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density functional theory

Amr A A Attia, Daniela Cioloboc, Alexandru Lupan, Radu Silaghi-Dumitrescu
The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer...
September 30, 2016: Journal of Inorganic Biochemistry
Richard A Manderville, Stacey D Wetmore
The formation of DNA adducts by the attack of intermediates derived from toxic substances at the C8 position of 2-deoxyguanosine (dG) is a common damaging event. Although the majority of studies on C8-dG adducts have focused on lesions containing a C8-N-C tether between the bulky moiety and the nucleobase, the formation of O-linked lesions with a similar tether topology and C-linked adducts involving direct C8-C connectivity have also been uncovered. Several studies have been done to try to better understand the structural impact and mutagenicity of O-linked and C-linked aryl C8-dG adducts, including lesions arising from unsubstituted and chloro substituted phenols, and the food mutagen ochratoxin A (OTA)...
October 21, 2016: Chemical Research in Toxicology
David A Mazziotti
A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T2 condition...
October 7, 2016: Physical Review Letters
Jinchun Qiu, Daniel K Unruh, Anthony Frank Cozzolino
Density Functional Theory calculations were used to design an anion receptor that utilizes antimony(III) secondary bonding interactions. Calculations were performed on promising motifs found in the chemical literature where two antimony sites were found in close proximity to a halide anion. The study was extended to a structurally related class of 1,3,2-benzodioxastibole derivatives to elucidate their potential for binding halide ions. Multiple geometric conformations were evaluated and various ratios of halide anions were considered...
October 21, 2016: Journal of Physical Chemistry. A
Radwan Elzein, Chun-Min Chang, Inna Ponomareva, Wen-Yang Gao, Shengqian Ma, Rudy Schlaf
Metal-organic frameworks (MOFs) deposited from solution have the potential to form 2-dimensional supramolecular thin films suitable for molecular electronic applications. However, the main challenges lie in achieving selective attachment to the substrate surface, and the integration of organic conductive ligands into the MOF structure to achieve conductivity. The presented results demonstrate that photoemission spectroscopy combined with preparation in a system-attached glovebox can be used to characterize the electronic structure of such systems...
October 21, 2016: ACS Applied Materials & Interfaces
Rocío Donamaría, M Concepción Gimeno, Vito Lippolis, José M López-de-Luzuriaga, Miguel Monge, M Elena Olmos
In this paper the reaction products of the basic gold(I) species [Au(C6Cl5)2](-) against the acid salt Ag(OClO3) in the presence of the S-donor macrocyclic ligand 1,4,7-trithiacyclononane ([9]aneS3) are studied in different solvents. Two different isomers of stoichiometry [{Au(C6Cl5)2}Ag([9]aneS3)]2 were isolated depending on the solvent used, dichloromethane or tetrahydrofuran, which show different luminescence in the solid state. X-ray diffraction studies of these compounds reveals that both show the same heteropolynuclear Ag···Au···Au···Ag system but with different Au···Au interaction distances and different relative positions of the cationic fragment [Ag([9]aneS3)](+) in the structure with respect the bimetallic Au···Au core...
October 21, 2016: Inorganic Chemistry
Giorgio Lanzani, Ari P Seitsonen, Marcella Iannuzzi, Kari Laasonen, Simo Olavi Pehkonen
The chemistry of aluminium or oxo-aluminium in water is still relatively unknown, although it is the basis for many chemical and industrial processes, including floc- culation in water treatment plants. Trimeric species have a predominant role in the formation of the Keggin cations, which are the basic building block of aluminium- based chemicals. Despite this, the details of the structural evolution of these small solvated clusters and how this is related to the processes leading to the formation of larger aggregates is still an open issue...
October 21, 2016: Journal of Physical Chemistry. B
Ivan Ljubic, Aleksandar Sabljic, Marija Bonifacic
The reactions of α-hydroxyalkyl radicals in aqueous medium are of interest because they exhibit a rich variety of fundamentally important competing mechanisms, such as proton-coupled electron transfer (PCET), hydrogen atom transfer, free radical substitutions, abstractions and additions etc. We present a theoretical study of the mechanism and kinetics of the aqueous reactions of α-hydroxyisopropyl (2-propanol) radical with four halogenated organic substrates: iodoacetate (IAc), iodoacetamide (IAm), 5-bromouracil (5-BrU), and carbon tetrachloride (CCl4)...
October 21, 2016: Journal of Physical Chemistry. B
Michael Thomas Ruggiero, J Axel Zeitler
Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterisation can be made...
October 21, 2016: Journal of Physical Chemistry. B
Yu Harabuchi, Rina Yamamoto, Satoshi Maeda, Satoshi Takeuchi, Tahei Tahara, Tetsuya Taketsugu
Ab initio molecular dynamics (AIMD) simulations were carried out for *-excited 1,1'-dimethylstilbene (dmSB) at the spin-flip time-dependent density functional theory (SF-TDDFT) level with the TSF-index technique, to get insights into the substitution effects on the photoisomerization dynamics of stilbene (SB). It is found that the reaction path from the Franck-Condon structure of cis-dmSB is oriented toward the 4,4-dihydrophenanthrene (DHP) side from the beginning, which is in contrast to the case of SB where the pathway is oriented toward the twist-side in the initial stage...
October 21, 2016: Journal of Physical Chemistry. A
Michel Alain Cuendet, Harel Weinstein, Michael V LeVine
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery...
October 21, 2016: Journal of Chemical Theory and Computation
Mingzhu Xia, Yuting Chu, Tianyi Wang, Wu Lei, Fengyun Wang
As a kind of promising energetic materials, the double furazan-based and furoxan-based compounds have raised concerns of many researchers in recent years. In this paper, the optimized structures, energetic properties, heat of formation (HOF), detonation properties, and bond dissociation energies of these compounds were calculated by density functional theory (DFT) method. The results show that the N-O bond, which is close to the adjacent coordinated oxygen atom in furoxan ring, is more fragile than the other N-O bonds in the ring...
November 2016: Journal of Molecular Modeling
Carlos E Hernandez-Tamargo, Ransel Barzaga, Hans Mikosch, Javier A Martínez, José A Herrera, M H Farías, Mayra P Hernández
The adsorption of sulphur multilayers on Au(100) has been studied using density functional theory (DFT) within the generalized gradient approximation (GGA). The first sulphur layer was adsorbed on the four-fold sites of the unreconstructed Au(100) surface forming a lattice. The experimental parameters of the lattice were reproduced taking into account the surface expansion of the topmost Au(100) layer. This expansion should occur when gold islands are formed after the lifting of hex-reconstruction, which allows the lateral movement of the gold atoms...
October 21, 2016: Physical Chemistry Chemical Physics: PCCP
Urszula K Komarnicka, Radosław Starosta, Agnieszka Kyzioł, Michał Płotek, Małgorzata Puchalska, Małgorzata Jeżowska-Bojczuk
In this paper we present lomefloxacin's (HLm, 2nd generation fluoroquinolone antibiotic agent) organic and inorganic derivatives: aminomethyl(diphenyl)phosphine (PLm), its oxide as well as new copper(I) iodide or copper(I) thiocyanate complexes with PLm and 2,9-dimethyl-1,10-phenanthroline (dmp) or 2,2'-biquinoline (bq) as the auxiliary ligands. The synthesized compounds were fully characterised by NMR, UV-Vis and luminescence spectroscopies. Selected structures were analysed by theoretical DFT (density functional theory) methods...
September 30, 2016: Journal of Inorganic Biochemistry
Hui-Hsu Gavin Tsai, Jia-Cheng Hu, Chun-Jui Tan, Yung-Ching Sheng, Chih-Chiang Chiu
The loading of dye sensitizers on a semiconductor is crucial for determining the light harvesting efficiency of dye-sensitizer solar cells (DSSCs). The interfacial properties of dyes adsorbed on TiO2 film such as adsorption configurations and adsorption energy can influence the total amount of dye sensitizers that loads and the stability of a DSSC device. Therefore, it is important to characterize the adsorption properties of dye sensitizers on TiO2 film atomically and electronically to ensure rational structure-based dye design for high-performance DSSCs...
October 20, 2016: Journal of Physical Chemistry. A
Qi Wu, Hongming Liu, Lei Kang, Zheshuai Lin, Xianggao Meng, Xingguo Chen, Jingui Qin
An alkali metal selenite chloride, Rb2SeOCl4·H2O, has been hydrothermally synthesized and structurally characterized. It is the first example of an alkali metal selenite halide in the literature. The compound crystallizes in the noncentrosymmetric (NCS) space group, Cmc21(36), of the orthorhombic system with a = 10.342(3) Å, b = 10.124(3) Å, c = 9.158(3) Å, and α = β = γ = 90°. The anionic [SeOCl4](2-) groups are arranged in the crystal in nearly the same direction, giving rise to a relatively large macroscopic dipole moment, causing the compound to display second harmonic generation (SHG) eight times as strong as that of KDP, measured using the Kurtz-Perry method on powders...
October 20, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Zhi-Hao Cui, Feng Wu, Hong Jiang
The relative stability of TiO2 in the rutile and anatase structure is wrongly described by density functional theory in various local, semilocal, or even hybrid functional approximations. In this work, we have found that by considering high-order correlations in the adiabatic connection fluctuation-dissipation theory with the random phase approximation (ACFDT-RPA), rutile is correctly predicted to be more stable than anatase, which can be physically attributed to different characters in the electronic band structure of rutile and anatase, including, in particular, that rutile has a smaller band gap than anatase...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
Tao Jiang, Menghua Wang, Li Li, Jinguang Si, Bo Song, Cao Zhou, Meng Yu, Xuewei Wang, Yonggang Zhang, Gang Ding, Zhongmei Zou
Overexpression of laeA in Chaetomium globosum CBS148.51 up-regulated expression of the chaetoglobosin gene cluster and resulted in the isolation of a new cytochalasan, chaetoglobosin Z (1), together with six known analogues, chaetoglobosins A (2), B (3), D (4), E (5), O (6), and V (7). RT-PCR analysis confirmed that the key genes in the chaetoglobosin gene cluster were significantly up-regulated. The structure of the new compound chaetoglobosin Z (1) was elucidated using NMR data. The relative and absolute configurations were determined by NOESY and electronic circular dichroism combined with quantum-chemical calculations adopting time-dependent density functional theory methods, respectively...
October 19, 2016: Journal of Natural Products
Shogo Okumura, Shu-Wei Tang, Teruhiko Saito, Kazuhiko Semba, Shigeyoshi Sakaki, Yoshiaki Nakao
We report a method that ensures the selective alkylation of benzamides and aromatic ketones at the para-position via cooperative nickel/aluminum catalysis. Using a bulky catalyst/co-catalyst system allows reactions between benzamides with alkenes to afford the corresponding para-alkylated products. The origin of the high para-selectivity has also been investigated by density functional theory calculations.
October 19, 2016: Journal of the American Chemical Society
Donghee Chang, Anton Van der Ven
A first-principles study was performed to elucidate the electrochemical properties of CaTi5O11, a recently discovered compound that is a crystallographic variant of TiO2(B) and that shows promise as an anode material for Li-ion batteries. The crystal structure of CaTi5O11 was further refined and two symmetrically distinct interstitial sites that can accommodate Li at positive voltage were identified. A statistical mechanics study relying on density functional theory (DFT) calculations predicted that interstitial Li in CaTi5O11 forms a solid solution with Li insertion resulting in a sloping voltage profile...
October 19, 2016: Physical Chemistry Chemical Physics: PCCP
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