Conformations and charge transport characteristics of biphenyldithiol self-assembled-monolayer molecular electronic devices: a multiscale computational study

We report a computational study of conformations and charge transport characteristics of biphenyldithiol (BPDT) monolayers in the (sqrt.3 x sqrt.3)R30 degrees packing ratio sandwiched between Au(111) electrodes. From force-field molecular-dynamics and annealing simulations of BPDT self-assembled monolayers (SAMs) with up to 100 molecules on a Au(111) substrate, we identify an energetically favorable herringbone-type SAM packing configuration and a less-stable parallel packing configuration. Both SAMs are described by the (2sqrt.3 x sqrt.3)R30 degrees unit cell including two molecules. With subsequent density-functional theory calculations of one unit cell of the (i) herringbone SAM with the molecular tilt angle theta approximately 15 degrees , (ii) herringbone SAM with theta approximately 30 degrees , and (iii) parallel SAM with theta approximately 30 degrees, we confirm that the herringbone packing configuration is more stable than the parallel one but find that the energy variation with respect to the molecule tilting within the herringbone packing is very small. Next, by capping these SAMs with the top Au(111) electrode, we prepare three molecular electronic device models and calculate their coherent charge transport properties within the matrix Green's function approach. Current-voltage (I-V) curves are then obtained via the Landauer-Buttiker formula. We find that at low-bias voltages (|V| < or = 0.2 V) the I-V characteristics of models (ii) and (iii) are similar and the current in model (i) is smaller than that in (ii) and (iii). On the other hand, at higher-bias voltages (|V| > or 0.5 V), the I-V characteristics of the three models show noticeable differences due to different phenyl band structures. We thus conclude that the BPDT SAM I-V characteristics in the low-bias voltage region are mainly determined by the -Au [corrected] interaction within the individual molecule-electrode contact, while both intramolecular conformation and intermolecular interaction can affect the BPDT SAM I-V characteristics in the high-bias voltage region.     

Crystal and molecular structure of a 4-nitro-6(5H)-phenanthridinone

L. Ya. Karpov Scientific Research Institute of Physical Chemistry. Translated from Zhurnal Strukturnoi Khimii, Vol. 28, No. 5, pp. 177–179, September–October, 1987.     

The mechanisms of the reactions of W and W+ with COx (x=1, 2): a computational study

The mechanisms of the reactions of W and W+ with COx (x=1, 2) were studied at the CCSD(T)/[SDD+6-311G(d)]//B3LYP/[SDD+6-31G(d)] level of theory. It was shown that the gas-phase reaction of W with CO2 proceeds with a negligible barrier via an insertion pathway, W(7S)+CO2(1A1)-->W(eta2-OCO)(6A')-->OW(eta1-CO)(1A)-->WO (3Sigma+)+CO(1Sigma). This oxidation process is calculated to be exothermic by 32.4 kcal/mol. Possible intermediates of this reaction are the W(eta2-OCO) and OWCO complexes, among which the latter is 37.4 kcal/mol more stable and lies 39.7 and 7.3 kcal/mol lower than the reactants, W(7S)+CO2(1A1), and the products, WO (3Sigma+)+CO(1Sigma), respectively. The barrier separating W(eta2-OCO) from OWCO is 8.0 kcal/mol (relative to the W(eta2-OCO) complex), which may be characterized as a W+delta-(CO2)-delta charge-transfer complex. Ionization of W does not change the character of the reaction of W with CO2: the reaction of W+ with CO2, like its neutral analog, proceeds via an insertion pathway and leads to oxidation of the W-center. The overall reaction W+(6D) + CO2(1A1)-->W(eta1-OCO)+(6A)-->OW(eta1-CO)+(4A)-->WO+(4Sigma+)+CO(1Sigma) is calculated to be exothermic by 25.4 kcal/mol. The cationic reaction proceeds with a somewhat large (9.9 kcal/mol) barrier and produces two intermediates, W(eta1-OCO)+(6A) and OW(eta1-CO)+(4A). Intermediate W(eta1-OCO)+(6A) is 20.0 kcal/mol less stable than OW(eta1-CO)+(4A), and separated from the latter by a 35.2 kcal/mol barrier. Complex W(eta1-OCO)+(6A) is characterized as an ion-molecular complex type of W+-(CO2). Gas-phase reactions of M=W/W+ with CO lead to the formation of a W-carbonyl complex M(eta1-CO) for both M=W and W+. The C-O insertion product, OMC, lies by 5.2 and 69.3 kcal/mol higher than the corresponding M(eta1-CO) isomer, for M=W and W+, respectively, and is separated from the latter by a large energy barrier.     

A plethora of carbene interconversions on the C(5)H(4)S energy surface: a computational study

The potential energy surface for the reaction of atomic carbon with thiophene has been studied computationally. Intermediates which are energetically viable include the 2- and 3-thienylcarbenes 8 and 11, thiacyclohexa-3,5-dien-2-ylidene, 10, and thiacyclohexa-2,3,5-triene, 6. In accord with experimental data, 6 and 8 are in equilibrium. The lowest-energy pathway for rearrangement of 6 to 8, which is endothermic by 14.5 kcal/mol, involves ring opening to Z-2-penten-4-ynthial which then recloses to carbene 8. A 1,4 addition of C across the diene system in thiophene generates an ylid which rearranges with little or no barrier to cyclopentadienethione, the global minimum on this potential energy surface.     

Crystal structure, coloring problem and magnetism of Gd(5-x)Zr(x)Si4

Ternary Gd(5-x)Zr(x)Si(4) silicides were synthesized by arc melting of the constituent elements and subsequent heat treatments. The Gd(5-x)Zr(x)Si(4) phases adopt the orthorhombic Gd(5)Si(4)-type (space group Pnma) structure for x≤ 0.25 and the tetragonal Zr(5)Si(4)-type (space group P4(1)2(1)2) structure for x≥ 1.0, respectively. The samples with intermediate compositions contain two phases. Single-crystal X-ray diffraction reveals a preferential site occupancy for Zr on the three metal sites in the order of M3 > M2 > M1. Size arguments based on the local coordination environments suggest that the larger Gd atoms preferentially occupy the larger M1 site, while the smaller Zr atoms tend to occupy the smaller metal sites, M2 and M3. Tight-binding linear-muffin-tin orbital calculations illustrate a role of the metal-silicon bonds in the metal site occupation. An increase in the valence electron concentration through the Zr substitution weakens the Si-Si interactions but enhances the metal-silicon and metal-metal interactions. The Curie temperature of Gd(5-x)Zr(x)Si(4) decreases gradually with the increasing Zr content.     

Synthesis and molecular structure of bis(areno)piperidinoaza-14(17)-crowns-4(5)

The condensation of dialkyl ketones with α,ω-bis(2-formylphenoxy)- or α,ω-bis(1-formylnaphthalen-2-yloxy)-3-oxapentane and-3,6-dioxaoctane in the presence of ammonium acetate according to Petrenko-Kritchenko gave 14–41% of new bis(areno) aza crowns, bis(areno)piperidinoaza-14-crown-4 and bis(benzo)-piperidinoaza-17-crown-5, having functional substituents in the piperidine fragment. The yield of the aza crown ether appreciably decreases upon extension of the polyether chain in the aldehyde component. The molecular structure of two of the obtained macrocyclic compounds and the relative configuration of asymmetric carbon atoms in the piperidine ring were determined by X-ray analysis, and the size of their internal cavities was estimated.     

The elusive structure of CrCl(2): a combined computational and gas-phase electron-diffraction study

Chromium dichloride poses a challenge to the structural chemist. Its different forms of aggregation and association display all well-known structural distortions induced by vibronic interactions. The monomeric molecule has a Renner-Teller distorted bent geometry, the crystal exhibits strong Jahn-Teller distortion, and the oligomers have slightly distorted four-membered-ring structures due to the pseudo-Jahn-Teller effect. In this paper we report on the low-energy structures of the monomer and its clusters, Cr(2)Cl(4), Cr(3)Cl(6), and Cr(4)Cl(8), from unrestricted Kohn-Sham (broken-symmetry) density functional calculations. CrCl(2) was also investigated at higher level, including coupled-cluster and state-average CASSCF computations. The global minima of the gas-phase clusters consist of two-dimensional, antiferromagnetically coupled chains of CrCl(2) units forming four-membered, doubly bridged Cr(2)Cl(2) rings, closely resembling the solid-state structure of alpha-CrCl(2). Each Cr atom in these chains has spin quantum number S=2. This suggests that the CrCl(2) nucleation starts very early on the structural chain motif found in the solid. There is only a very small change in energy from the antiferromagnetically to the ferromagnetically coupled Cr atoms, which indicates little spin-coupling between the metal centers. There is an approximately constant change in energy, about 50 kcal mol(-1), with every new CrCl(2) unit during cluster formation. Information about the structure of these clusters was used in the re-analysis of high-temperature electron-diffraction data. The vapor at 1170 K contained about 77 % monomeric molecules, 19 % dimers, and a small amount of trimers. Monomeric CrCl(2) was found to be bent with a bond angle of 149(10) degrees, in good agreement with our computations, which resulted in a Renner-Teller distortion of the lowest-energy (5)Pi(g) electronic state into the bent (5)B(2) ground state. The vibrational spectrum of chromium dichloride is discussed and the thermodynamics of cluster formation from 1000-2000 K is examined.     

Crystal and molecular structure of 2-(p-tolylimino)-4-methyl-4-ethyl-5-methylenethiazolidine

It was found by an x-ray diffraction study of 2-(p-tolylimino)-4-methyl-4-ethyl-5-methylenethiazolidine that the thiazolidine molecules in the crystal are joined together to form centrosymmetric dimers due to the formation of N-H...N hydrogen bonds. The structure of the dimer and the bond lengths and angles of the thiazolidine are presented. The study confirmed the imino structure of the investigated compound. The pathway of fragmentation of the alkyl groups attached to C₄ during mass-spectroscopic analysis was analyzed thoroughly.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1617–1619, December, 1981.     

A molecular dynamics study of the atomic structure of (CaO)x(SiO2)1-x glasses

The local atomic environment of Ca in (CaO)x(SiO2)1-x glasses is of interest because of the role of Ca in soda-lime glass, the application of calcium silicate glasses as biomaterials, and the previous experimental measurement of the Ca-Ca correlation in CaSiO(3) glass. Molecular dynamics has been used to obtain models of (CaO)x(SiO2)1-x glasses with x = 0, 0.1, 0.2, 0.3, 0.4, and 0.5, and with approximately 1000 atoms and size approximately 25 A. As expected, the models contain a tetrahedral silica network, the connectivity of which decreases as x increases. In the glass-forming region, i.e., x = 0.4 and 0.5, Ca has a mixture of 6- and 7-fold coordination. Bridging oxygen makes an important contribution to the coordination of Ca, with most bridging oxygens coordinated to 2 Si plus 1 Ca. The x = 0.5 model is in reasonable agreement with previous experimental studies, and does not substantiate the previous theory of cation ordering, which predicted Ca arranged in sheets. In the phase-separated region, i.e., x = 0.1 and 0.2, there is marked clustering of Ca.     

Chemical structure and orientation of ethylene on Si(114)-(2 x 1)/c(2 x 2)

The basic chemical structure and orientation of ethylene chemisorbed on Si(114)-(2 x 1) at submonolayer coverage is characterized in ultrahigh vacuum using transmission Fourier transform infrared (FTIR) spectroscopy. The spectra are consistent with di-sigma bonding of ethylene to the surface with a preferential molecular orientation over macroscopic lengths. These results are supported by density functional theory (DFT) calculations of vibrational frequencies for optimized ethylene-Si(114) structures occupying the dimer and rebonded atom surface sites. A detailed analysis of the strong angular and polarization dependence of the C-H stretching mode intensities is also consistent with the adsorption structures identified by DFT, indicating that ethylene chemisorbs with the C-C bond axis parallel to the structural rows oriented along the [10] direction on the Si(114)-(2 x 1) surface. The results indicate that the unique structure of this surface makes it an excellent template for elucidating relationships between surface structure and organic reaction mechanisms on silicon.     

Conformations of the glycine tripeptide analog Ac-Gly-Gly-NHMe: a computational study including aqueous solvation effects

A computational study of the conformational preferences of the glycine tripeptide analog, Ac-Gly-Gly-NHMe, has been carried out. The molecule is considered in isolation as well as with a continuum model of aqueous solvation. In the absence of solvent, several low-energy conformers are found that exhibit turnlike structures including type I and type II β turns. Upon consideration of aqueous solvation, two conformers, corresponding to the type I and II turn structures are found to be significantly lower in energy than all others. Results from ab initio molecular orbital theory calculations at MP2/aug-cc-pVTZ//MP2/6-311+G(d,p) are compared with those from density functional theory with B3LYP, ωB97X-D, B97-D, and M06-2X as well as several empirical force fields.     

Statics and dynamics of ethane molecules in AlPO(4)-5: a molecular dynamics simulation study.

From an experimental perspective, there has been disagreement among researchers on whether ethane would display single-file or normal diffusive behavior in the channels of AlPO(4)-5. Pulsed field gradient nuclear magnetic resonance measurements implied single-file diffusion, while quasielastic neutron scattering showed normal diffusion. In this paper we present the results of extensive classical molecular dynamics simulations of the diffusion of ethane molecules adsorbed in AlPO(4)-5. Our aim is to provide microscopic details of the static and dynamic properties of the adsorbed molecules in order to verify whether the conditions for the single-file regime can be achieved in a nondefective AlPO(4)-5 crystal structure.     

Electron correlation effects at semiconductor surfaces and interfaces: Si(111)-5x5, Si(111)-7x7 and Sn/Ge(111)

Electron correlation effects associated with the dangling bond surface states of Si(111)-5×5, Si(111)-7×7 and Sn/Ge(111)-3×3 are analyzed. In all the cases, extensive LDA-calculations are performed and effective two-dimensional Hamiltonians are deduced. Our analysis of these Hamiltonians shows that: (a) the Si(111)-5×5 surface states exhibits a metal-insulator transition; (b) the Si(111)-7×7 surface shows important similarities with the Si(111)-5×5 case, but it has a dangling bond surface band having a metallic character; (c) finally, the Sn/Ge(111)-3×3 dangling bond surface bands also shows important correlation effects that are found, however, not to affect the metallic character of the surface bands.     

Synthesis and proposed crystal structure of a disordered cadmium arsenate apatite Cd5(AsO4)3Cl(1-2x-y)O(x)[symbol: see text](x)OH(y)

During a study into the synthesis of minerals composed of mining wastes aimed at improving their immobilisation, a cadmium arsenate apatite has been prepared by hydrothermal methods. The structure of this apatite was analysed by single crystal X-ray diffraction, and was found to consist of a standard apatite framework based on Cd(5)(AsO(4))(3)X, where X represents an anion resident on the (0,0,0.25) site. The framework is hexagonal with the space group P6(3)/m(no 176), a= 9.9709(8), c= 6.4916(4)[Angstrom]. The X ion site is predominantly occupied by Cl(-) ions; however due to significant shortening of the c axis exhibited by all cadmium containing apatite phases, a pure chlorapatite is not possible without a significant cation deficiency. No evidence of the necessary deficiency was found in the crystal structure. For larger bromo- and iodo-apatites significant modulations along the c-axis are required to accommodate the halide. This paper examines a number of compensation mechanisms and proposes that a minor disorder of chloride, oxide and hydroxide located on the X ion site provides the required charge compensation mechanism. This is contrary to previous complex modulations proposed in the literature. The proposed chemical formula is Cd(5)(AsO(4))(3)Cl(1-2x-y)O(x)[symbol:see text](x)OH(y) where [symbol: see text] represents a vacancy.     

H(x)TeV9O28]((5-x)-) (x=1 and 2): vanadotellurates with decavanadate structure

Two new vanadotellurates, [HTeV(9)O(28)](4-) and [H(2)TeV(9)O(28)](3-) have been synthesized and structurally characterized as tetra-n-butylammonium (TBA) salts: TBA(4)[HTeV(9)O(28)]·2CH(3)CN [triclinic, space group P ?1, a = 16.7102(6) ?, b = 17.4680(7) ?, c = 17.9634(7) ?, α = 74.412(1)°, β = 67.494(1)°, γ = 74.160(2)°, Z = 2] and TBA(3)[H(2)TeV(9)O(28)] [monoclinic, space group P2(1)/c, a = 13.0013(5) ?, b = 19.157(1) ?, c = 28.453(1) ?, β = 97.222(2)°, Z = 4]. The results of the structural analyses indicate that the four O atoms that bridge two V atoms on the Te side are the most basic ones in the structure. The results of density-functional theory (DFT) calculations support this view.     

Surface structures of SrTiO3 (001): a TiO2-rich reconstruction with a c(4 x 2) unit cell

We report the solution of the c(4 x 2) reconstruction of SrTiO(3) (001), obtained through a combination of high-resolution transmission electron microscopy, direct methods analysis, and density functional theory. The structure is characterized by a single overlayer of TiO(2) stoichiometry in which TiO(5) polyhedra are arranged into edge-shared structures, in contrast to the corner-shared TiO(6) polyhedra in bulk. This structural pattern is similar to that reported by us earlier for the (2 x 1) reconstruction of the same crystal face formed at higher temperature. We discuss probable mechanisms of surface stabilization as revealed by these two solutions which are likely to apply to other reconstructions of SrTiO(3) (001) and, possibly, other perovskites in general.     

The structure of uracil: a laser ablation rotational study

The jet-cooled rotational spectrum of uracil has been investigated using laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. The quadrupole structure originated by the two 14N nuclei of uracil has been completely resolved and assigned. This provides a definitive method to establish the pyrrolic or pyrimidinic nature of the N nuclei and allows us to conclude that the observed tautomer of uracil in the gas phase is the diketo form. From the rotational constants of the isotopic species detected, a structure of uracil has been determined.     

Basis set effects on Cu(I) coordination in Cu-ZSM-5: a computational study

DFT calculations on the coordination of Cu⁺ to the framework oxygen atoms of Al-substituted ZSM-5 were performed by using combinations of different basis sets in order to investigate the dependence of the results on the adopted computational level. With low-end basis sets, a large basis set superposition error (BSSE) favors the coordination of Cu⁺ to three to four oxygen atoms of the framework, only two of which belong to the AlO₄ tetrahedron corresponding to the investigated T-site. More extended basis sets considerably lower the BSSE and favor the coordination of Cu⁺ to only two oxygen atoms of the AlO₄ tetrahedron. Upon interaction with NO, the Cu⁺ ion is always coordinated by two oxygen atoms of the AlO₄ tetrahedron, independently of the basis set adopted and of the coordination number before NO adsorption. The shift from three- to twofold coordination caused by the Cu⁺–NO interaction requires a deformation energy that lowers the final adsorption energy. Such an effect is relevant with low-end basis sets, whereas it is substantially absent with more extended basis sets, which favor the twofold coordination of Cu⁺ even before NO adsorption. As a result, high-end basis sets increase the NO interaction energy with respect to that calculated by low-end basis sets, in agreement with experiments and suggesting a possible re-interpretation of the catalytic properties of the investigated sites. Provided suitable scale factors are employed, the N–O stretching frequencies of adsorbed nitrogen oxide calculated by sufficiently extended basis sets turned out in fair agreement with experimental findings.     

Thermal decomposition of branched silanes: a computational study on mechanisms

The initial steps of the thermal decomposition of silanes in the gas phase were examined by DFT-B3LYP calculations, with particular attention being paid to the way in which the reactivity pattern changes with the degree of branching of the silane. Besides the established pathways-1,2-hydrogen shift, H(2) elimination, and homolytic dissociation-1,3-hydrogen shift was also explored as an initial reaction step which leads to disilene structures. Subsequent silylene insertion and initial steps of radical chain reactions were also studied. To estimate the energetic changes with temperature, various reaction free energies and the corresponding activation free energies up to 650?°C were calculated. Accordingly, the leading reaction channel at room temperature is 1,2-hydrogen shift with subsequent silylene insertion; for higher degrees of branching, competing pathways (homolytic dissociation, 1,3-hydrogen shift, and radical polymerization) gain in relative importance. At high temperatures, the rate-determining step changes to homolytic dissociation, and thereby the apparent rates of decomposition become dependent on the degree of branching.