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https://www.readbyqxmd.com/read/28719733/characterizing-a-mouse-model-for-evaluation-of-countermeasures-against-hydrogen-sulfide-induced-neurotoxicity-and-neurological-sequelae
#1
Poojya Anantharam, Elizabeth M Whitley, Belinda Mahama, Dong-Suk Kim, Paula M Imerman, Dahai Shao, Monica R Langley, Arthi Kanthasamy, Wilson K Rumbeiha
Hydrogen sulfide (H2 S) is a highly neurotoxic gas. It is the second most common cause of gas-induced deaths. Beyond mortality, surviving victims of acute exposure may suffer long-term neurological sequelae. There is a need to develop countermeasures against H2 S poisoning. However, no translational animal model of H2 S-induced neurological sequelae exists. Here, we describe a novel mouse model of H2 S-induced neurotoxicity for translational research. In paradigm I, C57/BL6 mice were exposed to 765 ppm H2 S for 40 min on day 1, followed by 15-min daily exposures for periods ranging from 1 to 6 days...
July 18, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28719672/the-effects-of-ice-on-methane-hydrate-nucleation-a-microcanonical-molecular-dynamics-study
#2
Zhengcai Zhang, Guang-Jun Guo
Although ice powders are widely used in gas hydrate formation experiments, the effects of ice on hydrate nucleation and what happens in the quasi-liquid layer of ice are still not well understood. Here, we used high-precision constant energy molecular dynamics simulations to study methane hydrate nucleation from vapor-liquid mixtures exposed to the basal, prismatic, and secondary prismatic planes of hexagonal ice (ice Ih). Although no significant difference is observed in hydrate nucleation processes for these different crystal planes, it is found, more interestingly, that methane hydrate can nucleate either on the ice surface heterogeneously or in the bulk solution phase homogeneously...
July 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28719208/quantification-of-hydrogen-bond-strength-based-on-interaction-coordinates-a-new-approach
#3
Sarvesh Kumar Kumar Pandey, Dhivya Manogaran, Sadasivam Manogaran, Henry F Schaefer
A new approach to quantify hydrogen bond strengths based on interaction coordinates (HBSBIC) is proposed and is very promising. In this research, it is assumed that the projected force field of the fictitious three atoms fragment (DHA) where D is the proton donor and A is the proton acceptor from the full molecular force field of the H-bonded complex characterizes the hydrogen bond. The "interaction coordinate (IC)" derived from the internal compliance matrix elements of this three atoms fragment measures how the DH covalent bond (its electron density) responds to constrained optimization when the HA hydrogen bond is stretched by a known amount (its electron density is perturbed by a specified amount)...
July 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28719207/elevation-of-the-energy-threshold-for-isomerization-of-5-hydroxyindole-tert-butyl-alcohol-1-cluster-cations
#4
Takamasa Ikeda, Kenji Sakota, Hiroshi Sekiya
Isomerization between two hydrogen-bonded (H-bonded) isomers of 5-hydroxyindole-(tert-butyl alcohol)1 cluster cations ([5HI-(t-BuOH)1](+)) was investigated in the gas phase. In the S0 state, jet-cooled 5HI-(t-BuOH)1 has two structural isomers, 5HI(OH)-(t-BuOH)1 and 5HI(NH)-(t-BuOH)1, in which the t-BuOH molecule is bound to the OH or the NH group of 5HI. The IR photodissociation spectrum of [5HI-(t-BuOH)1](+) generated by two-color resonant two-photon ionization (2C-R2PI) via the S1-S0 origin of 5HI(NH)-(t-BuOH)1 provided evidence of both [5HI(OH)-(t-BuOH)1](+) and [5HI(NH)-(t-BuOH)1](+) coexisting in the D0 state, indicating that [5HI(NH)-(t-BuOH)1](+) isomerizes to [5HI(OH)-(t-BuOH)1](+) after 2C-R2PI of 5HI(NH)-(t-BuOH)1...
July 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28719205/theoretical-investigations-on-the-mechanism-and-kinetics-of-oh-radical-initiated-reactions-of-monochloroacetic-acid
#5
Ravichandran Bhuvaneswari, Lakshmanan Sandhiya, Kittusamy Senthilkumar
The oxidation mechanism of monochloroacetic acid (CH2ClCOOH) by OH radical has been systematically investigated employing quantum mechanical methods coupled with kinetic calculation using canonical variational transition state theory. Three distinct transition states were identified for the titled reaction, two corresponding to the hydrogen atom abstraction and one corresponding to the chlorine atom abstraction. The rate constant of the titled reactions are computed over the temperature range of 278-350 K and the branching ratios calculated for the hydrogen atom abstraction from -C(O)OH site and -CH2Cl site is 25% and 75%, respectively at 298K...
July 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28719194/molecular-modeling-of-the-major-dna-adduct-formed-from-the-food-mutagen-ochratoxin-a-in-nari-2-base-deletion-duplexes-impact-of-sequence-context-and-adduct-ionization-on-conformational-preference-and-mutagenicity
#6
Preetleen Kathuria, Purshotam Sharma, Richard A Manderville, Stacey D Wetmore
Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C(8)-dG aromatic amine adducts to analyze the conformational features of post-replication 2-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C(8) position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens...
July 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28719182/atomic-white-out-enabling-atomic-circuitry-through-mechanically-induced-bonding-of-single-hydrogen-atoms-to-a-silicon-surface
#7
Taleana Rochelle Huff, Hatem Labidi, Mohammad Rashidi, Mohammad Koleini, Roshan Achal, Mark Henry Salomons, Robert A Wolkow
We report the mechanically induced formation of a silicon-hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a non-contact atomic force microscope (NC-AFM), a single hydrogen atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen passivated surface and can be transferred to the tip apex as evidenced from a unique signature in frequency shift curves. In the absence of tunnel electrons and electric field in the scanning probe microscope junction at 0 V, the hydrogen atom at the tip apex is brought very close to a silicon dangling bond, inducing the mechanical formation of a silicon-hydrogen covalent bond and the passivation of the dangling bond...
July 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28718966/dft-studies-on-the-mechanism-of-ag2-co3-catalyzed-hydroazidation-of-unactivated-terminal-alkynes-with-tms-n3-an-insight-into-the-silver-i-activation-mode
#8
Haiyan Yuan, Pin Xiao, Yiying Zheng, Jingping Zhang
Silver-mediated hydroazidation of unactivated alkynes has been developed as a new method for the synthesis of vinyl azides. Density functional theory calculations toward this reaction reveal that terminal alkynes with TMS-N3 participated hydroazidation proceed through HN3 formation, deprotonation and silver acetylides formation, nucleophilic addition, and protonation of terminal carbon by AgHCO3 . It is also found that water molecules and activation modes of Ag (I) have a significant influence on the title reaction mechanism...
July 18, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28718923/using-homology-modeling-to-interrogate-binding-affinity-in-neutralization-of-ricin-toxin-by-a-family-of-single-domain-antibodies
#9
Andrea Bazzoli, David J Vance, Michael J Rudolph, Yinghui Rong, Siva Krishna Angalakurthi, Ronald T Toth, C Russell Middaugh, David B Volkin, David D Weis, John Karanicolas, Nicholas J Mantis
In this report we investigated, within a group of closely related single domain camelid antibodies (VH Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like VH Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer...
July 18, 2017: Proteins
https://www.readbyqxmd.com/read/28718673/ameliorative-effect-of-gallic-acid-in-doxorubicin-induced-hepatotoxicity-in-wistar-rats-through-antioxidant-defense-system
#10
Temidayo Olutayo Omobowale, Ademola Adetokunbo Oyagbemi, Uchechukwu Enwiwe Ajufo, Olumuyima Abiola Adejumobi, Olufunke Eunice Ola-Davies, Adeolu Alex Adedapo, Momoh Audu Yakubu
Hepatotoxicity has been found to be one of the main side effects associated with doxorubicin (Dox) administration in cancer therapy. The aim of the present study was to examine the ameliorative effect of gallic acid (GA) in Dox-induced hepatotoxicity. Sixty male Wistar rats of 10 rats per group were used in this study and were randomly divided into 6 experimental groups (A-F). Rats in Group A served as the control group and received distilled water orally for 7 days; Group B was given Dox at 15 mg/kg body weight intraperitoneally (IP) on Day 8...
July 18, 2017: Journal of Dietary Supplements
https://www.readbyqxmd.com/read/28718645/fourfold-interpenetrated-mof-ni-pybz-2-as-coating-material-in-gas-chromatographic-capillary-column-for-separation
#11
Yan Zhang, Li Wang, Ru-Xin Yao, Xian-Ming Zhang
A fourfold interpenetrated diamond-like topological metal-organic framework (MOF), Ni(pybz)2 [pybz = 4-(4-pyridyl)benzoate] was successfully synthesized and fully characterized. This MOF can serve as coating material in gas chromatographic capillary column for the separation of some low boiling point essential oils. The prepared columns have good recognition ability and excellent selectivity toward a series of organic compounds, including alcohols, aldehydes, ketones, carboxylic acid, ethers, ester, and amines...
July 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28718640/smi2-h2o-n-reductions-of-electron-rich-enamines-by-concerted-proton-coupled-electron-transfer
#12
Scott S Kolmar, James M Mayer
Samarium diiodide in the presence of water and THF (SmI2(H2O)n) has in recent years become a versatile and useful reagent, mainly for reducing carbonyl-type substrates. This work reports the reduction of several enamines by SmI2(H2O)n. Mechanistic experiments implicate a concerted proton-coupled electron transfer (PCET) pathway, based on various evidence against initial outer-sphere electron transfer, proton transfer or substrate coordination. A thermochemical analysis indicates that the C-H bond formed in the rate determining step has a bond dissociation free energy (BDFE) of ~32 kcal mol-1...
July 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28718617/initial-reduction-of-co2-on-pd-ru-and-cu-doped-ceo2-111-surfaces-effects-of-surface-modification-on-catalytic-activity-and-selectivity
#13
Chen Guo, Shuxian Wei, Sainan Zhou, Tian Zhang, Zhaojie Wang, Siu Pang Ng, Xiaoqing Lu, Chi-Man Lawrence Wu, Wenyue Guo
Surface modification by metal doping is an effective treatment technique for improving surface properties for CO2 reduction. Herein, the effects of doped Pd, Ru, and Cu on the adsorption, activation, and reduction selectivity of CO2 on CeO2(111) were investigated by periodic density functional theory. The doped metals distorted the configuration of a perfect CeO2(111) by weakening the adjacent Ce-O bond strength, and Pd doping was beneficial for generating a highly active O vacancy. The analyses of adsorption energy, charge density difference, and density of states confirmed that the doped metals were conducive for enhancing CO2 adsorption, especially for Cu/CeO2(111)...
July 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28718467/how-to-make-an-efficient-and-robust-molecular-catalyst-for-water-oxidation
#14
Pablo Garrido-Barros, Carolina Gimbert-Suriñach, Roc Matheu, Xavier Sala, Antoni Llobet
Energy has been a central subject for human development from Homo erectus to date. The massive use of fossil fuels during the last 50 years has generated a large CO2 concentration in the atmosphere that has led to the so-called global warming. It is very urgent to come up with C-neutral energy schemes to be able to preserve Planet Earth for future generations to come and still preserve our modern societies' life style. One of the potential solutions is water splitting with sunlight (hν-WS) that is also associated with "artificial photosynthesis", since its working mode consists of light capture followed by water oxidation and proton reduction processes...
July 18, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28718462/-preventive-dentistry-7-getting-rid-of-halitosis
#15
T M H de Jong, M L Laine
Halitosis or bad breath is a problem that affects many people and its source is generally found in the oral cavity (intra-oral halitosis). Bacteria in the oral cavity produce volatile sulphur compounds such as hydrogen sulphide and methyl mercaptan that not only emit an unpleasant odour, but may also have toxic effects on the periodontal tissues. Good oral hygiene, a healthy periodontium and healthy teeth are the basis for the prevention of intra-oral halitosis and dentists and dental hygienists therefore play an essential role in its prevention...
July 2017: Nederlands Tijdschrift Voor Tandheelkunde
https://www.readbyqxmd.com/read/28718450/dynamics-and-energetics-of-the-mammalian-phosphatidylinositol-transfer-protein-phospholipid-exchange-cycle
#16
Aby Grabon, Adam Orlowski, Ashutosh Tripathi, Joni Vuorio, Matti Javanainen, Tomasz Róg, Max Lönnfors, Mark I McDermott, Garland Siebert, Pentti Somerharju, Ilpo Vattulainen, Vytas A Bankaitis
Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. Yet, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics (MD) simulations of the mammalian StART-like PtdIns/ phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the MD simulations...
July 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28718449/the-dual-function-chaperone-hych-improves-assembly-of-the-formate-hydrogenlyase-complex
#17
Ute Lindenstrauß, Philipp Skorupa, Jennifer S McDowall, Frank Sargent, Constanze Pinske
The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membrane-bound formate hydrogenlyase (FHL) complex is the primary hydrogen-producing enzyme in Escherichia coli and is composed of seven subunits mostly encoded within the hycA-I operon for [NiFe]-hydrogenase-3 (Hyd-3). The HycH protein is predicted to have an accessory function and is not part of the final structural FHL complex. In this work, a mutant strain devoid of HycH was characterized and found to have significantly reduced FHL activity due to instability of the electron transfer subunits...
July 17, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28717993/probing-the-binding-affinities-of-imipenem-and-ertapenem-for-outer-membrane-carboxylate-channel-d1-occd1-from-p-aeruginosa-simulation-studies
#18
Kamolrat Somboon, Jitti Niramitranon, Prapasiri Pongprayoon
Pseudomonas aeruginosa is an important nosocomial human pathogen. The major difficulty in the fight against this pathogen is the relative impermeability of its outer membrane (OM). Only specific substrates can penetrate through the OM of P. aeruginosa via substrate-specific porins, so this has become one of the most problematic drug-resistant pathogens. Carbapenems are the most effective drugs for treating P. aeruginosa infections. One such carbapenem that is applied in cases of P. aeruginosa infection is imipenem (IMI), which uses outer membrane carboxylate channel D1 (OccD1) as a point of entry into the pathogen...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28717992/melting-of-polymeric-dna-double-helix-at-elevated-temperature-a-molecular-dynamics-approach
#19
Sangeeta Kundu, Sanchita Mukherjee, Dhananjay Bhattacharyya
Genomic DNA of higher organisms exists as extremely long polymers, while in bacteria and other lower organisms it is circular with no terminal base pairs. Temperature-induced melting of the DNA double helix by localized strand separation has been unattainable by molecular dynamic simulations due to more rapid fraying of the terminal base pairs in oligomeric DNA. However, local-sequence-dependent unfolding of the DNA double helix is extremely important for understanding various biochemical phenomena, and can be addressed by simulating a model polymeric DNA duplex...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28717802/a-computational-study-on-the-mechanism-of-ynamide-mediated-amide-bond-formation-from-carboxylic-acids-and-amines
#20
Song-Lin Zhang, Hai-Xing Wan, Zhu-Qin Deng
This paper reports a computational study elucidating the reaction mechanism for ynamide-mediated amide bond formation from carboxylic acids and amines. The mechanisms have been studied in detail for ynamide hydrocarboxylation and the subsequent aminolysis of the resulting adduct by an amine. Ynamide hydrocarboxylation is kinetically favorable and thermodynamically irreversible, resulting in the formation of a key low-lying intermediate CP1 featuring geminal vinylic acyloxy and sulfonamide groups. The aminolysis of CP1 by the amine is proposed to be catalyzed by the carboxylic acid itself that imparts favourable bifunctional effects...
July 18, 2017: Organic & Biomolecular Chemistry
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