The gold-ammonia bonding patterns of neutral and charged complexes Au m 0+/-1-(NH3)n. I. Bonding and charge alternation

The gold-ammonia bonding patterns of the complexes which are formed between the ammonia clusters (NH(3))(1< or =n< or =3) and gold clusters of different sizes that range from one gold atom to the tri-, tetra-, and 20-nanogold clusters are governed by two basic and fundamentally different ingredients: the anchoring Au-N bond and the nonconventional N-H...Au hydrogen bond. The latter resembles, by all features, a conventional hydrogen bond and is formed between a typical conventional proton donor N-H group and the gold cluster that behaves as a nonconventional proton acceptor. We provide strong computational evidence that the gold-ammonia bonding patterns exhibit distinct characteristics as the Z charge state of the gold cluster varies within Z=0,+/-1. The analysis of these bonding patterns and their effects on the N-H...N H-bonded ammonia clusters are the subject of this paper.     

Where gold meets a hydrogen bond?

This is a short survey of the area of the hydrogen bonding where the noble and coinage metal gold enters its manifold of the proton acceptors. It is largely focused on the nonconventional hydrogen bonds that are formed in the complexes of the auride anion Au⁻ with HF, (HF)₂, H₂O, (H₂O)₂, NH₃, and (NH₃)₂, as mostly experimentally investigated to date. A thorough comparison of the experimental and computational data on these nonconventional hydrogen bonds is the main motif of the present work.     

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.     

Interactions of glutathione tripeptide with gold cluster: influence of intramolecular hydrogen bond on complexation behavior

Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au(3) cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Au-X (X = N, O, and S) anchoring bond and Au···H-X nonconventional hydrogen bonding. The influence of the intramolecular hydrogen bonding of glutathione on the interaction of this peptide with the gold cluster has been investigated. To gain insight on the role of intramolecular hydrogen bonding on Au-GSH interaction, we compared interaction energies of Au-GSH complexes with those of cystein and glycine components. Our results demonstrated that, in spite of the ability of cystein to form highly stable metal-sulfide interaction, complexation behavior of glutathione is governed by its intramolecular backbone hydrogen bonding. The quantum theory of atom in molecule (QTAIM) and natural bond orbital analysis (NBO) have also been applied to interpret the nature of interactions in Au-GSH complexes. Finally, conformational flexibility of glutathione during complexation with the Au(3) cluster was investigated by means of monitoring Ramachandran angles.     

Blue-shifted A-H stretching modes and cooperative hydrogen bonding. 1. Complexes of substituted formaldehyde with cyclic hydrogen fluoride and water clusters

The structures and vibrational spectra of the intermolecular complexes formed by insertion of substituted formaldehyde molecules HRCO (R = H, Li, F, Cl) into cyclic hydrogen fluoride and water clusters are studied at the MP2/aug-cc-pVTZ computational level. Depending on the nature of the substituent R, the cluster type, and its size, the C-H stretching modes of HRCO undergo large blue and partly red shifts, whereas all the F-H and O-H stretching modes of the conventional hydrogen bonds are strongly red-shifted. It is shown that (i) the mechanism of blue shifting can be explained within the concept of the negative intramolecular coupling between C-H and C=O bonds that is inherent to the HRCO monomers, (ii) the blue shifts also occur even if no hydrogen bond is formed, and (iii) variation of the acceptor X or the strength of the C-H...X hydrogen bond may either amplify the blue shift or cause a transition from blue shift to red shift. These findings are illustrated by means of intra- and intermolecular scans of the potential energy surfaces. The performance of the negative intramolecular coupling between C-H and C=O bonds of H(2)CO is interpreted in terms of the NBO analysis of the isolated H(2)CO molecule and H(2)CO interacting with (H2O)n and (HF)n clusters.     

Electron and hydrogen transfer in small hydrogen fluoride anion clusters

A new stable structure has been found for the anion clusters of hydrogen fluoride. The ab initio method was used to optimize the structures of the (HF)(3)(-), (HF)(4)(-), (HF)(5)(-), and (HF)(6)(-) anion clusters with an excess "solvated" electron. Instead of the well-known "zig-zag" (HF)(n)(-) structure, a new form, (HF)(n-1)F(-)···H, was found with lower energy. In this new form, the terminal hydrogen atom in the (HF)(n)(-) chain is separated from the other part of the cluster and the inner hydrogens transfer along the hydrogen bonds toward the outside fluoride. The negative charge also transfers from the terminal HF molecule of the chain to the center fluoride atoms. The (HF)(n)(-) clusters for n = 4, 5, and 6 have not yet been observed experimentally. These results should assist in the search for these systems and also provide a possible way to study the proton and electron transfer in some large hydrogen bonding systems.     

Cooperativity in hydrogen-bonded interactions: ab initio and "atoms in molecules" analyses

The H(2)CO...(HF)(n) (n = 1, ..., 9) complexes were investigated using the MP2 method and the following basis sets: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. It was found that the cooperativity effect enhances significantly the F-H...O hydrogen bond; in some of cases one can detect the covalent nature of hydrogen bonding. To deepen the nature of the interactions investigated, the scheme of decomposition of the interaction energy was applied; for stronger H-bonds where the cooperativity is more important, the delocalization energy term increases. The ratio of delocalization energy to electrostatic energy increases for stronger hydrogen bonds where the proton...acceptor distance is shorter. The Bader theory was also applied, and it was found that for stronger H-bonds the electronic energy density at the proton...acceptor bond critical point is negative and may be attributed to the partly covalent interaction.     

On the chemical bonding of gold in auro-boron oxide clusters AunBO- (n = 1-3)

During experiment on Au-B alloy clusters, an auro-boron oxide cluster Au2BO- was observed to be an intense peak dominating the Au-B mass spectra, along with weaker signals for AuBO- and Au3BO-. Well-resolved photoelectron spectra have been obtained for the three new oxide clusters, which exhibit an odd-even effect in electron affinities. Au2BO- is shown to be a closed shell molecule with a very high electron detachment energy, whereas AuBO and Au3BO neutrals are shown to be closed shell species with large HOMO-LUMO gaps, resulting in relatively low electron affinities. Density functional calculations were performed for both AunBO- (n = 1-3) and the corresponding HnBO- species to evaluate the analogy between bonding of gold and hydrogen in these clusters. The combination of experiment and theory allowed us to establish the structures and chemical bonding of these tertiary clusters. We find that the first gold atom does mimic hydrogen and interacts with the BO unit to produce a linear AuBO structure. This unit preserves its identity when interacting with additional gold atoms: a linear Au-[AuBO] complex is formed when adding one extra Au atom and two isomeric Au2-[AuBO] complexes are formed when adding two extra Au atoms. Since BO- is isoelectronic to CO, the AunBO- species can be alternatively viewed as Aun interacting with a BO- unit. The structures and chemical bonding in AunBO- are compared to those in the corresponding AunCO complexes.     

Strongly blue-shifted C-H stretches: interaction of formaldehyde with hydrogen fluoride clusters

The equilibrium structures, binding energies, and vibrational spectra of the cyclic, hydrogen-bonded complexes formed between formaldehyde, H(2)CO, and hydrogen fluoride clusters, (HF)(1< or =n < or =4), are investigated by means of large-scale second-order M?ller-Plesset calculations with extended basis sets. All studied complexes exhibit marked blue shifts of the C-H stretching frequencies, exceeding 100 cm(-1) for n = 2-4. It is shown that these blue shifts are, however, only to a minor part caused by blue-shifting hydrogen bonding via C-H...F contacts. The major part arises due to the structural relaxation of the H(2)CO molecule under the formation of a strong C=O...H-F hydrogen bond which strengthens as n increases. The close correlation between the different structural parameters in the studied series of complexes is demonstrated, and the consequences for the frequency shifts in the complexes are pointed out, corroborating thus the suggestion of the primary role of the C=O...H-F hydrogen bonding for the C-H stretching frequency shifts. This particular behavior, that the appearance of an increasingly stronger blue shift of the C-H stretching frequencies is mainly induced by the formation of a progressively stronger C=O...H-F hydrogen bond in the series of H(2)CO...(HF)(1< or =n < or =4), complexes and only to a lesser degree by the formation of the so-called blue-shifting C-H...F hydrogen bond, is rationalized with the aid of selected sections of the intramolecular H(2)CO potential energy surface and by performing a variety of structural optimizations of the H(2)CO molecule embedded in external, differently oriented dipole electric fields, and also by invoking a simple analytical force-field model.     

Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters

The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-H...Au hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Anomalous behavior of atomic hydrogen interacting with gold clusters

The change in the electronic structure of Au(n)- clusters induced by the exchange of an Au atom by hydrogen is studied using photoelectron spectroscopy. Au anion clusters react with one hydrogen atom but not with molecular hydrogen. The spectra of Au(n)- and Au(n-1)H- clusters show almost identical features for n > 2 suggesting that hydrogen behaves as a protonated species by contributing one electron to the valence pool of the Au(n)- cluster. This behavior is in sharp contrast to that of the commonly understood electronic structure of hydrogen in metals; namely, it attracts an electron from the conduction band of the metal and remains in an "anionic" form or forms covalent bonding. We discuss the influence of the unique electronic structure of H on the unusual catalytic behavior of Au clusters.     

Supramolecular gold(I) thiobarbiturate chemistry: combining aurophilicity and hydrogen bonding to make polymers,sheets, and networks

The cooperative forces of aurophilic and hydrogen bonding have been used in the self-assembly of phosphine or diphosphine complexes of gold(I) with the thiolate ligands derived from 2-thiobarbituric acid, SC(4)H(4)N(2)O(2), by single or double deprotonation. The reaction of the corresponding gold(I) trifluoroacetate complex with SC(4)H(4)N(2)O(2) gave the complexes [Au(SC(4)H(3)N(2)O(2))(PPh(3))], 1, [(AuSC(4)H(3)N(2)O(2))(2)(micro-LL)], with LL = Ph(2)PCH(2)PPh(2), 2a, Ph(2)P(CH(2))(3)PPh(2), 2b, or Ph(2)PCH=CHPPh(2), 2c, or the cyclic complex [Au(2)(micro-SC(4)H(2)N(2)O(2))(micro-Ph(2)PCH(2)CH(2)PPh(2))], 3. In the case with LL = Ph(2)P(CH(2))(6)PPh(2), the reaction led to loss of the diphosphine ligand to give [Au(6)(SC(4)H(3)N(2)O(2))(6)], 4, a hexagold(I) cluster complex in which each gold(I) center has trigonal AuS(2)N coordination. Structure determinations show that 1 has no aurophilic bonding, 2b, 3, and 4 have intramolecular aurophilic bonding, and 2c has intermolecular aurophilic bonding that contributes to the supramolecular structure. All the complexes undergo supramolecular association through strong NH...O and/or OH...N hydrogen bonding, and complex 3 also takes part in CH...O hydrogen bonding. The supramolecular association leads to formation of interesting polymer, sheet, or network structures, and 4 has a highly porous and stable lattice structure.     

Density functional investigation of the interaction of acetone with small gold clusters

The structural evolution of Au(n) (n=2, 3, 5, 7, 9, and 13) clusters and the adsorption of organic molecules such as acetone, acetaldehyde, and diethyl ketone on these clusters are studied using a density functional method. The detailed study of the adsorption of acetone on the Au(n) clusters reveals two main points. (1) The acetone molecule interacts with one gold atom of the gold clusters via the carbonyl oxygen. (2) This interaction is mediated through back donation mainly from the spd-hybridized orbitals of the interacting gold atom to the oxygen atom of the acetone molecule. In addition, a hydrogen bond is observed between a hydrogen atom of the methyl group and another gold atom (not involved in the bonding with carbonyl oxygen). Interestingly, the authors notice that the geometries of Au(9) and Au(13) undergo a significant flattening due to the adsorption of an acetone molecule. They have also investigated the role of the alkyl chain attached to the carbonyl group in the adsorption process by analyzing the interaction of Au(13) with acetaldehyde and diethyl ketone.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Glucose interaction with Au,Ag, and Cu clusters: Theoretical investigation

Interactions of α‐D ‐glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM‐B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α‐D ‐glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M…H? O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy calculations indicate that the silver cluster has the lowest and gold cluster has the highest affinity to interact with glucose. Natural bond orbital analysis is performed to calculate natural population analysis and charge transfers in the complexes. Quantum theory of atoms in molecules was also applied to interpret the nature of bonds. © 2012 Wiley Periodicals, Inc.     

Structure of adducts of the intermolecular interaction of dimethylpyrazole and diphenylformamidine with hydrogen halides in the solution

The structure of adducts forming in the solution due to the interaction of bifunctional azo compounds (dimethylpyrazole (DMP) and diphenylformamidine (DPFA)) with hydrogen halides (HF, HCl, and HBr) is found from the data of the IR absorption spectra and quantum chemical calculations. It is shown that in the interaction with HCl or HBr proton donors, proton transfer via the hydrogen bond to the basic N atom of the azo compound occurs with the formation of an NH⁺…Hal⁻ ionic pair. Strong evidences of proton transfer and the anion-cation pair formation are not found for the DMP-_F structure, and complexes with the molecular N…HF hydrogen bond are the dominant structures. Geometric parameters of the formed structures are calculated. The formation of trimers, containing two molecules of the azo compound and one HHal molecule, with an increase in the nitrogenous base concentration is experimentally proved, and the trimer structure is determined.     

Do aurophilic interactions compete against hydrogen bonds? Experimental evidence and rationalization based on ab initio calculations

[M(C6F5)(N(H)=CPh2)] (M = Ag (1) and Au (2)) complexes have been synthesized and characterized by X-ray diffraction analysis. Complex 1 shows a ladder-type structure in which two [Ag(C6F5)(N(H)=CPh2)] units are linked by a Ag(I)-Ag(I) interaction in an antiparallel disposition. The dimeric units are associated through hydrogen bonds of the type N-H...F(ortho). On the other hand, gold(I) complex 2 displays discrete dimers also in an antiparallel conformation in which both Au(I)-Au(I) interactions and N-H.F(ortho) hydrogen bonds appear within the dimeric units. The features of these coexisting interactions have been theoretically studied by ab initio calculations based on four different model systems in order to analyze them separately. The interactions have been analyzed at HF and MP2 levels of theory showing that, in this case, even at larger distances. The Au(I)-Au(I) interaction is stronger than Ag(I)-Ag(I) and that N-H.F hydrogen bonding and Au(I)-Au(I) contacts have a similar strength in the same molecule, which permits a competition between these two structural motifs giving rise to different structural arrangements.     

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.