Communication: Accurate determination of side-chain torsion angle χ1 in proteins: Phenylalanine residues

The following article appeared in Journal of Chemical Physics 134.6 (2011): 061101 and may be found at http://scitation.aip.org/content/aip/journal/jcp/134/6/10.1063/1.3553204Quantitative side-chain torsion angle χ1 determinations of phenylalanine residues in Desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined Karplus equations. Karplus coefficients for nine vicinal coupling related with the torsion angle χ1 were calculated using the B3LYP functional and basis sets of different size. Optimized χ1 angles are in outstanding agreement with those previously reported by employing x ray and NMR measurementsFinancial support from the MICINN of Spain (Project No. CTQ2007-66547 and CTQ2010-19232), the Comunidad de Madrid (Project Nos. S2009/ENE-1743) and AECID (Project No. D/023653/09) is gratefully acknowledged. Computational facilities have been provided by CCC-UA

Engineering the electronic and optical properties of 2D porphyrin paddlewheel metal-organic frameworks

Metal organic frameworks (MOFs) are promising photocatalytic materials due to their high surface area and tuneability of their electronic structure. We discuss here how to engineer the band structures and optical properties of a family of two-dimensional (2D) porphyrin-based MOFs, consisting of M tetrakis(4 carboxyphenyl) porphyrin structures (M TCPP, where M = Zn or Co) and metal (Co, Ni, Cu or Zn) paddlewheel clusters, with the aim of optimising their photocatalytic behaviour in solar fuel synthesis reactions (water splitting and/or CO2 reduction). Based on density functional theory (DFT) and time-dependent DFT simulations with a hybrid functional, we studied three types of composition/structural modifications: a) varying the metal centre at the paddlewheel or at the porphyrin centre to modify the band alignment; b) partially reducing the porphyrin unit to chlorin, which leads to stronger absorption of visible light; and c) substituting the benzene bridging between the porphyrin and paddlewheel, by ethyne or butadiyne bridges, with the aim of modifying the linker to metal charge transfer behaviour. Our work offers new insights on how to improve the photocatalytic behaviour of porphyrin- and paddlewheel-based MOFs

New Insights into the State Trapping of UV-Excited Thymine

Ljiljana Stojanović, Shuming Bai, and Mario Barbatti thank the support of the Aix-Marseille Initiative d’Excellence (A*MIDEX) grant (No. ANR-11-IDEX-0001-02) funded by the French Government “Investissements d’Avenir” program supervised by the Agence Nationale de la Recherche. This work was granted access to the HPC resources of Aix-Marseille Université financed by the project Equip@Meso (ANR-10-EQPX-29-01) also within the “Investissements d’Avenir” program. Artur F. Izmaylov acknowledges funding from a Sloan Research Fellowship and the Natural Sciences and Engineering Research Council of Canada (NSERC) through the Discovery Grants Program

Silicon Radical-Induced CH4 Dissociation for Uniform Graphene Coating on Silica Surface

Due to the manufacturability of highly well-defined structures and wide-range versatility in its microstructure, SiO2 is an attractive template for synthesizing graphene frameworks with the desired pore structure. However, its intrinsic inertness constrains the graphene formation via methane chemical vapor deposition. This work overcomes this challenge by successfully achieving uniform graphene coating on a trimethylsilyl-modified SiO2 (denote TMS-MPS). Remarkably, the onset temperature for graphene growth dropped to 720 °C for the TMS-MPS, as compared to the 885 °C of the pristine SiO2 . This is found to be mainly from the Si radicals formed from the decomposition of the surface TMS groups. Both experimental and computational results suggest a strong catalytic effect of the Si radicals on the CH4 dissociation. The surface engineering of SiO2 templates facilitates the synthesis of high-quality graphene sheets. As a result, the graphene-coated SiO2 composite exhibits a high electrical conductivity of 0.25 S cm-1 . Moreover, the removal of the TMP-MPS template has released a graphene framework that replicates the parental TMS-MPS template on both micro- and nano- scales. This study provides tremendous insights into graphene growth chemistries as well as establishes a promising methodology for synthesizing graphene-based materials with pre-designed microstructures and porosity

Steady and Time-Resolved Photoelectron Spectra Based on Nuclear Ensembles

Semiclassical methods to simulate both steady and time-resolved photoelectron spectra are presented. These approaches provide spectra with absolute band shapes and vibrational broadening beyond the Condon approximation, using an ensemble of nuclear configurations built either via distribution samplings or nonadiabatic dynamics simulations. Two models to account for the electron kinetic energy modulation due to vibrational overlaps between initial and final states are discussed. As illustrative examples, the steady photoelectron spectra of imidazole and adenine and the time- and kinetic-energy-resolved photoelectron spectrum of imidazole were simulated within the frame of time-dependent density functional theory. While for steady spectra only electrons ejected with maximum allowed kinetic energy need to be considered, it is shown that to properly describe time-resolved spectra, electrons ejected with low kinetic energies must be considered in the simulations as well. The results also show that simulations based either on full computation of photoelectron cross section or on simple Dyson orbital norms provide results of similar quality

Endoplasmic reticulum targeting fluorescent probes to image mobile Zn2+

Zn2+ plays an important role in the normal function of the endoplasmic reticulum (ER) and its deficiency can cause ER stress, which is related to a wide range of diseases. In order to provide tools to better understand the role of mobile Zn2+ in ER processes, the first custom designed ER-localised fluorescent Zn2+ probes have been developed through the introduction of a cyclohexyl sulfonylurea as an ER-targeting unit with different Zn2+ receptors. Experiments in vitro and in cellulo show that both probes have a good fluorescence switch on response to Zn2+, high selectivity over other cations, low toxicity, ER-specific targeting ability and are efficacious imaging agents for mobile Zn2+ in four different cell lines. Probe 9 has been used to detect mobile Zn2+ changes under ER stress induced by both tunicamycin or thapsigargin, which indicates that the new probes should allow a better understanding of the mechanisms cells use to respond to dysfunction of zinc homeostasis in the ER and its role in the initiation and progression of diseases to be developed

Electronic excitations in molecular solids:bridging theory and experiment

As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments

Photochemical Fingerprinting Is a Sensitive Probe for the Detection of Synthetic Cannabinoid Receptor Agonists; Toward Robust Point-of-Care Detection

With synthetic cannabinoid receptor agonist (SCRA) use still prevalent across Europe and structurally advanced generations emerging, it is imperative that drug detection methods advance in parallel. SCRAs are a chemically diverse and evolving group, which makes rapid detection challenging. We have previously shown that fluorescence spectral fingerprinting (FSF) has the potential to provide rapid assessment of SCRA presence directly from street material with minimal processing and in saliva. Enhancing the sensitivity and discriminatory ability of this approach has high potential to accelerate the delivery of a point-of-care technology that can be used confidently by a range of stakeholders, from medical to prison staff. We demonstrate that a range of structurally distinct SCRAs are photochemically active and give rise to distinct FSFs after irradiation. To explore this in detail, we have synthesized a model series of compounds which mimic specific structural features of AM-694. Our data show that FSFs are sensitive to chemically conservative changes, with evidence that this relates to shifts in the electronic structure and cross-conjugation. Crucially, we find that the photochemical degradation rate is sensitive to individual structures and gives rise to a specific major product, the mechanism and identification of which we elucidate through density-functional theory (DFT) and time-dependent DFT. We test the potential of our hybrid "photochemical fingerprinting"approach to discriminate SCRAs by demonstrating SCRA detection from a simulated smoking apparatus in saliva. Our study shows the potential of tracking photochemical reactivity via FSFs for enhanced discrimination of SCRAs, with successful integration into a portable device.</p

Photochemical fingerprinting is a sensitive probe for the detection of synthetic cannabinoid receptor agonists; towards robust point-of-care detection

With synthetic cannabinoid receptor agonist (SCRA) use still prevalent across Europe and structurally advanced generations emerging, it is imperative that drug detection methods advance in parallel. SCRAs are a chemically diverse and evolving group, which makes rapid detection challenging. We have previously shown that fluorescence spectral fingerprinting (FSF) has the potential to provide rapid assessment of SCRA presence directly from street material with minimal processing and in saliva. Enhancing the sensitivity and discriminatory ability of this approach has high potential to accelerate the delivery of a point-of-care technology that can be used confidently by a range of stakeholders, from medical to prison staff. We demonstrate that a range of structurally distinct SCRAs are photochemically active and give rise to distinct FSFs after irradiation. To explore this in detail, we have synthesized a model series of compounds which mimic specific structural features of AM-694. Our data show that FSFs are sensitive to chemically conservative changes, with evidence that this relates to shifts in the electronic structure and cross-conjugation. Crucially, we find that the photochemical degradation rate is sensitive to individual structures and gives rise to a specific major product, the mechanism and identification of which we elucidate through density-functional theory (DFT) and time-dependent DFT. We test the potential of our hybrid “photochemical fingerprinting” approach to discriminate SCRAs by demonstrating SCRA detection from a simulated smoking apparatus in saliva. Our study shows the potential of tracking photochemical reactivity via FSFs for enhanced discrimination of SCRAs, with successful integration into a portable device

Photochemical fingerprinting Is a sensitive probe for the detection of synthetic cannabinoid receptor agonists; toward robust point-of-care detection

With synthetic cannabinoid receptor agonist (SCRA) use still prevalent across Europe and structurally advanced generations emerging, it is imperative that drug detection methods advance in parallel. SCRAs are a chemically diverse and evolving group, which makes rapid detection challenging. We have previously shown that fluorescence spectral fingerprinting (FSF) has the potential to provide rapid assessment of SCRA presence directly from street material with minimal processing and in saliva. Enhancing the sensitivity and discriminatory ability of this approach has high potential to accelerate the delivery of a point-of-care technology that can be used confidently by a range of stakeholders, from medical to prison staff. We demonstrate that a range of structurally distinct SCRAs are photochemically active and give rise to distinct FSFs after irradiation. To explore this in detail, we have synthesized a model series of compounds which mimic specific structural features of AM-694. Our data show that FSFs are sensitive to chemically conservative changes, with evidence that this relates to shifts in the electronic structure and cross-conjugation. Crucially, we find that the photochemical degradation rate is sensitive to individual structures and gives rise to a specific major product, the mechanism and identification of which we elucidate through density-functional theory (DFT) and time-dependent DFT. We test the potential of our hybrid “photochemical fingerprinting” approach to discriminate SCRAs by demonstrating SCRA detection from a simulated smoking apparatus in saliva. Our study shows the potential of tracking photochemical reactivity via FSFs for enhanced discrimination of SCRAs, with successful integration into a portable device