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.     

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.     

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.     

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.     

Phenylalanine transfer RNA: molecular dynamics simulation

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.     

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.     

Electron solvation in finite systems: femtosecond dynamics of iodide. (Water)n anion clusters

Electron solvation dynamics in photoexcited anion clusters of I-(D2O)n=4-6 and I-(H2O)4-6 were probed by using femtosecond photoelectron spectroscopy (FPES). An ultrafast pump pulse excited the anion to the cluster analog of the charge-transfer-to-solvent state seen for I- in aqueous solution. Evolution of this state was monitored by time-resolved photoelectron spectroscopy using an ultrafast probe pulse. The excited n = 4 clusters showed simple population decay, but in the n = 5 and 6 clusters the solvent molecules rearranged to stabilize and localize the excess electron, showing characteristics associated with electron solvation dynamics in bulk water. Comparison of the FPES of I-(D2O)n with I-(H2O)n indicates more rapid solvation in the H2O clusters.     

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.     

Picometer-scale electronic control of molecular dynamics inside a single molecule

Tunneling electrons from a low-temperature (5 kelvin) scanning tunneling microscope were used to control, through resonant electronic excitation, the molecular dynamics of an individual biphenyl molecule adsorbed on a silicon(100) surface. Different reversible molecular movements were selectively activated by tuning the electron energy and by selecting precise locations for the excitation inside the molecule. Both the spatial selectivity and energy dependence of the electronic control are supported by spectroscopic measurements with the scanning tunneling microscope. These experiments demonstrate the feasibility of controlling the molecular dynamics of a single molecule through the localization of the electronic excitation inside the molecule.     

An ab initio molecular dynamics study of the aqueous liquid-vapor interface

We present an ab initio molecular dynamics simulation of the aqueous liquid-vapor interface. Having successfully stabilized a region of bulk water in the center of a water slab, we were able to reproduce and further quantify the experimentally observed abundance of surface "acceptor-only"(19%) and "single-donor"(66%) moieties as well as substantial surface relaxation approaching the liquid-vapor interface. Examination of the orientational dynamics points to a faster relaxation in the interfacial region. Furthermore, the average value of the dipole decreases and the average value of the highest occupied molecular orbital for each water molecule increases approaching the liquid-vapor interface. Our results support the idea that the surface contains, on average, far more reactive states than the bulk.     

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity of transport proteins and enzymes. Different minima correspond to changes in the relative orientation of the helices coupled with side-chain rearrangements that preserve the close packing of the protein interior. The conformational space sampled by the simulation is similar to that found in the evolutionary development of the globins. Glasslike behavior is expected at low temperatures. The minima obtained from the trajectory do not satisfy certain criteria for ultrametricity.     

基于分子动力学的miRNA 3'端与Argonaute蛋白PAZ功能域相互作用的研究

应用分子动力学方法研究了人类miRNA 3'末端3碱基与PAZ功能域的结合模式,并采用线性相互作用能方法计算miRNA 3'末端片段与PAZ之间的结合自由能。结果表明:miRNA 3'末端碱基组成决定了其和PAZ功能域的结合模式以及结合自由能,UGU与PAZ的结合最为稳定,结合自由能为-37.248kJ/mol,而CGA与PAZ的结合情况相对不太稳定,结合自由能为-5.418 kJ/mol;miRNA 3'端与PAZ的结合自由能与其在人类miRNA基因中的分布频率存在一定的相关性,UGU在人类基因中占6.768%,而CGA仅占0.414%。本研究结果可为进一步研究miRNA与Argonaute蛋白的相互作用以及对人类疾病防治和生物进化探索提供重要信息。     

Generation of femtosecond pulses of synchrotron radiation

Femtosecond synchrotron pulses were generated directly from an electron storage ring. An ultrashort laser pulse was used to modulate the energy of electrons within a 100-femtosecond slice of the stored 30-picosecond electron bunch. The energy-modulated electrons were spatially separated from the long bunch and used to generate approximately 300-femtosecond synchrotron pulses at a bend-magnet beamline, with a spectral range from infrared to x-ray wavelengths. The same technique can be used to generate approximately 100-femtosecond x-ray pulses of substantially higher flux and brightness with an undulator. Such synchrotron-based femtosecond x-ray sources offer the possibility of applying x-ray techniques on an ultrafast time scale to investigate structural dynamics in condensed matter.     

High-resolution protein structure determination by serial femtosecond crystallography

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.     

Phase-coherent optical pulse synthesis from separate femtosecond lasers

We generated a coherently synthesized optical pulse from two independent mode-locked femtosecond lasers, providing a route to extend the coherent bandwidth available for ultrafast science. The two separate lasers (one centered at 760 nanometers wavelength, the other at 810 nanometers) are tightly synchronized and phase-locked. Coherence between the two lasers is demonstrated via spectral interferometry and second-order field cross-correlation. Measurements reveal a coherently synthesized pulse that has a temporally narrower second-order autocorrelation width and that exhibits a larger amplitude than the individual laser outputs. This work represents a new and flexible approach to the synthesis of coherent light.     

Investigation of ultrafast phenomena in the femtosecond time domain

Rapid progress has taken place in the generation and application of femtosecond optical pulses. The impact of these developments is being felt in a broad range of scientific fields, including physics, chemistry, biology, and engineering. These rapidly evolving techniques have been applied to such diverse problems as phase transitions in highly excited semiconductors, molecular photofragment spectroscopy, impulsive phonon generation in solids, and optical radar ranging through biological tissue.