Adsorption of small molecules on helical gold nanorods: A relativistic density functional study

We study the adsorption of a variety of small molecules on helical gold nanorods using relativistic density functional theory. We focus on Au₄₀ which consists of a central linear strand of five gold atoms with seven helical strands of five gold atoms on a coaxial tube. All molecules preferentially adsorb at a single low‐coordinated gold atom on the coaxial tube at an end of Au₄₀. In most cases, there is significant charge transfer (CT) between Au₄₀ and the adsorbate, for CO and NO₂, there is CT from the Au₄₀ to adsorbate while for all other molecules there is CT from the adsorbate to Au₄₀. Thus, Au₄₀‐adsorbate can be described as a donor–accepter complex and we use charge decomposition analysis to better understand the adsorption process. We determine the adsorption energy order to be C₅H₅N >NO₂ > CO > NH₃ > CH₂?CH₂ > CH₂?CH? CHO > NO > HC?CH > H₂S > SO₂ > HCN > CH₃OH > H₂C?O > O₂ > H₂O > CH₄ > N₂. We find that the Au? C, Au? N, Au? S, and Au? O bonds are surprisingly strong, with clear implications for reactivity enhancement of the adsorbate. The Au? H bond is relatively weak but, for interactions via an H atom that is bonded to a carbon atom (e.g., CH₄), we find that there is large charge polarization of the Au? H? C moiety and partial activation of the inert C? H bond. Although the Au? S and Au? O bonds are generally weaker than the Au? C and Au? N bonds, we find that adsorption of H₂S or H₂O causes greater distortion of Au₄₀ in the binding region. However, the degree of distortion is small and the helical structure is retained, demonstrating the stability of the helical Au₄₀ nanorod under perturbations. © 2014 Wiley Periodicals, Inc.     

Density functional study on electronic structures and reactivity in methyl‐substituted chelates used in organic light‐emitting diodes

The electronic structure and reactivity trends of a set of tris‐(n‐methyl‐8‐quinolinolato) metal (III) (n = 0, 3, 4, 5; metal = Al⁺³, Ga⁺³) used as electron‐transport layer in organic light‐emitting diodes were studied and compared. All geometries were optimized at B3LYP/6‐31G(d,p) level of theory. The geometries of the ground state (S₀) of unsubstituted molecules AlQ3 and GaQ3 were found to be slightly affected by the methyl group, which is in agreement with previous works. Methyl‐derivatives conserve largely the electronic structures of AlQ3 and GaQ3. The energies of the frontier orbitals highest occupied and lowest unoccupied molecular orbital are raised by the electron‐releasing effect of methyl group. Molecular orbital contribution analysis reveals that the orbital population is essentially the same for both MQ3 and their derivatives. Analyses of the ionization potential and electron affinity showed that MQ3 tend to be better hole‐blockers than methylated analogues and 5Me‐MQ3 have higher hole‐injection capability than the other methyl‐substituted derivatives. The global reactivity analysis showed that the electrophilicity index can be an indicator of electron‐injection capability in these complexes. Local reactivity analysis showed that atomic sites that are prone to nucleophilic/electrophilic attack are atoms C‐4 in L3/C‐5 in L1. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Crystal overgrowth on gold nanorods: tuning the shape, facet, aspect ratio, and composition of the nanorods

Electrochemically prepared Au nanorods were used as seeds for the overgrowth of thin shells of gold, silver, and palladium by using a mild reducing agent, ascorbic acid, in the presence of surfactants at ambient condition. The unique crystal facets of the starting nanorods results in anisotropic crystal overgrowth. The overgrowth rates along different crystallographical directions can be further regulated by adding foreign ions or by using different metal reduction methods. This overgrowth study provides insights on how different metal ions could be reduced preferentially on different Au nanorod surfaces, so that the composition, aspect ratio, shape, and facet of the resulting nanostructures can be rationally tuned. These surfactant-stabilized bimetallic Au(core)M(shell) (M=Au, Ag, Pd) nanorod colloids might serve as better substrates in surface-enhanced Raman spectroscopy as well as exhibiting enhanced catalytic properties.     

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.     

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.     

Theoretical study of the structure and antimicrobial activity of horminone

The structural and electronic parameters of the horminone molecule, an abietan diterpene quinone, were studied by means of all‐electron calculations using Hartree–Fock and density functional theory‐based methods, as implemented in the Gaussian98 program. The 6‐31G orbital basis sets were used for the C, H, O, and Mg atoms. The results allow the identification of the negative site of horminone (HM) most favorable for its binding to the Mg²⁺ ion. The HM–Mg²⁺ complex is assumed to play a significant role in the antibacterial activity. First, it penetrates the membrane cell. Then, through its interaction with rRNA, it inhibits the protein synthesis in several types of bacteria. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 411–421, 2003     

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     

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     

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.     

DFT study on the effects of substituents on the structure and properties of dithiophosphate collectors

The structures and properties of seven substituted dithiophosphate (DTP) collectors containing three types of functional groups (O₂PS₂, C₂PS₂, and N₂PS₂) were studied using density functional theory. The collectors studied were dibutyl dithiophosphate (DNBDTP), diisobutyl dithiophosphate (DIBDTP), dibutoxyethyl dithiophosphate (DBOEDTP), xylenol dithiophosphate (DMPDTP), diisobutyl dithiohypophosphite (3418A), diphenylamine dithiophosphate (DTADTP), and dicyclohexylamine dithiophosphate (DCADTP). The structural analysis showed that the P S bond lengths in the C₂PS₂ and N₂PS₂ types are longer than those in the O₂PS₂ type, indicating that the strength of the P S bond is weaker in the former two. The frontier molecular orbital studies showed that the energy differences between the highest occupied molecular orbitals (HOMO) of 3418A (C₂PS₂ type) and DCADTP (N₂PS₂ type) and the lowest unoccupied molecular orbital (LUMO) of galena are significantly lower than those of the other collectors, suggesting that C₂PS₂ type and N₂PS₂ type with cyclohexane could enhance the interaction with galena. Using the Fukui function to calculate the nucleophilicity and electrophilicity of the sulfur atom indicated that the S atom exhibits nucleophilicity, especially in DMPDTP and DTADTP, which contain benzene rings, and the S atom exhibits strong nucleophilicity without electrophilicity. However, due to the lack of contribution from S atoms to the LUMO orbitals, the S atoms in these two compounds are not participate in any LUMO reactions. The adsorption results demonstrated that 3418A (C₂PS₂ type) and DCADTP (N₂PS₂ type) exhibit the strongest adsorption on Pb²⁺ ions, while DMPDTP (C₂PS₂ type) and DTADTP (O₂PS₂ type) which contain benzene rings, as well as DBOEDTP (C₂PS₂ type) which does not contain a benzene ring, exhibit weaker interaction compared to the other compounds. These are consistent with the results of the frontier molecular orbital and electrophilic nucleophilicity calculations.     

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     

Molecular analysis of water clusters: Calculation of the cluster structures and vibrational spectrum using density functional theory

Density functional theory (DFT) is applied to obtain absorption spectra at THz frequencies for molecular clusters of H₂O. The vibrational modes of the clusters are calculated. Coupling among molecular vibrational modes explains their spectral features associated with THz excitation. THz excitation is associated with vibrational frequencies which are here calculated within the DFT approximation of electronic states. This is done for both isolated molecules and collections of molecules in a cluster. The principal result of the paper is that a crystal-like cluster of 38 water molecules together with a continuum solvent background is sufficient to replicate well the experimental vibrational frequencies.     

Controlling the oxidative addition of aryl halides to Au(I)

By means of density functional theory calculations, we computationally analyze the physical factors governing the oxidative addition of aryl halides to gold(I) complexes. Using the activation strain model of chemical reactivity, it is found that the strain energy associated with the bending of the gold(I) complex plays a key role in controlling the activation barrier of the process. A systematic study on how the reaction barrier depends on the nature of the aryl halide, ligand, and counteranion allows us to identify the best combination of gold(I) complex and aryl halide to achieve a feasible (i.e., low barrier) oxidative addition to gold(I), a process considered as kinetically sluggish so far. © 2014 Wiley Periodicals, Inc.     

Two hydrogen ligands on tetrairidium clusters: a relativistic density functional study

Structural and energetic properties of Ir(4)H(2) have been determined by applying a relativistic density functional method. As previously obtained for Ir(4)H, terminal coordination of H ligands is preferred, in contrast to some other transition metals. Square-planar Ir(4) isomers with an H binding energy of up to 318 kJ mol(-1) per atom were determined as the most stable structures of Ir(4)H(2). Isomers with a tetrahedral or butterfly structure of the metal framework exhibit average H atom binding energies of up to approximately 300 kJ mol(-1). For all three types of isomers, a surprisingly large number of stable minima was identified. Unexpectedly, structural as well as energetic properties of Ir(4)H(2) complexes are very similar to Ir(4)H. Thus binding of an H atom to Ir(4) is only slightly affected by the presence of a second H ligand. In all cases examined, the reaction H(2)+ Ir(4)--> H(2)Ir(4) was found to be exothermic with reaction energies of up to 170 kJ mol(-1).