Geometric, electronic, and bonding properties of AuNM (N = 1-7, M = Ni, Pd, Pt) clusters

Employing first-principles methods, based on density functional theory, we report the ground state geometric and electronic structures of gold clusters doped with platinum group atoms, Au(N)M (N = 1-7, M = Ni, Pd, Pt). The stability and electronic properties of Ni-doped gold clusters are similar to that of pure gold clusters with an enhancement of bond strength. Due to the strong d-d or s-d interplay between impurities and gold atoms originating in the relativistic effects and unique properties of dopant delocalized s-electrons in Pd- and Pt-doped gold clusters, the dopant atoms markedly change the geometric and electronic properties of gold clusters, and stronger bond energies are found in Pt-doped clusters. The Mulliken populations analysis of impurities and detailed decompositions of bond energies as well as a variety of density of states of the most stable dopant gold clusters are given to understand the different effects of individual dopant atom on bonding and electronic properties of dopant gold clusters. From the electronic properties of dopant gold clusters, the different chemical reactivity toward O(2), CO, or NO molecule is predicted in transition metal-doped gold clusters compared to pure gold clusters.     

DOPA醌在Cu（100）表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

A spectroscopic study of self-assembled monolayer of porphyrin-functionalized oligo(phenyleneethynylene)s on gold: the influence of the anchor moiety

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules () with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH(3) (), an acetyl protected thiol with methylene linker, -CH(2)-S-COCH(3) (), and a trimethylsilylethynyl group, -C[triple bond, length as m-dash]C-Si(CH(3))(3) () have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared. The integrity and structural properties of these films were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The results suggest that the films formed from have a high orientational order with an almost upright orientation and dense packing of the molecular constituents, i.e. represent a high quality SAM. In contrast, molecule formed disordered molecular layers on Au, even though the molecule-surface bonding (thiolate) is the same as in the case of molecule . This suggests that the methylene linker in molecule has a strong impact on the quality of the resulting film, so that a well-ordered SAM cannot be formed. The silane system, , is also able to bind to the gold surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised of strongly inclined molecules. The above results suggest that the nature of the anchor group along with a possible linker is an important parameter which, to a high extent, predetermines the entire quality of OPE-based molecular layers.     

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.     

Electronic structure and luminescence of [AuS2PPh(OCH2CHCH2)]2 complex

The complex [AuS₂PPh(OCH₂CHCH₂)]₂ (1) presents an Au(I)–Au(I) intramolecular and intermolecular bonding with luminescence properties. To understand the nature of these features, fully optimized geometries were obtained by three computational methods, DFT/B3LYP, MPW1B95 and MP2. An Au(I)–Au(I) intramolecular bond was found in the ground state, at the three levels of theory, exhibiting an aurophilic interaction between the two gold atoms. Two molecules of the complex were optimized using DFT/B3LYP, in order to analyze the intermolecular interaction between them. The resulting intermolecular bonding distance between the two adjacent gold atoms on each molecule is 3.16 Å, indicating a strong aurophilic attraction. Time dependent calculations indicate that the first excited state with nonzero oscillator strength is a singlet, with an excitation energy equal to 3.16 eV. This should correspond to the absorption band seen experimentally at 3.10 eV. The lowest energy emission of (1) was obtained at 2.73 eV, which corresponds to the emission peak resulting from phosphorescence and located at 2.53 eV. This transition comes from an excited electron on the p orbitals of the ligands that is transferred to the d orbitals of the gold atoms on the HOMO. This interaction may be attributed to Ligand to Ligand–Metal Charge Transfer (LL–MCT).     

Rapid Estimation of Basis Set Error and Correlation Energy Based on Mulliken Charges and Mulliken Matrix with the Small 6-31g* Basis Set

Good, density functional quality (B3LYP/6-31G*) ground state total electronic energies have been approximated using single point Hartree–Fock-self consistent field (HF-SCF/6-31G*) total energies and Mulliken partial charges versus. Mulliken matrix (electrons assigned to atoms and atoms pairs from Mulliken population analysis). This is a development of our rapid estimation of basis set error and correlation energy from partial charges (REBECEP) method, published earlier (see references [21,22,30]. The development is as follows: (1) A larger set of atoms (H, C, N, O, F, Si, P and S) are considered as building blocks for closed shell, neutral, ground state molecules at their equlibrium geometry; (2) geometries near equilibrium geometry are also considered; (3) A larger set, containing 115 molecules, was used to fit REBECEP parameters; (4) most importantly, electrons belonging to chemical bonds (between atom pairs) are also considered (Mulliken matrix) in addition to the atoms (Mulliken charges), using more REBECEP parameters to fit and yielding a more flexible algorithm. With these parameters a rather accurate closed shell ground state electronic total energy can be obtained from a small basis set HF-SCF calculation in the vicinity of optimal geometry. The 3.3 kcal/mol root mean square deviation of REBECEP improves to 1.5 kcal/mol when using Mulliken matrix instead of Mulliken charges.     

Experimental and Theoretical Evidence for an Agostic Interaction in a Gold(III) Complex

The first agostic interaction in a gold complex is described. The presence of a bonding C?H???Au interaction in a cationic “tricoordinate” gold(III) complex was suggested by DFT calculations and was subsequently confirmed by NMR spectroscopy at low temperature. The agostic interaction was analyzed computationally using NBO and QTAIM analyses (NBO=natural bond orbital; QTAIM=quantum theory of atoms in molecules).     

Single molecule electron transport junctions: charging and geometric effects on conductance

A p-benzenedithiolate (BDT) molecule covalently bonded between two gold electrodes has become one of the model systems utilized for investigating molecular transport junctions. The plethora of papers published on the BDT system has led to varying conclusions with respect to both the mechanism and the magnitude of transport. Conductance variations have been attributed to difficulty in calculating charge transfer to the molecule, inability to locate the Fermi energy accurately, geometric dispersion, and stochastic switching. Here we compare results obtained using two transport codes, TRANSIESTA-C and HUCKEL-IV, to show that upon Au-S bond lengthening, the calculated low bias conductance initially increases by up to a factor of 30. This increase in highest occupied molecular orbital (HOMO) mediated conductance is attributed to charging of the terminal sulfur atom and a corresponding decrease in the energy gap between the Fermi level and the HOMO. Addition of a single Au atom to each terminal of the extended BDT molecule is shown to add four molecular states near the Fermi energy, which may explain the varying results reported in the literature.     

环四甲撑四硝胺(HMX)结构和性质的DFT研究

用密度泛函理论(DFT)B3LYP方法,取6-31G基组,求得环四甲撑四硝胺分子的几何构型、电子结构、 IR谱和298～1200 K的热力学性质.全优化几何构型和电子结构均具有Ci对称性.在相邻原子之间以N-NO2键的Mulliken集居数最小,表明其间电子分布较少,预示其为热解和起爆的引发键.IR谱与实验结果良好相符.     

环三甲撑三硝胺(RDX)结构和性质的DFT研究

环三甲撑三硝胺(RDX)是综合性能好、使用极广的高能炸药。本文用密度泛函理论(DFT)B3LYP方法,取6-31G*基组,求得其分子几何构型、电子结构、IR谱和热力学性质。全优化几何构型和电子结构均具有C3V对称性。在相邻原子之间以NNO2键的Mulliken集居数最小,表明其间电子分布较少,预示其为热解和起爆的引发键。IR谱与实验结果良好相符。计算所得298-1200K的热力学性质,对进一步深入研究RDX的反应和性质有助。     

Conformation and dynamics of arylthiol self-assembled monolayers on Au(111)

We report a computational investigation of the conformation and the dynamics of self-assembled monolayers (SAMs) of a set of aromatic thiols arranged in the ( radical3 x radical3)-R30 degrees packing ratio on a Au(111) surface using molecular dynamics (MD) simulations. It was found that the molecular conformations were better defined for the arylthiol with two phenyl groups as compared to those with a single phenyl group and that the chemical structure of the head and tail groups had a considerable influence on the system geometry. In line with the density functional theory (DFT) calculations of small thiol molecules, we found for the SAMs that the face-centered cubic (fcc) site on the Au(111) surface was the most preferred, followed by the hexagonal close-packed (hcp) site, while the bridge position showed the characteristics of a local energy maximum. The dynamics of thiol head groups on these three Au sites was found to govern the overall dynamics of SAMs as measured by the mean square displacement. We also report that both the conformation and the dynamics on the studied time scale were driven by the SAM formation energy.     

Tris(bis(trimethylsilyl)amido)samarium: X-ray structure and DFT study

The compound Sm[N(SiMe(3))(2)](3) has been investigated experimentally by X-ray crystallography and computationally by DFT methods. The structure is analogous to that of other tris[bis(trimethylsilyl)amido]lanthanides, featuring positional disorder of the metal atom above and below the plane defined by the three N donor atoms, resulting in a trigonal pyramidal configuration. One of the methyl groups of each amido ligand is placed above the apex of the pyramid at close distance to the metal center suggesting the presence of agostic interactions. The DFT calculations have been carried out on the real molecule and on a Si[N(SiH(3))(SiH(2)Me)](3) model where the unique Me group was placed above the apex of the pyramid to probe the agostic interaction. In both cases, the optimized geometry reproduces very well the experimental structure and indicates the presence of beta-Si-C agostic interactions. A comparison of the optimized geometries obtained in the presence/absence of the Sm d and the Si d orbitals serves to illustrate the relevance of these orbitals for (i). the establishment of the pyramidal configuration at Sm, (ii). the Sm-N bond length, and (iii). the Sm-(beta-Si-C) bond length. The bonding analysis, which was carried out by both Mulliken and NBO methods, not only confirms the importance of the metal d orbitals for the Sm-N and Sm-(beta-Si-C) chemical bonding but also illustrates the relevance of electrostatic terms in the agostic interaction. Sm-N and N-Si pi bonding is present according to the bonding analysis but is not important for enforcing the planar configuration at N, nor the pyramidal configuration at Sm.     

Molecular Dynamics Simulation of the Self-assembled Monolayers of 1-Adamantanethiolate and Its Derivatives on Au（111） Surfaces

The self-assembled monolayers （SAMs） of 1-adamantanethiolate and its derivatives on Au（111） surface were investigated. Density functional theory （DFT） calculation indicates that the most stable configuration for absorption is at the face centered cubic （fcc）-bridge site. Canonical ensemble molecular dynamics （MD） simulations were carried out to study the structures and energies of the SAMs. The ordered structures of the SAMs were analyzed by means of radial distribution function and the relative stability of the SAMs was compared. It was concluded by the comparison of various contributions to the SAM formation energy that the formation of the SAMs was determined by the intermolecular nonbonding interaction and the chemical bonding interaction of sulfur and gold.     

Effect of green solvents physical,chemical, biological and bonding nature on 5-acetyl-thiophene-2-carboxylic acid by DFT and TD-DFT approach – An antiviral agent

The density functional theory (DFT) is applied to 5-acetyl-thiophene-2-carboxylic acid (5AT2CA). To determine the optimal structure and different physical, chemical, and biological characteristics, the B3LYP technique and 6–311++G(d,p) basis set are employed. The binding energies and ellipticity are determined using the atoms in molecules theory (AIM). NBO analysis is used to study the exchanges between the contributor and receiver by energies. By utilizing HOMO-LUMO values and important electronic parameters, stability is determined. The molecular electrostatic potential (MEP) and Fukui function from Mulliken charges are used to determine the reactive regions of the molecule. The TD-DFT technique obtains the electronic transition using UV–Vis spectrum with various solvents. NLO studies were carried out on this molecule. Studies of temperature effect on 5AT2CA are done by thermodynamic parameters. Drug-likeness and molecular docking tests are used to evaluate the bioactivity and antiviral properties.     

Geometries, stabilities, and electronic properties of small anion Mg-doped gold clusters: a density functional theory study

First-principle density functional theory is used for studying the anion gold clusters doped with magnesium atom. By performing geometry optimizations, the equilibrium geometries, relative stabilities, and electronic and magnetic properties of [Au(n)Mg]? (n = 1-8) clusters have been investigated systematically in comparison with pure gold clusters. The results show that doping with a single Mg atom dramatically affects the geometries of the ground-state Au(n+1)? clusters for n = 2-7. Here, the relative stabilities are investigated in terms of the calculated fragmentation energies, second-order difference of energies, and highest occupied?lowest unoccupied molecular orbital energy gaps, manifesting that the ground-state [Au(n)Mg]? and Au(n+1)? clusters with odd-number gold atoms have a higher relative stability. In particular, it should be noted that the [Au?Mg]? cluster has the most enhanced chemical stability. The natural population analysis reveals that the charges in [Au(n)Mg]? (n = 2-8) clusters transfer from the Mg atom to the Au frames. In addition, the total magnetic moments of [Au(n)Mg]? clusters exhibit an odd-even oscillation as a function of cluster size, and the magnetic effects mainly come from the Au atoms.     

Investigation of correlation between impact sensitivities and nitro group charges in nitro compounds

A new method of calculating the Mulliken net charges of the nitro group, Q(NO)()2, to assess impact sensitivities for nitro compounds is established. All calculations including optimizations and Mulliken population and frequency analyses are performed by density functional theory (DFT) and the general gradient approximation (GGA) method in Acceryls' code Dmol(3) with the Beck-LYP hybrid functional and the DNP basis set. As a result, the charges on nitro group can be regarded as a structural parameter to estimate the impact sensitivity on the bond strength, oxygen balance, and molecular electrostatic potential. The compound with more -Q(NO)()2 will be insensitive and gives a large value of impact sensitivity H(50)(). This method considering the molecular structure is applicable for almost all nitro compounds when the C-NO(2), N-NO(2), or O-NO(2) bond is the weakest in the molecule. According to the results in this paper, the compounds with -Q(NO)()2 >0.23e show H(50)() 相似文献   

An ab initio study of crystal field effects,part 3: Solid- and gas-phase geometry of formamide,modeling the changes in a peptide group due to hydrogen bonds

A model of the solid state of formamide is constructed by optimizing a central molecule in an electrostatic field of the proper symmetry. Attention is paid to the way the electrostatic charges are obtained. Point charges obtained from a Mulliken population analysis yield a final set of atomic charges in the central molecule that agree reasonably well with those obtained experimentally after ak-refinement of formamide. Point charges from a so-called stockholder partitioning agree slightly less. Furthermore, the simple crystal field adaptation of standard ab initio methods reproduces within experimental limits the differences in C=O and C-N lengths, observed between the gas-phase and the solid state geometry. Again, a Mulliken field agrees slightly better than a stockholder field, but the difference in performance is statistically insignificant. In a survey of 221 high-quality single-crystal x-ray determinations of compounds containing the peptide group N-C=O, we found evidence supporting quantitatively the conclusion that the increase of C=O and the decrease of C-N bond length in the gas-to-solid transition is dominated by the effects of hydrogen bonding. It was shown that the C=O bond lengthens by about 0.011 å per H-bond it accepts, while the N-C bond diminishes by about 0.015 å per H-bond it donates.Part 2, see Ref. [5].     

Theoretical and Experimental Investigation of the 2-Hydroxyquinoxaline Structure: Study of the Tautomerization Equilibrium System and Analysis of the Electronic Properties

All reasonable tautomers of 2-hydroxyquinoxaline (2HQ) are investigated by the DFT B3LYP/6-311G(d) method. The optimized geometries corresponding to the minimum energy show that the keto form QX2 is the most stable form. The geometry optimization parameters (bond lengths, bond angles) are compared to the X-ray values. Calculated FTIR, UV, and NMR spectra of QX2 are compared to the experimental data to achieve a synergetic computational and spectroscopic approach for the structure analysis of 2HQ. The electronic properties, frontier molecular orbitals, and Mulliken atomic charges are calculated.     

Inhibition at perimeter sites of Au/TiO2 oxidation catalyst by reactant oxygen

TiO(2)-supported gold nanoparticles exhibit surprising catalytic activity for oxidation reactions compared to noble bulk gold which is inactive. The catalytic activity is localized at the perimeter of the Au nanoparticles where Au atoms are atomically adjacent to the TiO(2) support. At these dual-catalytic sites an oxygen molecule is efficiently activated through chemical bonding to both Au and Ti(4+) sites. A significant inhibition by a factor of 22 in the CO oxidation reaction rate is observed at 120 K when the Au is preoxidized, caused by the oxygen-induced positive charge produced on the perimeter Au atoms. Theoretical calculations indicate that induced positive charge occurs in the Au atoms which are adjacent to chemisorbed oxygen atoms, almost doubling the activation energy for CO oxidation at the dual-catalytic sites in agreement with experiments. This is an example of self-inhibition in catalysis by a reactant species.     

Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields

We apply density functional theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew-Burke-Ernzerhof exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an electronvolt. The DFT+U technique, parametrized to B3LYP-predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than that of PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP and approximately 0.1 A changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first-row transition metal ion complexes in a condensed-matter setting.