Ternary uranyl hydroxo acetate complexes: A computational study of structure, energetics, and stability constants

We studied computationally uranyl monohydroxo monoacetate complexes in aqueous solution using a scalar relativistic all-electron density functional method. Such ternary uranyl complexes may serve as models of ternary uranyl humate complexes which are important for the speciation of uranyl in the environment. As for simple uranyl monocarboxylate complexes, we calculated bidentate coordination to be slightly preferred due to entropy and solvation effects. Compared to uranyl acetate, uranyl hydroxo acetate exhibits an elongated uranyl bond and a short U-OH bond of ∼214 pm. The latter may provide a signature for direct identification of such ternary complexes by EXAFS. As expected from the lower charge of uranyl monohydroxide, complexation by acetate is less exoenergetic than acetate complexation of uranyl. In contrast, experimental complexation constants of uranyl humate and uranyl hydroxo humate are quite similar. Thus, one may question the interpretation of experimental results that assign simple ternary complexes as result of uranyl humate complexation at neutral pH.     

Ligand effects due to resonance character in LAuCCH<Superscript>−</Superscript> (L = F,Cl, Br,I, CCH) complexes: an NBO/NRT analysis

The organogold complexes of LAuCCH^? (L?=?F, Cl, Br, I, CCH) were investigated using natural bond orbital/natural resonance theory (NBO/NRT) methods. The NBO/NRT results strongly support the general resonance-type three-center-four-electron (3c/4e) picture of LAuCCH: L^?: Au–CCH ? L–Au :CCH^?, arising from hyperconjugation interactions. The sums of ionic and covalent contributions to both L–Au and Au–CCH bonds are all slightly larger than that due to the additional π-back bonding within the 3c/4e hyperbonded triad. This complementary relationship between L–Au and Au–CCH bond orders implies a competing relationship between the ancillary ligand and CCH around the gold atom. We discuss the ligand effects in the LAuCCH^? series on the basis of this competing relationship.     

A (U)MP2(full) and (U)CCSD(T) theoretical investigation into the substituent effects on the intermolecular T-shaped F–H…π interactions between HF and LBBL (L = ?H, ∶CO, :NN, –Cl, –CN and –NC)

The substituent effects on the intermolecular T-shaped F-H...π interactions are investigated between HF and LBBL (L = -H, : CO, :NN, -Cl, -CN and -NC) using the (U)MP2(full) and (U)CCSD(T) methods with the 6-311++G(2 d,p) basis set. The B ≡ B triple-bond contraction is found in the complexes with lone-pair-electron donors while the B = B double-bond is lengthened in the systems with the single-electron substituents upon complexation. The T-shaped F-H...π interaction energies follow the order of ClB = BCl...HF>HB = BH...HF>NNB ≡ BNN...HF>OCB ≡ BCO...HF>CNB = BNC...HF>NCB = BCN...HF. The electron-donating substituents : CO and :NN increases electron density of the B ≡ B triple bond by the delocalization interaction E ((2)) π ((CO/NN) → Lp(B)) while the electron-withdrawing substituents -CN and -NC decrease electron density of the B = B double bond by means of the π-π conjugative effect. The analyses of the APT atomic charge, "truncated" model, natural bond orbital (NBO), atoms in molecules (AIM) and electron density shifts reveal the nature of the substituent effect and explain the origin of the B ≡ B bond contraction.     

Theoretical investigations on the hydrogen bonding of nitrile isomers with H2O,HF, NH3 and H2S

The hydrogen bonds formed by the interaction of nitriles with water, hydrogen fluoride, ammonia and hydrogen sulphide have been studied using B3LYP and second-order Møller–Plesset perturbation (MP2) methods and 6-311+ + G(d,p) basis set. The energies and structures of 80 hydrogen-bonded complexes between nitriles and small molecules were examined systematically using B3LYP and MP2 procedure. Categorisation of the hydrogen bonds involved in the various complexes led to an ordering of hydrogen bond donor and acceptor abilities for some functional groups. The interaction energies have been corrected for the basis set superposition error using Boy's counterpoise correction method. The Morokuma energy decomposition analysis reveals that the strong interactions are due to the attractive contributions from the electrostatic (ES), polarisation (PL) and charge transfer (CT) components. The topological parameters, electron density and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital (NBO) analysis has also been performed to study the CT from proton acceptor to the antibonding orbital of the H–Y bond in the proton donor part of complexes. The frequency analysis of C–H…Y bond in the complexes indicates the blue-shifting nature largely in case of sp² hybridised carbon atom.     

First-principles investigation of the interaction of gold and palladium with armchair carbon nanotube

In this paper, we investigate the adsorption mechanisms at the interface between carbon nanotubes and metal electrodes that can influence the Schottky barrier (SB). We developed a theoretical model based on the first-principles density functional theory for the interaction of an armchair single-wall carbon nanotube (SWNT) with either Au(111) or Pd(111) surface. We considered the side-wall contact by modelling the full SWNT as well as the end-contact geometry using the graphene ribbon model to mimic the contact with very large diameter nanotubes. Strong interaction has been found for the Pd–SWNT interface where the partial density of states (DOS) shows that d-orbitals of palladium are dominant at the Fermi energy so that the hybrid Pd-orbitals have the correct symmetry to overlap with π-electrons and form covalent bonds. The SWNT can only be physisorbed on the gold surface for which the contribution to the DOS of the d-orbitals is very low. Moreover, the filling of antibonding states makes the Au–SWNT bond unstable. The average and ‘atom to atom’ energy barriers at the interface have been evaluated. The matching of open-edge carbon dimers with metal lattice in the end-contact geometry is more likely for large diameter SWNTs and this makes lower the SB at the interface.     

Influence of chitosan structure on the formation and stability of DNA-chitosan polyelectrolyte complexes

The interactions between DNA and chitosans varying in fractional content of acetylated units (FA), degree of polymerization (DP), and degree of ionization were investigated by several techniques, including an ethidium bromide (EtBr) fluorescence assay, gel retardation, atomic force microscopy, and dynamic and electrophoretic light scattering. The charge density of the chitosan and the number of charges per chain were found to be the dominating factors for the structure and stability of DNA-chitosan complexes. All high molecular weight chitosans condensed DNA into physically stable polyplexes; however, the properties of the complexes were strongly dependent on FA, and thereby the charge density of chitosan. By employing fully charged oligomers of constant charge density, it was shown that the complexation of DNA and stability of the polyplexes is governed by the number of cationic residues per chain. A minimum of 6-9 positive charges appeared necessary to provide interaction strength comparable to that of polycations. In contrast, further increase in the number of charges above 9 did not increase the apparent binding affinity as judged from the EtBr displacement assay. The chitosan oligomers exhibited a pH-dependent interaction with DNA, reflecting the number of ionized amino groups. The complexation of DNA and the stability of oligomer-based polyplexes became reduced above pH 7.4. Such pH-dependent dissociation of polyplexes around the physiological pH is highly relevant in gene delivery applications and might be one of the reasons for the high transfection activity of oligomer-based polyplexes observed.     

Complexation of lysozyme with poly(sodium(sulfamate-carboxylate)isoprene)

The complexation between hen egg white lysozyme (HEWL) and a novel pH-sensitive and intrinsically hydrophobic polyelectrolyte poly(sodium(sulfamate-carboxylate)isoprene) (SCPI), was investigated by means of dynamic, static, and electrophoretic light scattering and isothermal titration calorimetry measurements. The complexation process was studied at both pH 7 and 3 (high and low charge density of the SCPI, respectively) and under low ionic strength conditions for two polyelectrolyte samples of different molecular weights. The solution behavior, structure, and effective charge of the formed complexes proved to be dependent on the pH, the [-]/[+] charge ratio, and the molecular weight of the polyelectrolyte. Increasing the ionic strength of the solution led to vast aggregation and eventually precipitation of the complexes. The interaction between HEWL and SCPI was found to be mainly electrostatic, associated with an exothermic enthalpy change. The structural investigation of the complexed protein by fluorescence, infrared, circular dichroism spectroscopic, and differential scanning calorimetric measurements revealed no signs of denaturation upon complexation.     

Intermolecular interactions between gold clusters and selected amino acids cysteine and glycine: a DFT study

The intermolecular interactions between Au_n (n = 3–4) clusters and selected amino acids cysteine and glycine have been investigated by means of density functional theory (DFT). Present calculations show that the complexes possessing Au-NH₂ anchoring bond are found to be energetically favored. The results of NBO and frontier molecular orbitals analysis indicate that for the complex with anchoring bonds, lone pair electrons of sulfur, oxygen, and nitrogen atoms are transferred to the antibonding orbitals of gold, while for the complex with the nonconventional hydrogen bonds (Au···H–O), the lone pair electrons of gold are transferred to the antibonding orbitals of O-H bonds during the interaction. Furthermore, the interaction energy calculations show that the complexes with Au-NH₂ anchoring bond have relatively high intermolecular interaction energy, which is consistent with previous computational studies.     

Possible sequestration of polar gas molecules by superhalogen supported aluminum nitride nanoflakes

The feasibility of having MF₃ (where M?=?Rh, Ir, Pd, Pt, Ag, Au) supported AlN nanoflakes (AlNF) was investigated through density functional theory based calculations. The thermodynamic analysis reveals that the superhalogen MF₃ molecules can bind with the host AlNF in a thermodynamically favorable way. The nature of interaction in between the metal centers and the host is of partly covalent type whereas the F centers bind with the host in a non-covalent fashion as vindicated by natural bond orbital and atoms-in a-molecule analyses. An ab initio molecular dynamics study carried out at 298 K temperature confirms the stability of the MF₃@AlNF moieties in a dynamical context. The MF₃ guests can reduce the HOMO-LUMO gaps of the host nanoflakes. In general, the MF₃@AlNF complexes can sequestrate polar adsorbates such as CO, NO, and H₂O in a thermodynamically favorable way in most of the cases. An ab initio molecular dynamics calculation illustrates that the MF₃@AlNF can adsorb the chosen representative polar molecules in a more favorable way as compared to the corresponding adsorption scenario in the case of pristine AlNF.     

Inhibition of several enzymes by gold compounds. II. beta-Glucuronidase, acid phosphatase and L-malate dehydrogenase by sodium thiomalatoraurate (I), sodium thiosulfatoaurate (I) and thioglucosoaurate (I)

Bovine liver beta-D-glucuronide glucuronohydrolase, EC 3.2.1.32), wheat germ acid phosphatase (orthophosphoric monoesterphosphohydrolase, EC 3.1.3.2) and bovine liver L-malate dehydrogenase (L-malate: NAD oxidoreductase, EC 1.1.1.37) were inhibited by a series of gold (I) complexes that have been used as anti-inflammatory drugs. Both sodium thiosulfatoaurate (I) (Na AuTs) and sodium thiomalatoraurate (NaAuTM) effectively inhibited all three enzymes, while thioglucosoaurate (I) (AuTG) only inhibited L-malate dehydrogenase. The equilibrium constants (K1) ranged from nearly 4000 microM for the NaAuTM-beta-glucuronidase interaction to 24 microM for the NaAuTS-beta-glucuronidase interaction. The rate of covalent bond formation (kp) ranged from 0.00032 min-1 for NaAuTM-beta-glucuronidase formation to 1.7 min-1 for AuTG-L-malate dehydrogenase formation. The equilibrium data shows that the gold (I) drugs bind by several orders lower than the gold (III) compounds, suggesting a significantly stronger interaction between the more highly charged gold ion and the enzyme. Yet the rate of covalent bond formation depends as much on the structure of the active site as upon the lability of the gold-ligand bond. It was also observed that the more effective the gold inhibition the more toxic the compound.     

Density functional study on size-dependent structures, stabilities, electronic and magnetic properties of Au n M (M = Al and Si, n?=?1–9) clusters: comparison with pure gold clusters

The density functional theory (DFT) method has been employed to systematically investigate the geometrical structures, relative stabilities, and electronic and magnetic properties of Au(n)M (M = Al and Si, n = 1-9) clusters for clarifying the effect of Al(Si) modulation on the gold nanostructures. Of all the clusters studied, the most stable configurations adopt a three-dimensional structure for Au(n)Al at n = 4-8 and Au(n)Si at n = 3-9, while for pure gold systems, no three-dimensional lowest energy structures are obtained. Through a careful analysis of the fragmentation energy, second-order difference of energy, HOMO-LUMO energy gap, and magnetic moment as a function of cluster size, an odd-even alternative phenomenon has been observed. The results show that the clusters with even-number valence electrons have a higher relative stability, but lower magnetic moments. Furthermore, Al(Si) doping is found to enhance the stabilities of gold frameworks. In addition, the charge analysis has been given to understand the different effects of individual doped atom on electronic properties and compared further.     

Ab initio and DFT study of luminescent cyclometalated N-heterocyclic carbene organogold(III) complexes

The structures of versatile N-heterocyclic carbene-containing Au(III) complexes in the ground and low-lying excited states have been optimized at the B3LYP functional and the single-excitation configuration interaction (CIS) method, respectively. The spectral properties are predicted with time-dependent density functional theory (TDDFT). In addition, the charge transport quality has been estimated approximately by the predicted reorganization energy (λ). As revealed from the calculations, the introduction of methyl has a bigger influence on the spectral properties than phenyl. Furthermore, we find that changing the auxiliary ligand could tune the charge transfer properties.     

Structure of alginate gels: interaction of diuronate units with divalent cations from density functional calculations

The complexation of (1→4) linked α-L-guluronate (G) and β-D-mannuronate (M) disaccharides with Mg(2+), Ca(2+), Sr(2+), Mn(2+), Co(2+), Cu(2+), and Zn(2+) cations have been studied with quantum chemical density functional theory (DFT)-based method. A large number of possible cation-diuronate complexes, with one and two GG or MM disaccharide units and with or without water molecules in the inner coordination shells have been considered. The computed bond distances, cation interaction energies, and molecular orbital composition analysis revealed that the complexation of the transition metal (TM) ions to the disaccharides occurs via the formation of strong coordination-covalent bonds. On the contrary, the alkaline earth cations form ionic bonds with the uronates. The unidentate binding is found to be the most favored one in the TM hydrated and water-free complexes. By removing water molecules, the bidentate chelating binding also occurs, although it is found to be energetically less favored by 1 to 1.5 eV than the unidentate one. A good correlation is obtained between the alginate affinity trend toward TM cations and the interaction energies of the TM cations in all studied complexes, which suggests that the alginate affinities are strongly related to the chemical interaction strength of TM cations-uronate complexes. The trend of the interaction energies of the alkaline earth cations in the ionic complexes is opposite to the alginate affinity order. The binding strength is thus not a limiting factor in the alginate gelation in the presence of alkaline earth cations at variance with the TM cations.     

Theoretical study of the interaction between 5-methylcytosine and acrylamide

The hydrogen-bonded complexes between 5-methylcytosine and acrylamide have been investigated using the density function theory (DFT) method. Five stable complexes have been found with no imaginary frequencies. Complex C3 is the most stable one with interaction energies of -69.01?kJ?mol(-1) corrected for basis set superposition error (BSSE). The charge change in the process of these complexes formation has also been examined. The atoms in molecules (AIM) theory and natural bond orbital (NBO) method have been performed to investigate the hydrogen bonds involved in all the complexes. The electron density and its corresponding Laplacian at the bond and ring critical points have been analyzed. In C3 complex, there is the largest stabilization energy (18.17?kJ?mol(-1)) between N11-H12 antibonding orbital and lone electron pair of O17. It can be seen that the hydrogen bonds play a crucial role in the stability of all the complexes between 5-methylcytosine and acrylamide. The theoretical results could provide helpful information for other researchers in further work.     

The computational study of the γ-Fe2O3 nanoparticle as Carmustine drug delivery system: DFT approach

In the present study, it is attempted to scrutinize the properties of the maghemite nanoparticle as a Carmustine drug delivery system by means of the density functional theory calculations regarding their geometries, adsorption energies, vibrational frequencies, and topological features of the electron density. Based on the density functional theory results, it is found that the interaction between Carmustine drug molecule and maghemite nanoparticle is weak; so that, the adsorption of the Carmustine drug is typically physisorption. It is also found that the intermolecular hydrogen bonds between the drug and the nanoparticle play the significant role in the stability of the physisorption configurations. The nature of the intermolecular interactions has been explored by calculation of the electron densities and their Laplacian at the bond critical points using Atoms-in-Molecule theory. Moreover, natural bond orbital analysis indicates that the Carmustine molecule can be adsorbed on the nanoparticle surface with a charge transfer from the Carmustine drug to the nanoparticle.     

Density functional theory investigation of cocaine water complexes

Twenty cocaine–water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C?=?O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H?·?·?·?O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.     

Stabilization of gold nanowires inside nanoaggregates of cyclo[8]thiophene, cyclo[8]selenophene, and cyclo[8]tellurophene: a theoretical study

The stabilities and electronic properties of gold clusters containing up to six atoms trapped inside cyclo[8]thiophene (CS8), cyclo[8]selenophene (CSe8), and cyclo[8]tellurophene (CTe8) nanoaggregates have been studied using the M06 functional. The 6-31G(d) basis set was used for all atoms except Au and Te, for which the LANL2DZ(d,p) pseudopotential basis set was applied. Single-point energy calculations were performed with the 6-311G(d,p) basis set for all atoms except for Au and Te, for which the cc-TZVP-pp pseudopotential basis set was used. Among the three studied macrocycles, only CS8 and CSe8 were found to be capable of nanoaggregate formation. In the lowest-energy conformer of CTe8, the tellurophene fragments adopt an anti orientation, thus impeding a tubular arrangement of the macrocycles. The formation of gold clusters inside the CS8 and CSe8 nanoaggregates is a thermodynamically favorable process, and could represent a potentially useful method of stabilizing metal nanowires. The binding energy between the nanoaggregate and the gold cluster is always higher for selenium-containing complexes than for sulfur-containing ones because Se has a higher affinity than S for Au in such complexes. Interactions of the gold cluster with the nanoaggregate walls can change the geometry of the most stable isomer for the cluster. The relative energies of different isomers are rather similar, suggesting that they coexist. For nanoaggregates containing Au₆ clusters, the cluster geometry when it is inside a nanoaggregate is different from the geometry of the cluster when it is not inside the nanoaggregate, due to the geometric restrictions imposed by the nanoaggregate cavity. The reorganization energy needed to change the geometry leads to lower binding energies for these complexes compared to those of some smaller systems, although the formation of a complex between Au₆ and a nanoaggregate with six CS8 or CSe8 macrocycles is still thermodynamically viable.     

Catalytic activity of iron phthalocyanine for the oxidation of thiocyanate and L-cysteine anchored on Au(111) clusters

ABSTRACT

We studied the oxidation reactions of thiocyanate and L-cysteine on iron phthalocyanine (FePc) coupled via a bridging ligand of the 4-mercatopyridine (4MP) type to a gold cluster (Au₂₆), aiming to simulate a modified gold electrode. Theoretical models have been used based on the framework of density functional theory. Several mechanistic pathways are explored for the study of these reactions, finding that the most favorable mechanism involves an electron transfer process as the rate-determining step. Along the process, the ability of the gold cluster to act as an electron acceptor facilitating the reactions was detected. In addition, the proposed models presented a correlation between the energy obtained for the rate-determining step of the reaction and the experimental oxidation potentials of the thiocyanate and L-cysteine.     

A 1.4-nm gold cluster covalently attached to antibodies improves immunolabeling.

A large gold cluster (Au1.4nm) was covalently coupled to IgG and Fab' fragments. Its gold core is 1.4 nm in diameter and the Fab'-Au1.4nm immunoconjugate is the smallest gold immunoprobe that can be seen directly in the conventional electron microscope. It is useful in high-resolution immunolabeling, providing a resolution of 7.0 nm. The cluster's visibility can be enhanced with silver development for use in EM or light microscopy for histological purposes, or to detect less than or equal to 0.2 pg of antigen in immunoblots. By using a gold compound with covalent attachment, a number of advantages over colloidal gold probes are realized, including better resolution, stability, uniformity, sensitivity, and complete absence of aggregation; its small size should also improve penetration and more quantitative labeling of antigenic sites.     

Role of aliphatic and phenolic hydroxyl groups in uranyl complexation by humic substances

Relativistic density functional calculations of uranyl complexes with alcohols were carried out to study how phenolic and aliphatic hydroxyl groups of humic substances may contribute to uranyl complexation by humic substances. According to recent experimental work, blocking of phenolic OH groups decreases the loading capacity, but has no effect on the key geometric parameters of uranyl humate complexes. This can be understood on the basis of our calculations which showed uranium-oxygen distances to be very similar for complexes with rather different types of O-donor ligands, with average U-O_eq ∼ 237 pm for fivefold coordinated uranyl (VI) complexes, both for O⁻ and OH functional groups. Uranyl complexation by alcohol moieties seems unlikely at environmental conditions as a high pH is required for the deprotonation of these groups; we confirm an alternative complexation mechanism that overcomes the ligand deprotonation problem. Similarities in structures and energetic suggest that complexes of both aliphatic and phenolic alcoholates may well contribute in comparable fashion to the complexation of uranyl by humic acids.