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density functional theory

Jonas C Ott, Clemens K Blasius, Hubert Wadepohl, Lutz H Gade
This study focused on the synthesis and characterization of a range of low-valent, high-spin iron(II) complexes supported by a carbazole-based PNP pincer-type ligand. The addition of the lithiated ligand (PNP)Li to FeCl2 (THF)1.5 yielded the chlorido complex (PNP)FeCl (1), which could be readily converted to the four-coordinate iron(II) alkyl complexes (PNP)FeR [R = CH2 SiMe3 (3a), Me (3b), CH2 Ph (3c)]. These iron(II) complexes were fully characterized by X-ray analysis and a comprehensive, density-functional-theory-assisted study with complete assignment of their paramagnetic1 H and13 C NMR spectra...
February 23, 2018: Inorganic Chemistry
Andrea N L Batista, Fernando M Dos Santos, João M Batista, Quezia B Cass
Chiral natural product molecules are generally assumed to be biosynthesized in an enantiomerically pure or enriched fashion. Nevertheless, a significant amount of racemates or enantiomerically enriched mixtures has been reported from natural sources. This number is estimated to be even larger since the enantiomeric purity of secondary metabolites is rarely checked in the natural product isolation pipeline. This latter fact may have drastic effects on the evaluation of the biological activity of chiral natural products...
February 23, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jie Tan, Xiaoming Zhang, Wenguan Liu, Xiujie He, Mingwen Zhao
Using non-equilibrium Green's function formalism combined with density functional theory (DFT) calculations, we investigate the significant changes in electronic and transport properties of triangle graphene spirals (TGSs) in response to external strain. Tunable negative differential resistance (NDR) behavior is predicted. The NDR bias region, NDR width, and peak-to-valley ratio can be well tuned by external strain. Further analysis shows that these peculiar properties can be attributed to the dispersion widths of the pz orbitals...
February 23, 2018: Nanotechnology
Yassin Aweis Jeilani, Brooke Ross, Nasrin Aweis, Chelesa Fearce, Huynh Minh Hung, Minh Tho Nguyen
The prebiotic synthesis of nucleobases is of particular interest, given the experimental evidence that indicated formation of the nucleobases under abiotic conditions on the Early Earth under high temperature conditions. Biomolecules have been formed under meteoritic impact scenarios that lead to high-temperature and the generation of high-energy. Free radical pathways for the formation of biomolecules are appropriate under these conditions. Density functional theory computations were used to study the free radical routes for the formation of nucleobases at the UB3LYP/6-311G(d,p) level...
February 23, 2018: Journal of Physical Chemistry. A
Peter Werner Roesky, Christoph Schoo, Ralf Köppe, Martin Piesch, Michael T Gamer, Sergey Konchenko, Manfred Scheer
The reaction of [(Cp'''Co)2(μ,η2:2-As2)2] with the decamethylsamarocenes [Cp*2Sm(thf)2] or [Cp*2Sm], or the di(tetramethyl-n-propyl)samarocene [(C5Me4(n-propyl))2Sm] resulted in the mixed d/f polyarsendies [(Cp'''Co)2As4Sm(η5-C5Me4R)2] (R = Me, n-propyl). They are the first structural representatives of open chain-like polyarsenides as ligands in the coordination sphere of lanthanides. Their formation can be explained by an intramolecular As-As coupling within the cobalt polyarsenide complex after reduction by the divalent samarium complex...
February 23, 2018: Chemistry: a European Journal
Gauthier Deblonde, Morgan Kelley, Jing Su, Enrique Batista, Ping Yang, Corwin Booth, Rebecca J Abergel
The chemistry of trivalent transplutonium ions (Am3+, Cm3+, Bk3+, Cf3+, Es3+) is usually perceived as monotonic and parallel to that of the trivalent lanthanide series. Herein, we present the first extended X-ray absorption fine structure (EXAFS) study performed on a series of aqueous heavy actinide chelates, extending past Cm. The results obtained on diethylenetriaminepentaacetic acid (DTPA) complexes of trivalent Am, Cm, Bk, and Cf show a break to a much shorter metal-oxygen nearest-neighbor bond lengths in the case of Cf3+...
February 22, 2018: Angewandte Chemie
Timothy J Boyle, Diana Perales, Jessica M Rimsza, Todd M Alam, Daniel M Boye, Jeremiah M Sears, Jeffery A Greathouse, Richard A Kemp
A pair of thallium salen derivatives was synthesized and characterized for potential use as monitors (or taggants) or as models for Group 13 complexes for subterranean fluid flows. These precursors were isolated from the reaction of thallium ethoxide with N,N'-bis(3,5-di-tert-butylsalicylidene)-ethylenediamine (H2 -salo-But ), or N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-phenylenediamine (H2 -saloPh-But ). The products were identified by single crystal X-ray diffraction as: [((μ-O)2 ,κ1 -(N)(N')salo-But )Tl2 ] (1) and {[((μ-O)2 saloPh-But )Tl2 ][((μ-O)2 ,κ1 -(N)(N')saloPh-But )Tl2 ]} (2)...
February 23, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Wei-Shan Chiang, Daniel Georgi, Taner Yildirim, Jin-Hong Chen, Yun Liu
It is extremely challenging to measure the variation of pore surface properties in complex porous systems even though many porous materials have widely differing pore surface properties at microscopic levels. The surface heterogeneity results in different adsorption/desorption behaviors and storage capacity of guest molecules in pores. Built upon the conventional Porod's law scattering theory applicable mainly to porous materials with relatively homogeneous matrices, here we develop a generalized Porod's scattering law method (GPSLM) to study heterogeneous porous materials and directly obtain the variation of scattering length density (SLD) of pore surfaces...
February 22, 2018: Nature Communications
Víctor M Trejos, Jacqueline Quintana-H
In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential...
February 21, 2018: Journal of Chemical Physics
Bruno Nunes Cabral Tenorio, Marco Antonio Chaer Nascimento, Alexandre Braga Rocha
The time-dependent version of the density functional theory (TDDFT) has been used to calculate the total photoabsorption cross section of a number of molecules, namely, benzene, pyridine, furan, pyrrole, thiophene, phenol, naphthalene, and anthracene. The discrete electronic pseudo-spectra, obtained in a L2 basis set calculation were used in an analytic continuation procedure to obtain the photoabsorption cross sections. The ammonia molecule was chosen as a model system to compare the results obtained with TDDFT to those obtained with the linear response coupled cluster approach in order to make a link with our previous work and establish benchmarks...
February 21, 2018: Journal of Chemical Physics
Jolyon Aarons, Chris-Kriton Skylaris
Density Functional Theory (DFT) calculations with computational effort which increases linearly with the number of atoms (linear-scaling DFT) have been successfully developed for insulators, taking advantage of the exponential decay of the one-particle density matrix. For metallic systems, the density matrix is also expected to decay exponentially at finite electronic temperature and linear-scaling DFT methods should be possible by taking advantage of this decay. Here we present a method for DFT calculations at finite electronic temperature for metallic systems which is effectively linear-scaling (O(N))...
February 21, 2018: Journal of Chemical Physics
Tianyang Wu, Joseph Derrick, Minal Nahin, Xi Chen, Carlos Larriba-Andaluz
The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential...
February 21, 2018: Journal of Chemical Physics
Jianmin Tao, John P Perdew, Hong Tang, Chandra Shahi
Nanostructures can be bound together at equilibrium by the van der Waals (vdW) effect, a small but ubiquitous many-body attraction that presents challenges to density functional theory. How does the binding energy depend upon the size or number of atoms in one of a pair of identical nanostructures? To answer this question, we treat each nanostructure as a whole object, not as a collection of atoms. Our calculations start from an accurate static dipole polarizability for each considered nanostructure, and an accurate equilibrium center-to-center distance for the pair (the latter from experiment or from the vdW-DF-cx functional)...
February 21, 2018: Journal of Chemical Physics
Silio Lima Moura, Laura Martinez Fajardo, Leonardo Dos Anjos Cunha, Maria Del Pilar Taboada Sotomayor, Francisco Bolivar Correto Machado, Luiz Fernando Araújo Ferrão, Maria Isabel Pividori
This study addresses the rational design of a magnetic molecularly imprinted polymer (magnetic-MIP) for the selective recognition of the hormone levothyroxine. The theoretical study was carried out by the density functional theory (DFT) computations considering dispersion interaction energies, and using the D2 Grimme's correction. The B97-D/def2-SV(P)/PCM method is used not only for studying the structure of the template the and monomer-monomer interactions, but also to assess the stoichiometry, noncovalent binding energies, solvation effects and thermodynamics properties such as binding energy...
January 31, 2018: Biosensors & Bioelectronics
Jinlu Xing, Yuejie Ai, Yang Liu, Jia Du, Weiqiang Chen, Zhanhui Lu, Xiangke Wang
Cytosine methylation and demethylation play crucial roles in understanding the genomic DNA expression regulation. The epigenetic modification of cytosine and its continuous oxidative products-the "new four bases of DNA" including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC). However, compared to the abundant studies on the classical DNA bases, the photophysical and photochemical properties of those new bases have not yet aroused people's excessive attention...
February 22, 2018: Journal of Physical Chemistry. B
Nathan J Beal, Thomas A Corry, Patrick J O'Malley
Broken Symmetry Density Functional Theory (BS-DFT) g-tensor, 55Mn, 14N, and 17O hyperfine couplings have been calculated for active site models of superoxidised Mn(III)/Mn(IV) manganese catalase both in its native and azide inhibited form. While good agreement is found between calculated and experimental g-tensor and 55Mn hyperfine couplings for all models, the active site geometry and Mn ion oxidation state can only be readily distinguished based on comparison of calculated and experimental 14N azide and 17O HFCs...
February 22, 2018: Journal of Physical Chemistry. B
Dooshaye Moonshiram, Pablo Garrido-Barros, Carolina Gimbert-Suriñach, Antonio Picon, Cunming Liu, Xiaoyi Zhang, Michael Karnahl, Antoni Llobet
We report the light-induced electronic and geometric changes taking place within a heteroleptic Cu(I) photosensitizer, namely [(xant)Cu(Me2phenPh2)]PF6 (xant = xantphos, Me2phenPh2 = bathocuproine), by time-resolved X-ray absorption spectroscopy in the ps-µs time-regime. Time-resolved X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis enabled the elucidation of the electronic and structural configuration of the copper centre in the excited state as well as its decay dynamics in different solvent conditions with and without triethylamine acting as a sacrificial electron donor...
February 22, 2018: Chemistry: a European Journal
Yuanyuan Zheng, Wenrui Zheng, Jiaoyang Wang, Huifang Chang, Danfeng Zhu
The hydrazine derivatives have been regarded as the important building blocks in organic chemistry for the synthesis of organic N-containing compounds. It is important to understand the structure-activity relationship of the thermodynamics of N-N bonds, in particular, their strength as measured by using the homolytic bond dissociation enthalpies (BDEs). We calculated the N-N BDEs of 13 organonitrogen compounds by 8 composite high-level ab initio methods including G3, G3B3, G4, G4MP2, CBS-QB3, ROCBS-QB3, CBS-Q and CBS-APNO...
February 22, 2018: Journal of Physical Chemistry. A
Brian J Levandowski, Trevor A Hamlin, Roger C Helgeson, F Matthias Bickelhaupt, Kendall N Houk
The endo and exo stereoselectivities of Diels-Alder reactions of cyclopropenone, iminocyclopropene, and substituted triafulvenes with butadiene were rationalized using density functional theory calculations. When cyclopropenone is the dienophile there is a 1.8 kcal/mol preference for the exo cycloaddition with butadiene. While the reaction of 3-difluoromethylene triafulvene with butadiene favors the endo cycloaddition by 2.8 kcal/mol. The influence of charge transfer and secondary orbital interactions on the stereoselectivity of Diels-Alder reactions involving triafulvenes and heteroanalogs is discussed...
February 22, 2018: Journal of Organic Chemistry
Di-Ming Chen, Chun-Xiao Sun, Nan-Nan Zhang, Huan-Huan Si, Chun-Sen Liu, Miao Du
As a modulatable class of porous crystalline materials, metal-organic frameworks (MOFs) have gained intensive research attention in the domain of gas storage and separation. In this study, we report on the synthesis and gas adsorption properties of two robust MOFs with the general formula [Co3 (μ3 -OH)(cpt)3 Co3 (μ3 -OH)(L)3 (H2 O)9 ](NO3 )4 (guests)n [L = 3-amino-1,2,4-triazole (1) and 3,5-diamino-1,2,4-triazole (2); Hcpt = 4-(4-carboxyphenyl)-1,2,4-triazole], which show the same pacs topology. Both MOFs are isostructural to each other and show MIL-88-type frameworks whose pore spaces are partitioned by different functionlized trinuclear 1,2,4-triazolate-based clusters...
February 22, 2018: Inorganic Chemistry
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