Molecular Dynamic Structure Investigations of the Surface Stability and Adsorption of H, H2, CH3, C2H2: (100) Diamond

1992 ◽  
Vol 270 ◽  
Author(s):  
Th. Frauenheim ◽  
P. Blaudeck ◽  
D. Porezag
Keyword(s):  
Density Functional ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Minimal Basis ◽  
Surface Stability ◽  
Hydrogen Supply ◽  
Reaction Processes ◽  
Structure Investigations

ABSTRACTSurface properties - stability and reconstruction - of clean and hydrogenated diamond (100) have been studied by real temperature molecular dynarnic (MD) simulations using an approximate density functional (DF) theory expanding the total electronic wave function in a minimal basis of localized atomic valence electron orbitals (LCAO - ansatz). The clean surface is highly unstable against a spontaneous dimerization resulting in a 2×1 reconstruction. Atomic hydrogen in the gas phase above the top surface at all temperatures and H2 molecules approaching the center of the dimer bond at room temperature are reactive in breaking the dimer π-bonds forming a monohydrogenated surface which maintains a stable 2×1 structure but with elongated surface C-C dimer bonds remaining stable against continuing hydrogen supply. The dihydrogenated surface taking a 1×1 structure, because of steric overcrowding dynamically becomes unstable against forming a 1×1 (alternating) di-, monohydrogenated surface. As first elementary reaction processes which may be discussed in relation to diamond growth we studied the thermal adsorption of CH3 and C2H2 onto a clean 2×l reconstructed (100) diamond surface.

Density Functional Based Tight Binding Study of C2 and CN Deposition On (100) Diamond Surface

2001 ◽  
Vol 675 ◽  
Author(s):  
Michael Sternberg ◽  
Peter Zapol ◽  
Thomas Frauenheim ◽  
John Carlisle ◽  
Dieter M. Gruen ◽  
...  
Keyword(s):  
Experimental Evidence ◽  
Density Functional ◽  
Tight Binding ◽  
Nitrogen Addition ◽  
Binding Study ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Elementary Steps ◽  
Argon Plasmas ◽  
Tight Binding Method

ABSTRACTA density-functional based tight binding method was used to study elementary steps in the growth of ultrananocrystalline (UNCD) diamond. It was shown previously that C2 dimers are the dominant growth species in hydrogen-poor argon plasmas. Recent experimental evidence shows that nitrogen addition to the plasma profoundly changes the morphology of the UNCD film. CN species are believed to play a major role. Reactions of C2 and CN molecules with reconstructed diamond (100) surfaces were studied. A single CN prefers an end-on attachment to a surface atom on the unhydrided (100) surface with its C end down. It is shown how further C2 addition to the surface leads to CN-mediated diamond growth and how the CN species remain on top of the growing diamond layer.

scholarly journals Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study

2021 ◽  
Author(s):  
Hongwei Chen ◽  
Changchang Lv ◽  
Lin Guo ◽  
Ming Ma ◽  
Xiangfeng Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lactic Acid ◽  
Calcium Phosphate ◽  
Coordination Number ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Surface Stability ◽  
Ph Values ◽  
Phosphate Species

The ubiquitous mineralization of calcium phosphate (CaP) facilitates biological organisms to produce hierarchically structured minerals. The coordination number and strength of Ca2+ ions with phosphate species, oxygen-containing additives, and solvent molecules played a crucial role in tuning nucleation processes and surface stability of CaP under the simulated body fluid (SBF) or aqueous solutions upon the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values. As revealed by ab initio molecular dynamics (AIMD), density functional theory (DFT), and molecular dynamics (MD) simulations as well as high-throughput experimentation (HTE), the binding of LAC molecules with Ca2+ ions and phosphate species could stabilize both pre-nucleation clusters and brushite (DCPD, CaHPO4·2H2O) surface through intermolecular electrostatic and hydrogen bonding interactions. When the concentration of Ca2+ ions ([Ca2+]) is very low, the amount of the formed precipitation decreased with the addition of LAC based on UV-Vis spectroscopic analysis due to the reduced chance for the LAC capped Ca2+ ions to coordinate with phosphates and the increased solubility in acid solution. With the increasing [Ca2+] concentration, the kinetically stable DCPD precipitation was obtained with high Ca2+ coordination number and low surface energy. Morphologies of DCPD precipitation are in plate, needle, or rod, depending on the initial pH values that tuned by adding NH3·H2O, HCl, or CH3COOH. The prepared samples at pH ≈ 7.4 with different Ca/P ratios exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications.

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

scholarly journals Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Lütgert ◽  
J. Vorberger ◽  
N. J. Hartley ◽  
K. Voigt ◽  
M. Rödel ◽  
...  
Keyword(s):  
Equation Of State ◽  
Polyethylene Terephthalate ◽  
Density Functional ◽  
Equations Of State ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Shock Hugoniot ◽  
Highly Correlated

AbstractWe present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, $$({\hbox {C}}_{10} {\hbox {H}}_8 {\hbox {O}}_4)_n$$ ( C 10 H 8 O 4 ) n , also called mylar) shock-compressed to ($$155 \pm 20$$ 155 ± 20 ) GPa and ($$6000 \pm 1000$$ 6000 ± 1000 ) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

scholarly journals Effect of Nitrogen on the Growth of (100)-, (110)-, and (111)-Oriented Diamond Films

2020 ◽  
Vol 11 (1) ◽  
pp. 126
Author(s):  
Jen-Chuan Tung ◽  
Tsung-Che Li ◽  
Yen-Jui Teseng ◽  
Po-Liang Liu
Keyword(s):  
Growth Mechanism ◽  
Density Functional ◽  
Film Growth ◽  
Hydrogen Abstraction ◽  
Diamond Films ◽  
Activation Energies ◽  
Diamond Surface ◽  
Nitrogen Doped ◽  
Nitrogen Substitution ◽  
Diamond Film Growth

The aim of this research is the study of hydrogen abstraction reactions and methyl adsorption reactions on the surfaces of (100), (110), and (111) oriented nitrogen-doped diamond through first-principles density-functional calculations. The three steps of the growth mechanism for diamond thin films are hydrogen abstraction from the diamond surface, methyl adsorption on the diamond surface, and hydrogen abstraction from the methylated diamond surface. The activation energies for hydrogen abstraction from the surface of nitrogen-undoped and nitrogen-doped diamond (111) films were −0.64 and −2.95 eV, respectively. The results revealed that nitrogen substitution was beneficial for hydrogen abstraction and the subsequent adsorption of methyl molecules on the diamond (111) surface. The adsorption energy for methyl molecules on the diamond surface was generated during the growth of (100)-, (110)-, and (111)-oriented diamond films. Compared with nitrogen-doped diamond (100) films, adsorption energies for methyl molecule adsorption were by 0.14 and 0.69 eV higher for diamond (111) and (110) films, respectively. Moreover, compared with methylated diamond (100), the activation energies for hydrogen abstraction were by 0.36 and 1.25 eV higher from the surfaces of diamond (111) and (110), respectively. Growth mechanism simulations confirmed that nitrogen-doped diamond (100) films were preferred, which was in agreement with the experimental and theoretical observations of diamond film growth.

scholarly journals H2 Transformations on Graphene Supported Palladium Cluster: DFT-MD Simulations and NEB Calculations

Catalysts ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1306
Author(s):  
Francesco Ferrante ◽  
Antonio Prestianni ◽  
Marco Bertini ◽  
Dario Duca
Keyword(s):  
Atomic Hydrogen ◽  
Density Functional ◽  
Hydrogen Molecule ◽  
Md Simulations ◽  
Vacant Site ◽  
Functional Theory ◽  
H2 Adsorption ◽  
Palladium Cluster ◽  
Supported Palladium ◽  
Dynamics Simulations

Molecular dynamics simulations based on density functional theory were employed to investigate the fate of a hydrogen molecule shot with different kinetic energy toward a hydrogenated palladium cluster anchored on the vacant site of a defective graphene sheet. Hits resulting in H2 adsorption occur until the cluster is fully saturated. The influence of H content over Pd with respect to atomic hydrogen spillover onto graphene was investigated. Calculated energy barriers of ca. 1.6 eV for H-spillover suggest that the investigated Pd/graphene system is a good candidate for hydrogen storage.

Kinetic Monte Carlo Simulation of Diamond Film Growth with the Inclusion of Surface Migration

1998 ◽  
Vol 527 ◽  
Author(s):  
Armando Netto ◽  
Michael Frenklach
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Film Growth ◽  
Kinetic Monte Carlo ◽  
Diamond Films ◽  
State Theory ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Gaseous Species ◽  
Surface Migration

ABSTRACTDiamond films are of interest in many practical applications but the technology of producing high-quality, low-cost diamond is still lacking. To reach this goal, it is necessary to understand the mechanism underlying diamond deposition. Most reaction models advanced thus far do not consider surface diffusion, but recent theoretical results, founded on quantum-mechanical calculations and localized kinetic analysis, highlight the critical role that surface migration may play in growth of diamond films. In this paper we report a three-dimensional time-dependent Monte Carlo simulations of diamond growth which consider adsorption, desorption, lattice incorporation, and surface migration. The reaction mechanism includes seven gas-surface, four surface migration, and two surface-only reaction steps. The reaction probabilities are founded on the results of quantum-chemical and transition-state-theory calculations. The kinetic Monte Carlo simulations show that, starting with an ideal {100}-(2×1) reconstructed diamond surface, the model is able to produce a continuous film growth. The smoothness of the growing film and the developing morphology are shown to be influenced by rate parameter values and by deposition conditions such as temperature and gaseous species concentrations.

Diamond {111} Surface: Graphitization or Reconstruction?

1995 ◽  
Vol 383 ◽  
Author(s):  
G. Jungnickel ◽  
D. Porezag ◽  
Th. Frauenheim ◽  
W. R. L. Lambrecht ◽  
B. Segall ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Density Functional ◽  
Tight Binding ◽  
Diamond Growth ◽  
Functional Theory ◽  
Surface Phases ◽  
Surface Graphitization

ABSTRACTThe reconstruction of the diamond {1111} surface is re-examined by means of density functional theory based tight-binding molecular dynamics. Evidence is found for competition between a graphitizing tendency leading to an unreconstructed but relaxed 1 × 1 surface and a π-bonded chain-like 2 × 1 reconstruction. The implications of the possible co-existence of these two distinct surface phases for diamond growth are discussed.

Multiscale Simulations of Domains in Ferroelectrics

Domain Walls ◽  
2020 ◽  
pp. 311-339
Author(s):  
S. Liu ◽  
I. Grinberg ◽  
A. M. Rappe
Keyword(s):  
Density Functional ◽  
Large Scale ◽  
Mean Field Theory ◽  
Mean Field ◽  
Md Simulations ◽  
Relaxor Ferroelectrics ◽  
Ferroelectric Materials ◽  
Multiscale Simulations ◽  
Challenges And Opportunities ◽  
Physically Based

This chapter focuses on recent studies of ferroelectrics, where large-scale molecular dynamics (MD) simulations using first-principles-based force fields played a central role in revealing important physics inaccessible to direct density functional theory (DFT) calculations but critical for developing physically-based free energy functional for coarse-grained phase-field-type simulations. After reviewing typical atomistic potentials of ferroelectrics for MD simulations, the chapter describes a progressive theoretical framework that combines DFT, MD, and a mean-field theory. It then focuses on relaxor ferroelectrics. By examining the spatial and temporal polarization correlations in prototypical relaxor ferroelectrics with million-atom MD simulations and novel analysis techniques, this chapter shows that the widely accepted model of polar nanoregions embedded in a non-polar matrix is incorrect for Pb-based relaxors. Rather, the unusual properties of theses relaxor ferroelectrics stem from the presence of a multi-domain state with extremely small domain sizes (2–10 nanometers), giving rise to a greater flexibility for polarization rotations and the ultrahigh dielectric and piezoelectric responses. Finally, this chapter discusses the challenges and opportunities for multiscale simulations of ferroelectric materials.

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