Mechanisms for H2O decomposition on the Si(111)‐7 × 7 surface: A DFT cluster model study

The mechanisms for the complete decomposition of water molecules on the Si (111)‐7 × 7 surface were investigated theoretically. The reaction pathways for dissociation of four water molecules over the adatom and rest atom sites were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional. The calculated results demonstrated that the initial O? H bond dissociation from the first H₂O to form the adsorbed OH species is more preferential on the adatom site (Si_a) than the rest atom site (Si_r) of Si (111)‐7 × 7. Four water molecules dissociate successively over the adatom site, backbonds of adatoms which are saturated by OH species can reasonably be the place of insertion of oxygen atoms, yielding a tetrahedral SiO₄ structure with one on top and three inserted oxygen atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Formation of Au nanocluster ordered array on Si(111)‐7 × 7 surface

We report a successful approach in fabricating well shape two‐dimensional Au nanocluster hexagonal array on an Si(111)‐7 × 7 surface. The size of Au hexagons is about 2.5 × 2.5 nm². The easiness of preparing large scale Au hexagonal array makes this approach usable to fabricate a wide range of other metal nanocluster arrays. Further deposition of small amount of Au nanoclusters on the Au hexagonal array surface will prefer to occupy the holes of the hexagonal array at room temperature. Finally, a reasonable structure of formatting the hexagonal Au nanocluster array on the Si(111)‐7 × 7 surface was proposed. Copyright © 2015 John Wiley & Sons, Ltd.     

Plane‐wave density functional theory investigation of adsorption of 2,4,6‐trinitrotoluene on al‐hydroxylated (0001) surface of (4 × 4) α‐alumina

This article reports the results of the theoretical investigation of adsorption of 2,4,6‐trinitrotoluene (TNT) on Al‐hydroxylated (0001) surface of (4 × 4) α‐alumina (α‐Al₂O₃) using plane‐wave Density Functional Theory. Sixteen water molecules were used to hydroxylate the alumina surface. The Perdew–Burke–Ernzerhof functional and the recently developed van der Waals functional (vdW‐DF2) were used. The interaction of electron with core was accounted using the Vanderbilt ultrasoft pseudopotentials. It was found that hydroxylation has significant influence on the geometry of alumina and such changes are prominent up to few layers from the surface. Particularly, due to the Al‐hydroxylation the oxygen layers are decomposed into sublayers and such partitioning becomes progressively weaker for interior layers. Moreover, the nature of TNT adsorption interaction is changed from covalent type on the pristine alumina surface to hydrogen‐bonding interaction on the Al‐hydroxylated alumina surface. TNT in parallel orientation forms several hydrogen bonds compared to that in the perpendicular orientation with hydroxyl groups of the Al‐hydroxylated alumina surface. Therefore, the parallel orientation will be present in the adsorption of TNT on Al‐hydroxylated (0001) surface of α‐alumina. Further, the vdW‐DF2 van der Waals functional was found to be most suitable and should be used for such surface adsorption investigation. © 2014 Wiley Periodicals, Inc.     

A Model Calculation for the Isomerization and Decomposition of Chemisorbed HCN on the Si(100)-2×1 Surface

Ab initio molecular orbital and hybrid density functional theory calculations have been performed to study the adsorption, isomerization, and decomposition of HCN on Si(100)-2×1 using the Si₉H₁₂ cluster model of the surface. The results of our calculations indicate that the HCN can adsorb molecularly without a barrier onto the surface with both end-on (LM1) and side-on (LM2) positions. LM1 can isomerize to LM2 with a small barrier of 8 kcal/mol. The isomerization of LM2 by H-migration from C to the N atom, requires 76 kcal/mol activation energy (c.f. 47.5 kcal/mol in the gas phase) because of surface stabilization. Both HCN(a) and HNC(a) end-on adsorbates were found to dissociate readily, as concluded in our earlier experiment, to produce H and CN adspecies. The computed vibrational frequencies of HCN, CN, and also HCNH adspecies agree reasonably well with those observed experimentally. HCNH was found to be stable, with either the C or the N attaching to the surface.     

Selective oxidation of styrene on an oxygen-adsorbed Au(111): A density functional theory study

The reaction mechanism for the styrene selective oxidation on the oxygen preadsorbed Au(111) surface has been studied by the density functional theory calculation with the periodic slab model. The calculated results showed that the process of reaction includes two steps: forming the oxametallacycle intermediate (OMME) and then producing the products. It was found that the second step, from OMME to product is the rate-controlling step, which is similar to ethylene selective oxidation on Ag. Importantly, the present density-functional-theory calculation results suggested that the mechanism via the OMME (2) (i.e. the preadsorbed atomic oxygen bound to the CH2 group involved in C6H5--CH=CH2) to produce styrene epoxide is kinetically favored than that of OMME (1).     

Functionalization of diamond (001)‐2 × 1 surface by cycloaddition of 1,3‐cyclohexadiene: A theoretical study

Density functional theory calculations have been used to study [4 + 2] and [2 + 2] cycloaddition reaction between 1,3‐cyclohexadiene and diamond (001)‐2 × 1 surface. The calculations revealed four possible reaction pathways for 1,3‐cyclohexadiene with the surface dimmers of diamond. Full geometry‐optimized structures were obtained for all products, including intradimer and interdimer reaction products. These results were analyzed both in terms of the total energy values and the detailed optimized geometries. We found that the intradimer [4 + 2] product is energetically favored over the other products, and the barrier to intradimer [4 + 2] addition is lower than the other additions, so the intradimer [4 + 2] product is expected to be the dominant product on the surface. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Tris[3‐hydroxy‐2(1 H)‐pyridinonato]‐Komplexe von Al3+, Cr3+ und Fe3+ – Kristall‐ und Molekülstrukturen von 3‐Hydroxy‐2(1 H)‐pyridinon und Tris[3‐hydroxy‐2(1 H)‐pyridinonato]chrom(III)

Tris[3‐hydroxy‐2(1 H)‐pyridinonato] Complexes of Al³⁺, Cr³⁺, and Fe³⁺ – Crystal and Molecular Structures of 3‐Hydroxy‐2(1 H)‐pyridinone and Tris[3‐hydroxy‐2(1 H)‐pyridinonato]chromium(III) Tris[3‐hydroxy‐2(1 H)‐pyridinonato] complexes of Al³⁺, Cr³⁺ and Fe³⁺ are obtained by reactions of 3‐hydroxy‐2(1 H)pyridinone with the hydrates of AlCl₃, CrCl₃ or Fe(NO₃) in aqueous alkaline solutions as polycrystalline precipitates. The compounds are isotypic. X‐ray structure determinations were performed on single crystals of the uncoordinated 3‐hydroxy‐2(1 H)‐pyridinone ( 1 ) (orthorhombic, space group P2₁2₁2₁, a = 405.4(1), b = 683.0(1), c = 1770.3(3) pm, Z = 4) and of the chromium compound 3 (rhombohedral with hexagonal setting, space group R3c, a = 978.1(1), c = 2954.0(1) pm, Z = 6).     

Syntheses,and Crystal Structures of Indium Complexes with η2‐Piperidinyldithiocarbamate and η2‐Pyridine‐2‐Thionate Containing Ligands: Structures of [In(η2‐S2CNC5H10)3] and [In(η2‐pyS)3]

The η²‐thio‐indium complexes [In(η²‐thio)₃] (thio = S₂CNC₅H₁₀, 2 ; SNC₄H₄, (pyridine‐2‐thionate, pyS, 3 ) and [In(η²‐pyS)₂(η²‐acac)], 4 , (acac: acetylacetonate) are prepared by reacting the tris(η²‐acac)indium complex [In(η²‐acac)₃], 1 with HS₂CNC₅H₁₀, pySH, and pySH with ratios of 1:3, 1:3, and 1:2 in dichloromethane at room temperature, respectively. All of these complexes are identified by spectroscopic methods and complexes 2 and 3 are determined by single‐crystal X‐ray diffraction. Crystal data for 2 : space group, C2/c with a = 13.5489(8) Å, b = 12.1821(7) Å, c = 16.0893(10) Å, β = 101.654(1)°, V = 2600.9(3) ų, and Z = 4. The structure was refined to R = 0.033 and Rw = 0.086; Crystal data for 3 : space group, P2₁ with a = 8.8064 (6) Å, b = 11.7047 (8) Å, c = 9.4046 (7) Å, β = 114.78 (1)°, V = 880.13(11) ų, and Z = 2. The structure was refined to R = 0.030 and Rw = 0.061. The geometry around the metal atom of the two complexes is a trigonal prismatic coordination. The piperidinyldithiocarbamate and pyridine‐2‐thionate ligands, respectively, coordinate to the indium metal center through the two sulfur atoms and one sulfur and one nitrogen atoms, respectively. The short C‐N bond length in the range of 1.322(4)–1.381(6) Å in 2 and C‐S bond length in the range of 1.715(2)–1.753(6) Å in 2 and 3 , respectively, indicate considerable partial double bond character.     

Ability of fullerenes to act as η6 ligands in transition metal complexes. A comparative PM3(tm)–density functional theory study

High‐quality DFT calculations are employed to estimate the arene exchange energies for reactions of general formula: For C₆₀ and C₇₀ complexes of Cr(CO)₃, full geometry optimizations at the DFT level using moderately large basis sets were performed, while for the other systems a hybrid approach was developed in which the geometries were obtained at the PM3(tm) level and the energetics were evaluated at the DFT level. C₇₀ is shown to be a slightly better arene ligand than C₆₀; however, no enhancements of arene‐like bonding capabilities are seen for C₇₈ and C₈₄ relative to C₇₀. Explicit calculation of a series of exchange energies at the DFT level using both DFT and PM3(tm) geometries demonstrates that PM3(tm) geometries are sufficiently accurate for the calculation of energetics at a higher theoretical level, but PM3(tm) calculations are inadequate for a quantitative assessment of exchange energies. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1881–1886, 2001     

Synthesis and Nucleophilic Addition Reactions of Tricarbonyl[η5‐2‐(phenylthio)hexadienyl]iron Hexafluorophosphate

3‐Phenylthio‐3‐sulfolene ( 1 ) was readily converted to a C‐5 substituted product 2 , which upon thermolysis and complexation with Fe₂(CO)₉ gave (η⁴‐diene)iron complexes 3a and 3b . Treatment of 3a and 3b with aq. HPF₆ and Ac₂O provided the title compound 5 , which reacted regio‐ and stereospecifically with some nucleophiles to give the addition products 3b and 7 .     

Adsorption and migration growth of the Ce,O, and F adatoms on the CeO2 (111) surface: A density functional theory study

In order to investigate the microscopic behavior of the crystal surface growth of the fluorinated cerium dioxide polishing powder, the adsorption and migration of the Ce, O, and F atoms on the CeO₂ (111) surface were studied by using density functional theory with Hubbard correction +U. The adsorption energies of three single atoms at five high-symmetry sites and the migration activation energies along the migration pathway on the CeO₂ (111) surface were calculated. Results show that the most stable adsorption sites of the Ce, O, and F atoms were the O_h, Ce_bri, and Ce_t sites, respectively. The Ce atom migrated from the O_h to the O_t site. The O atom migrated from the Ce_bri to the O_bri site. The F atom migrated from the Ce_t to the O_h site. The migration activation energies of the Ce, O, and F atoms along the migration pathways were 1.526, 0.597, and 0.263 eV, respectively. The F adatom does not change the spatial configuration of the Ce and the O atoms. When the O vacancy occurs on the CeO₂ (111) surface, the F adatom can make up for the O vacancy defect.     

Insight into the π‐hole···π‐electrons tetrel bonds between F2ZO (Z = C,Si, Ge) and unsaturated hydrocarbons

The intermolecular π‐hole···π‐electrons interactions between F₂ZO (Z = C, Si, Ge) molecules and unsaturated hydrocarbons including acetylene, ethylene, 1,3‐butadiene and benzene were constructed to reveal the differences of tetrel bonds forming by carbon and heavier tetrel atoms. The ab initio computation in association with topological analysis of electron density, natural bond orbital, and energy decomposition analysis demonstrate that the strength of Si···π and Ge···π tetrel bonds is much stronger than that of C···π tetrel bonds. The Si···π and Ge···π tetrel bonds exhibit covalent or partially covalent interaction nature, while the weak C···π tetrel bonds display the hallmarks of noncovalent interaction, the electrostatic interaction is the primary influencing factor. The Si···π and Ge···π interactions are determined by both the σ‐ and π‐electron densities, while the C···π interactions are dominated mainly by the π‐electron densities. The π‐hole···π‐electrons tetrel bonds are dominated by electrostatic interaction, and polarization has a comparable contribution in the Si···π and Ge···π tetrel bonds.     

Reaktionen des [η2-{P–PtBu2}Pt(PPh3)2] und [η2-{P–PtBu2}Pt(dppe)] mit Metallcarbonylen. Bildung von [η2-{(CO)5M · PPtBu2}Pt(PPh3)2] (M = Cr,W) und [η2-{(CO)5Cr · PPtBu2}Pt(dppe)]

Coordination Chemistry of P-rich Phosphanes and Silylphosphanes. XVI [1] Reactions of [g²-{P–P^tBu₂}Pt(PPh₃)₂] and [g²-{P–P^tBu₂}Pt(dppe)] with Metal Carbonyls. Formation of [g²-{(CO)₅M · PP^tBu₂}Pt(PPh₃)₂] (M = Cr, W) and [g²-{(CO)₅Cr · PP^tBu₂}Pt(dppe)] [η²-{P–P^tBu₂}Pt(PPh₃)₂] 4 reacts with M(CO)₅ · THF (M = Cr, W) by adding the M(CO)₅ group to the phosphinophosphinidene ligand yielding [η²-{(CO)₅Cr · PP^tBu₂}Pt(PPh₃)₂] 1 , or [η²-{(CO)₅W · PP^tBu₂}Pt(PPh₃)₂] 2 , respectively. Similarly, [η²-{P–P^tBu₂}Pt(dppe)] 5 yields [η²-{(CO)₅Cr · PP^tBu₂}Pt(dppe)] 3 . Compounds 1 , 2 and 3 are characterized by their ¹H- and ³¹P-NMR spectra, for 2 and 3 also crystal structure determinations were performed. 2 crystallizes in the monoclinic space group P2₁/n (no. 14) with a = 1422.7(1) pm, b = 1509.3(1) pm, c = 2262.4(2) pm, β = 103.669(9)°. 3 crystallizes in the triclinic space group P1 (no. 2) with a = 1064.55(9) pm, b = 1149.9(1) pm, c = 1693.2(1) pm, α = 88.020(8)°, β = 72.524(7)°, γ = 85.850(8)°.     

Synthesis,X‐ray characterization and density functional theory studies of N6‐benzyl‐N6‐methyladenine–M(II) complexes (M = Zn,Cd): The prominent role of π–π, C–H···π and anion–π interactions

We report the synthesis and X‐ray characterization of the N⁶‐benzyl‐N⁶‐methyladenine ligand (L) and three metal complexes, namely [Zn(HL)Cl₃]·H₂O ( 1 ), [Cd(HL)₂Cl₄] ( 2 ) and [H₂L]₂[Cd₃(μ‐L)₂(μ‐Cl)₄Cl₆]·3H₂O ( 3 ). Complex 1 consists of the 7H‐adenine tautomer protonated at N3 and coordinated to a tetrahedral Zn(II) metal centre through N9. The octahedral Cd(II) in complex 2 is N⁹‐coordinated to two N⁶‐benzyl‐N⁶‐methyladeninium ligands (7H‐tautomer protonated at N3) that occupy apical positions and four chlorido ligands form the basal plane. Compound 3 corresponds to a trinuclear Cd(II) complex, where the central Cd atom is six‐coordinated to two bridging μ‐L and four bridging μ‐Cl ligands. The other two Cd atoms are six‐coordinated to three terminal chlorido ligands, to two bridging μ‐Cl ligands and to the bridging μ‐L through N3. Essentially, the coordination patterns, degree of protonation and tautomeric forms of the nucleobase dominate the solid‐state architectures of 1 – 3 . Additionally, the hydrogen‐bonding interactions produced by the endocyclic N atoms and NH groups stabilize high‐dimensional‐order supramolecular assemblies. Moreover, energetically strong anion–π and lone pair (lp)–π interactions are important in constructing the final solid‐state architectures in 1 – 3 . We have studied the non‐covalent interactions energetically using density functional theory calculations and rationalized the interactions using molecular electrostatic potential surfaces and Bader's theory of atoms in molecules. We have particularly analysed cooperative lp–π and anion–π interactions in 1 and π⁺–π⁺ interactions in 3 .     

A novel series of M(II) complexes of 6‐methylpyridine‐2‐carboxylic acid with 4(5)methylimidazole: Synthesis,crystal structures, α‐glucosidase activity,density functional theory calculations and molecular docking

Novel complexes of 6‐methylpyridine‐2‐carboxylic acid and 4(5)methylimidazole, namely [Mn(6‐mpa)₂(4(5)MeI)₂] ( 1 ), [Zn(6‐mpa)₂(4(5)MeI)₂] ( 2 ), [Cd(6‐mpa)₂(4(5)MeI)₂] ( 3 ), [Co(6‐mpa)₂(4(5)MeI)₂] ( 4 ), [Ni(6‐mpa)₂(4(5)MeI)(OAc)] ( 5 ) and [Cu(6‐mpa)₂(4(5)MeI)] ( 6 ), were synthesized for the first time. The structures of complexes 1 – 4 and complexes 5 and 6 were determined using X‐ray diffraction and mass spectrometric techniques, respectively. The experimental spectral analyses for these complexes were performed using Fourier transform infrared and UV–visible techniques. The α‐glucosidase inhibition activity values (IC₅₀) of complexes 1 – 6 were identified in view of genistein reference compound. Moreover, the DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level was used to obtain optimal molecular geometry and vibrational wavenumbers for complexes 1 – 6 . Electronic spectral behaviours and major contributions to the electronic transitions were investigated using TD‐DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level with conductor‐like polarizable continuum model and SWizard program. Finally, in order to investigate interactions between the synthesized complexes ( 1 – 6 ) and target protein (template structure S. cerevisiae isomaltase), a molecular docking study was carried out.     

Adsorption of polyfunctional 5‐fluorouracil and 2,4‐dithio‐5‐fluorouracil on Au(111) surface: Structure,energy, and electronic transmission

Adsorption of 5‐fluorouracil (5‐FU) and 2,4‐dithio‐5‐fluorouracil (2,4‐DT‐5‐FU) on Au(111) surface at low coverage is studied by using periodic‐slab‐density functional theory calculation. Isolated 5‐FU molecule adsorbs preferentially at bridge site in a vertical configuration via N? H group by forming the N? H···Au nonconventional H‐bond. The formation of the anchor Au? O bond is not observed. Substitution of oxygen atoms of 5‐FU with sulfur strongly influences the nature of adsorption and leads to the Au? S anchor bond and the N? H···Au nonconventional H‐bond of single 2,4‐DT‐5‐FU molecule on Au(111) surface. The adsorption site and orientation of 2,4‐DT‐5‐FU molecule on the surface are similar to those of 5‐FU. The metal–molecule coupling effects at asymmetric Au/S(N? H)S/mol/C? H/Au and Au/N? H/mol/O/Au transport junctions and symmetric Au/S(N? H)S/mol/mol/S(N? H)S/Au and Au/O/mol/mol/O/Au transport junctions are also investigated. The electronic structure is analyzed in detail, and the obtained results are used for illustrating the electron transmission in metal–molecule–metal systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Adsorption and Decomposition Mechanism of 1,1‐Diamino‐2,2‐dinitroethylene on Al(111) Surface by Periodic DFT Calculations

The adsorption of 1,1‐diamino‐2,2‐dinitroethylene (FOX‐7) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×2) slab model and three‐dimensional periodic boundary conditions. The strong attractive forces between oxygen and aluminum atoms induce the N? O bond breaking of the FOX‐7. Subsequently, the dissociated oxygen atoms and radical fragment of FOX‐7 oxidize the Al surface. The largest adsorption energy is ?940.5 kJ/mol. Most of charge transfer is 3.31e from the Al surface to the fragment of FOX‐7 molecule. We also investigated the adsorption and decomposition mechanism of FOX‐7 molecule on the Al(111) surface. The activation energy for the dissociation steps of P2 con?guration is as large as 428.8 kJ/mol, while activation energies of other con?gurations are much smaller, in range of 2.4 to 147.7 kJ/mol.     

Reaktionen von 1,1,3,3‐Tetrakis(dimethylamino)‐1 λ5, 3 λ5‐diphosphet mit 5‐Cyano‐1‐pentin und mit 2‐(Cyanmethyl)‐1‐methylpyrrol

Diphosphabenzenes. VII. Reactions of 1,1,3,3‐Tetrakis(dimethylamino)‐1 λ⁵, 3 λ⁵‐diphosphete with 5‐Cyano‐1‐pentine and 2‐(Cyanomethyl)‐1‐methylpyrrol 5‐Cyano‐1‐pentine reacts with the equimolar amount of the λ⁵‐diphosphete 1 to give the λ⁵‐diphosphinine (λ⁵‐diphosphabenzene) ( 3 ), while reaction with the double equimolar amount of 1 yields the λ⁵‐diphosphinine ( 4 ). The acyclic compount 6 is the main product of the reaction between 1 and 2‐(cyanomethyl)‐1‐methylpyrrol, 5 . Melting points of 4 · CH₃CN and 6 , and mass, nmr and ir spectra of 3 , 4 , and 6 are reported. The crystal structure of 4 · CH₃CN shows an open‐chain ylidic CPCP‐sequence, which is linked to a λ⁵‐diphosphinine via an ethylene bridge. The X‐ray structure analysis of 6 confirms the existence as an acyclic conjugated double ylid.     

Synthesis and Structures of Gallium‐β‐Diketiminate Complexes: Isolation of a Dinuclear Gallium(II) Complex

The sterically demanding β‐diketiminate ligand L^dmp [L^dmp = HC{(CMe)N(dmp)}₂, dmp = C₆H₃‐2,6‐Me₂] was used to stabilize various gallium complexes in the formal oxidation states +II and +III. The reaction of in situ generated [L^dmpLi] with gallium chloride affords [L^dmpGaCl₂] ( 1 ), which was used as starting complex to synthesize a variety of gallium(III) compounds [L^dmpGaX₂] [X = F ( 2 ), I ( 3 ), H ( 4 ), and Me ( 5 )]. Synthesis of the dinuclear complex [L^dmpGaI]₂ ( 6 ), with gallium in the formal oxidation state +II was accomplished by converting “GaI” with in situ generated [L^dmpLi] in toluene. All compounds were characterized by elemental analyses, NMR spectroscopy, LIFDI‐TOF‐MS, and single‐crystal X‐ray diffraction. Additionally DFT calculations were performed for analysis of the bonding in 6 .     

Effect of spin polarization for hydrogen adsorbed on Si(111)(1×1) surface: First‐principles calculations

The role of spin polarization on adsorption of atomic and molecular hydrogen on Si(111)(1×1) surface is examined by comparing the results of the local spin density approximation (LSD) and those of the local density approximation (LDA). A large improvement of the adsorption energies (around 0.8 eV/H) was found for the H atom adsorbed on Si(111)(1×1) surface. The inclusion of spin polarization reduces the overbinding between the H atom and the silicon surface and its effect is much more pronounced when the H atom is far away from the surface. Despite of the large changes in the adsorption energies, the main character of the potential energy surface of the H atom on Si(111)(1×1) surface is retained. An opposite effect is found in the charge‐density‐transfer map of LSD results as compared to LDA results for the H atom approaching the surface through the H3 path, in which the H atom loses electrons rather than gains electrons from the surface. The fact that the H atom tends to lose electrons in the silicon bulk has already been reported by the experimental studies for the behavior of the H atom in the p‐type silicon. For the molecular hydrogen on Si(111)(1×1) surface, the effect of the spin polarization is so small that it can be neglected. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 47–55, 2000