Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2

Classical trajectory calculations were performed to simulate state-resolved energy transfer experiments of highly vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) and CO(2), which were conducted using a high-resolution transient infrared absorption spectrometer. The goal here is to use classical trajectories to simulate the supercollision energy transfer pathway wherein large amounts of energy are transferred in single collisions in order to compare with experimental results. In the trajectory calculations, Newton's laws of motion are used for the molecular motion, isolated molecules are treated as collections of harmonic oscillators, and intermolecular potentials are formed by pairwise Lennard-Jones potentials. The calculations qualitatively reproduce the observed energy partitioning in the scattered CO(2) molecules and show that the relative partitioning between bath rotation and translation is dependent on the moment of inertia of the bath molecule. The simulations show that the low-frequency modes of the vibrationally excited pyrazine contribute most to the strong collisions. The majority of collisions lead to small DeltaE values and primarily involve single encounters between the energy donor and acceptor. The large DeltaE exchanges result from both single impulsive encounters and chattering collisions that involve multiple encounters.     

Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations

We present a combined theoretical approach based on analyzing molecular dynamics trajectories (at the nanosecond scale) generated by use of classical polarizable force fields and on quantum calculations to compute averaged hyperfine coupling constants. That method is used to estimate the constant of a prototypical nitroxide: the dimethylnitroxide. The molecule is embedded during the simulations in a cubic box containing about 500 water molecules and the molecular dynamics is generated using periodic conditions. Once the trajectories are achieved, the nitroxide and its first hydration shell molecules are extracted, and the coupling constants are computed by considering the latter aggregates by means of quantum computations. However, all the water molecules of the bulk are also accounted for during those computations by means of the electrostatic potential fitted method. Our results exhibit that in order to predict accurate and reliable coupling constants, one needs to describe carefully the out-of-plane motion of the nitroxide nitrogen and to sample trajectories with a time interval of 400 fs at least to generate an uncorrelated large set of nitroxide structures. Compared to Car-Parrinello molecular dynamics techniques, our approach can be used readily to compute hyperfine coupling constants of large systems, such as nitroxides of great size interacting with macromolecules such as proteins or polymers.     

Organized arrays of individual DNA molecules tethered to supported lipid bilayers

An unappreciated aspect of many single-molecule techniques is the need for an inert surface to which individual molecules can be anchored without compromising their biological integrity. Here, we present new methods for tethering large DNA molecules to the surface of a microfluidic sample chamber that has been rendered inert by the deposition of a supported lipid bilayer. These methods take advantage of the "bio-friendly" environment provided by zwitterionic lipids, but still allow the DNA molecules to be anchored at fixed positions on the surface. We also demonstrate a new method for constructing parallel arrays of individual DNA molecules assembled at defined positions on a bilayer-coated, fused silica surface. By using total internal reflection fluorescence microscopy to visualize the arrays, it is possible to simultaneously monitor hundreds of aligned DNA molecules within a single field-of-view. These molecular arrays will significantly increase the throughput capacity of single-molecule, fluorescence-based detection methods by allowing parallel processing of multiple individual reaction trajectories.     

氧在C－Ni（100）表面反应动力学的研究──Ⅱ．动力学计算结果

根据Ｏ２＋Ｃ－Ｎｉ（１００）表面反应的推广ＬＥＰＳ势能面，并用ＱＣＴ方法研究了该体系的反应动力学行为．结果给出了分子化学吸附和解离原子化学吸附及ＣＯ脱附反应的分子动态特征，以及态－态过程的吸附几率．考察了各种能量形式对吸附、脱附几率的影响和各类吸附、脱附几率的变化规律．     

气体分子在二维石墨烯纳米孔中的选择性渗透特性

二维石墨烯纳米孔中气体分子的选择性渗透对多孔石墨烯分离膜非常重要。本文采用分子动力学方法研究了气体分子在氮氢修饰石墨烯纳米孔中的渗透特性,从分子的大小和结构、纳米孔的构型以及分子与石墨烯之间的作用强度等角度阐明了分子出现选择性渗透的原因。结果表明,不同分子的渗透率不同,即H₂O＞H₂S＞CO₂＞N₂＞CH₄。渗透率跟分子的质量和直径以及分子在石墨烯表面上的吸附密度有关;根据气体分子动理学理论,渗透率跟分子质量成反比关系;而分子在石墨烯表面上的高吸附密度对渗透起促进作用。对于H₂O和CH₄分子,分子直径起主导作用;H₂O分子直径最小,其渗透率最大;同理,CH₄分子的渗透率最小。对于H₂S和CO₂分子,H₂S分子的直径较大,但其与石墨烯之间的作用强度较大(吸附密度较高),导致渗透率较高;对于CO₂和N₂分子,CO₂分子的直径较小,并且与石墨烯之间的作用强度较大,渗透率较高。同时发现,分子在纳米孔中的渗透使得其在石墨烯表面的密度分布极不均匀。纳米孔左右两侧的功能化氮原子使CH₄分子容易从孔两侧区域穿过,而其它分子由于直径较小在纳米孔中心区域穿过的概率最大。分子与石墨烯之间的作用越强,导致分子在石墨烯表面区域内停留的时间越长,最终使其在渗透纳米孔的过程中所经历的时间越长。本文所采用的氮氢修饰石墨烯纳米孔中,分子渗透速率达到~10^-3 mol·s^-1·m^-2·Pa^-1,并且其它分子相对于CH₄分子的选择性也很高,说明基于该类型纳米孔的多孔石墨烯分离膜在天然气处理等工业气体分离领域具有很好的应用前景。     

Comparative FTIR spectroscopy of HX adsorbed on solid water: Ragout-jet water clusters vs ice nanocrystal arrays

In addition to revealing the stretch-mode bands of the smallest mixed clusters of HCl and HBr (HX) with water, the ragout-jet FTIR spectra of dense mixed water-acid supersonic jets include bands that result from the interaction of HX with larger water clusters. It is argued here that low jet temperatures prevent the water-cluster-bound HX molecules from becoming sufficiently solvated to induce ionic dissociation. The molecular nature of the HX can be deduced directly from the observed influence of changing from HCl to HBr and from replacing H2O with D2O. Furthermore, the band positions of HX are roughly coincidental with bands assigned to molecular HCl and HBr adsorbed on ice nanocrystal surfaces at temperatures below 100 K. It is also interesting that the HX band positions and widths approximate those of HX bound to the surface of amorphous ice films at <60 K. Though computational results suggest the adsorbed HX molecules observed in the jet expansions are weakly distorted by single coordination with surface dangling-oxygen atoms, on-the-fly trajectories indicate that the cluster skeletons undergo large-amplitude low-frequency vibrations. Local HX solvation, the extent of proton sharing, and the HX vibrational spectra undergo serious modulation on a picosecond time scale.     

Microenvironment control of methyl rotation induced by proton transfer

Methyl rotation induced by proton transfer was found for cis-N-methylacetamide (NMA). More interestingly, it was found that the microenvironment could control the methyl rotation. The atom-centered density matrix propagation (ADMP) method, a recently developed ab initio molecular dynamics, was further carried out to depict the trajectories for methyl rotation of NMA. Moreover, trajectories for methyl rotation of NMA complexed with water molecules were also calculated, and water molecules at the two different sites of NMA were found to reverse or cease the rotational direction of the methyl groups of NMA. This finding that microenvironment can not only control rotational direction of methyl groups but can also cease the rotation may be of significant importance for the control of molecular machines.     

Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites

We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwald's rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus.     

Theoretical calculations of CH4 and H2 associative desorption from Ni(111): could subsurface hydrogen play an important role?

The results of theoretical calculations of associative desorption of CH(4) and H(2) from the Ni(111) surface are presented. Both minimum-energy paths and classical dynamics trajectories were generated using density-functional theory to estimate the energy and atomic forces. In particular, the recombination of a subsurface H atom with adsorbed CH(3) (methyl) or H at the surface was studied. The calculations do not show any evidence for enhanced CH(4) formation as the H atom emerges from the subsurface site. In fact, there is no minimum-energy path for such a concerted process on the energy surface. Dynamical trajectories started at the transition state for the H-atom hop from subsurface to surface site also did not lead to direct formation of a methane molecule but rather led to the formation of a thermally excited H atom and CH(3) group bound to the surface. The formation (as well as rupture) of the H-H and C-H bonds only occurs on the exposed side of a surface Ni atom. The transition states are quite similar for the two molecules, except that in the case of the C-H bond, the underlying Ni atom rises out of the surface plane by 0.25 A. Classical dynamics trajectories started at the transition state for desorption of CH(4) show that 15% of the barrier energy, 0.8 eV, is taken up by Ni atom vibrations, while about 60% goes into translation and 20% into vibration of a desorbing CH(4) molecule. The most important vibrational modes, accounting for 90% of the vibrational energy, are the four high-frequency CH(4) stretches. By time reversibility of the classical trajectories, this means that translational energy is most effective for dissociative adsorption at low-energy characteristic of thermal excitations but energy in stretching modes is also important. Quantum-mechanical tunneling in CH(4) dissociative adsorption and associative desorption is estimated to be important below 200 K and is, therefore, not expected to play an important role under typical conditions. An unexpected mechanism for the rotation of the adsorbed methyl group was discovered and illustrated a strong three-center C-H-Ni contribution to the methyl-surface bonding.     

Display of the flow of energy in molecules

In this article, we develop a method to graphically display the flow of energy within molecules. An energy continuity equation is derived leading to a molecular energy flux vector field. Computation of the flux calls for the intramolecular potential, any external interactions, and the phase space trajectories of the molecular motion. The flux provides a means to display energy flow in still frames and as a tool to visualize hitherto undiscovered dynamic pathways in molecules. Examples are presented that show energy flow in three molecular systems and illustrate the point that depiction of energy flux patterns has increasing utility and meaning as one moves to larger molecules. Simple extensions to this work would also allow visualization of the flux of such quantities as linear and angular momentum. © 1994 by John Wiley & Sons, Inc.     

Physisorption of molecular oxygen on C60 thin films

The interaction of oxygen molecules with a fullerene surface has been studied using high resolution electron energy loss spectroscopy and temperature programmed desorption. Vibrational excitation of the adsorbed oxygen is observed at 190 meV, an energy value comparable with that for molecular oxygen in the gas phase. We take this to indicate physisorption of molecular oxygen on the C(60) surface. Thermal desorption results also show that the bonding of oxygen molecules to the C(60) overlayer is comparable to that on a graphite surface. A detailed study of the energy dependence of the vibrational excitation reveals an inelastic electron resonance scattering process. The angular dependence of the resonant vibrational excitation exhibits features distinctively different from those for molecular oxygen physisorbed on the related graphite surface, at a comparable coverage. One possible reason is that the corrugated surface potential, due to the curvature of the C(60) molecules, promotes the preferential ordering of the physisorbed oxygen molecules perpendicular to the surface plane of the C(60) overlayer.     

Molecular dynamics simulations of amphiphilic graft copolymer molecules at a water/air interface

Fully atomistic molecular dynamics simulations of amphiphilic graft copolymer molecules have been performed at a range of surface concentrations at a water/air interface. These simulations are compared to experimental results from a corresponding system over a similar range of surface concentrations. Neutron reflectivity data calculated from the simulation trajectories agrees well with experimentally acquired profiles. In particular, excellent agreement in neutron reflectivity is found for lower surface concentration simulations. A simulation of a poly(ethylene oxide) (PEO) chain in aqueous solution has also been performed. This simulation allows the conformational behavior of the free PEO chain and those tethered to the interface in the previous simulations to be compared.     

Ab initio MD simulations of a prototype of methyl chloride hydrolysis with explicit consideration of three water molecules: a comparison of MD trajectories with the IRC path

Ab initio molecular dynamics simulations at the Hartree-Fock/6-31G level of theory are performed on methyl chloride hydrolysis with explicit consideration of one solute and two solvent water molecules at a temperature of 298 K. The reaction involves the formation of a reactant complex and the energy surface to the transition state is found to be simple. Two types of trajectories toward the product are observed. In the first type, the system reaches an intermediate complex (complex-P1) region after two nearly concerted proton transfers involving the attacking water molecule and the solvent water molecules. These trajectories resemble the intrinsic reaction coordinate trajectory. The thermal motion of the atoms leads the system to another intermediate complex (complex-P2) region. A second type of trajectory is found in which the system reaches the complex-P2 region directly after the proton transfers. In both of these forward trajectories, back proton transfers lead the system to a final complex-F region which resembles protonated methanol. Received: 3 July 1998 / Accepted: 2 September 1998 / Published online: 15 February 1999     

Real-time dipole orientational imaging as a probe of ligand-protein interactions

Single-molecule orientational imaging using total internal reflection fluorescence microscopy has been employed to investigate the dynamics of a protein-ligand system. Emission patterns from single tetramethylrhodamine (TMR)-biocytin molecules bound to streptavidin show that the TMR dipole adopts a limited number of favored orientations. The angular trajectories of individual dipoles exhibit remarkably similar patterns that are characteristic of single TMR molecules interacting with a relatively homogeneous population of nanoenvironments. Analysis of the polar and azimuthal angle distributions reveals a tendency for the dipole to assume three primary and two secondary orientations. Autocorrelation analysis of the dipole trajectories shows a predominantly bimodal behavior in the reorientation rates with the slow and fast components corresponding to the primary and secondary orientations, respectively. A number of mechanisms by which the observed orientations might be stabilized have been considered, in particular specific interactions between the zwitterionic TMR probe and charged residues on the streptavidin surface. Variations in the reorientation rates have been discussed in terms of local thermal fluctuations in the protein.     

Molecular Dynamics Simulations of the First Steps of the Formation of Polysiloxane Layers at a Zinc Oxide Surface

Three different dissolved silane molecules adsorbed at a polar ZnO surface (000&1macr;) are studied by means of constant temperature molecular dynamics simulations. The adsorbed single silane molecules exhibit a different behavior depending on the chemical nature of their tail. For octyltrihydroxysilane molecules with their rather unpolar tail an orthogonal orientation at the polar metal oxide surface is statistically favored with all three polar hydroxide groups of the head being in contact with the polar ZnO surface and the unpolar tail remaining in the isopropanol phase. On the contrary, due to their highly polar tail, aminopropyltrihydroxysilane molecules show a more or less parallel orientation at the surface. Apart from some minor fluctuations two hydroxide groups as well as the amino group of the tail are in contact with the surface. The behavior of the thiolpropyltrihydroxysilane molecules is somehow located in between resulting in parallel as well as orthogonal orientations of the molecule at the surface. Though many of the results obtained for single adsorbed silane molecules can also be transferred to adsorbed silane molecules within whole layers a remarkable difference appears: Now even for aminopropyltrihydroxysilane molecules a mixture of parallel and orthogonal alignment of the molecules can be observed whereas some of the octyltrihydroxysilane molecules also show a parallel orientation.     

Surface polarity of beta-HMX crystal and the related adhesive forces with Estane binder

Here I present the results on the study of surface properties of beta-HMX crystal utilizing molecular dynamics simulations. The surface polarity of three principal crystal surfaces, (011), (010), and (110), is investigated by measuring the water contact angles. The calculated contact angles are in excellent agreement with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain (with and without surrounding nitroplasticizer molecules) from the three principal crystal surfaces are also calculated using the umbrella sampling method. I find that the force for Estane detachment increases with the increasing HMX surface polarity. In addition, my results show that the nitroplasticizer also plays an important role in the adhesion between Estane and HMX surfaces.     

Effect of SDBS solution on the surface potential properties of the Zhaozhuang coal

It is of great significance to study the effect of surfactants on the coal surface potential for effective dust suppression in mining faces. The effect of different concentrations of sodium dodecyl benzene sulfonate (SDBS) solution on the surface potential of the Zhaozhuang coal was measured by atomic force microscopy (AFM). The experimental results show that the SDBS solution has significant influence on the surface potential of the Zhaozhuang coal. The electrical characteristics of the coal surface at the nanometer scale are different from those of macroscopic or the mesoscopic level. The surface potential of coal is basically a normal distribution, showing certain electrical characteristics. The mean value of the surface potential of the Zhaozhuang coal is increased with the increase in concentration of the SDBS solution; when the concentration of the SDBS solution is 0.3%, the mean value of surface potential is 5.59 mv, which is about two times of the mean value of the surface potential without SDBS solution added. With the increase of the concentration of the SDBS solution, the maximum value of the surface potential of the Zhaozhuang coal increases, and the minimum value decreases. It shows that the SDBS solution has a significant effect on the potential distribution law and the magnitude of the coal surface. Subsequently, on the basis of the constructed Zhaozhuang coal macromolecule model, xtb and Multiwfn simulation software were used to calculate the molecular surface electrostatic potential value and electron density value of the Zhaozhuang coal molecules after adding water molecules. The variation law for the electrostatic potential surface of the molecule was obtained after adding numbers of water molecules to the surface of the coal molecule. The simulation results show that the area proportion of absolute molecular surface electrostatic potential greater than 10 kcal/mol is increased with the growth in the number of water molecules, while the area proportion of absolute molecular surface electrostatic potential less than 10 kcal/mol is decreased. Because of the free state O─H bond polarity of water molecules, the charges on the molecular surface are rearranged in order to change the electron density on the surface of coal molecules, which affects the overall electrostatic potential of the configuration.     

Six-dimensional quantum dynamics of H2 dissociative adsorption on the Pt(211) stepped surface

Results of experimental studies, and theoretical calculations utilizing classical trajectories, have shown that dissociation of H2 on the Pt(211) stepped surface is enhanced at low energies by a molecular trapping mechanism. Because quantum effects can play a large role at the low energies and long lifetimes that characterize molecular trapping, we have undertaken quantum dynamics calculations for this system, the first to treat all molecular degrees of freedom of a gas molecule reacting on a stepped metallic surface. The calculations show that molecular trapping persists in the quantum system, but only at much lower energies than experimentally seen, pointing to possible deficiencies in the potential energy surface. Classical and quasiclassical trajectory calculations on the same potential provide a reasonable picture of reaction overall, but many of the finer details are inaccurate, and certain classical reaction mechanisms are entirely invalid. We conclude that some skepticism should be shown toward any classical study for which long-lived trapping states play a role.     

Comparative study of normal and branched alkane monolayer films adsorbed on a solid surface. I. Structure

The structure of a monolayer film of the branched alkane squalane (C30H62) adsorbed on graphite has been studied by neutron diffraction and molecular dynamics (MD) simulations and compared with a similar study of the n-alkane tetracosane (n-C24H52). Both molecules have 24 carbon atoms along their backbone and squalane has, in addition, six methyl side groups. Upon adsorption, there are significant differences as well as similarities in the behavior of these molecular films. Both molecules form ordered structures at low temperatures; however, while the melting point of the two-dimensional (2D) tetracosane film is roughly the same as the bulk melting point, the surface strongly stabilizes the 2D squalane film such that its melting point is 91 K above its value in bulk. Therefore, squalane, like tetracosane, will be a poor lubricant in those nanoscale devices that require a fluid lubricant at room temperature. The neutron diffraction data show that the translational order in the squalane monolayer is significantly less than in the tetracosane monolayer. The authors' MD simulations suggest that this is caused by a distortion of the squalane molecules upon adsorption on the graphite surface. When the molecules are allowed to relax on the surface, they distort such that all six methyl groups point away from the surface. This results in a reduction in the monolayer's translational order characterized by a decrease in its coherence length and hence a broadening of the diffraction peaks. The MD simulations also show that the melting mechanism in the squalane monolayer is the same footprint reduction mechanism found in the tetracosane monolayer, where a chain melting drives the lattice melting.