The stability of small helical gold nanorods: a relativistic density functional study

Multistrand 7-1 helical Au(24), Au(32), and Au(40) structures with three, four, and five gold atoms in the central strand and 21, 28, and 35 gold atoms in the coaxial tube are investigated using relativistic density functional theory. We demonstrate that these helical gold nanorods are stable structures with a rather large HOMO-LUMO gap, a large binding energy per atom, a very large vertical dissociation energy, and an extremely large electron affinity. On the basis of the atomic charges and the nature of the frontier orbitals, they are also expected to have strong selective reactivity toward electrophiles and nucleophiles. Furthermore, we show that these helical Au(n) structures and, in particular, the helical Au(40) structure are competitive energetically and chemically with respect to alternate cage and compact Au(n) structures. We consider two fragmentations of the helical Au(40) structure and perform a density of states analysis to examine both charge transfer and electronic polarization.     

Adsorption of CO on oxygen preadsorbed neutral and charged gas phase Pd4 clusters: A density functional study

We present the results of a density functional calculation on adsorption of O₂, CO, and their coadsorption at various sites of neutral, cationic, and anionic Pd₄ clusters. For all the clusters, the dissociative adsorption of oxygen sitting on Pd bridge sites is found to be preferable. Both O₂ and CO binding energies are found to be higher for the anionic Pd₄ cluster followed by cationic and neutral cluster. However, binding energies of O₂ or CO in the coadsorption complexes follow the trend: anionic > neutral > cationic. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Interaction of copernicium with gold: Assessment of applicability of simple density functional theories

Interactions of Cn (element 112) atom with small Au clusters are studied using accurate ab initio scalar relativistic coupled cluster method for correlation treatment and two‐component relativistic density functional theory (RDFT) to take account of spin‐dependent relativistic effects. The results demonstrate the failure of RDFT with simple generalized‐gradient and hybrid functionals in describing Cn–Au bonds in complex systems. © 2013 Wiley Periodicals, Inc.     

The RTAM electronic bibliography,version 17.0, on relativistic theory of atoms and molecules

The RTAM bibliography is freely available at rtam.csc.fi and the Version 17.0 of August 22, 2013 now contains 16,566 items from the year 1916–2013. “Production works” were systematically covered until 1999. Since the year 2000, mainly methodological papers were included. The methods and principles behind RTAM are described. © 2013 Wiley Periodicals, Inc.     

Yb、YbO电子激发态的相对论含时密度泛函理论研究

本文用基于精确二分量哈密顿（exact two—component Hamiltonian）的相对论含时密度泛函理论（time-dependent relativistic density functional theory）计算了Yb和YbO的电子激发态,并利用对称性、自然原子轨道对激发态性质和归属进行了详细分析,所得结果支持实验对YbO基态与激发态的指认．     

Nanoengineered micro gold shells for LDI-TOF analysis of small molecules

This paper reports on analyses of small molecules with laser desorption/ionization time of flight (LDI-TOF) mass spectrometry (MS) using nanostructure-embedded micro gold shells (μAuSs). The mass analyses of amino acids, sugars, peptides, and their mixtures gave apparent mass peaks for analytes without any significant background interferences. μAuSs afforded a better limit of detection (LOD) and a higher signal-to-noise ratio than gold nanoparticles, which are commonly used for LDI-TOF analysis of small molecules. We believe μAuSs have advantages in terms of simplicity, detection limit, and reproducibility, and therefore, they constitute a significant addition to the organic matrix-free analytical tools that are currently in wide use.     

Cyanide adsorbed on coinage metal electrodes: A relativistic density functional investigation

The adsorptive properties of cyanide (CN⁻) on coinage metal (M) electrodes (M=Cu, Ag, Au) have been investigated using a relativistic density functional method. The way to model the electrochemical potential applied to the electrodes is to consider the systems in the presence of a perturbative external field F. The field-perturbative approach is proven to be a suitable method in interpreting the observed spectral shifts with electrode potential. The calculated potential-dependent shifts of ω_{M(SINGLE BOND)CN} and ω_{C(SINGLE BOND)M} are similar for the three metals, in agreement with experiment observations. The relativistic effects are required to account for the similarity in the frequency shifts of ω_{M(SINGLE BOND)CN}. The calculated vibrational tuning rates dω_{C(SINGLE BOND)N}/dF are 6.61×10⁻⁷, 6.61×10⁻⁷, and 5.64×10⁻⁷ cm⁻¹/(V/cm) for M=Cu, Ag, and Au, respectively. The coupling of the M(SINGLE BOND)CN and C(SINGLE BOND)N internal modes contributes significantly (about 25%) to the size of the frequency shifts Δω_{C(SINGLE BOND)N} of the ligand. The effect of electric fields on the metal(SINGLE BOND)CN⁻ bonding is also investigated. It is shown that changes in the magnitude of CN⁻ to the metal donation and M(SINGLE BOND)CN bond strength occur under the influence of the electric field. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 175–185, 1998     

Predicting whether aromatic molecules would prefer to enter a carbon nanotube: A density functional theory study

The interaction of a carbon nanotube (CNT) with various aromatic molecules, such as aniline, benzophenone, and diphenylamine, was studied using density functional theory able to compute intermolecular weak interactions (B3LYP-D3). CNTs of varying lengths were used, such as 4-CNT, 6-CNT, and 8-CNT (the numbers denoting relative lengths), with the lengths being chosen appropriately to save computation times. All aromatic molecules were found to exhibit strong intermolecular binding energies with the inner surface of the CNT, rather than the outer surface. Hydrogen bonding between two aromatic molecules that include N and O atoms is shown to further stabilize the intermolecular adsorption process. Therefore, when benzophenone and diphenylamine were simultaneously allowed to interact with a CNT, the aromatic molecules were expected to preferably enter the CNT. Furthermore, additional calculations of the intermolecular adsorption energy for aniline adsorbed on a graphene surface showed that the concavity of graphene-like carbon sheet is in proportion to the intermolecular binding energy between the graphene-like carbon sheet and the aromatic molecule.     

Uranyl complexation by monodentate nitrogen donor ligands. A relativistic density functional study

To examine the interaction of uranyl with nitrogen containing groups of humic substances, the model complexes [UO₂(H₂O)₄L_N]²⁺, L_N = NH₂CH₃, N(CH₃)₃, and NC₅H₅ in aqueous solution were studied computationally with an all‐electron relativistic density functional method. Results are compared with the corresponding penta‐aqua complex of uranyl. Although pyridine coordinates with about the same strength as L = H₂O, methylamine binds ～10 kJ mol^?1 stronger and trimethylamine ～40 kJ mol^?1 weaker than a fifth aqua ligand. Yet, each of these ligands L_N donates about the same amount of charge to uranyl as L = H₂O. U? N bonds are ～10 pm longer than the U? O bonds of the aqua ligands. From the present model results, one does not expect that, when compared with carboxyl groups, monodentate N‐containing functional groups contribute significantly to uranyl complexation by humic substances. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Interaction of NO molecules with Pd clusters: Ab initio density–functional study

The adsorption of NO molecules on small Pd_n (n = 1?6) clusters has been studied using first‐principles density‐functional theory. Three adsorption sites were considered: vertex (on–top), bridge, and hollow. Adsorption is strong, ranging from 2 to 3 eV. In all cases NO adsorbs in a bent configuration. Calculated shifts in N–O bond vibration frequencies (with anharmonic corrections) agree very well with available experimental data. In contrast to metallic Pd surfaces, adsorption of NO on palladium clusters causes considerable changes in geometry around adsorption site because palladium d‐orbitals rehybridize to maximize the overlap with NO orbitals (mainly the antibonding π*). Thus, the overall energetic effect of NO adsorption is the result of two competing processes: lowering of the total energy through tighter bonding with NO and rising the energy due to cluster deformation. The Pd_n–NO bond creation is governed by electron transfer from Pd–d orbitals into the NO π*. As a result, the Pd cluster becomes locally demagnetized (with total magnetic moment of 1 μ_B located at Pd atoms not connected to NO) and the NO molecule is activated: the N–O bond length is increased and the vibration frequency is redshifted. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study

The mechanism of the action of copper-dependent quercetin 2,3-dioxygenase(2,3QD) has been investigated by means of hybrid density functional theory.The 2,3QD enzyme cleaves the O-heterocycle of a quercetin by incorporation of both oxygen atoms into the substrate and releases carbon monoxide.The calculations show that dioxygen attack on the copper complex is energetically favorable.The adduct has a possible near-degeneracy of states between [Cu 2+-(substrate-H +)] and [Cu +-(substrate-H).],and in addition the pyramidalized C 2 atom is ideally suited for forming a dioxygen-bridged structure.In the next step,the C 3-C 4 bond is cleaved and intermediate Int 5 is formed via transition state TS 4.Finally,the O a-O b and C 2-C 3 bonds are cleaved,and CO is released in one concerted transition state(TS 5) with the barrier of 63.25 and 61.91 kJ/mol in the gas phase and protein environments,respectively.On the basis of our proposed reaction mechanism,this is the rate-limiting step of the whole catalytic cycle and is strongly driven by a relatively large exothermicity of 100.86 kJ/mol.Our work provides some valuable fundamental insights into the behavior of this enzyme.     

Adsorption change of cyclohexyl acetylene on gold nanoparticle surfaces

The conformational changes of cyclohexyl acetylene (CHAL) on gold nanoparticle surfaces were investigated by means of concentration- and temperature-dependent surface-enhanced Raman scattering (SERS). Depending on concentrations and temperatures, the spectral changes of the acetylene ν(C≡C) stretching vibration on gold nanoparticles appeared to be more conspicuous than those of cyclohexyl ring modes. The density functional theory (DFT) calculation was performed at the level of B3LYP/6-31G++(d,p) to compare the energetic stability and vibrational frequencies of the various conformers of cyclohexanethiol (CHT) and CHAL. The DFT calculations were also carried out at the level of B3LYP/LACVP** on the CHAL molecule adsorbed on Au clusters at several sites to explain the spectral changes of the acetylene ν(C≡C) stretching vibration.     

Understanding hydrogenation of the adenine‐thymine base pairs and their anions: A density functional study

The B3LYP/DZP++ approach has been used to investigate the properties of hydrogenated radicals and anions of adenine‐thymine (A‐T) base pairs. Our calculations show that the hydrogenated radicals and anions have relatively high stabilities compared with the single adenine and thymine base. The conformations and hydrogen‐bond interactions of A‐T base pairs have obviously changed once the hydrogen atoms attached to the A‐T base pairs and their anion. As for the hydrogenated A‐T radicals, all of them exhibit relatively high electron affinities and different hydrogenation properties with respect to their components. The process of the bond formations of (C6)‐H (adenine) and (C6)‐H (thymine) are the most favorable in energetics. The two hydrogenation channels have the reaction Gibbs free energies (ΔG°) of ?51.8 and ?54.2 kcal mol^?1, respectively. Also, the calculations on the basis of CPCM model imply that the solvent effect plays an important role in the electron attachment and hydrogenation reactions, and can stabilize the hydrogenated A‐T anions. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Reaction mechanism of platinum dimer cation with ammonia based on the relativistic density functional study

The gas‐phase reactions between Pt and NH₃ have been investigated using the relativistic density functional approach (ZORA‐PW91/TZ2P). The quartet and doublet potential energy surfaces of Pt + NH₃ have been explored. The minimum energy reaction path proceeds through the following steps: Pt(⁴Σ_u) + NH₃ → q‐1 → d‐2 → d‐3 → d‐4 → d‐Pt₂NH⁺ + H₂. In the whole reaction pathway, the step of d‐2 → d‐3 is the rate‐determining step with a energy barrier of 36.1 kcal/mol, and exoergicity of the whole reaction is 12.0 kcal/mol. When Pt₂NH⁺ reacts with NH₃ again, there are two rival reaction paths in the doublet state. One is degradation of NH and another is loss of H₂. In the case of degradation of NH, the activation energy is only 3.4 kcal/mol, and the overall reaction is exothermic by 8.9 kcal/mol. Thus, this reaction is favored both thermodynamically and kinetically. However, in the case of loss of H₂, the rate‐determining step's energy barrier is 64.3 kcal/mol and the overall reaction is endothermic by 8.5 kcal/mol, so it is difficult to take place. Predicted relative energies and barriers along the suggested reaction paths are in reasonable agreement with experimental observations. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Computational study of water and ammonia dimers with density functional theory methods

The structures and energies for the dimerization of water and ammonia molecules were computed with density functional theory (DFT) and ab initio methods. For all studies the same 6-311+G(2d,2p) basis set was used. Two linear hydrogen-bonded and cyclic ammonia dimer structures were computed and their relative stability is discussed. From the systematic studies, hybrid DFT methods were selected as reliable for computing the parameters of these types of van der Waals' complex.     

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

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     

The capture of carbonyl sulfide by N-methyldiethanolamine: A systematic density functional theory investigation

In this contribution, the mechanism of carbonyl sulfide (COS) absorption by N-methyldiethanolamine (MDEA) aqueous solution was explored via theoretical computations. Detailed reaction mechanisms were analyzed using density functional theory (DFT) calculations at the B3LYP-D3 level of theory. In total, four different pathways for COS absorption by MDEA have been considered. The most favorable pathway for the removal of COS is a three-step mechanism including the hydrolysis, proton transfer, and dissociation of CO₂, and hydrolysis is the rate-determining step. The mechanisms of the COS absorption by different amines were investigated, and the calculated results suggest that the total energy barrier for the COS absorption by MDEA is comparable to that by monoethanolamine (MEA), diethanolamine (DEA), and diisopropylamine (DIPA), indicating the COS absorption by all the four amines are feasible, while MDEA gives a better performance in terms of thermodynamics.     

A DFT Study of Thiophene Adsorption on the Rh（111） Surfaces

Thiophene adsorption on the Rh(111) surfaces has been investigated by density functional theory.The results show that the adsorption at the hollow and bridge sites is the most stable.The molecular plane of the thiophene ring is distorted,the C=C bond is stretched to 1.448  and the C-C bond is shortened to 1.390.The C-H bonds tilt 22～42oaway from the surface.The calculated adsorption geometries are in reasonable agreement with population analysis and density of states.The thiophene molecule obtains 0.74 electrons,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.The reaction paths and transition states for desulfurization of the molecule have been investigated.The bridge adsorption structure of thiophene leads to a thiol via an activated reaction with an energetic barrier of 0.30 eV.This second step is slightly difficult,and dissociation into a C4H4 fragment and a sulfur atom is possible,with an energetic barrier of 0.40 eV.     

Theoretical density functional theory studies on interactions of small biologically active molecules with isolated heme group

We present ab-initio density functional theory studies on the interactions of small biologically active molecules, namely NO, CO, O(2), H(2)O, and NO(2) (-) with the full-size heme group. Our results show that the small molecule-iron bond is the strongest in carbonyl and the weakest in nitrite system. Trans influence induced by NO binding to the five-coordinate heme complex is shown. Nitric oxide in the resulting complex might be described as NO(-). The differences among the small ligands of XO type (CO, NO, O(2)), and their distant chemical behavior from H(2)O and NO(2) (-) ligands in binding to the Fe(II) ion, are shown. Moreover, the role of the heme ring as a reservoir of electrons in the studied complexes is invoked. The analysis of the parameters defining the iron-histidine bond indicates that this bond is longer and weaker in nitrosyl and carbonyl complexes than in the other systems. Our findings support the proposed mechanism of soluble guanylate cyclase (sGC) activation and suggest that the first step of sGC activation by CO may be the same as during the activation by NO. Obtained results are then compared with the data concerning smaller model of the heme, the porphyrin complexes, available in the literature.