Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins

New sounds and extended composition techniques

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This commentary supports my PhD composition portfolio. The composition processes of each piece are related to my central research questions, which concern the creation of new sounds using overtone-based scales and extended instrumental techniques. I have developed four main conceptual composition themes and these are represented in the thirteen compositions in the portfolio. In this commentary I consider how each composition was developed around these conceptual themes.Nomura Foundation, Japan for a research grant, Brunel Graduate School for the Vice Chancellor’s Travel Prizes (2010 and 2012), and for the PRSF and Bliss Trust Composer Bursarie

Normal & reversed spin mobility in a diradical by electron-vibration coupling

π−conjugated radicals have great promise for use in organic spintronics, however, the mechanisms of spin relaxation and mobility related to radical structural flexibility remain unexplored. Here, we describe a dumbbell shape azobenzene diradical and correlate its solid-state flexibility with spin relaxation and mobility. We employ a combination of X-ray diffraction and Raman spectroscopy to determine the molecular changes with temperature. Heating leads to: i) a modulation of the spin distribution; and ii) a “normal” quinoidal → aromatic transformation at low temperatures driven by the intramolecular rotational vibrations of the azobenzene core and a “reversed” aromatic → quinoidal change at high temperatures activated by an azobenzene bicycle pedal motion amplified by anisotropic intermolecular interactions. Thermal excitation of these vibrational states modulates the diradical electronic and spin structures featuring vibronic coupling mechanisms that might be relevant for future design of high spin organic molecules with tunable magnetic properties for solid state spintronics

Normal & reversed spin mobility in a diradical by electron-vibration coupling

π−conjugated radicals have great promise for use in organic spintronics, however, the mechanisms of spin relaxation and mobility related to radical structural flexibility remain unexplored. Here, we describe a dumbbell shape azobenzene diradical and correlate its solid-state flexibility with spin relaxation and mobility. We employ a combination of X-ray diffraction and Raman spectroscopy to determine the molecular changes with temperature. Heating leads to: i) a modulation of the spin distribution; and ii) a “normal” quinoidal → aromatic transformation at low temperatures driven by the intramolecular rotational vibrations of the azobenzene core and a “reversed” aromatic → quinoidal change at high temperatures activated by an azobenzene bicycle pedal motion amplified by anisotropic intermolecular interactions. Thermal excitation of these vibrational states modulates the diradical electronic and spin structures featuring vibronic coupling mechanisms that might be relevant for future design of high spin organic molecules with tunable magnetic properties for solid state spintronics.The authors acknowledge financial support from the National Natural Science Foundation of China (61805034) and the Scientific Research Foundation of UESTC for Young Teachers (Y03019023601008007). We thank MINECO/FEDER of the Spanish Government (PGC2018-098533-B-I00), Junta de Andalucía (UMA18FEDERJA057) and Research Central Services (SCAI) of the University of Málaga. F.N. and Y.D. gratefully acknowledge the financial support from the University of Bologna (RFO) and computational resources from CINECA through an ISCRA (Italian Super Computing Resource Allocation) C project. Y.D. acknowledges MIUR for her Ph.D. fellowship

The Mechanics of the Bicycle Pedal Photoisomerization in Crystalline <em>cis,cis-</em>1,4-Diphenyl-1,3-butadiene

Direct irradiation of crystalline cis,cis-1,4-diphenyl-1,3-butadiene (cc-DPB) forms trans,trans-1,4-diphenyl-1,3,-butadiene via a concerted two-bond isomerization called the bicycle pedal (BP) mechanism. However, little is known about photoisomerization pathways in the solid state and there has been much debate surrounding the interpretation of volume-conserving isomerization mechanisms. The bicycle pedal photoisomerization is investigated using the quantum mechanics/molecular mechanics complete active space self-consistent field/Amber force-field method. Important details about how the steric environment influences isomerization mechanisms are revealed including how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. Specifically, in the bicycle pedal, the phenyl rings of cc-DPB are locked in place and the intermolecular packing allows a passageway for rotation of the central diene in a volume-conserving manner. In contrast, the bicycle pedal rotation in the gas phase is not a stable pathway, so single-bond rotation mechanisms become operative instead. Furthermore, the crystal BP mechanism is an activated process that occurs completely on the excited state; the photoproduct can decay to the ground state through radiative and non-radiative pathways. The present models, however, do not capture the quantitative activation barriers, and more work is needed to better model reactions in crystals. Last, the reaction barriers of the different crystalline conformations within the unit cell of cc-DPB are compared to investigate the possibility for conformation-dependent isomerization. Although some difference in reaction barriers is observed, the difference is most likely not responsible for the experimentally observed periods of fast and slow conversion.8897-890

Microgravity: A Teacher's Guide With Activities in Science, Mathematics, and Technology

The purpose of this curriculum supplement guide is to define and explain microgravity and show how microgravity can help us learn about the phenomena of our world. The front section of the guide is designed to provide teachers of science, mathematics, and technology at many levels with a foundation in microgravity science and applications. It begins with background information for the teacher on what microgravity is and how it is created. This is followed with information on the domains of microgravity science research; biotechnology, combustion science, fluid physics, fundamental physics, materials science, and microgravity research geared toward exploration. The background section concludes with a history of microgravity research and the expectations microgravity scientists have for research on the International Space Station. Finally, the guide concludes with a suggested reading list, NASA educational resources including electronic resources, and an evaluation questionnaire

Development of Reaction Discovery Tools in Photochemistry and Condensed Phases

Photochemistry obeys different rules than ground-state chemistry and by doing so opens avenues for synthesis and materials properties. However, the different rules of photochemistry make understanding the fine details of photochemical reactions difficult. Computational chemistry can provide the details for understanding photochemical reactions, but the field of computational photochemistry is still new, and many techniques developed for ground-state reactions are not directly applicable to photochemical reactions. As a result, many photochemical mechanisms are not understood, and this hinders the rational design and synthesis of new photochemistry. To address this need, this thesis develops techniques to search for and study photochemical reactions. Chapter 2 and 3 develop methods to calculate photochemical reactions in gas- and condensed-phases via minimum energy reaction paths. First, Chapter 2 develops a method to search the molecular 3N-6 space for photochemical reactions. This space, although vast, is not chaotic and can be efficiently searched using a concept familiar to chemists: breaking and adding bonds and driving angles and torsions. Furthermore, this procedure can be automated to predict new chemistry not previously identified by experiments. Chapter 3 furthers this research by leveraging the concept of molecules to enable the computational study of reactions in large multi-molecular systems like crystals. Specifically, the use of a new coordinate system involving translational and rotational coordinates allows decoupling of the coordinate systems of the individual molecules, which is necessary for the efficient algebra. Importantly, these methods are general, they can be used to study single molecules and crystals, and much in between. These methods are demonstrated on complex chemical problems including the isomerization pathways of ethylene and stilbene (Chapter 2), the photocycloaddition of butadiene (Chapter 2), the rotation of a crystalline gyroscope (Chapter 3), the bicycle pedal rotation of cis,cis-diphenylbutadiene (Chapter 4), and the mechanism of a reversible photoacid (Chapter 5). These problems have value in understanding the processes of vision, optomechanics, and high-energy materials, and through their xx study much needed insight is gained that can be useful for designing new syntheses and materials. Furthermore, the new computational methods open the possibility for many future investigations. The results of Chapter 2 find a novel roaming-atom and hula-twist isomerization pathway and use automated reaction discovery tools to identify a missing butadiene photoproduct and why the [4+2] cycloaddition is forbidden. The results of Chapter 3 and 4 build on Chapter 2 by including the influence of a steric environment. Chapter 3 demonstrates by application to a molecular gyroscope that extreme long-range correlated motion can be captured with GSM, and Chapter 4 details how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. For example, the bicycle pedals rotate through the passageway in the adjacent monomers. However, the models do not capture the quantitative activation barriers and more work is needed. Finally, Chapter 5 provides the ultrafast details of how the photoacid isomerizes and ring-closes with experimental and computational evidence. Unfortunately, quantitative calculation of pKa cannot be provided with the computations employed herein. In summary, this thesis provides an advancement in the knowledge of photochemical mechanisms that can be used for the development of new syntheses and offers new tools with capacity to study complex photochemical problems.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163005/1/craldaz_1.pd

A viscoelastic deadly fluid in carnivorous pitcher plants

Background : The carnivorous plants of the genus Nepenthes, widely distributed in the Asian tropics, rely mostly on nutrients derived from arthropods trapped in their pitcher-shaped leaves and digested by their enzymatic fluid. The genus exhibits a great diversity of prey and pitcher forms and its mechanism of trapping has long intrigued scientists. The slippery inner surfaces of the pitchers, which can be waxy or highly wettable, have so far been considered as the key trapping devices. However, the occurrence of species lacking such epidermal specializations but still effective at trapping insects suggests the possible implication of other mechanisms. Methodology/Principal Findings : Using a combination of insect bioassays, high-speed video and rheological measurements, we show that the digestive fluid of Nepenthes rafflesiana is highly viscoelastic and that this physical property is crucial for the retention of insects in its traps. Trapping efficiency is shown to remain strong even when the fluid is highly diluted by water, as long as the elastic relaxation time of the fluid is higher than the typical time scale of insect movements. Conclusions/Significance : This finding challenges the common classification of Nepenthes pitchers as simple passive traps and is of great adaptive significance for these tropical plants, which are often submitted to high rainfalls and variations in fluid concentration. The viscoelastic trap constitutes a cryptic but potentially widespread adaptation of Nepenthes species and could be a homologous trait shared through common ancestry with the sundew (Drosera) flypaper plants. Such large production of a highly viscoelastic biopolymer fluid in permanent pools is nevertheless unique in the plant kingdom and suggests novel applications for pest control