Complexation of small organic molecules by Cu+

Signatures of Size-Dependent Structural Patterns in Hydrated Copper(I) Clusters, Cu+(H2O)n=1-10

The isomers of a hydrated Cu(I) ion with n = 1-10 water molecules were investigated by using ab initio quantum chemistry and an automated isomer-search algorithm. The electronic structure and vibrational spectra of the hundreds of resulting isomers were used to analyze the source of the observed bonding patterns. A structural evolution from dominantly two-coordinate structures (n = 1-4) toward a mixture of two- and three-coordinate structures was observed at n = 5-6, where the stability provided by expanded hydrogen-bonding was competitive with the dominantly electrostatic interaction between the water ligand and remaining binding sites of the metal ion. Further hydration (n = 7-10) led to a mixture of three- and four-coordinate structures. The metal ion was found, through spectroscopic signatures, to appreciably perturb the O-H bonds of even third-shell water molecules, which highlighted the ability of this nominally simple ion to partially activate the surrounding water network.

Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study

The coordination number of various experimentally known Cu(I) compounds is studied using density functional theory. Various basis sets are tested, aiming to establish a reliable level for prediction of the coordination number of these and other Cu(I) complexes. It is found that most levels exhibit correct trends, namely, the bulkier ligands demonstrate larger preference for coordination of two ligands. Proper absolute values are obtained when dispersion corrections are also included in the calculations. It is concluded that the fairly small modified 6-31+G* basis set due to Pulay represents a good compromise between accuracy and efficiency, followed by Balabanov and Peterson's all-electron aug-cc-pVDZ basis set. The overall energy is decomposed into various components whose relative contribution to the overall tendency of forming a complex with a particular coordination is examined. It is shown that two opposing contributions play a major role: the interaction energy of the ligand being added and the deformation energy of the copper's coordination sphere prior to the ligand addition. The former being a stabilizing contribution, leads to higher coordination numbers while the later, a destabilizing contribution, is shown to favor lower coordination numbers.

Gas-phase interactions between lead(II) ions and thiouracil nucleobases: a combined experimental and theoretical study

The gas-phase interactions between lead(II) ions and 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil have been investigated by combining mass spectrometry and theoretical calculations. The most abundant complexes observed, namely [Pb(thiouracil) - H](+), have been studied by MS/MS experiments. Cationization by the metal allows an unambiguous characterization of the sulfur position, several fragment ions being specific of each isomer. Moreover, compared with the uracil fragmentation, new fragmentation channels are observed: elimination of PbS or total reduction of the metal. Calculations performed on the different structures, including tautomers, show that sulfur is the preferred complexation site, suggesting the greater affinity of lead for sulfur. The most stable structures are always preferentially bidentate. Natural population analysis indicates a charge transfer from the base to the metal with a more pronounced covalent character for sulfur compared to oxygen. Energetic profiles associated with the main fragmentations have been described.

Coordination and solvation of copper ion: infrared photodissociation spectroscopy of Cu(+)(NH(3))(n) (n = 3-8)

Coordination and solvation structures of the Cu(+)(NH(3))(n) ions with n = 3-8 are studied by infrared photodissociation spectroscopy in the NH-stretch region with the aid of density functional theory calculations. Hydrogen bonding between NH(3) molecules is absent for n = 3, indicating that all NH(3) molecules are bonded directly to Cu(+) in a tri-coordinated form. The first sign of hydrogen bonding is detected at n = 4 through frequency reduction and intensity enhancement of the infrared transitions, implying that at least one NH(3) molecule is placed in the second solvation shell. The spectra of n = 4 and 5 suggest the coexistence of multiple isomers, which have different coordination numbers (2, 3, and 4) or different types of hydrogen-bonding configurations. With increasing n, however, the di-coordinated isomer is of growing importance until becoming predominant at n = 8. These results signify a strong tendency of Cu(+) to adopt the twofold linear coordination, as in the case of Cu(+)(H(2)O)(n).

Thermochemistry, bonding, and reactivity of Ni+ and Ni2+ in the gas phase

In this review, we present a general overview on the studies carried out on Ni(+-)- and Ni(2+)-containing systems in the gas phase since 1996. We have focused our attention in the determination of binding energies in parallel with an analysis of the structure and bonding of the complexes formed by the interaction of Ni(+) with one ligand, or in clusters where this metal ion binds several identical or different ligands. Solvation of Ni(2+) by different ligands is also discussed, together with the theoretical information available of doubly charged Ni-containing species. The final section of this review is devoted to an analysis of the gas-phase uni- and bimolecular reactivity of Ni(+) and Ni(2+) complexes.

Copper-biomolecule complexes in the gas phase. The ternary way

This review deals with copper complexes of a variety of organic and bioorganic molecules that have been produced as gas-phase ions by electrospray and other ionization methods and studied experimentally by mass spectrometry and theoretically by ab initio and density functional theory computations. Ternary complexes of Cu((II)) allow one to modify the oxidation state and coordination sphere of the copper ion and thus induce novel fragmentations that involve redox and radical-based reactions. Structure elucidation, distinction, and quantitation of leucine and isoleucine isomers in peptides, distinction of enantiomers in chiral compounds, and sensitive detection of antibiotics are some of the highlights of mass spectrometry of ternary copper complexes. Binary copper complexes are mainly represented by Cu((I)) species in which the copper ion displays the properties of a weak Lewis acid.

Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+)

Hartree-Fock and DFT (B3LYP) nonrelativistic (scalar relativistic pseudopotentials for the metallic cation) and relativistic (molecular four-component approach coupled to an all-electron basis set) calculations are performed on a series of six nd10 (n+1)s0 [M(H2O)]p+ complexes to investigate their geometry, either planar C2v or nonplanar C(s). These complexes are, formally, entities originating from the complexation of a water molecule to a metallic cation: in the present study, no internal reorganization has been found, which ensures that the complexes can be regarded as a water molecule interacting with a metallic cation. For [Au(H2O)]+ and [Hg(H2O)]2+, it is observed that both electronic correlation and relativistic effects are required to recover the C(s) structures predicted by the four-component relativistic all-electron DFT calculations. However, including the zero-point energy corrections makes these shallow C(s) minima vanish and the systems become floppy. In all other systems, namely [Cu(H2O)]+, [Zn(H2O)]2+, [Ag(H2O)]+, and [Cd(H2O)]2+, all calculations predict a C2v geometry arising from especially flat potential energy surfaces related to the out-of-plane wagging vibration mode. In all cases, our computations point to the quasi-perfect transferability of the atomic pseudopotentials considered toward the molecular species investigated. A rationalization of the shape of the wagging potential energy surfaces (i.e., single well vs. double well) is proposed based on the Constrained Space Orbital Variation decompositions of the complexation energies. Any way of stabilizing the lowest unoccupied orbital of the metallic cation is expected to favor charge-transfer (from the highest occupied orbital(s) of the water ligand), covalence, and, consequently, C(s) structures. The CSOV complexation energy decompositions unambiguously reveal that such stabilizations are achieved by means of relativistic effects for [Au(H2O)]+, and, to a lesser extent, for [Hg(H2O)]2+. Such analyses allow to numerically quantify the rule of thumb known for Au+ which, once again, appears as a better archetype of a relativistic cation than Hg2+. This observation is reinforced due to the especially high contribution of the nonadditive correlation/relativity terms to the total complexation energy of [Au(H2O)]+.

New model potentials for sulfur–copper(I) and sulfur–mercury(II) interactions in proteins: Fromab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).

ZEKE Spectroscopy and Theoretical Calculations of Copper−Methylamine Complexes

The copper-monomethylamine and -dimethylamine complexes were produced in a supersonic jet and examined using single-photon zero kinetic energy (ZEKE) photoelectron spectroscopy and theoretical calculations. The adiabatic ionization potentials (I.P.) of the complexes and vibrational frequencies of the corresponding ions were measured from their ZEKE spectra. The equilibrium geometries, binding energies, and vibrational frequencies of the neutral and ionized complexes were obtained from MP2 and B3LYP calculations. The observed vibrational frequencies of the ionic complexes were well-reproduced by both calculations, whereas the Franck-Condon intensity patterns of the spectra were simulated better by MP2 than B3LYP. The observed I.P. and vibrational frequencies of the Cu-NH(n)(CH3)(3-n) (n = 0-3) complexes were compared, and methyl substitution effects on their ZEKE spectra were discussed.

Pulsed-field ionization electron spectroscopy and conformation of copper-diammonia

Copper-diammonia, Cu(NH3)2, and its deuterated species, Cu(ND3)2, are produced in supersonic molecular beams and studied by pulsed-field ionization zero electron kinetic energy photoelectron spectroscopy and ab initio calculations. Structural isomers with a copper atom binding to an ammonia dimer or two ammonia molecules are obtained by the calculations. By comparing the experimental measurements to the theoretical calculations, the neutral and ionic forms of copper-diammonia are determined to be in a doubly bound linear conformation in their ground electronic states. The adiabatic ionization potentials of Cu(NH3)2 and Cu(ND3)2 are measured as 29,532 (5) and 29,313 (5) cm(-1), respectively. The metal-ligand symmetric stretching frequencies are measured to be 436 cm(-1) for Cu+-(NH3)2 and 398 cm(-1) for Cu+-(ND3)2, and the metal-ligand bending frequencies 75,139 cm(-1) for CuCu+-(NH3)2 and 70125 cm(-1) for CuCu+-(ND3)2. Moreover, the dissociation energy of Cu(NH3)2-->CuNH3+NH3 is determined to be 11(3) kcal mol(-1) through a thermodynamic relationship.

Reactions of Cu+(1S, 3D) with CH3Cl, CH2ClF, CHClF2, and CClF3

The reactions of gas-phase Cu+(1S) and Cu+(3D) with CH3Cl, CH2ClF, CHClF2, and CClF3 are examined using the drift cell technique at 3.5 Torr. State-specific product channels and overall bimolecular rate constants for depletion of the two Cu+ states are determined using electronic state chromatography. Cu+(1S) participates exclusively in association with all four neutrals, whereas Cl abstraction is the dominant product channel for Cu+(3D). The resulting CuCl+ product subsequently abstracts Cl- in a secondary process. Tertiary reactions are also observed, which include both hydride abstraction (with CH3Cl) and fluoride abstraction (with the fluorinated neutrals). All product channels can be understood in terms of the known thermochemical and quantum mechanical (i.e., spin) requirements. Cu+(1S) is depleted by all four neutrals at 30% to 40% of the ADO rate under these conditions, whereas Cu+(3D) is observed to react at approximately 80% of the ADO rate with CH3Cl, CH2ClF, and CHClF2. Reaction of excited state Cu+ with CClF3 occurs at only 7% of the ADO rate. The behavior of Cu+(3D) is consistent with a mechanism in which formation of CuCl+ occurs exclusively on the triplet surface via a mechanism in which the metal ion must interact exclusively with Cl.

Ring complexes of S-nitrosothiols with CU+: a density functional theory study

The density functional theory (DFT) method B3P86/6-311+G(2df,p) has been employed to investigate the complexes formed upon interaction of Cu(+) with nitrosylated cysteine (CysNO) and its decarboxylated (H(2)NCH(2)CH(2)SNO) and deaminated (HOOCCH(2)CH(2)SNO) derivatives. Optimized structures, relative enthalpies and relative free energies have been calculated and compared. In addition, the effects of binding an H(2)O molecule to the Cu(+) centre in the resulting complexes have also been considered. It is found that the most stable complexes are formed when Cu(+) coordinates to the S-nitrosothiol via S of the SNO group. This results in dramatic lengthenings of the SN bond with concomitant shortening of the NO bond. In contrast, when Cu(+) coordinates via the nitrogen of the SNO group, a shortening of the SN bond with lengthening of the NO bond is observed. These effects are tempered by the electron donating ability of other functional groups also coordinated with the Cu(+) centre in the complexes and on the coordination state of the Cu(+) ion.

Tandem mass spectrometry of Cu(II) complexes: the effects of ligand donor group on dissociation

A quadrupole ion trap mass spectrometer was used to study the dissociation patterns of Cu(II) complexes with various linear podand ligands. Cu(II) complexes having different combinations of nitrogen-, oxygen- and sulfur-containing terminal functionality attached to a diethylenetriamine (DIEN) framework were ionized by electrospray and collision-induced dissociation (CID) was used to generate product ions. Regardless of the particular functional groups present, the complexes undergo predominantly heterolytic cleavages of carbon-carbon bonds along the DIEN backbone with Cu remaining coordinated to one of the two terminal functional groups. Upon dissociation, Cu's preference to remain coordinated to a particular functional group follows the trend thioether > amine > imidazole > pyridine > ether. A simple evaluation of this trend based upon metal-functional group binding affinity appears not to be adequate for fully explaining these observations. The tendency of Cu(II) to be reduced upon dissociation helps explain the observed trend, as does the flexibility of the functional group, which affects its ability to orient its dipole effectively toward the metal.

Theoretical evidence that Cu(I) complexation promotes degradation of S-nitrosothiols

The degradation of S-nitrosothiols (RSNOs) to release NO is believed to be catalyzed by CuI ions, but the mechanism remains unclear. Kinetic experiments have shown that decomposition rates vary significantly with the chemical nature of the RSNO considered. On the basis of first-principles calculations, the catalytic role of CuI ion is investigated for the decomposition of S-nitrosocysteine and its N-acetylated and ethyl ester derivatives, and for S-nitrosohomocysteine. This preliminary study focuses on the CuI-RSNO intermediates involved in the decomposition pathway. The model chemistry has been validated by comparing calculated CuI-ligand binding energies and S-N bond homolysis energies with available experimental data. Calculations show that the formation of CuI-RSNO intermediates results in weakening of the S-N bond and strengthening of the N-O bond, which would promote S-N bond breaking and NO release from S-nitrosothiols.

Absolute configuration of secondary alcohols by 1H NMR: in situ complexation of alpha-methoxyphenylacetic acid esters with barium(II)

A novel methodology that allows the assignment of the absolute configuration of chiral secondary alcohols by NMR using only one derivative is presented. All that is needed is (a) the derivatization of the alcohol of unknown configuration with one enantiomer--either the (R)- or the (S)--of alpha-methoxyphenylacetic acid (MPA), (b) the recording of the 1H NMR spectrum of the resulting ester in MeCN-d3, and (c) addition of a barium(II) salt [i.e. Ba(ClO4)2] to the NMR tube till saturation and recording of a second spectrum. The assignment of the R/S configuration to the alcohol takes a few minutes and consists on the comparison of the signs of the shifts (Deltadelta(Ba)) produced by addition of the barium(II) with those predicted for the (R) and the (S) enantiomers in accordance to a simplified model that reflects the conformational changes produced by the complexation with barium and their consequences in the chemical shifts. These conformational changes are based on experimental NMR and CD results showing that the formation of a barium(II) complex with the MPA ester moves the conformational equilibrium between syn- (sp) and anti-periplanar (ap) forms toward the most stable ones (sp), and that this leads to the increase of the shielding caused by the MPA phenyl group on a certain substituent of the alcohol. In addition, ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations provide further evidence on the formation, structure, and stability of the complexes with Ba2+, Mg2+, and the influence of the solvent. The general applicability of this methodology and the reliability of the configurational assignment were assured by the study of about twenty alcohols of known configuration and diverse structural features. Its scope and limitations have also being established and other representative cations (i.e. Li+, Rb+, Cs+, Mg2+, Ca2+, Sc3+, V3+, Zn2+) were also evaluated. The procedure proposed is simple, fast, and cheap because it requires a very small amount of sample, only one derivatization, and the recording of only two 1H NMR spectra at rt. A graphical guide to facilitate the application of this new method is included at the end of the paper.