Cover Picture

The cover picture shows the experimental principles of femtochemistry, the field concerned with the real-time observation of physical, chemical, and biological changes on the femtosecond time scale. The clocking of the femtosecond events is made using laser pulses, one to initiate the change and others to take snapshots. Studies of the motion at atomic-scale resolution provide a telescopic view of the molecular world. More information about this fascinating topic is described by A. H. Zewail in his Nobel Lecture on page 2586 ff. It is quite fitting that at the back of this issue is the inaugural issue of ChemPhysChem, announced in earlier editorials.     

Femtosecond lasers in gas phase chemistry

This critical review is intended to provide an overview of the state-of-the-art in femtosecond laser technology and recent applications in ultrafast gas phase chemical dynamics. Although "femtochemistry" is not a new subject, there have been some tremendous advances in experimental techniques during the last few years. Time-resolved photoelectron spectroscopy and ultrafast electron diffraction have enabled us to observe molecular dynamics through a wider window. Attosecond laser sources, which have so far only been exploited in atomic physics, have the potential to probe chemical dynamics on an even faster timescale and observe the motions of electrons. Huge progress in pulse shaping and pulse characterisation methodology is paving the way for exciting new advances in the field of coherent control.     

Ultrafast spin-state photoswitching in a crystal and slower consecutive processes investigated by femtosecond optical spectroscopy and picosecond X-ray diffraction

We report the spin state photo-switching dynamics in two polymorphs of a spin-crossover molecular complex triggered by a femtosecond laser flash, as determined by combining femtosecond optical pump-probe spectroscopy and picosecond X-ray diffraction techniques. The light-driven transformations in the two polymorphs are compared. Combining both techniques and tracking how the X-ray data correlate with optical signals allow understanding of how electronic and structural degrees of freedom couple and play their role when the switchable molecules interact in the active crystalline medium. The study sheds light on crossing the border between femtochemistry at the molecular scale and femtoswitching at the material scale.     

Femtosecond-technology-based chemical research

The review concerns the mechanisms of physicochemical processes occurring on the femtosecond-subpicosecond time scale; coherent chemistry; coherent control of the dynamics and yield of reaction products; femtosecond optical, electron, and X-ray microscopies; and structural dynamics during chemical reactions. The results of research on molecular, nanoscale, and also on biological systems. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 722–739, April, 2008.     

Femtochemie. Elementare Schritte chemischer Reaktionen

Femtochemistry is about the investigation and control of ultrafast elementary molecular dynamics, which are the basis of every chemical reaction. The processes finally resulting in breaking of chemical bonds or molecular structure changes take place on a time scale of only femto to picoseconds. Solely femtosecond laser pulses are fast enough to resolve these fast processes. Different techniques were developed, which make use of a combination of femtosecond pulses having a relative temporal delay, in order to get access to the dynamics even in complex molecules. The knowledge of the elementary processes allows for a better understanding of the reaction mechanisms and their dependence on environmental conditions. The interaction with the molecules even before the final reaction path is entered, opens up new exciting possibilities for the control of chemical processes. A specific manipulation of the molecular dynamics using adapted pulse shapes appears to be realistic also for complex reactions and systems. The evolutionary optimization strategies, which exploit the experimental results as feedback, make selective chemistry come true even without knowledge of all system parameters.     

Observing the Femtoworld of Molecules: The 1999 Nobel Prize in Chemistry

The Egyptian-born chemist Ahmed H. Zewail of the California Institute of Technology, Pasadena was awarded the 1999 Nobel Prize for Chemistry for his studies of the transition states of chemical reactions using femtosecond spectroscopy. Zewails career is described from his youth in Egypt to his latest discoveries in the field that he almost single-handedly developed, with extensive quotations from the laureate. The advances in chemical dynamics from the turn of the 20th century to the present are reviewed with emphasis on Zewails contributions. Applications and future possibilities for femtochemistry are also considered.Series Editor contribution.     

Chemistry in solution: recent techniques and applications using soft X-ray spectroscopy

The aim of a more precise knowledge about molecular structures and the nature of chemical bonds is the driving force behind the development of numerous experimental methods and theories. Recent soft X-ray based techniques provide novel opportunities for tackling the structure and the dynamics of chemical and biochemical systems in solution. In our research group we are developing experimental methods for mapping the electronic structure and dynamics of molecular systems in solution during bond-building and breaking using soft X-ray absorption and emission spectroscopy. The combination of such recent developments with conventional spectroscopy as well as theoretical modeling allows us to address open questions about hydrogen bonds, thermodynamics and active centers of biological systems. Based on the core-hole clock and pump-probe spectroscopy dynamics on the time scale from sub-femtoseconds up to picoseconds can be revealed.     

Chemistry and biology in the new age

Ahmed Zewail won the 1999 Nobel Prize in chemistry for his visionary work in probing the motions of atoms at the femtosecond level. This pioneering research, a decade earlier, opened up a new frontier of scientific knowledge. Zewail and his multidisciplinary team at Caltech are now pushing further into the realm of molecular complexity, with the ultimate aim of exploring the global dynamics of biological systems at atomic resolution. This requires a new method of 'watching' reactions--ultrafast electron diffraction.     

Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet.

Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.     

Optical molecular imaging for systems biology: from molecule to organism

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.     

A New Method for High-Resolution NMR Spectra in Inhomogeneous Fields with Efficient Solvent Suppression

High-resolution nuclear magnetic resonance （NMR） is one of the most powerful tools for analyzing molecular structures and dynamics. Magnetic field homogeneity is required for conventional high-resolution spectra. However, there are many chemical and/or biological circumstances where the spatial homogeneities of the magnetic fields are degraded. Intense solvent signal is another obstacle for obtaining high-resolution spectra, especially in in vivo and in situ NMR spectroscopy. In this paper, a new pulse sequence based on intermolecular multiple quantum coherence （iMQC） was reported. This sequence can effectively remove the effect of magnetic field inhomogeneity and suppress the solvent signal. It can recover the spectral information such as chemical shifts, coupling constants, multiplet patterns, and relative peak areas in inhomogeneous fields. Theoretical analyses and experimental verifications are presented to demonstrate the feasibility of this method.     

Femtosecond studies of tryptophan fluorescence dynamics in proteins: local solvation and electronic quenching

We report our systematic examination of tryptophan fluorescence dynamics in proteins with femtosecond resolution. Distinct patterns of femtosecond-resolved fluorescence transients from the blue to the red side of emission have been characterized to distinguish local ultrafast solvation and electronic quenching. It is shown that tryptophan is an ideal local optical probe for hydration dynamics and protein-water interactions as well as an excellent local molecular reporter for ultrafast electron transfer in proteins, as demonstrated by a series of biological systems, here in melittin, human serum albumin, and human thioredoxin, and at lipid interfaces. These studies clarify the assignments in the literature about the ultrafast solvation or quenching dynamics of tryptophan in proteins. We also report a new observation of solvation dynamics at far red-side emission when the relaxation of the local environment is slower than 1 ps. These results provide a molecular basis for using tryptophan as a local molecular probe for ultrafast protein dynamics in general.     

Recovering Invisible Signals by Two‐Field NMR Spectroscopy

Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two‐field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low‐field dimension. Two‐field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields.     

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.     

Femtosecond Time-Resolved Stimulated Raman Spectroscopy: Application to the Ultrafast Internal Conversion in beta-Carotene

We have developed the technique of femtosecond stimulated Raman spectroscopy (FSRS), which allows the rapid collection of high-resolution vibrational spectra on the femtosecond time scale. FSRS combines a sub-50 fs actinic pump pulse with a two-pulse stimulated Raman probe to obtain vibrational spectra whose frequency resolution limits are uncoupled from the time resolution. This allows the acquisition of spectra with <100 fs time resolution and <30 cm(-1) frequency resolution. Additionally, FSRS is unaffected by background fluorescence, provides rapid (100 ms) acquisition times, and exhibits traditional spontaneous Raman line shapes. FSRS is used here to study the relaxation dynamics of beta-carotene. Following optical excitation to S(2) (1B(u) (+)) the molecule relaxes in 160 fs to S(1) (2A(g) (-)) and then undergoes two distinct stages of intramolecular vibrational energy redistribution (IVR) with 200 and 450 fs time constants. These processes are attributed to rapid (200 fs) distribution of the internal conversion energy from the S(1) C=C modes into a restricted bath of anharmonically coupled modes followed by complete IVR in 450 fs. FSRS is a valuable new technique for studying the vibrational structure of chemical reaction intermediates and transition states.     

Chasing charge localization and chemical reactivity following photoionization in liquid water

The ultrafast dynamics of the cationic hole formed in bulk liquid water following ionization is investigated by ab initio molecular dynamics simulations and an experimentally accessible signature is suggested that might be tracked by femtosecond pump-probe spectroscopy. This is one of the fastest fundamental processes occurring in radiation-induced chemistry in aqueous systems and biological tissue. However, unlike the excess electron formed in the same process, the nature and time evolution of the cationic hole has been hitherto little studied. Simulations show that an initially partially delocalized cationic hole localizes within ~30 fs after which proton transfer to a neighboring water molecule proceeds practically immediately, leading to the formation of the OH radical and the hydronium cation in a reaction which can be formally written as H(2)O(+) + H(2)O → OH + H(3)O(+). The exact amount of initial spin delocalization is, however, somewhat method dependent, being realistically described by approximate density functional theory methods corrected for the self-interaction error. Localization, and then the evolving separation of spin and charge, changes the electronic structure of the radical center. This is manifested in the spectrum of electronic excitations which is calculated for the ensemble of ab initio molecular dynamics trajectories using a quantum mechanics/molecular mechanics (QM∕MM) formalism applying the equation of motion coupled-clusters method to the radical core. A clear spectroscopic signature is predicted by the theoretical model: as the hole transforms into a hydroxyl radical, a transient electronic absorption in the visible shifts to the blue, growing toward the near ultraviolet. Experimental evidence for this primary radiation-induced process is sought using femtosecond photoionization of liquid water excited with two photons at 11 eV. Transient absorption measurements carried out with ~40 fs time resolution and broadband spectral probing across the near-UV and visible are presented and direct comparisons with the theoretical simulations are made. Within the sensitivity and time resolution of the current measurement, a matching spectral signature is not detected. This result is used to place an upper limit on the absorption strength and/or lifetime of the localized H(2)O(+) ((aq)) species.     

Ultrafast electron diffraction: dynamical structures on complex energy landscapes.

In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.     

Ultrafast 2D-IR spectroscopy of transient species.

Multidimensional spectroscopic experiments offer fascinating insights into molecular structure and dynamics in the field of NMR spectroscopy. With the introduction of ultrafast two-dimensional infrared spectroscopy (2D-IR), multidimensional concepts have entered the optical domain, measuring couplings and correlations between molecular vibrations with femtosecond time resolution. In the transient 2D-IR (T2D-IR) experiments described in this minireview we exploit the high time resolution of 2D-IR to study transient species during fast nonequilibrium processes in real time. Information on molecular structure and dynamics is obtained that is not available from one-dimensional spectroscopy. We discuss examples from chemistry, physics and biophysics.     

Micro- and nanomechanical sensors for environmental, chemical, and biological detection

Micro- and nanoelectromechanical systems, including cantilevers and other small scale structures, have been studied for sensor applications. Accurate sensing of gaseous or aqueous environments, chemical vapors, and biomolecules have been demonstrated using a variety of these devices that undergo static deflections or shifts in resonant frequency upon analyte binding. In particular, biological detection of viruses, antigens, DNA, and other proteins is of great interest. While the majority of currently used detection schemes are reliant on biomarkers, such as fluorescent labels, time, effort, and chemical activity could be saved by developing an ultrasensitive method of label-free mass detection. Micro- and nanoscale sensors have been effectively applied as label-free detectors. In the following, we review the technologies and recent developments in the field of micro- and nanoelectromechanical sensors with particular emphasis on their application as biological sensors and recent work towards integrating these sensors in microfluidic systems.     

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.