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Brenton Jennewine, Jonathan Fox, Anand Ramamurthi
: Abdominal Aortic Aneurysms (AAA) involve slow dilation and weakening of the aortic wall due to breakdown of structural matrix components, such as elastic fibers by chronically overexpressed matrix metalloproteinases (MMPs), primarily, MMPs-2 and -9. Auto-regenerative repair of disrupted elastic fibers by smooth muscle cells (SMCs) at the AAA site is intrinsically poor and together with chronic proteolysis prevents restoration of elastin homeostasis, necessary to enable AAA growth arrest or regression to a healthy state...
January 10, 2017: Acta Biomaterialia
Jing Huang, Ye Mei, Gerhard Koenig, Andrew C Simmonett, Frank C Pickard, Qin Wu, Lee-Ping Wang, Alexander D MacKerell, Bernard R Brooks, Yihan Shao
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges)...
January 12, 2017: Journal of Chemical Theory and Computation
Suzana Mustafa, Norul Badriah Hassan, Soo Choon Tan, Ahmad Kashfi Ab Rahman, Lee Lee Low, Wan Nazirah Wan Yusuf
BACKGROUND/AIM: Nevirapine is a reverse-transcriptase inhibitor widely used in combination therapy to treat HIV infection. Nevirapine is extensively metabolized in the liver and CYP2B6 is mainly responsible for oxidation of 3-hydroxynevirapine (3-OH NVP). This study aims to explore CYP2B6 activity by measuring 2-hydroxynevirapine (2-OH NVP) and 3-OH NVP in plasma and to identify factors associated with nevirapine pharmacokinetic parameters. MATERIALS AND METHODS: A total of 112 patients were recruited and treated with nevirapine-based antiretroviral therapy...
December 20, 2016: Turkish Journal of Medical Sciences
Oliver Hunold, Philipp Keuter, Pascal Bliem, Denis Music, Friederike Wittmers, Anna L Ravensburg, Daniel Primetzhofer, Jochen M Schneider
We have systematically studied the effect of transition metal valence electron concentration (VEC) of amorphous T 0.75Y0.75B14 (a-T 0.75Y0.75B14, T  =  Sc, Ti, V, Y, Zr, Nb) on the elastic properties, bonding, density and electronic structure using ab initio molecular dynamics. As the transition metal VEC is increased in both periods, the bulk modulus increases linearly with molar- and mass density. This trend can be understood by a concomitant decrease in cohesive energy. T'  =  Ti and Zr were selected to validate the predicted data experimentally...
January 12, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
N Tatemizo, S Imada, Y Miura, H Yamane, K Tanaka
The valence band (VB) structures of wurtzite AlCrN (Cr concentration: 0-17.1%), which show optical absorption in the ultraviolet-visible-infrared light region, were investigated via photoelectron yield spectroscopy (PYS), x-ray/ultraviolet photoelectron spectroscopy (XPS/UPS), and ab initio density of states (DOS) calculations. An obvious photoelectron emission threshold was observed ~5.3 eV from the vacuum level for AlCrN, whereas no emission was observed for AlN in the PYS spectra. Comparisons of XPS and UPS VB spectra and the calculated DOS imply that Cr 3d states are formed both at the top of the VB and in the AlN gap...
January 12, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Feng Shao, Benjamin Cahier, Eric Rivière, Régis Guillot, Nathalie Guihéry, Victoria E Campbell, Talal Mallah
This paper describes the correlation between Ising-type magnetic anisotropy and structure in trigonal bipyramidal Co(II) complexes. Three sulfur-containing trigonal bipyramidal Co(II) complexes were synthesized and characterized. It was shown that we can engineer the magnitude of the Ising anisotropy using ligand field theory arguments in conjunction with structural parameters. To prepare this series of compounds, we used, on the one hand, a tetradentate ligand containing three sulfur atoms and one amine (NS3(tBu)) and on the other hand three different axial ligands, namely, Cl(-), Br(-), and NCS(-)...
January 12, 2017: Inorganic Chemistry
Xuhui Lin, Zhenhua Chen, Wei Wu
To investigate the factors that may cause bond length alternation and π-bond localization in annelated benzenes, ab initio valence bond calculations were performed. The results reveal that the bond length alternation of annelated benzene is determined by the strain-induced hybridization change from the partially optimized geometries, in which the central benzene ring is constrained to a regular hexagon, to the equilibrium geometries rather than the previously recognized re-hybridization effect that the carbon atoms in the central ring are deviated from sp(2) hybridization...
January 12, 2017: Physical Chemistry Chemical Physics: PCCP
Ya-Sen Jiao, Pu-Feng Du
Predicting protein submitochondrial locations has been studied for about ten years. A dozen of methods were developed in this regard. Although a mitochondrion has four submitochondrial compartments, all existing studies considered only three of them. The mitochondrial intermembrane space proteins were always excluded in these studies. However, there are over 50 mitochondrial intermembrane space proteins in the recent release of UniProt database. We think it is time to incorporate these proteins in predicting protein submitochondrial locations...
January 8, 2017: Journal of Theoretical Biology
Yi Pan, Zhihong Luo, Yih-Chung Chang, Kai-Chung Lau, C Y Ng
The ionization energies (IEs) of TiO and TiO2 and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for TiO/TiO(+) and TiO2/TiO2(+) are predicted by the wave-function-based CCSDTQ/CBS approach. The CCSDTQ/CBS calculations involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation (HOC), core-valence (CV) electronic, spin-orbit (SO) coupling, and scalar relativistic (SR) effect corrections...
January 11, 2017: Journal of Physical Chemistry. A
Agnieszka Horala, Agata Swiatly, Jan Matysiak, Paulina Banach, Ewa Nowak-Markwitz, Zenon J Kokot
As cancer development involves pathological vessel formation, 16 angiogenesis markers were evaluated as potential ovarian cancer (OC) biomarkers. Blood samples collected from 172 patients were divided based on histopathological result: OC (n = 38), borderline ovarian tumours (n = 6), non-malignant ovarian tumours (n = 62), healthy controls (n = 50) and 16 patients were excluded. Sixteen angiogenesis markers were measured using BioPlex Pro Human Cancer Biomarker Panel 1 immunoassay. Additionally, concentrations of cancer antigen 125 (CA125) and human epididymis protein 4 (HE4) were measured in patients with adnexal masses using electrochemiluminescence immunoassay...
January 10, 2017: International Journal of Molecular Sciences
Nikolai A Smirnov
The paper presents first-principles FP-LMTO calculations on the relative stability of $fcc$, $bcc$, $hcp$ and $dhcp$ gold under pressure. They were done in Local Density Approximation (LDA), as well as in Generalized Gradient Approximation (GGA) with and without spin-orbit interaction. Phonon spectra for the considered gold structures were obtained from LDA calculations within linear response theory and the contribution of lattice vibrations to the free energy of the system was determined in quasiharmonic approximation...
January 11, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Katie L M Harriman, Jonathan L Brosmer, Liviu Ungur, Paula L Diaconescu, Muralee Murugesu
DyIII single-ion magnets (SIMs) with strong axial donors and weak equatorial ligands have recently been sought after as model systems with which to harness the maximum magnetic anisotropy of DyIII ions. Utilizing a rigid ferrocene diamide ligand (NNTBS), a DyIII SIM, (NNTBS)DyI(THF)2, 1-Dy (NNTBS = fc(NHSitBuMe2)2, fc = 1,1' ferrocenediyl), composed of a near linear arrangement of donor atoms, exhibits a large energy barrier to spin reversal (770.8 K) and magnetic blocking (14 K). The effects of the transverse ligands on the magnetic and electronic structure of 1-Dy were investigated through ab initio methods, eliciting significant magnetic axiality, even in the 4th Kramers doublet, thus, demonstrating the potential of rigid diamide ligands in the design of new SIMs with defined magnetic axiality...
January 11, 2017: Journal of the American Chemical Society
Yuzhen Ge, Wanyue Ye, Zameer Hussain Shah, Xi-Jie Lin, Rongwen Lu, Shufen Zhang
Ammonia-borane (NH3•BH3; AB) has been considered as an excellent chemical material for the hydrogen storage. However, developing highly efficient catalysts for continuous hydrogen generation from AB is still a challenge for the future fuel cell applications. The combination of Pt with Ni is an effective strategy to achieve active bimetallic nanocatalyst, and the particle size has been proved to play a crucial role in determining its final activity. However, the synthesis of PtNi bimetallic catalyst in the size of highly dispersed clusters has always been a challenge...
January 11, 2017: ACS Applied Materials & Interfaces
Motoaki Hirayama, Ryo Okugawa, Takashi Miyake, Shuichi Murakami
In nodal-line semimetals, the gaps close along loops in k space, which are not at high-symmetry points. Typical mechanisms for the emergence of nodal lines involve mirror symmetry and the π Berry phase. Here we show via ab initio calculations that fcc calcium (Ca), strontium (Sr) and ytterbium (Yb) have topological nodal lines with the π Berry phase near the Fermi level, when spin-orbit interaction is neglected. In particular, Ca becomes a nodal-line semimetal at high pressure. Owing to nodal lines, the Zak phase becomes either π or 0, depending on the wavevector k, and the π Zak phase leads to surface polarization charge...
January 11, 2017: Nature Communications
Wenzhong Xing, Xiaodong Chen, Dafei Ren, Kangru Zhan, Yining Wang
The objective of this study was to analyze the effects of ceramic material thickness and resin cement shade on the color matching of ceramic veneers at the gray tooth structures. Seventy-two artificial maxillary right central incisor teeth (C2 shade) were prepared according to veneer tooth preparation in practice. Ceramic materials (LT, A2 shade, IPS e.max Press) were selected to fabricate the 0.50- and 0.75-mm thick veneers at the body region. The ceramic veneer specimens were bonded to the artificial teeth by the 6 shades of resin cements (Variolink Veneer: shades of HV+3, LV-2, LV-3; and RelyX(TM) Veneer: shades of WO, TR, A3)...
January 10, 2017: Odontology
Chongqin Zhu, Sabre Kais, Xiao Cheng Zeng, Joseph S Francisco, Ivan Gladich
Interfacial chemistry involving glyoxal at aerosol surfaces is postulated to catalyze aerosol growth. This chemistry remains speculative due to a lack of detailed information concerning the physicochemical behavior of glyoxal at the interface of atmospheric aerosols. Here, we report results from high-level electronic structure calculations as well as both classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at the air/liquid water interface. When compared to the gas phase, the trans to cis isomerization of glyoxal at the liquid water interface is found to be catalyzed; additionally, the trans conformation is selectively solvated within the bulk to a greater degree than is the cis conformation...
January 11, 2017: Journal of the American Chemical Society
Erdal Benli, Abdullah Çırakoglu, Ercan Ögreden, Selamettin Demir, Yasemin Kaya, Mustafa Ibas, Ali Ayyıldız, Ahmet Yüce
AIM: The aim of this study was to investigate whether there is a relationship between erectile dysfunction (ED), thought to be a vascular disease, and AB0 blood group. MATERIAL AND METHOD: The study included 350 people abiding by the study criteria who applied to our clinic from April 2012-April 2015. The patients were divided into two groups including those with ED (Group 1) and those without (Group 2). Age, blood group, IIEF-5 score and presence of additional diseases were recorded...
December 30, 2016: Archivio Italiano di Urologia, Andrologia
Gui-Liang Xu, Tian Sheng, Lina Chong, Tianyuan Ma, Chengjun Sun, Xiaobing Zuo, Di-Jia Liu, Yang Ren, Xiaoyi Zhang, Yuzi Liu, Steve M Heald, Shi-Gang Sun, Zonghai Chen, Khalil Amine
Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It's well known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-ray scattering, X-ray diffraction and X-ray absorption spectroscopy...
January 10, 2017: Nano Letters
Chowdhury Ashraf, Adri C T van Duin
A detailed insight of key reactive events related to oxidation and pyrolysis of hydrocarbon fuels further enhances our understanding of combustion chemistry. Though comprehensive kinetic models are available for smaller hydrocarbons (typically C3 or lower), developing and validating reaction mechanisms for larger hydrocarbons is a daunting task, due to the complexity of their reaction networks. The ReaxFF method provides an attractive computational method to obtain reaction kinetics for complex fuel and fuel mixtures, providing an accuracy approaching ab-initio based methods, but with a significantly lower computational expense...
January 10, 2017: Journal of Physical Chemistry. A
Josue E Perez, Manoj Kumar, Joseph S Francisco, Amitabha Sinha
Atmospheric aerosols often contain a significant fraction of carbon-nitrogen functionality, which makes gas-phase aldehyde-amine chemistries an important source of nitrogen containing compounds in aerosols. Here we use high-level ab initio calculations to examine the key determinants of amine (ammonia, methylamine, and dimethylamine) addition onto three different aldehydes (acetaldehyde, glycolaldehyde, and 2-hydroperoxy acetaldehyde), with each reaction being catalyzed by a single water molecule. The model aldehydes reflect different degrees of oxygenation at a site adjacent to the carbonyl moiety, the α-site, and represent typical oxygenates that can arise from atmospheric oxidation especially under conditions where the concentration of NO is low...
January 10, 2017: Journal of Physical Chemistry. A
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