Femtosecond dynamics of hydrogen elimination: benzene formation from cyclohexadiene

Using femtosecond-resolved mass spectrometry in a molecular beam, we report real-time study of the hydrogen elimination reaction of 1,4-cyclohexadiene. The experimental observation of the ultrafast stepwise H-elimination elucidates the reaction dynamics and mechanism. With density-functional theory (ground-state) calculations, the nature of the reaction (multiple) pathways is examined. With the help of recent conical-intersection calculations, the excited-state and ground-state pathways are correlated. From these experimental and theoretical results we provide a unifying picture of the thermochemistry, photochemistry and the stereochemistry observed in the condensed phase

Dynamics in Self-assembled Organic Monolayers at the Liquid/Solid Interface Revealed by Scanning Tunneling Microscopy

The liquid/solid interface provides an interesting medium for molecular self-assembly and scanning tunneling microscopy is the preferred technique to analyse the structural features of the surface-supported self-assembled monolayers in this medium. An interesting aspect is the phenomenon of molecular dynamics at the liquid/solid interface. In this mini-review, we report on our efforts and strategies to investigate and even induce molecular dynamics at the liquid/solid interface, bringing insight to various kinds of processes such as conformational, translational and adsorption/desorption dynamics

Preferred Formation of Minority Concomitant Polymorphs in 2D Self‐Assembly under Lateral Nanoconfinement

Control over polymorph formation in the crystallization of organic molecules remains a huge scientific challenge. Now, preferential formation is presented of one polymorph, formed by chiral molecules, in controlled two‐dimensional (2D) nanoconfinement conditions at a liquid–solid interface. So‐called nanocorrals to control concomitant polymorph formation were created in situ via a nanoshaving protocol at the interface between 1‐phenyloctane and covalently modified highly‐oriented pyrolytic graphite (HOPG). The preferentially formed polymorphs, which were less stable in the large‐scale monolayers, could be selected simply by varying the orientation of the square nanocorrals with respect to the HOPG lattice

Direct observation of the femtosecond nonradiative dynamics of azulene in a molecular beam: The anomalous behavior in the isolated molecule

Using femtosecond-resolved mass spectrometry in a molecular beam, we report real-time observation of the nonradiative, anomalous dynamics of azulene. We studied both S_2 and S_1 state dynamics. The motion of the wave packet in S_1 involves two time scales, a dephasing time of less than 100 fs and a 900±100 fs internal conversion. We discuss the dynamical picture in relation to the molecular structures and the conical intersection, and we compare with theory

Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes revealed by scanning force microscopy

LEDGF/p75 is a transcriptional coactivator implicated in the pathogenesis of AIDS and leukemia. In these contexts, LEDGF/p75 acts as a cofactor by tethering protein cargo to transcriptionally active regions in the human genome. Our study - based on scanning force microscopy (SFM) imaging - is the first to provide structural information on the interaction of LEDGF/p75 with DNA. Two novel approaches that allow obtaining insights into the DNA conformation inside nucleoprotein complexes revealed (1) that LEDGF/p75 can bind at least in three different binding modes, (2) how DNA topology and protein dimerization affect these binding modes, and (3) geometrical and mechanical aspects of the nucleoprotein complexes. These structural and mechanical details will help us to better understand the cellular mechanisms of LEDGF/p75 as a transcriptional coactivator and as a cofactor in disease

High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ∼10 000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but in contrast to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Notably, centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes. Finally, our results reconcile previous conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability and to facilitate future high-throughput AFM studies that involve heterogeneous nucleoprotein complexes

Direct observation of the femtosecond nonradiative dynamics of azulene in a molecular beam: The anomalous behavior in the isolated molecule

Using femtosecond-resolved mass spectrometry in a molecular beam, we report real-time observation of the nonradiative, anomalous dynamics of azulene. We studied both S_2 and S_1 state dynamics. The motion of the wave packet in S_1 involves two time scales, a dephasing time of less than 100 fs and a 900±100 fs internal conversion. We discuss the dynamical picture in relation to the molecular structures and the conical intersection, and we compare with theory

Self-assembly under confinement: nanocorrals for understanding fundamentals of 2D crystallization

Nanocorrals with different size, shape, and orientation are created on covalently modified highly oriented pyrolytic graphite surfaces using scanning probe nanolithography, i.e., nanoshaving. Alkylated diacetylene molecules undergo laterally confined supramolecular self-assembly within these corrals. When nanoshaving is performed in situ, at the liquid–solid interface, the orientation of the supramolecular lamellae structure is directionally influenced by the gradual graphite surface exposure. Careful choice of the nanoshaving direction with respect to the substrate symmetry axes promotes alignment of the supramolecular lamellae within the corral. Self-assembly occurring inside corrals of different size and shape reveals the importance of geometric and kinetic constraints controlled by the nanoshaving process. Finally, seed-mediated crystallization studies demonstrate confinement control over nucleation and growth principles