Density Functional Theory Study (density + functional_theory_study)

Distribution by Scientific Domains
Distribution within Chemistry

Selected Abstracts

Beyond the Icosahedron: A Density Functional Theory Study of 14-Atom Germanium Clusters

R. Bruce King
Abstract Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge14z (z = ,8, ,6, ,4, ,2, 0, +2, +4) starting from seven different initial configurations. An Oh omnicapped cube structure is the most stable for Ge142, followed by a hexagonal antiprism structure with a relative energy of 42.7 kcal/mol. The lowest-energy structure for neutral Ge14 is a triplet omnicapped cube with full Oh symmetry followed by a singlet omnicapped cube compressed to D4h symmetry through Jahn,Teller distortion. The lowest energy Ge142+ structure is also an Oh structure derived from the omnicapped cube through elongation of the 12 edges of the underlying cube to give a rhomboidal dodecahedron with 12 rhombus faces. The lowest-energy Ge124+ structure is a bicapped icosahedron. Some D6h hexagonal wheel structures at higher energies are also found for the hypoelectronic systems Ge14, Ge142+, and Ge144+. The lowest-energy structures for the hyperelectronic Ge144,, Ge146,, and Ge148, are relatively unsymmetrical not readily recognizable open structures typically with some pentagonal or hexagonal faces. The D6d bicapped hexagonal antiprism found in 14-vertex C2B12 carborane and M2C2B10 dimetallacarborane structures is not the lowest-energy structure for any of the Ge14z clusters.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]

A Density Functional Theory Study of the Stille Cross-Coupling via Associative Transmetalation.

Coordinating Solvents, The Role of Ligands
Abstract An associative mechanism has been computationally characterized for the Stille cross-coupling of vinyl bromide and trimethylvinylstannane catalyzed by PdL2 (L=PMe3, AsMe3) with or without dimethylformamide as coordinating ligand. All the species along the catalytic cycles that start from both the cis - and the trans -PdL(Y)(vinyl)Br complexes (Y=L or S; L=PMe3, AsMe3 or PH3; S=DMF) have been located in the gas phase and in the presence of polar solvents. Computations support the central role of species trans -PdL(DMF)(vinyl)Br which react by ligand dissociation and stannane coordination in the rate-limiting transmetalation step via a puckered four-coordinate (at palladium) transition state comprised of Pd, Br, Sn and sp2 C atoms. A donating solvent may enter the catalytic cycle assisting isomerization of cis -PdL2(vinyl)Br to trans -PdL(DMF)(vinyl)Br complexes via a pentacoordinate square pyramidal Pd intermediate. In keeping with experimental observations, the activation energies of the catalytic cycles with arsines as Pd ligands are lower than those with phosphines. Polytopal rearrangements from the three-coordinate T-shaped Pd complexes resulting from transmetalation account for the isomerization and the CC bond formation on the reductive elimination step. [source]

ChemInform Abstract: Beyond the Icosahedron: A Density Functional Theory Study of 14-Atom Germanium Clusters.

CHEMINFORM, Issue 45 2008
R. Bruce King
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Density Functional Theory Study of Geometrical Structures and Electronic Properties of Silica Nanowires.

CHEMINFORM, Issue 12 2007
Dongju Zhang
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source]

Structure and Energy of Mo27SxCy Clusters: A Density Functional Theory Study

CHEMINFORM, Issue 11 2007
Xiao-Dong Wen
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source]

Density Functional Theory Study of the Structures and Properties of (H2AlN3)n (n = 1,4) Clusters.

CHEMINFORM, Issue 24 2004
Qi Ying Xia
No abstract is available for this article. [source]

Density Functional Theory Study of Nine-Atom Germanium Clusters: Effect of Electron Count on Cluster Geometry.

CHEMINFORM, Issue 50 2003
R. B. King
No abstract is available for this article. [source]

Periodic Density Functional Theory Study of the Dissociative Adsorption of Molecular Oxygen over La2O3.

CHEMINFORM, Issue 39 2002
Michael S. Palmer
No abstract is available for this article. [source]

ChemInform Abstract: The Nature of Superacid Electrophilic Species in HF/SbF5: A Density Functional Theory Study.

CHEMINFORM, Issue 21 2002
Pierre M. Esteves
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Structural, Electronic, and Bonding Properties of Zeolite Sn-Beta: A Periodic Density Functional Theory Study

Sharan Shetty
Abstract The structural, electronic, and the bonding properties of the zeolite Sn-beta (Sn-BEA) have been investigated by using the periodic density functional theory. Each of the nine different T-sites in BEA were substituted by Sn atoms and all the nine geometries were completely optimized by using the plane-wave basis set in conjunction with the ultra-soft pseudopotential. On the basis of the structural and the electronic properties, it has been demonstrated that the substitution of Sn atoms in the BEA framework is an endothermic process and hence the incorporation of Sn in the BEA is limited. The lowest unoccupied molecular orbitals (LUMO) energies have been used to characterize the Lewis acidity of each T-site. On the basis of the relative cohesive energy and the LUMO energy, the T2 site is shown to be the most favorable site for the substitution Sn atoms in the BEA framework. [source]

A Density Functional Theory Study on the Electrocyclization of 1,2,4,6-Heptatetraene Analogues: Converting a Pericyclic to a Pseudopericyclic Reaction

Enrique M. Cabaleiro-Lago Prof. Dr.
Abstract A comprehensive B3LYP/6-31+G* study on the electrocyclization of 1,2,4,6-heptatetraene analogues was conducted. Starting from the cyclization of (2Z)-2,4,5-hexatrienal, a pericyclic disrotatory process favored by the assistance of a electron lone pair, we incorporated small modifications in its molecular structure to obtain a truly pseudopericyclic process. To this purpose electronegative atoms (fluorine and nitrogen) were added to give a more electrophilic character on the carbon atom which is attacked by the electron lone pair of the oxygen atom. The complete pathway for each reaction was determined, and changes in magnetic properties were monitored with a view to estimating the aromatization associated with each process. This information, together with the energetic and structural results, allowed us to classify the reactions as pseudopericyclic or pericyclic. Among all studied reactions only one was a truly pseudopericyclic process and another was a borderline case. The features of this unequivocally pseudopericyclic case were analyzed in depth. Se ha llevado a cabo un exhaustivo estudio B3LYP/6-31+G* de la electrociclación de análogos del 1,2,4,6-heptatetraeno. Partiendo de la ciclación del (2Z)-2,4,5-hexatrienal, un proceso pericíclico disrotatorio favorecido por la ayuda de un par electrónico solitario, hemos incorporado pequeñas modificaciones en su estructura molecular con el fin de obtener un proceso verdaderamente pseudopericíclico. Con este propósito se añadieron átomos electronegativos (flúor y oxígeno) para conseguir un mayor carácter electrofílico en el átomo de carbono que es atacado por el par electrónico solitario del átomo de oxígeno. Se han determinado los caminos de reacción completos y se ha observado la variación de las propiedades magnéticas con el fin de estimar la aromatización asociada a cada proceso. Esta información, junto con los resultados energéticos y estructurales, nos han permitido clasificar las reacciones como pseudopericíclicas o pericíclicas. De todas las reacciones estudiadas sólo una resultó ser realmente pseudopericíclica y otra resultó ser un caso límite. Las características de este caso inequívocamente pseudopericíclico han sido analizadas en profundidad. [source]

Manganese, Iron, Cobalt, and Nickel Oxo-, Peroxo-, and Superoxoclusters: A Density Functional Theory Study

CHEMPHYSCHEM, Issue 2 2004
Ellie L. Uzunova Dr.
Abstract The 3d-transition-metal dioxo-, peroxo-, and superoxoclusters with the general composition MO2, M(O2), and MOO (M=Mn, Fe, Co, and Ni) were studied by DFT by the B1LYP functional. The dioxides in their ground states represent the global minima for the M+O2 system. Both ground-state dioxides and the lowest-energy peroxides are in their (d-only) highest spin states. The 6A1 state of Co(O2) exceeds the d-only spin-multiplicity value (quartet), being nearly isoenergetic with the 4A1 state of Co(O2). The energy gain on transforming the peroxides to the corresponding dioxides decreases in the order Mn(O2)>Fe(O2)>Co(O2)>Ni(O2) and varies in the range 0.27,1.8 eV. The dissociation energy to M+O2 for all studied peroxides is less than 1 eV being the lowest (0.47 eV) for Mn(O2). The Mn and Fe peroxides need less than 0.3 eV to rupture one of the MO bonds to form the corresponding superoxide. Mn and Fe superoxides are less stable than the corresponding peroxides; the superoxide of Co is more stable than its peroxide, while Ni superoxide is unstable,its energy is above the limit of dissociation to Ni+O2. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides, in which the terminal oxygen atom is more nucleophilic than the M-bonded oxygen atom. This result differs from the expectations based on charge-distribution analysis. [source]

Protonation of Pyrrole and Furan by H3O+ and NH4+ in the Gas Phase: A Density Functional Theory Study

Kuo Zeng
Abstract Density functional theory and ab initio calculations have been used to determine structures and stabilities of the protonated aromatics species AH+ and AH22+ (A=pyrrole, furan). Possible mechanisms and relative energetics for protonation of pyrrole and furan by H3O+ and AH4+ in the gas phase have been explored. Calculations show that the C, -protonated species was the most stable structure for AH+, and the protonated AH+ might accommodate the second proton to yield AH22+ if the free proton was available. The gas-phase H3O+ could protonate pyrrole and furan with significant exothermicity and almost without barrier. The proton transfer from AH4+ to pyrrole and furan has a barrier ranging from 33.5 to 39.3 kJ/mol in the gas phase. [source]

Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic

Pere Alemany
Abstract A first-principles Density Functional Theory study of several layered solids structurally related to rhombohedral arsenic has been carried out. The electronic structures of rhombohedral arsenic, CaSi2, CaAl2Si2, KSnSb, and SrSn2As2 are discussed in detail, emphasizing on the origins of their metallic or nonmetallic behaviours. It is found that all of these systems are metallic except KSnSb. Electronegativity differences between the elements in the anionic sublattice and/or direct interlayer interactions play the main role in controlling the conductivity behavior. CaSi2 exhibits a peculiar feature since the cation directly influences the conductivity but is not essential for its appearance. Cation-anion interactions are shown to have an important covalent contribution, but despite this fact and the metallic character found for most of these phases, the Zintl approach still provides a valid approximation to their electronic structure. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source]

Reactivation pathway of the hydrogenase H-cluster: Density functional theory study

Stefan Motiu
Abstract This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H-cluster, the active site of Fe-only hydrogenases. The H-cluster is a dimetal complex, Fe,Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H2O, and OH,, are bound to the distal iron (Fed). Density functional theory (DFT) calculations on the native and ruthenium-modified H-cluster have been performed using the B3LYP functional with 6-31+G** and 6-311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH, inhibited H-cluster, which proceeds by an initial protonation of the Fed,OH, complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

A hybrid density functional theory study of the low-temperature dimethyl ether combustion pathways.

I: Chain-propagation
Dimethyl ether (DME) has been proposed to be a promising alternative to conventional diesel fuel because of its favorable compression ignition property (high cetane number) and its soot-free combustion. A radical chain mechanism for hydrocarbon autoignition has been proposed for DME at low temperatures. In this mechanism, the chain initiation step consists of DME undergoing hydrogen abstraction by a highly reactive species (typically ·OH). The CH3O·H2 created in the initiation step then combines with O2; the subsequent CH3OCH2OO· radical is involved in a Lindemann-type mechanism, which can lead to the production of formaldehyde (CH2 = O) and ·OH. This concludes the chain-propagating step: the one ·OH produced then sustains the chain-reaction by creating another CH3O·H2. A relatively stable intermediate (·CH2OCH2OOH), formed via isomerization of CH3OCH2OO· in the chain-propagation step, can combine with a second O2 to produce a radical (·OOCH2OCH2OOH) that can potentially decompose into two ·OH radical (and other products). This path leads to chain-branching and an exponential increase in the rate of DME oxidation. We have used spin-polarized density functional theory with the Becke-3-parameter Lee,Parr,Yang exchange-correlation functional to calculate the structures and energies of key reactants, intermediates, and products involved in (and competing with) the chain-propagating and chain-branching steps of low-temperature DME oxidation. In this article, Part I, we consider only the chain-propagation mechanism and its competing mechanisms for DME combustion. Here, we show that only certain conformers can undergo the isomerization to ·CH2OCH2OOH. A new transition state has been discovered for the disproportionation reaction ·CH2OCH2OOH , 2CH2O + ·OH in the chain-propagating step of DME autoignition that is much lower than previous barriers. The key to making this decomposition pathway facile is initial cleavage of the O,O rather than the C,O bond. This renders all transition states along the chain-propagation potential energy surface below the CH3O·H2 + O2 reactants. In contrast with the more well-studied CH3·H2 (ethyl radical) + O2 system, the H-transfer isomerization of CH3OCH2OO· to ·CH2OCH2OOH in low-temperature DME oxidation has a much lower activation energy. This is most likely due to the larger ring strain of the analogous transition state in ethane oxidation, which is a five-membered ring opposed to a six-membered ring in dimethyl ether oxidation. Thus low-temperature ethane oxidation is much less likely to form the ·ROOH (where R is a generic group) radicals necessary for chain-branching, which leads to autoignition. Three competing reactions are considered: CH3O·H2 , CH2O + ·CH3; ·CH2OCH2OOH , 1,3-dioxetane + ·OH; and ·CH2OCH2OOH , ethylene oxide + HOO·. The reaction barriers of all these competing paths are much higher in energy (7,10 kcal/mol) than the reactants CH3O·H2 + O2 and, therefore, are unlikely low-temperature paths. Interestingly, an analysis of the highest occupied molecular orbital along the CH3O·H2 decomposition path shows that electronically excited (1A2 or 3A2) CH2O can form; this can also be shown for ·CH2OCH2OOH, which forms two formaldehyde molecules. This may explain the luminosity of DME's low-temperature flames. [source]

Excited states of OsO4: A comprehensive time-dependent relativistic density functional theory study

Yong Zhang
Abstract A large number of scalar as well as spinor excited states of OsO4, in the experimentally accessible energy range of 3,11 eV, have been captured by time-dependent relativistic density functional linear response theory based on an exact two-component Hamiltonian resulting from the symmetrized elimination of the small component. The results are grossly in good agreement with those by the singles and doubles coupled-cluster linear response theory in conjunction with relativistic effective core potentials. The simulated-excitation spectrum is also in line with the available experiment. Furthermore, combined with detailed analysis of the excited states, the nature of the observed optical transitions is clearly elucidated. It is found that a few scalar states of 3T1 and 3T2 symmetries are split significantly by the spin-orbit coupling. The possible source for the substantial spin-orbit splittings of ligand molecular orbitals is carefully examined, leading to a new interpretation on the primary valence photoelectron ionization spectrum of OsO4. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex

Yufang Liu
Abstract The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen-bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time-dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S1 state of this doubly hydrogen-bonded FN-2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen-bonded FN-2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm,1 observed in the IR spectra should be assigned as the doubly hydrogen-bonded FN-2MeOH complex from our calculated results. The electronic excited-state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S1 state of the doubly hydrogen-bonded FN-2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen-bonded FN-MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source]

N,N -Diethyl- N,-[(E)-4-pyridylmethylene]benzene-1,4-diamine: a combined X-ray and density functional theory study

Rüdiger W. Seidel
The crystal structure of the title compound, C16H19N3, comprises neutral molecules of a dipolar Schiff base chromophore. A density functional theory (DFT) optimized structure at the B3LYP/6-31G(d) level is compared with the molecular structure in the solid state. The compound crystallizes in the noncentrosymmetric space group Pna21 with a herring-bone packing motif and is therefore a potential candidate for nonlinear optical effects in the bulk. [source]

Condensed polyhedral boranes and analogous organometallic clusters: a molecular orbital and density functional theory study on the cap,cap interactions,

Eluvathingal D. Jemmis
Abstract The interactions between the non-bonded atoms on adjacent units were assumed to be one of the major factors that hinder the exploration and advancement of macropolyhedral borane chemistry. In sandwich complexes involving boron as the bridging atom, the interaction between non-bonded atoms tends to be antibonding, but a closer analysis of various condensed systems shows that this cannot be generalized. The overlap populations (OPs) calculated for structures optimized at the B3LYP/6-31g* level [B21H181, (5), B20H16 (6), [Al(C2B4H6)2]1, (7), B12H102, (8), B10H82, (9 and 14), B11H13 (10), B10H14 (11), C2B8H12 (13) and B20H182, (15)] indicate bonding interactions between the caps, except for 7 and 13. This is substantiated by a detailed extended Hückel-based molecular orbital (MO) study using B10H14 as a model system to represent macropolyhedral boranes with higher fusions. An isolobal equivalent structure, [C8H6(Ru(CO)2Me)2] (17), studied at the B3LYP/LANL2DZ level has weak RuRu interactions. An analysis of the nature of the MOs in B10H14 (11) shows that there is no direct head on overlap of the cap orbitals that are antibonding; this is in contradiction to sandwiched molecules (7), where there are two occupied MOs with antibonding interactions. The m + n + o electron pair count (m is the number of cages involved in condensation, n is the number of vertices and o is the number of single vertex condensations) of sandwich complexes requires the filling of these two MOs. The negative OP between the carbon atoms in 13 is attributed to the greater electronegativity of carbon and is substantiated by a fragment MO analysis. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Adsorption of 6-mercaptopurine and 6-mercaptopurine-ribosideon silver colloid: A pH-dependent surface-enhanced Raman spectroscopy and density functional theory study.

BIOPOLYMERS, Issue 6 2005

Abstract Surface-enhanced Raman spectroscopy (SERS) has been applied to characterize the interaction of 6-mercaptopurine-ribose (6MPR), an active drug used in chemotherapy of acute lymphoblastic leukemia, with a model biological substrate at therapeutic concentrations and as function of the pH value. Therefore, a detailed vibrational analysis of crystalline and solvated (6MPR) based on Density Functional Theory (DFT) calculations of the thion and thiol tautomers has been performed. 6MPR adopts the thion tautomeric form in the polycrystalline state. The SERS spectra of 6MPR and 6-mercaptopurine (6MP) recorded on silver colloid provided evidence that the ribose derivative shows different adsorption behavior compared with the free base. Under acidic conditions, the adsorption of 6MPR on the metal surface via the N7 and possibly S atoms was proposed to have a perpendicular orientation, while 6MP is probably adsorbed through the N9 and N3 atoms. Under basic conditions both molecules are adsorbed through the N1 and possibly S atoms, but 6MP has a more tilted orientation on the silver colloidal surface while 6MPR adopts a perpendicular orientation. The reorientation of the 6MPR molecule on the surface starts at pH 8 while in the case of 6MP the reorientation starts around pH 6. Under basic conditions, the presence of the anionic molecular species for both molecules is suggested. The deprotonation of 6MP is completed at pH 8 while the deprotonation of the riboside is finished at pH 10. For low drug concentrations under neutral conditions and for pH values 8 and 9, 6MPR interacts with the substrate through both N7 and N1 atoms, possibly forming two differently adsorbed species, while for 6MP only one species adsorbed via N1 was evidenced. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 298,310, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [source]

Electron Tunneling through Molecular Media: A Density Functional Study of Au/Dithiol/Au Systems

CHEMPHYSCHEM, Issue 9 2005
Qiang Sun Dr.
Abstract We report a density functional theory study of the electronic properties of n -alkanedithiols (CnS2, with n=4, 8 and 12) sandwiched between two Au(111) infinite slab electrodes. We investigate the influence of the distance between the two electrodes and of the molecular chain length, tilt angle, and coverage on the local density of states (LDOS) at the Fermi energy (Ef). We find that the (small) value of the LDOS at Efnear the center of the molecular wires,a quantity that is related to the tunneling current,is mainly determined by the length n of the alkane chains: it originates from the tails of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) which are broadened by the interaction with the electrodes, and decays exponentially with the length of the molecular wire. This opens a nonresonance tunneling channel for charge transport at small bias voltages. While the length of the hydrocarbon chain appears to be the determining factor, the tilt angle of the molecular wires with respect to the electrode surfaces, and therefore the distance between these, has a small influence on the LDOS at the center of the molecule, while the effect of coverage can be ignored. The picture which emerges from these calculations is totally consistent with a through-bond tunneling mechanism. [source]