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density functional theory

Felipe Polo-Garzon, Shi-Ze Yang, Victor Fung, Guo Shiou Foo, Elizabeth Erin Bickel, Matthew F Chisholm, De-En Jiang, Zili Wu
Although perovskites have been widely used in catalysis, tuning their surface terminations to control reaction selectivities has not been well established. In this work, we employ multiple surface sensitive techniques to characterize the surface termination (one aspect of surface reconstruction) of SrTiO3 (STO) after thermal pretreatment (Sr-enrichment) and chemical etching (Ti-enrichment). We show, using the conversion of 2-propanol as a probe reaction, that the surface termination of STO can be controlled to greatly tune catalytic acid/base properties and consequently the reaction selectivities in a wide range, which are inaccessible using single metal oxides, either SrO or TiO2...
June 21, 2017: Angewandte Chemie
Riccardo Spezia, Stefan Knecht, Benedetta Mennucci
Carotenoids can play multiple roles in biological photoreceptors thanks to their rich photophysics. In the present work, we have investigated six of the most common carbonyl containing carotenoids: echinenone, canthaxanthin, astaxanthin, fucoxanthin, capsanthin and capsorubin. Their excitation properties are investigated by means of a hybrid density functional theory (DFT) and multireference configuration interaction (MRCI) approach to elucidate the role of the carbonyl group: the bright transition is of ππ* character, as expected, but the presence of a C[double bond, length as m-dash]O moiety reduces the energy of nπ* transitions which may become closer to the ππ* transition, in particular as the conjugation chain decreases...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
C-Z Gao, P M Dinh, P-G Reinhard, E Suraud
We study from a theoretical perspective the ionization of molecules and clusters induced by irradiation of a combined two-color laser field consisting of a train of attosecond XUV pulses in the presence of an IR field. We use time-dependent density-functional theory (TDDFT) in real time and real space as a theoretical tool. The calculated results are compared to experimental data when available. We also compare TDDFT with results obtained using a time-dependent Schrödinger equation (TDSE), which is well suited to simple systems while TDDFT allows dealing with more complex molecules and clusters...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
Jörg Kussmann, Christian Ochsenfeld
We present a parallel integral algorithm for two-electron contributions occurring in Hartree-Fock and hybrid density functional theory that allows for a strong scaling parallelization on inhomogeneous compute clusters. With a particular focus on graphic processing units, we show that our approach allows an efficient use of CPUs and graphics processing units (GPUs) simultaneously, although the different architectures demand conflictive strategies in order to ensure efficient program execution. Furthermore, we present a general strategy to use large basis sets like quadruple-ζ split valence on GPUs and investigate the balance between CPUs and GPUs depending on l-quantum numbers of the corresponding basis functions...
June 21, 2017: Journal of Chemical Theory and Computation
Shuang Zhao, Bo Zhao, XinZhe Tian, Yun-Lai Ren, Kaisheng Yao, JianJi Wang, JunNa Liu, Yunli Ren
Density functional theory calculations were performed to investigate the structural and energetic properties of trimetallic AuxPdyPtz clusters with x+y+z=7. The possible stable geometrical configurations with their electronic states are determined. We analyze the chemical order, binding energies, vertical ionization potential, electron affinity and HOMO-LUMO gaps as a function of the whole concentration range. The affinity of AuxPdyPtz clusters towards one O2 molecule is also evaluated in terms of the changes in geometry, adsorption energy and charge transfer...
June 21, 2017: Journal of Physical Chemistry. A
Syed Awais Rouf, Jiří Mareš, Juha Vaara
We apply approximate relativistic methods to calculate the magnetic property tensors, i.e., the g-tensor, zero-field splitting (ZFS) tensor (D), and hyperfine coupling (HFC) tensors, for the purpose of constructing paramagnetic nuclear magnetic resonance (pNMR) shielding tensors. The chemical shift and shielding anisotropy are calculated by applying a modern implementation of the classic Kurland-McGarvey theory (J. Magn. Reson. 1970, 2, 286), which formulates the shielding tensor in terms of the g- and HFC tensors obtained for the ground multiplet, in the case of higher than doublet multiplicity defined by the ZFS interaction...
June 21, 2017: Journal of Chemical Theory and Computation
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
Jiří Brus, Martina Urbanová, Jiri Czernek, Miroslava Pavelkova, Katerina Kubova, Jakub Vyslouzil, Sabina Abbrent, Rafal Konefal, Jiri Horsky, David Vetchy, Jan Vysloužil, Pavel Kulich
Alginate gels are an outstanding biomaterial widely applicable in tissue engineering, medicine, and pharmacy for cell transplantation, wound healing and efficient bioactive agent delivery, respectively. This contribution provides new and comprehensive insight into the atomic-resolution structure and dynamics of polyvalent ion-crosslinked alginate gels in microbead formulations. By applying various advanced solid-state NMR (ssNMR) spectroscopy techniques, we verified the homogenous distribution of the crosslinking ions in the alginate gels and the high degree of ion exchange...
June 21, 2017: Biomacromolecules
Eduard Carbonell-Sanromà, Jeremy Hieulle, Manuel Vilas-Varela, Pedro Brandimarte, Mikel Iraola, Ana Barragán, Jingcheng Li, Mikel Abadía, Martina Corso, Daniel Sanchez-Portal, Diego Peña, Jose Ignacio Pascual
We report on the on-surface synthesis of 7 armchair graphene nanoribbons (7-AGNRs) substituted with nitrile (CN) functional groups. The CN groups are attached to the GNR backbone by modifying the 7-AGNR precursor. While many of these groups survive the on-surface synthesis, the reaction process causes the cleavage of some CN from the ribbon backbone and the on-surface cycloisomerization of few nitriles onto pyridine rings. Scanning Tunneling Spectroscopy and Density Functional Theory reveal that CN groups behave as very efficient n-dopants, significantly downshifting the bands of the ribbon, and introducing deep impurity levels associated to the nitrogen electron lone pairs...
June 21, 2017: ACS Nano
Mohamed-Elamir F Hegazy, Abdelsamed I Elshamy, Tarik A Mohamed, Ahmed R Hamed, Mahmoud A A Ibrahim, Shinji Ohta, Paul W Paré
Three new cembrene diterpenoids, sarcoehrenbergilid A-C (1-3), along with four known diterpenoids, sarcophine (4), (+)-7α,8β-dihydroxydeepoxysarcophine (5), sinulolide A (6), and sinulolide B (7), and one steroid, sardisterol (8), were isolated and characterized from a solvent extract of the Red Sea soft coral Sarcophyton ehrenbergi. Chemical structures were elucidated by NMR and MS analyses with absolute stereochemistry determined by X-ray analysis. Since these isolated cembrene diterpenes contained 10 or more carbons in a large flexible ring, conformer stabilities were examined based on density functional theory calculations...
June 21, 2017: Marine Drugs
Alejandro Morales-Bayuelo
Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity...
June 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Elaheh Sedghamiz, Balazs Nagy, Frank Jensen
We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ~900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles and torsional angles, and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields, and indications for how to design improved force fields...
June 21, 2017: Journal of Chemical Theory and Computation
Ulises Orozco-Valencia, José L Gázquez, Alberto Vela
The net charge transfer process that occurs between two species, A and B, interacting with each other, may be decomposed into two processes: one in which A receives charge from B, which can be identified as the electrophilic channel for A or the nucleophilic channel for B, and a second in which A donates charge to B, which can be identified as the nucleophilic channel for A or the electrophilic channel for B. By determining the amount of charge associated with both processes through the minimization of the interaction energy associated with each case, the expressions for the amount of charge involved in each case can be expressed in terms of the directional chemical potentials and the hardnesses of the interacting species...
July 2017: Journal of Molecular Modeling
Gi Rim Han, Doyk Hwang, Seunghoon Lee, Jong Woo Lee, Eunhak Lim, Jiyoung Heo, Seong Keun Kim
Excited state dynamics of common yellow dye quinophthalone (QPH) was probed by femtosecond transient absorption spectroscopy. Multi-exponential decay of the excited state and significant change of rate constants upon deuterium substitution indicate that uncommon nitrogen-to-oxygen excited state intramolecular proton transfer (ESIPT) occurs. By performing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations, we found that adiabatic surface crossing between the S1 and S2 states takes place in the photoreaction...
June 20, 2017: Scientific Reports
Daniel Halwidl, Wernfried Mayr-Schmölzer, David Fobes, Jin Peng, Zhiqiang Mao, Michael Schmid, Florian Mittendorfer, Josef Redinger, Ulrike Diebold
As complex ternary perovskite-type oxides are increasingly used in solid oxide fuel cells, electrolysis and catalysis, it is desirable to obtain a better understanding of their surface chemical properties. Here we report a pronounced ordering of hydroxyls on the cleaved (001) surface of the Ruddlesden-Popper perovskite Ca3Ru2O7 upon water adsorption at 105 K and subsequent annealing to room temperature. Density functional theory calculations predict the dissociative adsorption of a single water molecule (E ads = 1...
June 20, 2017: Nature Communications
Mehdi Shakourian-Fard, Hadiseh Heydari, Ganesh Kamath
Defect engineering could potentially allow for dramatic tuning of optoelectronic properties of two-dimensional materials. With the help of density functional theory (DFT) calculations, we present a systematic study of the DNA Nucleobases (NBs) adsorbed on hexagonal boron-nitride nanoflake (h-BNNF) and boron and nitrogen monovacancies. The presence of such VN and VB defects increases the binding strength of NBs by 9 kcal/mol and 34 kcal/mol, respectively (h-BNNF-VB> h-BNNF-VN> h-BNNF). A more negative electrostatic potential at the B vacancy-site makes h-BNNF-VB surface more reactive than h-BNNF-VN surface enabling H-bonding interactions with NBs...
June 20, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Qiucheng Li, Zifeng Zhao, Baoming Yan, Xiuju Song, Zhepeng Zhang, Jia Li, Xiaosong Wu, Zuqiang Bian, Xiaolong Zou, Yanfeng Zhang, Zhongfan Liu
The direct growth of high-quality, large-area, uniform, vertically stacked Gr/h-BN heterostructures is of vital importance for applications in electronics and optoelectronics. However, the main challenge lies in the catalytically inert nature of the hexagonal boron nitride (h-BN) substrates, which usually afford a rather low decomposition rate of carbon precursors, and thus relatively low growth rate of graphene. Herein, a nickelocene-precursor-facilitated route is developed for the fast growth of Gr/h-BN vertical heterostructures on Cu foils, which shows much improved synthesis efficiency (8-10 times faster) and crystalline quality of graphene (large single-crystalline domain up to ≈20 µm)...
June 20, 2017: Advanced Materials
Xiaoyan Mu, Justin Kai-Chi Lau, Cheuk-Kuen Lai, K W Michael Siu, Alan C Hopkinson, Ivan K Chu
Four isomers of the radical cation of tripeptide phenylalanylglycyltryptophan, in which the initial location of the radical center is well defined, have been isolated and their collision-induced dissociation (CID) spectra examined. These ions, the π-centered [FGWπ˙](+), α-carbon- [FGα˙W](+), N-centered [FGWN˙](+) and ζ-carbon- [Fζ˙GW](+) radical cations, were generated via collision-induced dissociation (CID) of transition metal-ligand-peptide complexes, side chain fragmentation of a π-centered radical cation, homolytic cleavage of a labile nitrogen-nitrogen single bond, and laser induced dissociation of an iodinated peptide, respectively...
June 20, 2017: Physical Chemistry Chemical Physics: PCCP
David Ayuso, Alicia Palacios, Piero Decleva, Fernando Martín
The combination of attosecond pump-probe techniques with mass spectrometry methods has recently led to the first experimental demonstration of ultrafast charge dynamics in a biomolecule, the amino acid phenylalanine [Calegari et al., Science, 2014, 346, 336]. Using an extension of the static-exchange density functional theory (DFT) method, the observed dynamics was explained as resulting from the coherent superposition of ionic states produced by the broadband attosecond pulse. Here, we have used the static-exchange DFT method to investigate charge migration induced by attosecond pulses in the glycine molecule...
June 20, 2017: Physical Chemistry Chemical Physics: PCCP
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