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atomic structure

Ivan Yu Chernyshov, Philip V Toukach
Motivation: Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results: The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule...
March 14, 2018: Bioinformatics
Deepak Reddy Gade, Amareswararao Makkapati, Rajesh Babu Yarlagadda, Godefridus J Peters, B S Sastry, V V S Rajendra Prasad
Overexpression of P-glycoprotein (P-gp) leads to the emergence of multidrug resistance (MDR) in cancer treatment. Acridones have the potential to reverse MDR and sensitize cells. In the present study, we aimed to elucidate the chemosensitization potential of acridones by employing various molecular modelling techniques. Pharmacophore modeling was performed for the dataset of chemosensitizing acridones earlier proved for cytotoxic activity against MCF7 breast cancer cell line. Gaussian-based QSAR studies also performed to predict the favored and disfavored region of the acridone molecules...
February 24, 2018: Computational Biology and Chemistry
A Garbout, M Férid
Considering the features in changing the structure and properties of rare earth titanates pyrochlores, the substituted Dy2 Ti2 O7 may be very attractive for various applications. Effect of Sm and Y substitution on the structural properties of Dy2 Ti2 O7 ceramic was established. These ceramics were prepared by solid-state reaction and characterized by X-ray diffraction and Raman spectroscopy. Both analysis show that YDyTi2 O7 with the pyrochlore structure is obtained after heating at 1400°C, but SmDyTi2 O7 has already formed after sintering at 1200°C...
March 10, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
David M Thal, Ziva Vuckovic, Christopher J Draper-Joyce, Yi-Lynn Liang, Alisa Glukhova, Arthur Christopoulos, Patrick M Sexton
G protein-coupled receptors (GPCRs) are the largest superfamily of cell surface receptor proteins and are important drug targets for many human diseases. In the last decade, remarkable progress has been made in the determination of atomic structures of GPCRs with over 200 structures from 53 unique receptors having been solved. Technological advances in protein engineering and X-ray crystallography have driven much of the progress to date. However, recent advances in cryo-electron microscopy have facilitated the structural determination of three new structures of active-state GPCRs in complex with heterotrimeric G protein...
March 13, 2018: Current Opinion in Structural Biology
Hendrik Göddeke, M Hadi Timachi, Cedric A Hutter, Laura Galazzo, Markus A Seeger, Mikko Karttunen, Enrica Bordignon, Lars V Schäfer
ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemo-mechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved...
March 16, 2018: Journal of the American Chemical Society
Marcin Maździarz, Adam Mrozek, Wacław Kuś, Tadeusz Burczyński
A potentially new, single-atom thick semiconducting 2D- graphene -like material, called Anisotropic-cyclicgraphene , has been generated by the two stage searching strategy linking molecular and ab initio approach. The candidate was derived from the evolutionary-based algorithm and molecular simulations was then profoundly analysed using first-principles density functional theory from the structural, mechanical, phonon, and electronic properties point of view. The proposed polymorph of graphene ( rP16 -P1m1) is mechanically, dynamically, and thermally stable and can achieve semiconducting with a direct band gap of 0...
March 16, 2018: Materials
Francesca Malvano, Luigi Maritato, Giovanni Carapella, Pasquale Orgiani, Roberto Pilloton, Marisa Di Matteo, Donatella Albanese
Due to their interesting ferroelectric, conductive and dielectric properties, in recent years, perovskite-structured materials have begun to attract increasing interest in the biosensing field. In this study, a strontium titanate perovskite layer (SrTiO₃) has been synthesized on a platinum electrode and exploited for the development of an impedimetric label-free immunosensor for Escherichia coli O157:H7 detection. The electrochemical characterization of the perovskite-modified electrode during the construction of the immunosensor, as well as after the interaction with different E...
March 16, 2018: Biosensors
Qiang Zhang, Tianyuan Xin, Xiaoke Lu, Yuexia Wang
We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method...
March 16, 2018: Materials
Rui Liu, Huimin Chen, Liping Fang, Cuihong Xu, Zuoliang He, Yujian Lai, Huachao Zhao, Deribachew Bekana Hirpa, Jing-Fu Liu
AuPd bimetallic nanocatalysts exhibit superior catalytic performance in the cleavage of carbon-halogen bonds (C-X) in the hazardous halogenated pollutants. A better understanding of how Au atoms promote the reactivity of Pd sites rather than vaguely interpreting as bimetallic effect, and determining which type of Pd sites are necessary for these reactions are crucial factors for the design of atomically precise nanocatalysts that make full use of both the Pd and Au atoms. Herein, we systematically manipulated the coordination number of Pd-Pd, d-orbital occupation state and Au-Pd interface of the Pd reactive centers, and studied the structure-activity relationship of Au-Pd in the catalyzed cleavage of C-X bonds...
March 16, 2018: Environmental Science & Technology
Joyce Pham, Gordon J Miller
Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co2 Si-type to distorted hexagonal Fe2 P-type and then Ni2 In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au-Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures...
March 16, 2018: Inorganic Chemistry
Qin Xiang, Yuping Liu, Xuefeng Zou, Bingbing Hu, Yujie Qiang, Danmei Yu, Wei Yin, Changguo Chen
In this work, g-C3N4@GO gel-like hybrid is obtained by assembling intentionally exfoliated g-C3N4 sheets on graphene oxide (GO) sheets under a hydrothermal condition. A specific N-doping process is firstly designed by heating the g-C3N4@GO interlaced hybrid in vacuum to form nitrogen-doped graphene nanosheets (NGS) with high level of pyridinic-N (56.0%) and edge-rich defect structure. The prepared NGS exhibited a great electrocatalysis for oxygen reduction reaction (ORR) in terms of the activity, durability, methanol tolerance, and the reaction kinetics...
March 16, 2018: ACS Applied Materials & Interfaces
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Iain M Aldous, Laurence J Hardwick
The deposition and dissolution of sodium superoxide (NaO2 ) was investigated by atomic force microscopy. Rectangular prisms consisting of 8 smaller sub-structures grew from NaO2 platelets, when discharged in 0.5 M NaClO4 , diethylene glycol dimethyl ether on highly ordered pyrolytic graphite. During oxidation the 8 sub-structures are conserved. Ring-like structures of Na2 CO3 of 200 nm diameter remain at the end of oxidation.
March 16, 2018: Chemical Communications: Chem Comm
Julia Tesch, Fabian Paschke, Mikhail Fonin, Marko Wietstruk, Stefan Böttcher, Roland J Koch, Aaron Bostwick, Chris Jozwiak, Eli Rotenberg, Anna Makarova, Beate Paulus, Elena Voloshina, Yuriy Dedkov
The implementation of graphene in semiconducting technology requires precise knowledge about the graphene-semiconductor interface. In our work the structure and electronic properties of the graphene/n-Ge(110) interface are investigated on the local (nm) and macro (from μm to mm) scales via a combination of different microscopic and spectroscopic surface science techniques accompanied by density functional theory calculations. The electronic structure of freestanding graphene remains almost completely intact in this system, with only a moderate n-doping indicating weak interaction between graphene and the Ge substrate...
March 16, 2018: Nanoscale
Sunandan Mukherjee, Chandran Nithin, Yasaswi Divakaruni, Ranjit Prasad Bahadur
We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a protein polar group is retained, we assign it as WP site; if it is lost, we assign it as WD site and if a new H-bond is created, we assign it as WH site. We find that the density of WD sites is highest followed by WH and WP sites except in antigen and (or) antibody complexes, where the density of WH sites is highest followed by WD and WP sites...
March 16, 2018: Journal of Biomolecular Structure & Dynamics
Fan Sun, Zhongnan Guo, Ning Liu, Dan Wu, Jiawei Lin, Erjian Cheng, Tianping Ying, Shiyan Li, Wenxia Yuan
In this work, we report the discovery of a new Ni-based quasi-one-dimensional selenide: Cs0.9 Ni3.1 Se3 . This compound adopts the TlFe3 Te3 -type structure with space group P63 / m, which consists of infinite [Ni3 Se3 ] chains with face-sharing Ni6 octahedra along the c direction. The lattice parameters are calculated as a = 9.26301(4) Å and c = 4.34272(2) Å, with the Ni-Ni distance in the ab plane as 2.582(3) Å, suggesting the formation of a Ni-Ni metallic bond in this compound. Interestingly, it has been found that Cs0...
March 16, 2018: Inorganic Chemistry
Ayori Mitsutake, Hiroshi Takano
Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i...
March 15, 2018: Biophysical Reviews
Shuai Zhang, Qinfu Liu, Hongfei Cheng, Feng Gao, Cun Liu, Brian J Teppen
Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space...
January 2018: Applied Clay Science
Sangmoon Yoon, Hyobin Yoo, Seoung-Hun Kang, Miyoung Kim, Young-Kyun Kwon
We report the existence of latent order during core relaxation in the high-angle grain boundaries (GBs) of GaN films using atomic-resolution scanning transmission electron microscopy and ab initio density functional theory calculations. Core structures in the high-angle GBs are characterized by two pairs of Ga-N bonds located next to each other. The core type correlates strongly with the bond angle differences. We identify an order of core relaxation hidden in the high-angle GBs by further classifying the 5/7 atom cores into a stable 5/7 core (5/7(S)) and a metastable 5/7 core (5/7(M))...
March 15, 2018: Scientific Reports
Hisao Tsukamoto, Masahiro Higashi, Hideyoshi Motoki, Hiroki Watanabe, Christian Ganser, Koichi Nakajo, Yoshihiro Kubo, Takayuki Uchihashi, Yuji Furutani
Canonical K+ channels are tetrameric and highly K+ selective, whereas two-pore domain K+ (K2P) channels form dimers, but with a similar pore architecture. A two-pore domain potassium channel TWIK1 (KCNK1 or K2P1) allows permeation of Na+ and other monovalent ions, resulting mainly from the presence of Thr118 in the P1 domain. However, the mechanistic basis for this reduced selectivity is unclear. Using ion-exchange-induced difference infrared spectroscopy, we analyzed WT TWIK1 and T118I (highly K+ selective) and L228F (substitution in the P2 domain) TWIK1 variants and found that in the presence of K+ ions, WT and both variants exhibit an amide-I band at 1680 cm-1 This band corresponds to interactions of the backbone carbonyls in the selectivity filter with K+ , a feature very similar to that of the canonical K+ channel KcsA...
March 15, 2018: Journal of Biological Chemistry
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