Understanding molecular dynamics quantum-state by quantum-state

It is now possible to resolve completely the initial and final quantum states in chemical processes. Spectra of reactive intermediates, of highly vibrationally excited molecules, and even of molecules in the process of falling apart have been recorded. This information has led to greater understanding of the molecular structure and dynamics of small gas-phase molecules. Many of the concepts and spectroscopic techniques that have been developed will be valuable throughout chemistry.     

Crystallographic R factor refinement by molecular dynamics

Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced. In crambin, the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.     

Real-space observation of molecular motion induced by femtosecond laser pulses

Femtosecond laser irradiation is used to excite adsorbed CO molecules on a Cu110 surface; the ensuing motion of individual molecules across the surface is characterized on a site-to-site basis by in situ scanning tunneling microscopy. Adsorbate motion both along and perpendicular to the rows of the Cu110 surface occurs readily, in marked contrast to the behavior seen for equilibrium diffusion processes. The experimental findings for the probability and direction of the molecular motion can be understood as a manifestation of strong coupling between the adsorbates' lateral degrees of freedom and the substrate electronic excitation produced by the femtosecond laser radiation.     

Dark structures in molecular radiationless transitions determined by ultrafast diffraction

The intermediate structures formed through radiationless transitions are termed "dark" because their existence is inferred indirectly from radiative transitions. We used ultrafast electron diffraction to directly determine these transient structures on both ground-state and excited-state potential energy surfaces of several aromatic molecules. The resolution in space and time (0.01 angstrom and 1 picosecond) enables differentiation between competing nonradiative pathways of bond breaking, vibronic coupling, and spin transition. For the systems reported here, the results reveal unexpected dynamical behavior. The observed ring opening of the structure depends on molecular substituents. This, together with the parallel bifurcation into physical and chemical channels, redefines structural dynamics of the energy landscape in radiationless processes.     

Subnanometer motion of cargoes driven by thermal gradients along carbon nanotubes

An important issue in nanoelectromechanical systems is developing small electrically driven motors. We report on an artificial nanofabricated motor in which one short carbon nanotube moves relative to another coaxial nanotube. A cargo is attached to an ablated outer wall of a multiwalled carbon nanotube that can rotate and/or translate along the inner nanotube. The motion is actuated by imposing a thermal gradient along the nanotube, which allows for subnanometer displacements, as opposed to an electromigration or random walk effect.     

Nonequilibrium molecular motion in a hypersonic shock wave

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

Dynamics of molecular motion at single-crystal surfaces

Dramatic advances in our understanding of the motion of individual atoms and molecules at single-crystal surfaces have been made within the past 5 years. Recent experimental and theoretical studies of the interaction of nitric oxide with metal surfaces illustrate the depth of understanding now obtainable. General principles, applicable to a broader range of molecule-surface encounters, have begun to emerge out of the systematic and in-depth analyses of these and related studies.     

20世纪90年代大众传媒规约下的“马桥论争”

20世纪90年代中国文坛上充满了论争,但那些看似自由的论争因为大众传媒的介入依旧不能自由地展开。本文仅以当年的“马桥论争”为例,从策划的噱头、失真的陷阱和仓促的表演三个层面,分析大众传媒对文学论争的规约与影响。     

Real-time observation of molecular motion on a surface

The laser-induced movement of CO molecules over a platinum surface was followed in real time by means of ultrafast vibrational spectroscopy. Because the CO molecules bound on different surface sites exhibit different C-O stretch vibrational frequencies, the site-to-site hopping, triggered by excitation with a laser pulse, can be determined from subpicosecond changes in the vibrational spectra. The unexpectedly fast motion--characterized by a 500-femtosecond time constant--reveals that a rotational motion of the CO molecules, rather than pure translation, is required for this diffusion process. This conclusion is corroborated by density functional theory calculations.     

Ultrafast x-ray diffraction of transient molecular structures in solution

We report direct structural evidence of the bridged radical (CH2ICH2.) in a polar solution, obtained using time-resolved liquid-phase x-ray diffraction. This transient intermediate has long been hypothesized to explain stereo-chemical control in many association and/or dissociation reactions involving haloalkanes. Ultrashort optical pulses were used to dissociate an iodine atom from the haloethane molecule (C2H4I2) dissolved in methanol, and the diffraction of picosecond x-ray pulses from a synchrotron supports the following structural dynamics, with approximately 0.01 angstrom spatial resolution and approximately 100 picosecond time resolution: The loss of one iodine atom from C2H4I2 leads to the C-I-C triangular geometry of CH2ICH2.. This transient C2H4I then binds to an iodine atom to form a new species, the C2H4I-I isomer, which eventually decays into C2H4 + I2. Solvent dynamics were also extracted from the data, revealing a change in the solvent cage geometry, heating, and thermal expansion.     

Crystal and molecular structures of rhenium heptafluoride

Rhenium heptafluoride, ReF(7), is one of only two stable binary compounds MX(7) with a heptacoordinated metal atom M and halide atom X. Its low-temperature crystal structure, as determined by high-resolution powder neutron diffraction, reveals the molecular structure, which has been the subject of speculation and debate for many years. Here it is shown within experimental error that at 1.5 kelvin the lowest energy configuration of ReF(7) has symmetry Cs (m) and is a distorted pentagonal bipyramid. The deviation of the two axial Re-F bonds from collinear and the puckering of the ring of equatorial fluorine atoms are similar to what has been postulated as one of the conformations of the pseudorotational motion observed at higher temperatures.     

The molecular mechanism of thermal noise in rod photoreceptors

Spontaneous electrical signals in the retina's photoreceptors impose a limit on visual sensitivity. Their origin is attributed to a thermal, rather than photochemical, activation of the transduction cascade. Although the mechanism of such a process is under debate, the observation of a relationship between the maximum absorption wavelength (λ(max)) and the thermal activation kinetic constant (k) of different visual pigments (the Barlow correlation) indicates that the thermal and photochemical activations are related. Here we show that a quantum chemical model of the bovine rod pigment provides a molecular-level understanding of the Barlow correlation. The transition state mediating thermal activation has the same electronic structure as the photoreceptor excited state, thus creating a direct link between λ(max) and k. Such a link appears to be the manifestation of intrinsic chromophore features associated with the existence of a conical intersection between its ground and excited states.     

Ultrafast flash thermal conductance of molecular chains

At the level of individual molecules, familiar concepts of heat transport no longer apply. When large amounts of heat are transported through a molecule, a crucial process in molecular electronic devices, energy is carried by discrete molecular vibrational excitations. We studied heat transport through self-assembled monolayers of long-chain hydrocarbon molecules anchored to a gold substrate by ultrafast heating of the gold with a femtosecond laser pulse. When the heat reached the methyl groups at the chain ends, a nonlinear coherent vibrational spectroscopy technique detected the resulting thermally induced disorder. The flow of heat into the chains was limited by the interface conductance. The leading edge of the heat burst traveled ballistically along the chains at a velocity of 1 kilometer per second. The molecular conductance per chain was 50 picowatts per kelvin.     

Large-scale molecular dynamics simulations of dislocation intersection in copper

The results of massively parallel three-dimensional molecular dynamics simulations of the perpendicular intersection of extended dislocations in copper are reported. The intersection process, which involves three of the four possible 111 glide planes in the face-centered cubic lattice, begins with junction formation, followed by unzipping, partial dislocation bowing, cutting, and, finally, unit jog formation. The investigation provides insights into this complex atomistic process, which is currently not accessible to experimental investigation.     

Large-scale molecular dynamics simulations of self-assembling systems

Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.     

Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle

A rotaxane is described in which a macrocycle moves reversibly between two hydrogen-bonding stations after a nanosecond laser pulse. Observation of transient changes in the optical absorption spectrum after photoexcitation allows direct quantitative monitoring of the submolecular translational process. The rate of shuttling was determined and the influence of the surrounding medium was studied: At room temperature in acetonitrile, the photoinduced movement of the macrocycle to the second station takes about 1 microsecond and, after charge recombination (about 100 microseconds), the macrocycle shuttles back to its original position. The process is reversible and cyclable and has properties characteristic of an energy-driven piston.     

Femtosecond pulse sequences used for optical manipulation of molecular motion

Optical control over elementary molecular motion is enhanced with timed sequences of femtosecond (10(-15) second) pulses produced by pulse-shaping techniques. Appropriately timed pulse sequences are used to repetitively drive selected vibrations of a crystal lattice, in a manner analogous to repetitively pushing a child on a swing with appropriate timing to build up a large oscillation amplitude. This process corresponds to repetitively "pushing" molecules along selected paths in the lattice. Amplification of selected vibrational modes and discrimination against other modes are demonstrated. Prospects for more extensive manipulation of molecular and collective behavior and structure are clearly indicated.     

Direct imaging of transient molecular structures with ultrafast diffraction

Ultrafast electron diffraction (UED) has been developed to study transient structures in complex chemical reactions initiated with femtosecond laser pulses. This direct imaging of reactions was achieved using our third-generation apparatus equipped with an electron pulse (1.07 +/- 0.27 picoseconds) source, a charge-coupled device camera, and a mass spectrometer. Two prototypical gas-phase reactions were studied: the nonconcerted elimination reaction of a haloethane, wherein the structure of the intermediate was determined, and the ring opening of a cyclic hydrocarbon containing no heavy atoms. These results demonstrate the vastly improved sensitivity, resolution, and versatility of UED for studying ultrafast structural dynamics in complex molecular systems.     

Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time

In general, the formation and dissociation of solute-solvent complexes have been too rapid to measure without disturbing the thermal equilibrium. We were able to do so with the use of two-dimensional infrared vibrational echo spectroscopy, an ultrafast vibrational analog of two-dimensional nuclear magnetic resonance spectroscopy. The equilibrium dynamics of phenol complexation to benzene in a benzene-carbon tetrachloride solvent mixture were measured in real time by the appearance of off-diagonal peaks in the two-dimensional vibrational echo spectrum of the phenol hydroxyl stretch. The dissociation time constant tau(d) for the phenol-benzene complex was 8 picoseconds. Adding two electron-donating methyl groups to the benzene nearly tripled the value of tau(d) and stabilized the complex, whereas bromobenzene, with an electron-withdrawing bromo group, formed a slightly weaker complex with a slightly lower tau(d). The spectroscopic method holds promise for studying a wide variety of other fast chemical exchange processes.