In this contribution we demonstrate structural control over a transport resonance in HS(CH2)n[1,4 −C6H4](CH2)nSH (n = 1, 3, 4, 6) metal-molecule-metal junctions, fabricated and tested using the scanning tunnelingmicroscopy-based I (z)method. The Breit-Wigner resonance originates from one of the arene π-bonding orbitals, which sharpens and moves closer to the contact Fermi energy as n increases. Varying the number of methylene groups thus leads to a very shallow decay of the conductance with the length of the molecule. We demonstrate that the electrical behavior observed here can be straightforwardly rationalized by analyzing the effects caused by the electrostatic balance created at the metal-molecule interface. Such resonances offer future prospects in molecular electronics in terms of controlling charge transport over longer distances, and also in single-molecule conductance switching if the resonances can be externally gated ; This research was supported by the EPSRC (Grant No. EP/H035184/1), by MINECO under Grant No. FIS2013-47328, by the European Union structural funds and the Comunidad de Madrid MAD2D-CM Program under Grant. P2013/MIT-2850, and by Generalitat Valenciana under Grant PROMETEO/2012/011.
[EN] To our knowledge, we have developed a novel temperature-jump optical tweezers setup that changes the temperature locally and rapidly. It uses a heating laser with a wavelength that is highly absorbed by water so it can cover a broad range of temperatures. This instrument can record several force-distance curves for one individual molecule at various temper- atures with good thermal and mechanical stability. Our design has features to reduce convection and baseline shifts, which have troubled previous heating-laser instruments. As proof of accuracy, we used the instrument to carry out DNA unzipping experi- ments in which we derived the average basepair free energy, entropy, and enthalpy of formation of the DNA duplex in a range of temperatures between 5 C and 50 C. We also used the instrument to characterize the temperature-dependent elasticity of single-stranded DNA (ssDNA), where we find a significant condensation plateau at low force and low temperature. Oddly, the persistence length of ssDNA measured at high force seems to increase with temperature, contrary to simple entropic models. ; The authors thank J. Camunas and S. Frutos for contributing the molecules used in the experiments, and J.M. Huguet for helpful discussion. F.R. is supported by grant Institucio Catalana de Recerca i Estudis Avancats Academia 2013 and J.R. A.-G. by an Explora grant from MINECO (MAT2013-49455-EXP). The research that led to the results presented here was funded by the European Union Seventh Framework Programme (FP7/2007-2013) under grant 308850 INFERNOS and European Research Council grant MagReps (No. 267862). ; De Lorenzo, S.; Ribezzi-Crivellari, M.; Arias-Gonzalez, JR.; Smith, S.; Ritort, F. (2015). A Temperature-Jump Optical Trap for Single-Molecule Manipulation. Biophysical Journal. 108(12):2854-2864. https://doi.org/10.1016/j.bpj.2015.05.017 ; S ; 2854 ; 2864 ; 108 ; 12
The activity of enzymes is traditionally characterised through bulk-phase biochemical methods that only report on population averages. Single-molecule methods are advantageous in elucidating kinetic and population heterogeneity but are often complicated, time consuming, and lacking statistical power. We present a highly generalisable and high-throughput single-molecule assay to rapidly characterise proteins involved in DNA metabolism. The assay exclusively relies on changes in total fluorescence intensity of surface-immobilised DNA templates as a result of DNA synthesis, unwinding or digestion. Combined with an automated data-analysis pipeline, our method provides enzymatic activity data of thousands of molecules in less than an hour. We demonstrate our method by characterising three fundamentally different nucleic-acid enzyme activities: digestion by the phage λ exonuclease, synthesis by the phage Phi29 polymerase, and unwinding by the E. coli UvrD helicase. We observe a previously unknown activity of the UvrD helicase to remove proteins tightly bound to the ends of DNA. ; The authors thank Dr Jacob Lewis (University of Wollongong) and Prof. Michael O'Donnell (Rockefeller University) for contributing reagents. ; This work was supported by the Australian Research Council (research grants DP150100956 and DP180100858 to A.M.v.O. and an Australian Laureate Fellowship FL140100027 to A.M.v.O.), the National Health and Medical Research Council (NHMRC Investigator grant 2007778 to L.M.S) and an Australian Government Research Training Program Scholarship (to S.H.M). Funding for open access charge: Australian Research Council.
2010 Spring. ; Includes bibliographic references. ; Covers not scanned. ; Print version deaccessioned 2022. ; Energetic materials have a wide variety of industrial, civil, and military applications. They include a number of organic compounds such as RDX (1,3,5- trinitroheahydro-s-triazine), HMX (octahydro-1,3,5,7-tetranitro-l ,3,5,7-tetrazocine), DAAF (3,3'-diamino-4,4'-azoxyfurazan), DAATO35 (3,3'-azobis(6-amino-l,2,4,5- tetrazine)-mixed N-oxides), etc. These materials release huge chemical energy during their decomposition. The decomposition of energetic materials is initiated with a shock or compression wave or a spark. Such events in solids generate molecules in the excited electronic states. Hence, in order to maximize release of the stored chemical energy in the most efficient and useful manner and to design new energetic materials, the unimolecular decomposition mechanisms and dynamics from excited electronic states should be understood for these systems. This thesis describes understanding about unimolecular decomposition of energetic materials from their excited electronic states. A few fundamental questions at molecular level dealing with electronic excitation of energetic materials are addressed here: (a) what happens immediately after electronic excitation of energetic molecules?; (b) how is excess energy partitioned among product molecules following electronic excitation?; (b) what are the mechanism and dynamics of molecular decomposition?; (d) does nonadiabatic chemistry (a process that span multiple electronic potential energy surfaces) through conical intersection (crossing of different potential energy surfaces) dominate system behavior? Both energy and time resolved spectroscopic techniques are used in this effort. The product internal state (rotational and vibrational) distributions are probed using mass and energy resolved spectroscopic techniques using time-of-flight mass spectrometry (TOFMS) and laser induced fluorescence (LIF) spectroscopy. Analyzing the product internal state distributions, the mechanisms of unimolecular decomposition of energetic molecules from excited electronic states are determined. The femtosecond pump-probe spectroscopic technique is utilized to determine ultrafast decomposition dynamics of these molecules. From a theoretical point of view, multiconfigurational methodologies such as, CASSCF and CASMP2 are used to model the processes involving excited electronic states of energetic molecules. Influence of nonadiabatic chemistry in the overall decomposition of energetic molecules is also theoretically judged. The primary energetic systems whose nonadiabatic chemistry discussed here are the nitramine (e.g., RDX, HMX), furazan (e.g., DAAF), and tetrazine-N-oxide (e.g., DAATO3.5) based energetic species. A number of model systems, which are simple analogue molecules of the large and more complex energetic materials, are studied in detail to understand nonadiabatic energetic behavior of a single energetic moiety of particular class. Subsequently, the decomposition mechanism for more complex energetic systems are studied and compared with that of their model systems. Nitramine energetic materials and model systems undergo nitro-nitrite isomerization followed by IV NO elimination. Nitramine energetic materials dissociates in the ground state generating rotationally cold (20 K) distribution of the NO product. Nitramine model systems dissociates in the excited state surface producing rotationally hot (-120 K) distribution of the NO product. The nitro-nitrite isomerization happens through conical intersection. Furazan based model molecules (e.g., furazan) possess two different pathways of decomposition: ring contraction and ring opening. These two pathways are electronically nonadiabatic. The ring contraction mechanism generates rotationally cold (20 K) product NO and the ring opening mechanism generates rotationally hot (100 K) product NO. Furazan based energetic material (DAAF), however, dissociates only through a ring contraction mechanism. Thus nonadiabatic pathways control the decomposition of furazan based molecules. Decomposition of tetrazine-2,4-dioxide based molecules involves a ring contraction mechanism through (Si/So)ci, producing only rotationally cold (20 K) but vibrationally hot (1200 K) distributions of the NO product. Tetrazine-l,4-dioxde undergoes similar decomposition pathway through (Si/So)ci; however, it produces rotationally hotter (50 K) but vibrationally colder distribution of the NO product. Thus the relative position of the oxygen atoms attached to the tetrazine ring is important parameter along with their nonadiabatic chemistry controlling their final energetic reactivity. Decomposition dynamics of all energetic materials is faster than 180 fs. Considering the influence of conical intersections in the excited electronic state decomposition of energetic materials, rotationally cold N2 product is predicted to be the major decomposition product of high nitrogen content energetic species. The present work infers that generation of internally cold product is an important characteristics of a true energetic molecule. Presence of low lying chemically relevant conical intersections provides a direct pathway of ultrafast decomposition chemistry of energetic molecules. The energy barrier to the low lying chemically relevant conical intersection, in principle, would be a point of interest to make a system more or less energetic.
The second law of photochemistry states that, in most cases, no more than one molecule is activated for an excited-state reaction for each photon absorbed by a collection of molecules. In this Letter, we demonstrate that it is possible to trigger a many-molecule reaction using only one photon by strongly coupling the molecular ensemble to a confined light mode. The collective nature of the resulting hybrid states of the system (the so-called polaritons) leads to the formation of a polaritonic "supermolecule" involving the degrees of freedom of all molecules, opening a reaction path on which all involved molecules undergo a chemical transformation. We theoretically investigate the system conditions for this effect to take place and be enhanced. ; This work has been funded by the European Research Council under Grants No. ERC-2011-AdG-290981 and No. ERC- 2016-STG-714870, by the European Union Seventh Framework Programme under Grant No. FP7-PEOPLE- 2013-CIG-618229, and the Spanish MINECO under Contract No. MAT2014-53432-C5-5-R and the "María de Maeztu" program for Units of Excellence in R&D (MDM-2014-0377).
