Pentameric Clusters Research Articles

Magnetic properties of FeCo nanoclusters on Cu(100):Ab initiocalculations

We present ab initio calculations of the magnetic moments and magnetic anisotropy energies of small FeCo clusters of varying composition on top of a Cu(100) substrate. Three different cluster layouts have been considered, namely, $2\ifmmode\times\else\texttimes\fi{}2$, $3\ifmmode\times\else\texttimes\fi{}3$, and crosslike pentamer clusters. The ratio of Co atoms with respect to the total number in a chosen cluster (``concentration'') was varied and all possible arrangements of the atomic species were taken into account. Calculations have been performed fully relativistic using the embedded-cluster technique in conjunction with the screened Korringa-Kohn-Rostoker method and the magnetocrystalline anisotropy energy (MAE) has been evaluated by means of the magnetic force theorem. A central result of the investigations is that the size of the magnetic moments of the individual Fe and Co atoms and their contributions to the anisotropy energy depend on the position they occupy in a particular cluster and on the type and the number of nearest neighbors. The MAE for the $2\ifmmode\times\else\texttimes\fi{}2$ and $3\ifmmode\times\else\texttimes\fi{}3$ clusters varies with respect to the concentration of Co atoms in the same manner as the corresponding monolayer case, whereas the pentamer clusters show a slightly different behavior. Furthermore, for the clusters with an easy axis along a direction in the surface plane, the MAE shows a significant angular dependence.

Investigation of the effects of ionic hydrogen bonds (C [dbnd]O −⋯H–C and +N–H⋯ −O [dbnd]C) in crystalline dl-proline by ab initio and DFT calculated NQR parameters

In this paper, we have calculated the nuclear quadrupole resonance (NQR) parameters of the quadrupole nuclei involved in the hydrogen bonds (C O −⋯H–C and +N–H⋯ −O C) in the monomer and pentameric cluster of dl-proline by HF and B3LYP methods and basis sets of 6-311+G ∗ and 6-311++G ∗∗. These computations are performed on the basis of X-ray diffraction structural data of dl-proline. The results indicate that the calculations including hydrogen-bonding (HB) interactions (in pentamer) are in better agreement with the experimental data than those in which these interactions are neglected (in monomer). The quantum chemical calculations show that the intermolecular hydrogen-bonding interactions play an important role in determination of the NQR parameters of 14N, 2H of NH 2 + group and 17O.

Atomic force microscopy investigation of Mason–Pfizer monkey virus and human immunodeficiency virus type 1 reassembled particles

Particles of ΔProCANC, a fusion of capsid (CA) and nucleocapsid (NC) protein of Mason–Pfizer monkey virus (M-PMV), which lacks the amino terminal proline, were reassembled in vitro and visualized by atomic force microscopy (AFM). The particles, of 83–84 nm diameter, exhibited ordered domains based on trigonal arrays of prominent rings with center to center distances of 8.7 nm. Imperfect closure of the lattice on the spherical surface was affected by formation of discontinuities. The lattice is consistent only with plane group p3 where one molecule is shared between contiguous rings. There are no pentameric clusters nor evidence that the particles are icosahedral. Tubular structures were also reassembled, in vitro, from two HIV fusion proteins, ΔProCANC and CANC. The tubes were uniform in diameter, 40 nm, but varied in length to a maximum of 600 nm. They exhibited left handed helical symmetry based on a p6 hexagonal net. The organization of HIV fusion proteins in the tubes is significantly different than for the protein units in the particles of M-PMV ΔProCANC.

Investigation of C–H…O [dbnd]C and N–H…O [dbnd]C hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters

A computational study at the level of density functional theory (DFT) was carried out to investigate C–H…O C and N–H…O C hydrogen-bonding interactions (HBs) in the real crystalline cluster of thymine by O-17, N-14 and H-2 calculated nuclear quadrupole resonance (NQR) parameters. To perform the calculations, a hydrogen-bonded pentameric cluster of thymine was created using X-ray coordinates where the hydrogen atoms positions are optimized and the electric field gradient (EFG) tensors were calculated for the target molecule. Additional EFG calculations were also performed for crystalline monomer and an optimized isolated gas-phase thymine. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G ⁎⁎ and CC-pVTZ basis sets were converted to those experimentally measurable NQR parameters, quadrupole coupling constants and asymmetry parameters. The results reveal that because of strong contribution to N–H…O C HBs, NQR parameters of O 2, N 1 and N 3 undergo significant changes from monomer to the target molecule in cluster. Furthermore, the NQR parameters of O 2 also undergo some changes because of non-classical C–H…O C HBs.

A Systematic Investigation of Hydrogen-Bonding Effects on the 17O, 14N, and 2H Nuclear Quadrupole Resonance Parameters of Anhydrous and Monohydrated Cytosine Crystalline Structures: A Density Functional Theory Study

A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.

A Unique Cyanide‐Bridged Three‐Dimensional (3‐D) Copper(II)—Copper(I) Mixed‐Valence Polymer Containing 1‐D Water Tapes with Cyclic Pentamer Units.

AbstractFor Abstract see ChemInform Abstract in Full Text.

A Unique Cyanide-Bridged Three-Dimensional (3-D) Copper(II)−Copper(I) Mixed-Valence Polymer Containing 1-D Water Tapes with Cyclic Pentamer Units

A unique cyano-bridged copper(II)-copper(I) mixed-valence polymer, {[Cu(3)(CN)(4)(H(2)O)(3)](H(2)O)(2)}(n) (1), has been prepared and structurally determined by X-ray diffraction. The cyanide anions with (mu(2),eta(2)) and (mu(3),eta(2)) bridging modes connect the copper centers into a complicated zeolite-like 3-D network. Of further interest, coordinated and lattice water molecules in this structure form 1-D hydrogen-bonded water tapes consisting of linked cyclic pentamer clusters.

How do small water clusters bind an excess electron?

The arrangement of water molecules around a hydrated electron has eluded explanation for more than 40 years. Here we report sharp vibrational bands for small gas-phase water cluster anions, (H2O)(4-6)- and (D2O)(4-6)-. Analysis of these bands reveals a detailed picture of the diffuse electron-binding site. The electron is closely associated with a single water molecule attached to the supporting network through a double H-bond acceptor motif. The local OH stretching bands of this molecule are dramatically distorted in the pentamer and smaller clusters because the excited vibrational levels are strongly coupled to the electron continuum. The vibration-to-electronic energy transfer rates, as revealed by line shape analysis, are mode-specific and remarkably fast, with the symmetric stretching mode surviving for less than 10 vibrational periods [50 fs in (H2O)4-].

Formation and dynamics of water clusters on Ru(001)

The adsorption kinetics of water on Ru(001) was simulated using molecular dynamics (MD) and equilibrium-model approach. The results nicely reproduce observations from STM imaging, work function change, and IR measurements. The agreement with experimental results is based on the formation of stable clusters already at very low surface coverage and temperature. Tetramers are predicted to be relatively stable compared to smaller and larger clusters. The dipole moment per water molecule continuously decreases from 2.2D for the monomer down to 1.1D for pentamer and larger clusters. Dimers are found to diffuse faster than monomers or larger clusters, with activation energy for diffusion of 2.9 kcal/mol, in agreement with recent STM measurements. A unique mechanism for dimers diffusion is proposed. Temperature programmed desorption (TPD) spectra from a metal surface were calculated by employing the MD scheme. These spectra were found identical to the standard Redhead line-shape analysis of the experimental TPD spectra of water from Pt(111) and Ru(001), an observation that was used to verify the consistency of the MD procedure. Finally, a kinetic model, fed by the MD calculated decreasing dipole moments per water molecule at larger clusters, explains well the highly nonlinear initial stages (up to 0.35BL) of the work function change data determined experimentally.

Electron attachment to CO2 clusters

Vertical and adiabatic electron attachment to carbon dioxide clusters (CO2)N (N=2–5) is studied at high ab initio levels of theory. As a first step the geometries of neutral and anionic CO2 clusters are reexamined. The potential energy surfaces of both neutral and anionic CO2 clusters show many minima, and several isomers have been reported so far. Here we present new lowest-energy isomers for the tetramer and pentamer anion clusters, as well as high-level results for relative and CO2 evaporation energies. Electron correlation is crucial for the computed properties, and since we had to make certain compromises about the theoretical level in order to include larger clusters, a thorough investigation of different ab initio methods is performed for the dimer. The vertical affinities of the investigated (CO2)N clusters are found to be clearly negative; i.e., vertical attachment into valence orbitals leads to temporary anion states. The energies of these resonances as well as the associated autodetachment lifetimes are computed using complex absorbing potentials at the frozen-orbital and correlated second-order Green’s function levels. Whereas the cluster environment has a surprisingly weak influence on the negative vertical affinities, solvation has a strong effect on the adiabatic electron affinities. The computed trends suggest that the tetramer is at the brink of stability and that the pentamer cluster is the smallest species possessing an appreciable positive electron affinity. Our findings have profound implications for the interpretation of the low-energy electron attachment experiments and provide a basis for the discussion and modeling the attachment process.

Clean Diesel to license NOx reduction technology for diesel vehicles in North America

A density functional method was applied to investigate the electronic structures of Cu ion adsorbed ZSM-5 zeolite and the interactions of NO molecules with zeolite. Two types of models were considered, the pentameric cluster model and the 5-membered ring cluster model. In the former, the Cu ion was bound to the two O atoms with larger stabilization energy (52 kcal/mol) than the single O atom. For the 5-membered ring model, a much smaller stabilization energy (38 kcal/mol) was calculated. The deNOx reaction mechanism was simulated as the reactions between two NO molecules or between NO and HNO (or NOH) molecules. The former did not produce N2 and O2 smoothly due to the activation barrier, whereas the latter is found to lead to N2O and OH more easily.

Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine, deoxyguanosine and uridine observed by ESI-MS/MS.

Electrospray ionization (ESI) mass spectra of nucleosides, recorded in the presence of alkali metals, display alkali metal ion-bound quartets and other clusters that may have implications for understanding non-covalent interactions in DNA and RNA. The tetramers of guanosine and deoxyguanosine and also their metaclusters (clusters of clusters), cationized by alkali metals, were observed as unusually abundant magic number clusters. The observation of these species in the gas phase parallels previous condensed-phase studies, which show that guanine derivatives can form quartets and metaclusters of quartets in solution in the presence of metal cations. This parallel behavior and also internal evidence suggest that bonding in the guanosine tetramers involves the bases rather than the sugar units. The nucleobases thymine and uracil are known to form magic number pentameric adducts with K+, Cs+ and NH4+ in the gas phase. In sharp contrast, we now show that the nucleosides uridine and deoxythymidine do not form the pentameric clusters characteristic of the corresponding bases. More subtle effects of the sugars are evident in the fact that adenosine and cytidine form numerous higher order clusters with alkali metals, whereas deoxyadenosine and deoxycytidine show no clustering. It is suggested that hydrogen bonding between the bases in the tetramers of dG and rG are the dominant interactions in the clusters, hence changing the ribose group to deoxyribose (and vice versa) generally has little effect. However, the additional hydroxyl group of RNA nucleosides enhances the non-selective formation of higher-order aggregates for adenosine and cytidine and results in the lack of highly stable magic number clusters. Some clusters are the result of aggregation in the course of ionization (ESI) whereas others appear to be intrinsic to the solution being examined.

An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.

Cucumber mosaic virus (CMV), the type member of the genus Cucumovirus (family Bromoviridae), is transmitted by aphids in a nonpersistent manner. Mutagenesis experiments identified the betaH-betaI loop of the capsid subunit as a potential key motif responsible for interactions with the insect vector. To further examine the functional characteristics of this motif, we generated monoclonal antibodies that bound to native virions but not to betaH-betaI mutants. Fab fragments from these antibodies were complexed with wild-type CMV and the virus-Fab structure was determined to 12-A resolution by using electron cryomicroscopy and image reconstruction techniques. The electron density attributed to the bound antibody has a turret-like appearance and protrudes from each of the 12 fivefold axes of the icosahedral virus. Thus, the antibody binds only to the pentameric clusters (pentons) of A subunits of the T=3 quasisymmetric virus and does not appear to bind to any of the B and C subunits that occur as hexameric clusters (hexons) at the threefold (quasi-sixfold) axes. Modeling and electron density comparisons were used to analyze the paratope-epitope interface and demonstrated that the antibody binds to three betaH-betaI loops in three adjacent A subunits in each penton. This antibody can discriminate between A and B/C subunits even though the betaH-betaI loop adopts the same structure in all 180 capsid subunits and is therefore recognizing differences in subunit arrangements. Antibodies with such character have potential use as probes of viral assembly. Our results may provide an additional rationale for designing synthetic vaccines by using symmetrical viral particles.

A theoretical study of the electronic spectrum of water

The electronic spectrum of water is investigated using coupled cluster electronic structure methods. Vertical excitation energies are calculated for both gas phase H2O, various water clusters, as well as from models designed to simulate condensed phase effects. Four different approaches for describing condensed phase effects on the electronic transitions are investigated: continuum (a single water molecule embedded in a dielectric medium), discrete (water clusters), semidiscrete (a water pentamer cluster embedded in a dielectric medium), and intermolecular perturbation methods. The results are compared with experimental results. The solvent shift on the lowest state appears to be reasonably described by discrete and semidiscrete methods. It is very difficult to model the condensed-phase effects for the higher states of the pure liquid.

The inelastic incoherent neutron spectrum of crystalline oxamide: experiment and simulation of a solid

The inelastic neutron scattering spectrum of crystalline oxamide, CO(NH 2)–CO(NH 2), is reported and compared with the results of Hartree–Fock and density functional theory calculations on a pentamer cluster model and the results of Car–Parrinello molecular dynamics calculations for the periodic crystal. All four hydrogen atoms of this centrosymmetric, planar sheet molecular crystal are involved in CO–H–N hydrogen bonds. It is shown that all three of these simulations provide reasonable descriptions of the inelastic neutron scattering spectra and thus of the hydrogen bond dynamics. There is no evidence for unusual structural or dynamic effects beyond those typically associated with H-bond formation. It is argued that a polymolecular approach is needed in order to provide an adequate treatment of such strongly hydrogen bonded systems.

Ab initio studies of anionic clusters of water pentamer

Conformers of water anionic pentamer cluster (H2O)5− have been reported here in using ab initio as well as density functional methods. Relative stabilities of these conformers obtained from inclusion of electron correlation at various levels indicate that they are very close in energies. The plots of singly occupied molecular orbital (SOMO) reveal that the excess electron exhibits stabilization selectively as either a surface state or an internal state. Vibrational frequencies of some of the conformers have also been reported at the MP2 level.

Dissociative photoionisation of acetylene-ethane van der Waals clusters

Intracluster ion–molecule reactions have been studied by dissociative photoionization of mixed acetylene–ethane van der Waals clusters in a supersonic molecular beam. The studies were carried out by recording threshold photoelectron–photoion coincidence mass spectra of the clusters at different photon energies between 10.8 and 11.3 eV. Intracluster reactions have been observed in mixed dimer, trimer, pentamer, and hexamer clusters. In the case of the mixed dimer ion [(C 2H 2)(C 2H 6)] +, two fragment ions result from intramolecular reactions: C 3H 5 + (CH 3 loss), and C 2H 4 + (C 2H 4 loss). This indicates that the dimer ion isomerizes into the 2-butene ion prior to dissociation, as is the case for ethylene dimer ions. Mixed trimer ions also dissociate by CH 3 loss. No intracluster hydride transfer prior to dissociation is observed, although this reaction channel is important in bimolecular C 2H 2 + + C 2H 6 collisions. Two very specific intracluster reactions leading to C 2H 4 loss were observed for pentamer and hexamer mixed cluster ions. A model involving evaporation and intracluster reactions leading to CH 3 and C 2H 4 loss is proposed to explain this surprising result.

Ab Initio Calculations of Cooperativity Effects on Clusters of Methanol, Ethanol, 1-Propanol, and Methanethiol

The results of ab initio calculations for cyclic clusters of methanol, ethanol, 1-propanol, and methanethiol are presented. Dimer, trimer, and tetramer clusters of all four compounds are studied, as are pentamer and hexamer clusters of methanol. From optimized clusters at HG/6--31G**, total energies and binding energies were calculated with both the HF and MP2 theories using the aug-cc-pVDZ basis set. Accurate binding energies were also calculated for the dimer and trimer of methanol using symmetry-adapted perturbation theory with the same basis set. Intermolecular and intramolecular distances, charge distribution of binding sites, binding energies, and equilibrium constants were computed to determine the hydrogen bond cooperativity effect for each species. The cooperativity effect, exclusive to hydrogen bonding systems, results form specific forces among the molecules, in particular charge-transfer processes and the greater importance of interactions between molecules not directly hydrogen bonded because of the longer range of the interactions. The ratios of equilibrium constants for forming multimer hydrogen bonds to that for dimer hydrogen bond formation increase rapidly with the cluster size, in contrast to the constant value commonly used in thermodynamic models for hydrogen bonding liquids.

Quantum cluster equilibrium theory of liquids: molecular clusters and thermodynamics of liquid ethanol

Quantum cluster equilibrium (QCE) theory is presented for liquid ethanol. The cluster equilibria that dictate phase composition are determined by the rigorous techniques of quantum statistical thermodynamics in the canonical ensemble, based on the ab initio partition function. The characteristic features of the supramolecular clusters which comprise the QCE model are discussed in terms of binding energies, geometries, cooperativity and charge transfer. The validity of the resulting QCE model is demonstrated by comparison with experimental ther-modynamic data: Clausius—Clapeyron pressure/temperature dependence and the specific heat. At room temperature, neat, liquid ethanol consists of approximately equal parts of monomer, cyclic tetramer and cyclic pentamer clusters.

Improved intermolecular water potential from global geometry optimization of small water clusters using local MP2

Global geometry optimizations of water pentamer and hexamer clusters were carried out using a model potential from the NEMO family [P.-O. Åstrand, A. Wallqvist, G. Karlström, J. Chem. Phys. 100 (1994) 3726], which is simultaneously improved by minimizing the interaction energy deviations from an ab initio reference (in our case local second-order Møller–Plesset perturbation theory, LMP2) at corresponding geometries. This procedure not only yields the most important local (and global) minima of these clusters at the LMP2 level, but also an improved parameter set for the NEMO potential that, in contrast to the original NEMO potential, reproduces these structures and their energy ordering faithfully. The use of local MP2 ensures that the optimized structures are virtually free of basis set superposition errors.