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proton density

Bardi Benediktsson, Ragnar Bjornsson
Nitrogenase is one of the most fascinating enzymes in nature, being responsible for all biological nitrogen reduction. Despite decades of research, it is among the enzymes in bioinorganic chemistry whose mechanism is the most poorly understood. The MoFe protein of nitrogenase contains an iron-molybdenum-sulfur cluster, FeMoco, where N2 reduction takes place. The resting state of FeMoco has been characterized by crystallography, multiple spectroscopic techniques, and theory (broken-symmetry density functional theory), and all heavy atoms are now characterized...
October 20, 2017: Inorganic Chemistry
Carlos Gueto-Tettay, Luis Pelaez-Bedoya, Juan Carlos Drosos-Ramirez
BACE1 is an aspartyl protease with a very relevant role in medicinal chemistry related to Alzheimer Disease since it has demonstrated to be a promising therapeutic target for inhibition and possible control for the progress of the peptide accumulation characteristic of this pathology. The enzymatic activity of this protein is given by the aspartic dyad, Asp93 and Asp289, which can adopt several protonation states depending on the chemical nature of its inhibitors, this is, monoprotonated, diprotonated and di-deprotonated states...
October 20, 2017: Journal of Biomolecular Structure & Dynamics
Matti Hellström, Jörg Behler
Density functional theory (DFT) is routinely used to calculate the adsorption energies of molecules on solid surfaces, which can be employed to derive surface phase diagrams. Such calculations become computationally expensive if the number of substrate atoms is large, which happens whenever the adsorbate coverage is small. Here, we propose an efficient method for calculating surface phase diagrams for redox-active adsorbates on semiconductors, that we apply to the important example of proton (H(+)) and hydride (H(-)) adsorbates on a ZnO surface...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
S N Chen, M Vranic, T Gangolf, E Boella, P Antici, M Bailly-Grandvaux, P Loiseau, H Pépin, G Revet, J J Santos, A M Schroer, Mikhail Starodubtsev, O Willi, L O Silva, E d'Humières, J Fuchs
We have investigated proton acceleration in the forward direction from a near-critical density hydrogen gas jet target irradiated by a high intensity (10(18) W/cm(2)), short-pulse (5 ps) laser with wavelength of 1.054 μm. We observed the signature of the Collisionless Shock Acceleration mechanism, namely quasi-monoenergetic proton beams with small divergence in addition to the more commonly observed electron-sheath driven proton acceleration. The proton energies we obtained were modest (~MeV), but prospects for improvement are offered through further tailoring the gas jet density profile...
October 18, 2017: Scientific Reports
K Yagi, H Yamamoto, R Uemura, Y Matsuda, K Okuyama, T Ishimoto, T Nakano, M Hayashi
The progress of caries has conventionally been evaluated by checking changes in mineral density using transverse microradiography (TMR). Recent advances have seen development of a new measurement system, using in-air micro proton induced X-ray/gamma-ray emission (PIXE/PIGE). PIXE/PIGE enables analysis of distributions and concentrations of multiple mineral elements in a carious lesion. The aim of this study was to evaluate the effectiveness of PIXE/PIGE for investigating the development of root caries. In summary, we successfully established a multi-elemental sequential measuring method using in-air micro-PIXE/PIGE to identify the dynamic distributions and concentrations of Ca and F in human root dentin...
October 18, 2017: Scientific Reports
Belén Hernández, Fernando Pflüger, Manuel Dauchez, Mahmoud Ghomi
Water interaction with peptide chains is one of the key structure stabilizing factors in an aqueous environment. Because of its strong polar character, water can bind to both anionic and cationic sites via electrostatic interactions. It can also act as a hydrogen-bond donor or acceptor according to its interactions with different polar groups in the backbone and side chains of peptides and proteins. Based on density functional theory calculations, the present report aims at illustrating the most energetically favorable interaction sites of aromatic side chains of phenylalanine, tyrosine, tryptophan, and histidine (neutral and protonated species) with surrounding water molecules...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
Carles Acosta-Silva, Joan Bertran, Vicenç Branchadell, Antoni Oliva
A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a non-bridged oxygen atom of the phosphate has been explored using the MO6-2X density functional method and the solvent continuum model (SMD). This reaction is the initial step of the RNA hydrolysis. We have used different solvents characterized by their dielectric constant and, for each of them, we have studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points...
October 17, 2017: Journal of Physical Chemistry. A
Haiyang Zhang, Yang Jiang, Hai Yan, Ziheng Cui, Chunhua Yin
Experimental observations for ionic hydration free energies are highly debated mainly due to the ambiguous absolute hydration free energy of proton, 〖∆G〗_hyd^* (H^+). Hydration free energies (HFEs) of the 112 singly-charged ions in the Minnesota solvation database were predicted by six methods with explicit and implicit solvent models, namely, Thermodynamic Integration (TI), Energy Representation module (ERmod), Three-Dimensional Reference Interaction Site Model (3D-RISM), and continuum Solvation Models based on the quantum mechanical charge Density (SMD) and on the Poisson-Boltzmann (PB) and Generalized Born (GB) theories...
October 17, 2017: Journal of Chemical Information and Modeling
S Chaiwongwattana, Đ Škalamera, N Došlić, C Bohne, N Basarić
Photophysical properties and excited state intramolecular proton transfer (ESIPT) reactivity for anthrol carbaldehydes 1-5 have been investigated computationally and experimentally by steady-state and time-resolved fluorescence and laser flash photolysis (LFP). 1,2-Disubstituted anthrol carbaldehydes 1 and 2 are not ESIPT reactive, contrary to naphthol analogues. The main deactivation channels from S1 for 1 and 2 are fluorescence (ΦF = 0.1-0.2) and intersystem crossing (ISC) to almost isoenergetic T2 states...
October 17, 2017: Physical Chemistry Chemical Physics: PCCP
V Conte, A Selva, P Colautti, G Hilgers, H Rabus, A Bantsar, M Pietrzak, S Pszona
The biological action of ionizing charged particles is initiated at the DNA level, and the effectiveness with which the initial physical effect changes into measurable biological damage is likely ruled by the stochastics of ionizations produced by the incident ions in subcellular nanometric volumes. Based on this hypothesis, experimental nanodosimetry aims at establishing a new concept of radiation quality that builds on measurable characteristics of the particle track structure at the nanometer scale. Three different nanodosimetric detection systems have been developed to date that allow measurements of the number of ionizations produced by the passage of a primary particle in a nanometer-size gas volume (in unit density scale)...
September 23, 2017: Radiation Protection Dosimetry
Martin Setvin, Xiao Shi, Jan Hulva, Thomas Simschitz, Gareth S Parkinson, Michael Schmid, Cristiana Di Valentin, Annabella Selloni, Ulrike Diebold
The photoactivity of methanol adsorbed on the anatase TiO2 (101) surface was studied by a combination of scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), X-ray photoemission spectroscopy (XPS), and density functional theory (DFT) calculations. Isolated methanol molecules adsorbed at the anatase (101) surface show a negligible photoactivity. Two ways of methanol activation were found. First, methoxy groups formed by reaction of methanol with coadsorbed O2 molecules or terminal OH groups are photoactive, and they turn into formaldehyde upon UV illumination...
October 6, 2017: ACS Catalysis
Moritz Kronlage, Véronique Schwehr, Daniel Schwarz, Tim Godel, Sabine Heiland, Martin Bendszus, Philipp Bäumer
PURPOSE: To establish normal values and to identify demographic determinants of quantitative biomarkers in magnetic resonance neurography (MRN). METHODS: In this study 60 healthy individuals (5 men and 5 women of every decade between 20 and 80 years) were examined according to a standardized MRN protocol at 3 T, including multiecho T2 relaxometry. Nerve cross-sectional area (CSA), transverse relaxation time (T2), and proton spin density (PSD) were assessed for the sciatic, tibial, median, ulnar, and radial nerves...
October 13, 2017: Clinical Neuroradiology
Mario E Flores, Toshimichi Shibue, Natsuhiko Sugimura, Hiroyuki Nishide, Ignacio Moreno-Villoslada
Upon titration of n-hexanol / cyclohexane mixtures of different molar compositions with water, water / n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in 1D 1H-NMR spectra, diffusion coefficients calculated by diffusion ordered NM R spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5 - 15 molecules of n-hexanol / cluster in the absence of water were observed in the whole range of n-hexanol / cyclohexane molar fractions studied...
October 13, 2017: Journal of Physical Chemistry. B
Michael S Middleton, Mark L Van Natta, Elhamy R Heba, Adina Alazraki, Andrew T Trout, Prakash Masand, Elizabeth M Brunt, David E Kleiner, Edward Doo, James Tonascia, Joel E Lavine, Wei Shen, Gavin Hamilton, Jeffrey B Schwimmer, Claude B Sirlin
We assessed the performance of magnetic resonance imaging (MRI) proton density fat fraction (PDFF) in children to stratify hepatic steatosis grade before and after treatment in the Cysteamine Bitartrate Delayed-Release for the Treatment of Nonalcoholic Fatty Liver Disease in Children (CyNCh) trial, using centrally-scored histology as reference. Participants had multi-echo 1.5T or 3T MRI on scanners from three manufacturers. Of 169 enrolled children, 110 (65%) and 83 (49%) had MRI and liver biopsy at baseline and at end-of-treatment (EOT; 52-weeks), respectively...
October 13, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Qian Wang, Hong Yan Zhao, Po-Kam Lo, William W Y Lam, Kai-Chung Lau, Tai-Chu Lau
We have previously reported that the oxidation of SO3(2-) to SO4(2-) by a trans-dioxoruthenium(VI) complex, [Ru(VI)(TMC)(O)2)](2+) (Ru(VI); TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazcyclotetradecane) in aqueous solutions occurs via an O-atom transfer mechanism. In this work, we have reinvestigated the effects of the pH on the oxidation of S(IV) by Ru(VI) in more detail in order to obtain kinetic data for the HSO3(-) pathway. The HSO3(-) pathway exhibits a deuterium isotope effect of 17.4, which indicates that O-H bond breaking occurs in the rate-limiting step...
October 13, 2017: Inorganic Chemistry
Kesong Tian, Ruifei Li, Haiyan Wang, Yan Chen, Wanchun Guo, Yaqi Wang, Zhaopeng Xu
Functional polymer-grafting silica nanoparticles hold great promise in diverse applications such as molecule recognition, drug delivery, and heterogeneous catalysis due to high density and uniform distribution of functional groups and their tunable spatial distance. However, conventional grafting methods from monomers mainly consist of one or more extra surface modification steps and a subsequent surface polymerization step. A monomer protonation-dependent surface polymerization strategy is proposed to achieve one-step uniform surface grafting of cross-linked poly(4-vinylpyridine) (P4VP) onto core-shell Fe3 O4 @SiO2 nanostructures...
October 13, 2017: Macromolecular Rapid Communications
Johann M E Jende, Gesa H Hauck, Ricarda Diem, Markus Weiler, Sabine Heiland, Brigitte Wildemann, Mirjam Korporal-Kuhnke, Wolfgang Wick, John M Hayes, Johannes Pfaff, Mirko Pham, Martin Bendszus, Jennifer Kollmer
OBJECTIVE: To detect and quantify peripheral nerve lesions in multiple sclerosis (MS) by magnetic resonance neurography (MRN). METHODS: 36 patients diagnosed with MS based on the 2010 McDonald criteria (34 with the relapsing-remitting form, 2 with clinically isolated syndrome) with and without disease modifying treatment were compared to 35 healthy age/sex-matched volunteers. All patients underwent detailed neurological and electrophysiological examinations. 3T MRN with large anatomical coverage of both legs and the lumbosacral plexus was performed by using 2D fat-saturated, T2-weighted and dual echo turbo-spin-echo sequences as well as a 3D T2-weighted, fat-saturated SPACE sequence...
October 10, 2017: Annals of Neurology
Bo-Kyeong Kang, Mimi Kim, Soon-Young Song, Dae Won Jun, Kiseok Jang
OBJECTIVE: To assess the feasibility of proton density fat fraction (PDFF) magnetic resonance imaging (MRI) for estimating hepatic fat fraction with magnetic resonance spectroscopy (MRS) and histology as references and to investigate intrahepatic fat distribution and variability. METHODS: Between November 2014 and September 2015, 85 adults (48 men, 47 women) who underwent MRI-PDFF (n=139), MRS-PDFF (n=49) and liver biopsy (n=29) were enrolled in this study. Data were compared using linear regression...
October 12, 2017: British Journal of Radiology
Felix Brockherde, Leslie Vogt, Li Li, Mark E Tuckerman, Kieron Burke, Klaus-Robert Müller
Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative...
October 11, 2017: Nature Communications
Rebecca J Abergel, Wibe A de Jong, Gauthier J-P Deblonde, Phuong D Dau, Ilya Captain, Teresa M Eaton, Jiwen Jian, Michael J van Stipdonk, Jonathan Martens, Giel Berden, Jos Oomens, John K Gibson
Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U(6+) chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidenced by CID, using deuterium and (18)O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy...
October 11, 2017: Inorganic Chemistry
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