Green's function formalism coupled with Gaussian broadening of discrete states for quantum transport: application to atomic and molecular wires

A Green's function formalism incorporating broadened density of states (DOS) is proposed for the calculation of electrical conductance. In cluster-molecule-cluster systems, broadened DOS of the clusters are defined as continuous DOS of electrodes and used to calculate Green's function of electrodes. This approach combined with density functional theory is applied to the electrical transmission of gold atomic wires and molecular wires consisting of benzene-1,4-dithiolate, benzene-1,4-dimethanethiolate, 4,4(')-bipyridine, hexane dithiolate, and octane dithiolate. The B3LYP, B3PW91, MPW1PW91, SVWN, and BPW91 functionals with the LANL2DZ, CEP, and SDD basis sets are employed in the calculation of conductance. The width parameter was successfully determined to reproduce the quantum unit of conductance 2e(2)/h in gold atomic wires. The combination of the B3LYP hybrid functional and the CEP-31G basis set is excellent in reproducing measured conductances of molecular wires by Tao et al. [Science 301, 1221 (2003); J. Am. Chem. Soc. 125, 16164 (2003); Nano Lett. 4, 267 (2004)].     

Structure and energetics of two- and three-dimensional neutral, cationic, and anionic gold clusters Au(5< or = n < or =9)Z (Z=0,+/-1)

Low-energy structures are found on the potential energy surfaces of the neutral, cationic, and anionic gold clusters Au(5< or = n < or =9)Z (Z=0,+/-1) and on the neutral potential energy surface of Au(9). These structures provide insights on the two to three dimensional (2D-->3D) transition in small neutral and charged gold clusters. It is demonstrated that the size threshold for the 2D-3D coexistence is lower for cationic than neutral gold clusters: the 2D-3D coexistence develops for Au(5) (+) and Au(7) (+) on the cationic potential energy surfaces while only for Au(9) on the neutral. Two metastable long-lived dianions of gold clusters are also reported.     

Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.     

Reactions of sulfur dioxide with neutral vanadium oxide clusters in the gas phase. I. Density functional theory study

Thermodynamics of reactions of vanadium oxide clusters with SO2 are studied at the BPW91/LANL2DZ level of theory. BPW91/LANL2DZ is insufficient to properly describe relative V-O and S-O bond strengths of vanadium and sulfur oxides. Calibration of theoretical results with experimental data is necessary to compute reliable enthalpy changes for reactions between VxOy and SO2. Theoretical results indicate SO2 to SO conversion occurs for oxygen-deficient clusters and SO2 to SO3 conversion occurs for oxygen-rich clusters. Stable intermediate structures of VOy (y = 1 - 4) clusters with SO2 are also obtained at the BPW91/TZVP level of theory. Some possible mechanisms for SO3 formation and catalyst regeneration for condensed-phase systems are suggested. These results are in agreement with, and complement, gas-phase experimental studies of neutral vanadium oxide clusters.     

Size dependence of the structures and energetic and electronic properties of gold clusters

The structures and stabilities of gold clusters with up to 14 atoms have been determined by density-functional theory. The structure optimizations and frequency analysis are performed with the Perdew-Wang 1991 gradient-corrected functional combined with the effective core potential and corresponding valence basis set (LANL2DZ). The turnover point from two-dimensional to three-dimensional geometry for gold clusters occurs at Au12. The energetic and electronic properties of the small gold clusters are strongly dependent on sizes and structures, which are in good agreement with experiment and other theoretical calculations. The even-odd oscillation in cluster stability and electronic properties predicted that the clusters with even numbers of atoms were more stable than the neighboring clusters with odd numbers of atoms. The stability and electronic structure properties of gold clusters are also characterized by the maximum hardness principle of chemical reactivity and minimum polarizability principle.     

Interaction of amino acids with gold and silver clusters

Binding of gold and silver clusters with amino acids (glycine and cysteine) was studied using density functional theory (DFT). Geometries of neutral, anionic, and cationic amino acids with Au3 and Ag3 clusters were optimized using the DFT-B3LYP approach. The mixed basis set used here was denoted by 6-31+G** (union or logical sum)LANL2DZ. This work demonstrated that the interaction of amino acids with gold and silver clusters is governed by two major bonding factors: (a) the anchoring N-Au(Ag), O-Au(Ag), and S-Au(Ag) bonds and (b) the nonconventional N-H...Au(Ag) and O-H...Au(Ag) hydrogen bonds. Among the three forms of amino acids, anionic ones exhibited the most tendency to interact with the Au and Ag clusters. Natural bond orbital analysis was performed to calculate charge transfer, natural population analysis, and Wiberg bond indices of the complexes. Atoms-in-molecules theory was also applied to determine the nature of interactions. It was shown that these bonds are partially electrostatic and partially covalent.     

Vibrational assignments of 2-iodopyridine

A review of the vibrational assignments for 2-iodopyridine has been proposed based on the FT-Raman (3500-50cm(-1)) and IR (4000-400cm(-1)) spectral measurements. Equilibrium geometries and vibrational frequencies have been computed from a variety of electronic structure methods: the ab initio (RHF), six DFT (BLYP, BP86, B3LYP, B3P86, B3PW91 and SVWN) and MP2 methods using 3-21G*, LANL2DZ and DGDZVP basis sets. A normal coordinate analysis has been carried out: the normal modes and their couplings are characterized in terms of potential energy distributions (PEDs). The comparison of assignments for pyridine and halopyridines shows that several of the normal modes arise from coupled vibrations in 2-iodopyridine. The BP86 and B3LYP methods with LANL2DZ basis set have performed reasonably well in reproducing the observed spectra, demonstrating that the LANL2DZ basis set (with effective core potential representations of electrons near the nuclei for post-third row atoms) is suitable for 2-iodopyridine.     

Density functional study of the interaction of carbon monoxide with small neutral and charged silver clusters

CO adsorption on small neutral, anionic, and cationic silver clusters Ag(n) (n = 1-7) has been studied with use of the PW91PW91 density functional theory (DFT) method. The adsorption of CO on-top site, among various possible sites, is energetically preferred irrespective of the charge state of the silver cluster. The cationic silver clusters generally have a greater tendency to adsorb CO than the anionic and neutral silver ones, except for n = 3 and 4, and the binding energies reach a local minimum at n = 5. The binding energies on the neutral clusters, instead, reach a local maximum at n = 3, which is about 0.87 eV, probably large enough to be captured in the experiments. Binding of CO to the silver clusters is generally weaker than that to the copper and gold counterparts at the same size and charge state. This is due to the weaker orbital interaction between silver and CO, which is caused by the larger atomic radius of the silver atom. In contrast, Au atoms with a larger nuclear charge but a similar atomic radius to silver owing to the lanthanide contraction are able to have a stronger interaction with CO.     

Density functional theory study of small vanadium oxide clusters

Density functional theory is employed to study structure and stability of small neutral vanadium oxide clusters in the gas phase. BPW91/LANL2DZ level of theory is used to obtain structures of VOy (y=1-5), V2Oy (y=2-7), V3Oy (y=4-9), and V4Oy (y=7-12) clusters. Enthalpies of growth and fragmentation reactions of the lowest energy isomers of vanadium oxide molecules are also obtained to study the stability of neutral vanadium oxide species under oxygen saturated gas-phase conditions. Our results suggest that cyclic and cage-like structures are preferred for the lowest energy isomers of neutral vanadium oxide clusters, and oxygen-oxygen bonds are present for oxygen-rich clusters. Clusters with an odd number of vanadium atoms tend to have low spin ground states, while clusters with even number of vanadium atoms have a variety of spin multiplicities for their ground electronic state. VO2, V2O5, V3O7, and V4O10 are predicted to be the most stable neutral clusters under the oxygen saturated conditions. These results are in agreement with and complement previous gas-phase experimental studies of neutral vanadium oxide clusters.     

双环金属铱(Ⅲ)异腈配合物的二阶非线性光学性质

采用密度泛函理论(DFT)方法对双环金属Ir(III)异腈配合物的非线性光学(NLO)性质进行计算研究。用B3PW91(UB3PW91)(金属原子采用LANL2DZ基组,非金属原子采用6-31G*基组)方法对配合物进行几何结构优化。在优化构型基础上,采用B3PW91(UB3PW91)和B3LYP(UB3LYP)方法计算了配合物的第一超极化率(βtot),并用CAM-B3LYP(UCAM-B3LYP)(金属原子采用LANL2DZ基组,非金属原子采用6-31G**基组)方法模拟配合物的吸收光谱。结果表明,主配体的取代基(R1)和副配体的取代基(R2)对第一超极化率值贡献不大。配合物发生氧化还原反应,电荷转移方式增多,电荷转移程度增大,使βtot值显著增加,其中1a+([(C∧N)2Ir(CNR)2]+(R=CH3))发生氧化反应和还原反应的βtot值分别增大了75倍和144倍。因此,这类双环金属铱(III)异腈配合物的氧化还原反应可以有效地调节其二阶NLO性质。     

Binding of gold clusters with DNA base pairs: a density functional study of neutral and anionic GC-Aun and AT-Aun (n = 4, 8) complexes

Binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs was studied using the density functional theory (DFT). Geometries of the neutral GC-Au(n) and AT-Au(n) and the corresponding anionic (GC-Au(n))(-1) and (AT-Au(n))(-1) (n = 4, 8) complexes were fully optimized in different electronic states, that is, singlet and triplet states for the neutral complexes and doublet and quartet states for the anionic complexes, using the B3LYP density functional method. The 6-31+G basis set was used for all atoms except gold. For gold atoms, the Los Alamos effective core potential (ECP) basis set LanL2DZ was employed. Vibrational frequency calculations were performed to ensure that the optimized structures corresponded to potential energy surface minima. The gold clusters around the neutral GC and AT base pairs have a T-shaped structure, which satisfactorily resemble those observed experimentally and in other theoretical studies. However, in anionic GC and AT base pairs, the gold clusters have extended zigzag and T-shaped structures. We found that guanine and adenine have high affinity for Au clusters, with their N3 and N7 sites being preferentially involved in binding with the same. The calculated adiabatic electron affinities (AEAs) of the GC-Au(n)complexes (n = 4, 8) were found to be much larger than those of the isolated base pairs.     

Adsorption energies of molecular oxygen on Au clusters

The adsorption properties of O(2) molecules on anionic, cationic, and neutral Au(n) clusters (n=1-6) are studied using the density functional theory (DFT) with the generalized gradient approximation (GGA), and with the hybrid functional. The results show that the GGA calculations with the PW91 functional systemically overestimate the adsorption energy by 0.2-0.4 eV than the DFT ones with the hybrid functional, resulting in the failure of GGA with the PW91 functional for predicting the adsorption behavior of molecular oxygen on Au clusters. Our DFT calculations with the hybrid functional give the same adsorption behavior of molecular oxygen on Au cluster anions and cations as the experimental measurements. For the neutral Au clusters, the hybrid DFT predicts that only Au(3) and Au(5) clusters can adsorb one O(2) molecule.     

金镍二元团簇结构和电子性质的理论研究

在UBP86/LANL2DZ和UBP86/def2-TZVP水平下详细研究了AumNin (m＋n≤6)团簇的几何结构和电子性质. 详细地分析了团簇的结构特征, 平均结合能, 垂直电离势, 垂直电子亲和能, 电荷转移以及成键特征. 所有混合团簇中, 镍原子趋于聚集到一起, 形成最多Ni—Ni键, 金原子分布在镍原子聚集体周围以形成最多Au—Ni键. Ni原子较少团簇的电子性质与纯金团簇类似, 呈现一定奇偶振荡. 混合团簇中存在镍到金原子间的电荷转移. Ni原子较少团簇中, 自旋电子主要定域在Ni原子上, Ni原子较多团簇中, Au原子明显受到自旋极化. 混合团簇的分波态密度表明, AuNi混合团簇对小分子的反应活性要高于纯金团簇.     

Bidimensionality of 8-atom clusters of Au: first principles study and comparison with Ag clusters

We have calculated the lowest energy structures of 8-atom neutral gold clusters using the density functional theory approach. In contrast with current literature that finds kinetic energy to be the determinant component, we have found that the 2D structure is energetically favored due to a higher electron delocalization that stems from the relativistic contraction of Au atom size which cause 3D clusters to deform. This higher delocalization lowers the total energy of the 2D structures against the 3D ones. Silver clusters do not suffer this size contraction, hence there is no higher delocalization in the 2D clusters, and their fundamental structure will be 3D.     

Adsorption of molecular hydrogen and hydrogen sulfide on Au clusters

The authors present theoretical results describing the adsorption of H2 and H2S molecules on small neutral and cationic gold clusters (Au(n)((0/+1)), n=1-8) using density functional theory with the generalized gradient approximation. Lowest energy structures of the gold clusters along with their isomers are considered in the optimization process for molecular adsorption. The adsorption energies of H2S molecule on the cationic clusters are generally greater than those on the corresponding neutral clusters. These are also greater than the H2 adsorption energies on the corresponding cationic and neutral clusters. The adsorption energies for cationic clusters decrease with increasing cluster size. This fact is reflected in the elongations of the Au-S and Au-H bonds indicating weak adsorption as the cluster grows. In most cases, the geometry of the lowest energy gold cluster remains planar even after the adsorption. In addition, the adsorbed molecule gets adjusted such that its center of mass lies on the plane of the gold cluster. Study of the orbital charge density of the gold adsorbed H2S molecule reveals that conduction is possible through molecular orbitals other than the lowest unoccupied molecular orbital level. The dissociation of the cationic Au(n)SH2+ cluster into Au(n)S+ and H2 is preferred over the dissociation into Au(m)SH2+ and Au(n-m), where n=2-8 and m=1-(n-1). H2S adsorbed clusters with odd number of gold atoms are more stable than neighboring even n clusters.     

金钯二元小团簇的几何结构与电子性质

在UBP86/LANL2DZ和UB3LYP/def2-TZVP水平下详细研究了AumPdn(m+n≤6)团簇的几何结构和电子性质.阐明了团簇的结构特征、平均结合能、垂直电离势、垂直电子亲和能、电荷转移以及成键特征.除单取代混合团簇(AunPd和AuPdn,n=5或6)外,五和六原子混合团簇中钯原子趋于聚集到一起形成Pdcore,金原子分布在Pdcore周围形成PdcoreAushell结构.含一个和两个钯原子团簇的电子性质与纯金团簇类似,呈现一定奇偶振荡.混合团簇的电子性质,如最高占据分子轨道(HOMO),最低未占据分子轨道(LUMO),垂直电离势,垂直电子亲和能,Fermi能级和化学硬度等均与团簇空间结构和金、钯原子数之比直接相关.混合团簇中存在钯原子到金原子间的电荷转移,表明团簇中存在明显金钯间成键作用.分析团簇的电荷分布、前线轨道和化学硬度表明,金钯混合团簇对小分子如O2、H2和CO等的反应活性要强于纯金团簇.     

Electronic structures of 4d transition metal monoxides by density functional theory

Bond distances, dissociation energies, ionization potentials and electron affinities of 4d transition metal monoxides from YO to CdO and their positive and negative ions were studied by use of density functional methods B3LYP, BLYP, B3PW91, BPW91, B3P86, BP86, SVWN, MPW1PW91 and PBE1PBE. It was found that calculated properties are highly dependent on the functionals employed, especially for dissociation energy. For most neutral species, pure density functionals BLYP, BPW91 and BP86 have good performance in predicting dissociation energy than hybrid density functionals B3LYP, B3PW91 and B3P86. In addition, BLYP gives the largest bond distance compared with other density functional methods, while SVWN gives shortest bond distance, largest dissociation energy and electron affinity. For the ground state, the spin multiplicity of the charged species can be obtained by ± 1 of their corresponding neutral species.     

铝原子团簇Al5、Al5-和Al5+稳定结构的密度泛函理论研究

采用密度泛函理论的四种方法:杂化密度泛函B3LYP与B3PW91、Perdew-Wang91交换与相关泛函WP91PW91、局域自旋密度近似SVWN,研究了A15、Al5-和Al5+团簇的多种可能结构,找到了它们稳定的结构与自旋态,与已有的理论结果作了比较,并计算了Al5-的绝热与垂直电子离解能、Al5的绝热与垂直电离势,同有关的实验数据比较,符合较好.同时对四种密度泛函方法的计算结果作了一些比较与讨论.     

Density functional study of small neutral and charged silver cluster hydrides

Small neutral, anionic, and cationic silver cluster hydrides AgnH and anionic HAgnH (n=1-7) have been studied using the PW91PW91 density functional method. It was found that the most stable structure of the AgnH complex (neutral or charged) does not always come from that of the lowest energy bare silver cluster plus an attached H atom. Among various possible adsorption sites, the bridge site is energetically preferred for the cationic and most cases of neutral Agn. For anionic Agn, the top site is preferred for smaller Agn within n相似文献   

杂硼原子簇XB6+ (X=C,Si, Ge,Sn, Pb)的稳定性和芳香性

利用从头算MP2方法和密度泛函理论B3LYP和B3PW91方法, 研究了杂硼原子簇XB₆⁺ (X=C, Si, Ge, Sn, Pb)的结构、稳定性及化学键合情况. 对C, Si, Ge, B使用6-311+G(d)基组, 对Sn和Pb使用LANL2DZ赝势基组. 研究结果表明, 具有C_s对称性的假平面XB₆⁺ (X=C, Si, Ge, Sn, Pb)结构是势能面上的全域极小点, 其稳定性要高于C_6v对称性的锥形结构和C₂对称性的假锥形结构. 在B3LYP水平上, 对这些异构体的势能面的极小点进行了自然键轨道(NBO)的分析; 对最稳定构型的最高占据分子轨道(HOMO)和最低空轨道(LUMO)能级差、分子轨道(MO)和核独立化学位移(NICS)进行了计算和讨论. 分析了杂原子和硼原子间、相邻硼原子间的键合情况, 讨论了最稳定构型的芳香性质.