan; Weber, William J

    2011-01-01

    The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

  13. Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second

    SciTech Connect

    Bylaska, Eric J.; Glass, Kevin A.; Baxter, Douglas J.; Baden, Scott B.; Weare, John H.

    2010-09-16

    An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. These algorithms make use of a two-dimensional processor geometry proposed by Gygi et al for use in AIMD algorithms. Using this strategy, a highly scalable algorithm for exact exchange has been developed and incorporated it into AIMD. This new algorithm for exact exchange employs an incomplete butterfly to overcome the bottleneck associated with exact exchange term, and it makes judicious use of data replication. Initial testing has shown that this algorithm can scale to over 20,000 CPUs even for modest size simulation.

  14. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-01

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  15. Ab initio molecular dynamics simulation of structural transformation in zinc blende GaN under high pressure

    SciTech Connect

    Xiao, Hai Yan; Gao, Fei; Zu, Xiaotao T.; Weber, William J.

    2010-02-04

    High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.

  16. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001).

    PubMed

    Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco

    2015-08-21

    We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer. PMID:26193818

  17. Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations.

    PubMed

    Gaigeot, M P; Vuilleumier, R; Sprik, M; Borgis, D

    2005-09-01

    The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated:  In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range. PMID:26641894

  18. Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments.

    PubMed

    Marinica, D C; Grégoire, G; Desfrançois, C; Schermann, J P; Borgis, D; Gaigeot, M P

    2006-07-20

    Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature. PMID:16836443

  19. 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)

  20. Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations

    PubMed Central

    Zhou, Yanzi; Wang, Shenglong; Zhang, Yingkai

    2010-01-01

    Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multi-step free energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack to the carbonyl carbon with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of His447 ring needs to be adjusted very slightly, and then the proton transfers from His447 to the product and the break of the scissile bond happen spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1 ~ 2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms. PMID:20550161

  1. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  2. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo

    2013-08-01

    Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

  3. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    SciTech Connect

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-31

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  4. Thermal expansion, diffusion and melting of Li2O using a compact forcefield derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Asahi, Ryoji; Freeman, Clive M.; Saxe, Paul; Wimmer, Erich

    2014-10-01

    This work shows a straightforward procedure to derive forcefields (FFs) which are able to describe the structural, thermal and transport properties of condensed phases. The approach is based on ab initio molecular dynamics trajectories and an empirical calibration such as the melting point. This is demonstrated for lithium oxide using a Buckingham-type potential and optimized effective atomic charges. The present FF reproduces the density and thermal expansion of Li2O very well, including an anomaly related to the known superionic behaviour, i.e. a pre-melting of the Li sublattice at a critical temperature of Tc = 1200 K. Calculations of the diffusion coefficient as a function of temperature show a strong dependence on vacancy concentration for temperatures below Tc, consistent with previous simulations. Extensions to other ionic systems and compositions are made straightforward by the compact form of the FF and the present methodology employed in the parameter fitting.

  5. Argon Interaction with Gold Surfaces: Ab Initio-Assisted Determination of Pair Ar-Au Potentials for Molecular Dynamics Simulations.

    PubMed

    Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline

    2015-07-01

    Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588

  6. Direct assessment of quantum nuclear effects on hydrogen bond strength by constrained-centroid ab initio path integral molecular dynamics.

    PubMed

    Walker, Brent; Michaelides, Angelos

    2010-11-01

    The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)(2) is about 30% weaker when quantum nuclear effects are included, while that in (H(2)O)(2) is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation. PMID:21054031

  7. Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

    2010-10-01

    The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

  8. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

    PubMed

    Giese, Timothy J; York, Darrin M

    2016-06-14

    A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914

  9. Melting of Fe and Fe120Si8 at the Earth's Core Pressures by ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Belonoshko, A. B.; Rosengren, A.; Burakovsky, L.; Preston, D. L.; Johansson, B.

    2008-12-01

    The solid Earth's inner core (IC) consists mainly of iron likely alloyed with some light elements. At low temperature iron is stable in hexagonal close packed (hcp) phase up to very high pressures. However, there is an accumulating evidence that under pressures (~ 364 GPa) and temperatures (above 6000 K) in the Earth's IC iron, either pure or alloyed with light elements (e.g. Si), might be stable in the body-centred cubic (bcc) phase1,2. The melting temperature of this phase in the IC is unknown. Conditions of the IC are not achieved in experiment. Previous theoretical studies concentrated mostly on the melting of the hcp phase3. We show, by combination of ab initio molecular dynamics and Z-method4 that pure bcc Fe melts at at the pressure in the center of IC at ~7000 K. Iron, alloyed with 6.25% of Si, melts at a temperature of ~7200 K. While light elements depress hcp Fe melting temperatures5, we show that Si addition has opposite effect on bcc Fe. Melting temperatures of bcc and hcp 2,3 are within mutual error bars, even though bcc melts at a higher temperature. However, the melting temperature of Si-alloyed bcc iron is clearly above that of Si-alloyed hcp phase5. This is because of different bonding of Si-Fe within the bcc as compared to the hcp structure. Therefore, the existing estimates of core temperatures have to be corrected upwards. 1. Brown, J.M. & McQueen, R.G. J. Geophys. Res. 91, 7485(1986). 2. Belonoshko, A.B., Ahuja, R. & Johansson, B. Nature 424, 1032(2003); Belonoshko, A.B., Skorodumova, N.V., Rosengren, A. & Johansson, B. Science 319, 797(2008). 3. Belonoshko, A.B., Ahuja, R. & Johansson, B. Phys. Rev. Lett. 84, 3638(2000); Alfé, D., Gillan, M.J. & Price, G.D. Nature 401, 462(1999). 4. Kresse, G. & Furthmüller, J. J. Phys. Rev. B 54, 11169(1996); Belonoshko, A.B., Skorodumova, N.V., Rosengren, A. & Johansson, B. Phys. Rev. B 73, 012201(2006). 5. Alfé, D., Price, G.D. & Gillan, M.J. Cont. Phys. 48, 63 (2007).

  10. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085

  11. Ab initio molecular dynamics with simultaneous electron and phonon excitations: Application to the relaxation of hot atoms and molecules on metal surfaces

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Juaristi, J. I.; Alducin, M.

    2015-11-01

    The relaxation dynamics of hot H, N, and N2 on Pd(100), Ag(111), and Fe(110), respectively, is studied by means of ab initio molecular dynamics with electronic friction. This method is adapted here to account for the electron density changes caused by lattice vibrations, thus treating on an equal footing both electron-hole (e -h ) pair and phonon excitations. We find that even if the latter increasingly dominate the heavier is the hot species, the contribution of e -h pairs is by no means negligible in these cases because it gains relevance at the last stage of the relaxation process. The quantitative details of energy dissipation depend on the interplay of the potential energy surface, electronic structure, and kinetic factors.

  12. New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics.

    PubMed

    Furmanchuk, Al'ona; Shishkin, Oleg V; Isayev, Olexandr; Gorb, Leonid; Leszczynski, Jerzy

    2010-09-01

    The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface. PMID:20532343

  13. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations.

    PubMed

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step. PMID:26133420

  14. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-01

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  15. A prototypical ionic liquid explored by ab initio molecular dynamics and Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Bodo, E.; Sferrazza, A.; Caminiti, R.; Mangialardo, S.; Postorino, P.

    2013-10-01

    We present an analysis of the liquid and of a small isolated cluster of n-ethyl ammonium nitrate based on "first principles" molecular dynamics. We discover that the peculiar properties of ionic liquids make such compounds ideal candidates for such an analysis. We have been able to characterize some important features of the liquid structure and we have validated our simulations by comparing our findings with experimental vibrational spectra of the liquid phase. Theoretical spectra, which present a remarkable agreement with the measurements, besides the assignment of the main spectra features, allow an interpretation of the spectra at high frequencies where the vibrational motions involve the hydrogen-bonded atoms, thus providing a picture of the hydrogen bonding network that exists in such compounds.

  16. A prototypical ionic liquid explored by ab initio molecular dynamics and Raman spectroscopy.

    PubMed

    Bodo, E; Sferrazza, A; Caminiti, R; Mangialardo, S; Postorino, P

    2013-10-14

    We present an analysis of the liquid and of a small isolated cluster of n-ethyl ammonium nitrate based on "first principles" molecular dynamics. We discover that the peculiar properties of ionic liquids make such compounds ideal candidates for such an analysis. We have been able to characterize some important features of the liquid structure and we have validated our simulations by comparing our findings with experimental vibrational spectra of the liquid phase. Theoretical spectra, which present a remarkable agreement with the measurements, besides the assignment of the main spectra features, allow an interpretation of the spectra at high frequencies where the vibrational motions involve the hydrogen-bonded atoms, thus providing a picture of the hydrogen bonding network that exists in such compounds. PMID:24116621

  17. Sound velocity in shock compressed molybdenum obtained by ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Lukinov, T.; Simak, S. I.; Belonoshko, A. B.

    2015-08-01

    The sound velocity of Mo along the Hugoniot adiabat is calculated from first principles using density-functional theory based molecular dynamics. These data are compared to the sound velocity as measured in recent experiments. The theoretical and experimental Hugoniot and sound velocities are in very good agreement up to pressures of 210 GPa and temperatures of 3700 K on the Hugoniot. However, above that point the experiment and theory diverge. This implies that Mo undergoes a phase transition at about the same point. Considering that the melting point of Mo is likely much higher at that pressure, the related change in the sound velocity in experiment can be ascribed to a solid-solid transition.

  18. Sound velocity in shock compressed molybdenum obtained by ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Lukinov, Tymofiy; Belonoshko, Anatoly; Simak, Sergey

    The sound velocity of Mo along the Hugoniot adiabat is calculated from first principles using density-functional theory based molecular dynamics. These data are compared to the sound velocity as measured in recent experiments. The theoretical and experimental Hugoniot and sound velocities are in very good agreement up to pressures of 210 GPa and temperatures of 3700 K on the Hugoniot. However, above that point the experiment and theory diverge. This implies that Mo undergoes a phase transition at about the same point. Considering that the melting point of Mo is likely much higher at that pressure, the related change in the sound velocity in experiment can be ascribed to a solid-solid transition.

  19. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    SciTech Connect

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  20. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    SciTech Connect

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2013-12-21

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

  1. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    NASA Astrophysics Data System (ADS)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  2. Ab initio molecular dynamics simulations of ion–solid interactions in Gd2Zr2O7 and Gd2Ti2O7

    SciTech Connect

    Wang, X. J.; Xiao, Haiyan Y.; Zu, Xiaotao; Zhang, Yanwen; Weber, William J.

    2012-12-21

    The development of the ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion–solid interactions in materials, with the determination of threshold displacement energies with ab initio accuracy, and prediction of a new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order–disorder is more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be [similar]0.15, [similar]0.11 to 0.27 and [similar]0.1 to 0.13 |e| for Gd, Zr (or Ti), and O, respectively. Neglecting the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

  3. Ab initio molecular dynamics simulations of ion-solid interactions in Gd2Zr2O7 and Gd2Ti2O7

    SciTech Connect

    Wang, X J; Xiao, Haiyan; Zu, X T; Zhang, Yanwen; Weber, William J

    2013-01-01

    The development of ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion-solid interactions in materials, with identification determination of threshold displacement energies with ab initio accuracy, and prediction of new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order-disorder are more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ~0.15, ~0.11-0.27 and ~0.1-0.13 |e| for Gd, Zr (or Ti), and O, respectively. Negligence of the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

  4. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

    NASA Astrophysics Data System (ADS)

    Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng

    2008-04-01

    Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, β-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

  5. Modification of Defect Structures in Graphene by Electron Irradiation: Ab Initio Molecular Dynamics Simulations

    SciTech Connect

    Wang, Zhiguo; Zhou, Yungang; Bang, Junhyeok; Prange, Micah P.; Zhang, Shengbai; Gao, Fei

    2012-08-02

    Defects play an important role on the unique properties of the sp2-bonded materials, such as graphene. The creation and evolution of mono-vacancy, di-vacancy, Stone-Wales (SW) and grain boundaries (GBs) under irradiation in graphene are investigated using density functional theory and time-dependent density functional theory molecular dynamics simulations. It is of great interest to note that the patterns of these defects can be controlled through electron irradiation. The SW defects can be created by electron irradiation with energy of above the displacement threshold energy (Td, {approx}19 eV) and can be healed with an energy (14-18 eV) lower than Td. The transformation between four types of divacancies, V2(5-8-5), V2(555-777), V2(5555-6-7777), and V2(55-77) can be realized through bond rotation induced by electron irradiation. The migrations of divancancies, SW defects, and GBs can also be controlled by electron irradiation. Thus, electron irradiation can serve as an important tool to modify morphology in a controllable manner, and to tailor the physical properties of graphene.

  6. CO2 capture in amine solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ma, Changru; Pietrucci, Fabio; Andreoni, Wanda

    2014-03-01

    The most mature technology for post-combustion CO2 capture exploits a cyclic process, in which CO2 is selectively and reversibly absorbed in an amine solution, typically monoethanolamine(MEA) at 30%wt concentration. Empirical efforts are ongoing worldwide to reduce the high energy penalty for amine regeneration and to increase the absorption rate. Computer simulations can help by providing new insights and the missing quantitative information. Using extensive large-scale Car-Parrinello molecular dynamics simulations, aided by accelerated sampling techniques, we have characterized the reactions leading to CO2 capture in MEA 30%wt solutions via the formation of the carbamate, and the subsequent CO2 release. Deprotonation and CO2 release turn out to be competitive for an intermediate zwitterion (free-energy barrier ~10kcal/mol), with sizable entropic contribution, whereas CO2 release from the carbamate has a much higher barrier (~50kcal/mol), mainly enthalpic and rather independent of temperature. An unprecedented characterization of structural and vibrational properties of the solution allows us to interpret recent experimental results. More results on other amines, allow us to rationalize their still unexplained better performance relative to MEA. We acknowledge PRACE for awarding us access to resource Juqueen based in Germany at Juelich.

  7. Fine-grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer

    SciTech Connect

    E. Bohm A. Bhatele L. V. Kale M. E. Tuckerman S. Kumar J. A. Gunnels G. J. Martyna; Bohm, E.; Bhatele, A.; Kale, L. V.; Tuckerman, M. E.; Kumar, S.; Gunnels, J. A.; Martyna, G. J.

    2008-01-01

    Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy Junction that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L(tm) system-specific optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).

  8. A molecular dynamics study of polymer/graphene interfacial systems

    SciTech Connect

    Rissanou, Anastassia N.; Harmandaris, Vagelis

    2014-05-15

    Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

  9. Molecular dynamic study of pressure fluctuations spectrum in plasma

    NASA Astrophysics Data System (ADS)

    Bystryi, R. G.

    2015-11-01

    Pressure of plasma is calculated by using classical molecular dynamics method. The formula based on virial theorem was used. Spectrum pressure's fluctuations of singly ionized non-ideal plasma are studied. 1/f-like spectrum behavior is observed. In other words, flicker noise is observed in fluctuations of pressure equilibrium non-ideal plasma. Relations between the obtained result and pressure fluctuations within the Gibbs and Einstein approaches are discussed. Special attention is paid to features of calculating the pressure in strongly coupled systems.

  10. Molecular dynamics studies of protein folding and aggregation

    NASA Astrophysics Data System (ADS)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  11. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-10-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.

  12. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    PubMed Central

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

  13. Dynamical structures of glycol and ethanedithiol examined by infrared spectroscopy, ab initio computation, and molecular dynamics simulations.

    PubMed

    Ma, Xiaoyan; Cai, Kaicong; Wang, Jianping

    2011-02-10

    Infrared (IR) experiment, ab initio computations, and molecular dynamics (MD) simulations were used to examine the dynamical structures of ethylene glycol (EG) and 1,2-ethanedithiol (EDT) in carbon tetrachloride and deuterated chloroform. Using the O-H and S-H stretching modes as structural probes, EG and EDT were found to exhibit different conformational preferences, even though they share similar molecular formula. Results suggest that the gauche conformation of EG presents and is stabilized by the intramolecular hydrogen bond (IHB), while both the trans and gauche EDT are possible in the two solvents. Exchangeable IHB donor and acceptor pairs were predicted in the case of EG. Anharmonic vibrational frequencies, anharmonicities, and couplings of the O-H and S-H stretching modes were predicted and found to be structurally dependent. Linear IR and two-dimensional IR spectra containing these structural signatures were simulated and discussed. These results demonstrate that a combination of the methods used here is very useful in revealing structural dynamics of small molecules in condensed phases. PMID:21208002

  14. Raman Spectra of Liquid Water from Ab Initio Molecular Dynamics: Vibrational Signatures of Charge Fluctuations in the Hydrogen Bond Network.

    PubMed

    Wan, Quan; Spanu, Leonardo; Galli, Giulia A; Gygi, François

    2013-09-10

    We report the first ab initio simulations of the Raman spectra of liquid water, obtained by combining first principles molecular dynamics and density functional perturbation theory. Our computed spectra are in good agreement with experiments, especially in the low frequency region. We also describe a systematic strategy to analyze the Raman intensities, which is of general applicability to molecular solids and liquids, and it is based on maximally localized Wannier functions and effective molecular polarizabilities. Our analysis revealed the presence of intermolecular charge fluctuations accompanying the hydrogen bond (HB) stretching modes at 270 cm(-1), in spite of the absence of any Raman activity in the isotropic spectrum. We also found that charge fluctuations partly contribute to the 200 cm(-1) peak in the anisotropic spectrum, thus providing insight into the controversial origin of such peak. Our results highlighted the importance of taking into account electronic effects in interpreting the Raman spectra of liquid water and the key role of charge fluctuations within the HB network; they also pointed at the inaccuracies of models using constant molecular polarizabilities to describe the Raman response of liquid water. PMID:26592405

  15. Ab initio molecular dynamics with noisy and cheap quantum Monte Carlo forces: accurate calculation of vibrational frequencies

    NASA Astrophysics Data System (ADS)

    Luo, Ye; Sorella, Sandro

    2014-03-01

    We introduce a general and efficient method for the calculation of vibrational frequencies of electronic systems, ranging from molecules to solids. By performing damped molecular dynamics with ab initio forces, we show that quantum vibrational frequencies can be evaluated by diagonalizing the time averaged position-position or force-force correlation matrices, although the ionic motion is treated on the classical level within the Born-Oppenheimer approximation. The novelty of our approach is to evaluate atomic forces with QMC by means of a highly accurate and correlated variational wave function which is optimized simultaneously during the dynamics. QMC is an accurate and promising many-body technique for electronic structure calculation thanks to massively parallel computers. However, since infinite statistics is not feasible, property evaluation may be affected by large noise that is difficult to harness. Our approach controls the QMC stochastic bias systematically and gives very accurate results with moderate computational effort, namely even with noisy forces. We prove the accuracy and efficiency of our method on the water monomer[A. Zen et al., JCTC 9 (2013) 4332] and dimer. We are currently working on the challenging problem of simulating liquid water at ambient conditions.

  16. Hydroxyl-functionalized 1-(2-hydroxyethyl)-3-methyl imidazolium ionic liquids: thermodynamic and structural properties using molecular dynamics simulations and ab initio calculations.

    PubMed

    Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza

    2014-12-11

    The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The

  17. Bond dissociation mechanism of ethanol during carbon nanotube synthesis via alcohol catalytic CVD technique: Ab initio molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Oguri, Tomoya; Shimamura, Kohei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu

    2014-03-01

    Dissociation of ethanol on a nickel cluster is investigated by ab initio molecular dynamics simulation to reveal the bond dissociation mechanism of carbon source molecules during carbon nanotube synthesis. C-C bonds in only CHxCO fragments are dissociated on the nickel cluster, whereas there is no preferential structure among the fragments for C-O bond dissociation. The dissociation preference is uncorrelated with the bond dissociation energy of corresponding bonds in freestanding molecules but is correlated with the energy difference between fragment molecules before and after dissociation on the nickel surface. Moreover, carbon-chain formation occurs after C-C bond dissociation in a continuous simulation. What determines the chirality of CNTs? What happens at the dissociation stage of carbon source molecules? Regarding the former question, many researchers have pointed out the good epitaxial relationship between a graphite network and a close-packed facet (i.e., fcc(1 1 1) or hcp(0 0 0 1)) of transition metals [17-19]. Therefore, the correlation between the chirality of CNTs and the angle of the step edge on metal (or metal carbide) surfaces has been closely investigated [20-22]. In association with this geometric matching, the epitaxial growth of graphene on Cu(1 1 1) and Ni(1 1 1) surfaces has recently been achieved via CCVD technique [23-25], which is a promising technique for the synthesis of large-area and monolayer graphene.Regarding the latter question, it is empirically known that the yield and quality of CNT products strongly depend on the choice of carbon source molecules and additives. For example, it is well known that the use of ethanol as carbon source molecules yields a large amount of SWNTs without amorphous carbons (called the alcohol CCVD (ACCVD) technique) compared with the CCVD process using hydrocarbons [4]. Moreover, the addition of a small amount of water dramatically enhances the activity and lifetime of the catalytic metal (called the

  18. A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL

    NASA Astrophysics Data System (ADS)

    Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.

    2009-03-01

    FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are

  19. Speciation and thermodynamic properties of zinc in sulfur-rich hydrothermal fluids: Insights from ab initio molecular dynamics simulations and X-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Etschmann, Barbara; Liu, Weihua; Sherman, David M.; Testemale, Denis; Brugger, Joël

    2016-04-01

    Chlorine and sulfur are the main elements involved in the complexing of metals in ore-forming fluids. The nature and thermodynamic properties of the Zn(II)-Cl complexes have been investigated by previous experimental and theoretical studies and are now well established up to high temperatures (600 °C). In contrast, the role of bisulfide complexes for zinc speciation in sulfur-bearing fluids remains poorly known, and a better understanding of Zn(II)-HS complexation is required for modeling zinc transport in magmatic and metamorphic fluids and for optimizing the hydrometallurgical processing of sulfide ores. We have conducted ab initio molecular dynamics (MD) simulations to calculate the speciation of Zn(II)-HS complexes from ambient to hydrothermal-magmatic conditions (25-600 °C, up to 2000 bar). These theoretical calculations were complemented by X-ray absorption spectroscopy (XAS) measurements of Zn(II) in HS--rich solutions at 200-500 °C and 600-1000 bar. The speciation and geometrical properties predicted by the ab initio MD simulations and the in situ XAS data are in excellent agreement. Upon heating from room temperature to 250 °C, Zn(II) speciation in HS--rich solutions shows a transition from the sixfold octahedral hexaaquo complex [Zn(H2O)6]2+ to fourfold tetrahedral [Zn(HS)n(H2O)4-n]2-n complexes (n = 1-4). Ab initio MD simulations also show that at temperatures > 250 °C, the threefold trigonal-planar [Zn(HS)3]- complex becomes increasingly stable, and predominates in S-rich solutions; in contrast, chloro-complexes display a tetrahedral geometry at 25-500 °C, while trigonal planar ZnCl3- predominates at temperatures > 500 °C. The stability constants of Zn(II)-HS complexes were calculated by thermodynamic integration of constrained ab initio MD simulations at 200, 350 and 600 °C. The stability constants generated from this study predict that zinc can be transported by HS- at high temperature in reduced, neutral to alkaline solutions, while Zn

  20. An energy dispersive x-ray scattering and molecular dynamics study of liquid dimethyl carbonate

    NASA Astrophysics Data System (ADS)

    Gontrani, Lorenzo; Russina, Olga; Marincola, Flaminia Cesare; Caminiti, Ruggero

    2009-12-01

    In this work, we report on the first x-ray diffraction study on liquid dimethyl carbonate. Diffraction spectra were collected with an energy-dispersive instrument, whose wide Q-range allows the structure determination of weakly ordered systems (such as liquids). The structural correlation in this liquid ranges up to about 20 Å. The observed patterns are interpreted with a structural model derived from classical molecular dynamics simulations. The simulations were run using OPLS force field, only slightly modified to restrain bond distances to the experimental values. The model structure function and radial distribution functions, averaged among the productive trajectory frames, are in very good agreement with the corresponding experimental ones. Molecular dynamics results show that the deviations from C2v cis-cis structure, predicted by ab initio calculations and observed by electron diffraction in the gas phase, are small. By analyzing the intra- and intermolecular pair distribution functions, it was possible to assign the peaks of the experimental radial distribution function to specific structural correlations, and to compute the different average intermolecular coordination numbers. The intermolecular methyl-carbonyl oxygen distance is thoroughly discussed to assess the presence of weak C-H⋯ṡO hydrogen bonds.

  1. Mobility of hydrogen-helium clusters in tungsten studied by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Grigorev, Petr; Terentyev, Dmitry; Bonny, Giovanni; Zhurkin, Evgeny E.; van Oost, Guido; Noterdaeme, Jean-Marie

    2016-06-01

    Tungsten is a primary candidate material for plasma facing components in fusion reactors. Interaction of plasma components with the material is unavoidable and will lead to degradation of the performance and the lifetime of the in-vessel components. In order to gain better understanding the mechanisms driving the material degradation at atomic level, atomistic simulations are employed. In this work we study migration, stability and self-trapping properties of pure helium and mixed helium-hydrogen clusters in tungsten by means of molecular dynamics simulations. We test two versions of an embedded atom model interatomic potential by comparing it with ab initio data regarding the binding properties of He clusters. By analysing the trajectories of the clusters during molecular dynamics simulations at finite temperatures we obtain the diffusion parameters. The results show that the diffusivity of mixed clusters is significantly lower, than that of pure helium clusters. The latter suggest that the formation of mixed clusters during mixed hydrogen helium plasma exposure will affect the helium diffusivity in the material.

  2. Thermal conductivity of penta-graphene from molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xu, Wen; Zhang, Gang; Li, Baowen

    2015-10-01

    Using classical equilibrium molecular dynamics simulations and applying the original Tersoff interatomic potential, we study the thermal transport property of the latest two dimensional carbon allotrope, penta-graphene. It is predicted that its room-temperature thermal conductivity is about 167 W/mK, which is much lower than that of graphene. With normal mode decomposition, the accumulated thermal conductivity with respect to phonon frequency and mean free path is analyzed. It is found that the acoustic phonons make a contribution of about 90% to the thermal conductivity, and phonons with mean free paths larger than 100 nm make a contribution over 50%. We demonstrate that the remarkably lower thermal conductivity of penta-graphene compared with graphene results from the lower phonon group velocities and fewer collective phonon excitations. Our study highlights the importance of structure-property relationship and provides better understanding of thermal transport property and valuable insight into thermal management of penta-graphene.

  3. Thermal conductivity of penta-graphene from molecular dynamics study.

    PubMed

    Xu, Wen; Zhang, Gang; Li, Baowen

    2015-10-21

    Using classical equilibrium molecular dynamics simulations and applying the original Tersoff interatomic potential, we study the thermal transport property of the latest two dimensional carbon allotrope, penta-graphene. It is predicted that its room-temperature thermal conductivity is about 167 W/mK, which is much lower than that of graphene. With normal mode decomposition, the accumulated thermal conductivity with respect to phonon frequency and mean free path is analyzed. It is found that the acoustic phonons make a contribution of about 90% to the thermal conductivity, and phonons with mean free paths larger than 100 nm make a contribution over 50%. We demonstrate that the remarkably lower thermal conductivity of penta-graphene compared with graphene results from the lower phonon group velocities and fewer collective phonon excitations. Our study highlights the importance of structure-property relationship and provides better understanding of thermal transport property and valuable insight into thermal management of penta-graphene. PMID:26493918

  4. Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Swanson, Jessica M. J.

    2011-05-01

    The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH/120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ = 340 a.u. and μ = 1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH/120 XC functional with μ = 340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.

  5. Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

    2015-02-01

    The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized

  6. Molecular Dynamical Study on Ion Channeling through Peptide Nanotube

    NASA Astrophysics Data System (ADS)

    Sumiya, Norihito; Igami, Daiki; Takeda, Kyozaburo

    2011-12-01

    We theoretically study the possibility of ion channeling through peptide nanotubes (PNTs). After designing the minimal peptide nanorings (PNRs) and their aggregated form (peptide nanotubes, PNT) computationally, we carry out molecular dynamics (MD) calculations for cation channeling. The present MD calculations show that cation channeling through PNTs occurs. Furthermore, inter-ring hydrogen bonds (HBs) survive and maintain the tubular form of PNTs during cation channeling. We introduce mobility such that cation channeling can be evaluated quantitatively. As the ionic radius of the cation becomes smaller, the effective relaxation time τ becomes larger. Accordingly, mobilities of 10-2˜10-3[cm2/volt/sec] are calculated. In contrast, when an anion (F-) passes through the PNT, the inter-ring HBs are broken, thus inducing breakdown of the peptide backbone. Consequently, H atoms from the broken HBs surround the channeling anion (F-) and halt its motion.

  7. Deformation of hypernuclei studied with antisymmetrized molecular dynamics

    SciTech Connect

    Isaka, M.; Kimura, M.; Dote, A.; Ohnishi, A.

    2011-04-15

    An extended version of antisymmetrized molecular dynamics was developed to study the structure of p-sd shell hypernuclei. By using an effective {Lambda}N interaction, we investigated the energy curves of {sub {Lambda}}{sup 9}Be, {sub {Lambda}}{sup 13}C, and {sub {Lambda}}{sup 20,21}Ne as a function of nuclear quadrupole deformation. The changes to nuclear deformation caused by {Lambda} particles are discussed. We found that {Lambda} in the p wave enhances nuclear deformation, while that in the s wave reduces it. This effect is most prominent in {sub {Lambda}}{sup 13}C. The possibility of parity inversion in {sub {Lambda}}{sup 20}Ne is also examined.

  8. Molecular dynamics studies of U1A-RNA complexes.

    PubMed Central

    Reyes, C M; Kollman, P A

    1999-01-01

    The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity. PMID:10024175

  9. Erbium Implantation in Silica Studied by Molecular Dynamics Simulations

    SciTech Connect

    Du, Jincheng; Corrales, Louis R.

    2007-02-01

    Defect formation induced by erbium implantation in silica glass and cristobalite was studied using molecular dynamics simulations employing a partial charge model in combination with the ZBL potential. The results show that the number of displaced atoms generated at the same PKA energy is similar in silica and cristobalite but the number of coordination defects created is much lower in the cristobalite than in silica glass. In both cases, the erbium ion is able to create an optimal coordination environment at the end of the collision cascade. Subsequent thermal annealing causes the relaxation of the silicon oxygen network structure along with a reduction of silicon and oxygen defects. This research is supported by the Divisions of Materials Sciences and Engineering and Chemical Science, Office of Basic Energy Sciences, U.S. Department of Energy. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  10. Anisotropic mechanical properties of graphene: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yu, Ming; Zeng, Anna; Zeng, Kevin

    2014-03-01

    The anisotropic mechanical properties of monolayer graphene with different shapes have been studied using an efficient quantum mechanics molecular dynamics scheme based on a semi-empirical Hamiltonian (refereed as SCED-LCAO) [PRB 74, 15540; PHYSE 42, 1]. We have found the anisotropic nature of the membrane stress. The stresses along the armchair direction are slightly stronger than that along the zigzag direction, showing strong direction selectivity. The graphene with the rectangular shape could sustain strong load (i . e ., 20%) in both armchair and zigzag directions. The graphene with the rhombus shape show large difference in the strain direction: it will quickly crack after 18 % of strain in armchair the direction, but slowly destroyed after 20% in the zigzag direction. The obtained 2D Young's modulus at infinitesimal strain and the third-order (effective nonlinear) elastic modulus are in good consistent with the experimental observation.