Thermal O-H Bond Activation of Water as Mediated by Heteronuclear [Al2Mg2O5]•+: Evidence for Oxygen-Atom Scrambling.

PubMed

Geng, Caiyun; Li, Jilai; Weiske, Thomas; Schwarz, Helmut

2018-06-25

Mechanistic insight into the thermal O-H bond activation of water by the cubane-like, prototypical heteronuclear oxide cluster [Al 2 Mg 2 O 5 ] •+ has been derived from a combined experimental/computational study. Experiments in the highly diluted gas phase using Fourier transform ion-cyclotron resonance mass spectrometry show that hydrogen-atom abstraction from water by the cluster cation [Al 2 Mg 2 O 5 ] •+ occurs at ambient conditions accompanied by the liberation of an OH • radical. Due to a complete randomization of all oxygen atoms prior to fragmentation about 83% of the oxygen atoms of the hydroxyl radical released originate from the oxide cluster itself. The experimental findings are supported by detailed high-level quantum chemical calculations. The theoretical analysis reveals that the transfer of a formal hydrogen atom from water to the metal-oxide cation can proceed mechanistically via proton- or hydrogen-atom transfer exploiting different active sites of the cluster oxide. In addition to the unprecedented oxygen-atom scrambling, one of the more general and quite unexpected findings concerns the role of spin density at the hydrogen-acceptor oxide atom. While this feature is so crucial for [M-O] + /CH 4 couples, it is much less important in the O-H bond activation of water.

Thermodynamics of the clusterization process of cis isomers of unsaturated fatty acids at the air/water interface.

PubMed

Vysotsky, Yu B; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Aksenenko, E V; Miller, R

2009-04-02

In the framework of the semiempirical PM3 method, the thermodynamic parameters of cis isomers of unsaturated carboxylic acids at the air/water interface are studied. The model systems used are unsaturated cis fatty acid of the composition Delta = 12-15 and omega = 6-11, where Delta and omega refer to the number of carbon atoms between the functional group and double bond, and that between the double bond and methyl group, respectively. For dimers, trimers, and tetramers of the four acid series, the thermodynamic parameters of clusterization are calculated. It is shown that the position of the double bond does not significantly affect the values of thermodynamic parameters of formation and clusterization of carboxylic acids for equal chain lengths (n = Delta + omega). The calculated results show that for cis unsaturated fatty acid with odd Delta values the spontaneous clusterization threshold corresponds to n = 17-18 carbon atoms in the alkyl chain, while for monounsaturated acids with even Delta values this threshold corresponds to n = 18-19 carbon atoms in the alkyl chain. These differences in the clusterization threshold between the acids with even and odd Delta values are attributed to the formation of additional intermolecular hydrogen bonds between the ketonic oxygen atom of one monomer and the hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with odd Delta values or between the hydroxyl oxygen atom of one monomer and hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with even Delta values. The results obtained in the study agree satisfactorily with our experimental data for cis unsaturated nervonic (Delta15, omega9) and erucic acids (Delta13, omega9), and published data for some fatty acids, namely cis-16-heptadecenoic (Delta16, omega1), cis-9-hexadecenoic (Delta7, omega9), cis-11-eicosenoic (Delta11, omega9) and cis-9-octadecenoic acid (Delta9, omega9).

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

Theoretical Study on the Catalytic Reduction Mechanism of NO by CO on Tetrahedral Rh4 Subnanocluster.

PubMed

Yang, Hua-Qing; Fu, Hong-Quan; Su, Ben-Fang; Xiang, Bo; Xu, Qian-Qian; Hu, Chang-Wei

2015-11-25

The catalytic mechanism of 2NO + 2CO → N2 + 2CO2 on Rh4 cluster has been systematically investigated on the ground and first excited states at the B3LYP/6-311+G(2d),SDD level. For the overall reaction of 2NO + 2CO → N2 + 2CO2, the main reaction pathways take place on the facet site rather than the edge site of the Rh4 cluster. The turnover frequency (TOF) determining transition states are characteristic of the second N-O bond cleavage with rate constant k4 = 1.403 × 10(11) exp (-181 203/RT) and the N-N bond formation for the intermediate N2O formation with rate constant k2 = 3.762 × 10(12) exp (-207 817/RT). The TOF-determining intermediates of (3)N(b)Rh4NO and (3)N(b)Rh4O(b)(NO) are associated with the nitrogen-atom molecular complex, which is in agreement with the experimental observation of surface nitrogen. On the facet site of Rh4 cluster, the formation of CO2 stems solely from the recombination of CO and O atom, while N2 originates partly from the recombination of two N atoms and partly from the decomposition of N2O. For the N-O bond cleavage or the synchronous N-O bond cleavage and C-O bond formation, the neutral Rh4 cluster exhibits better catalytic performance than the cationic Rh4(+) cluster. Alternatively, for N-N bond formation, the cationic Rh4(+) cluster possesses better catalytic performance than the neutral Rh4 cluster.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.

The Existence of a Designer Al=Al Double Bond in the LiAl2 H4- Cluster Formed by Electronic Transmutation.

PubMed

Lundell, Katie A; Zhang, Xinxing; Boldyrev, Alexander I; Bowen, Kit H

2017-12-22

The Al=Al double bond is elusive in chemistry. Herein we report the results obtained via combined photoelectron spectroscopy and ab initio studies of the LiAl 2 H 4 - cluster that confirm the formation of a conventional Al=Al double bond. Comprehensive searches for the most stable structures of the LiAl 2 H 4 - cluster have shown that the global minimum isomer I possesses a geometric structure which resembles that of Si 2 H 4 , demonstrating a successful example of the transmutation of Al atoms into Si atoms by electron donation. Theoretical simulations of the photoelectron spectrum discovered the coexistence of two isomers in the ion beam, including the one with the Al=Al double bond. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metallothionein-like multinuclear clusters of mercury(II) and sulfur in peat

USGS Publications Warehouse

Nagy, K.L.; Manceau, A.; Gasper, J.D.; Ryan, J.N.; Aiken, G.R.

2011-01-01

Strong mercury(II)-sulfur (Hg-SR) bonds in natural organic matter, which influence mercury bioavailability, are difficult to characterize. We report evidence for two new Hg-SR structures using X-ray absorption spectroscopy in peats from the Florida Everglades with added Hg. The first, observed at a mole ratio of organic reduced S to Hg (Sred/Hg) between 220 and 1140, is a Hg4Sx type of cluster with each Hg atom bonded to two S atoms at 2.34 ?? and one S at 2.53 ??, and all Hg atoms 4.12 ?? apart. This model structure matches those of metal-thiolate clusters in metallothioneins, but not those of HgS minerals. The second, with one S atom at 2.34 ?? and about six C atoms at 2.97 to 3.28 ??, occurred at S red/Hg between 0.80 and 4.3 and suggests Hg binding to a thiolated aromatic unit. The multinuclear Hg cluster indicates a strong binding environment to cysteinyl sulfur that might impede methylation. Along with a linear Hg(SR)2 unit with Hg - S bond lengths of 2.34 ?? at Sred/Hg of about 10 to 20, the new structures support a continuum in Hg-SR binding strength in natural organic matter. ?? 2011 American Chemical Society.

Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

NASA Astrophysics Data System (ADS)

Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

2016-05-01

Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

Structure and properties of B20Si-/0/+ clusters

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Li, Yi De; Huang, Shou Guo

2018-06-01

A global search for the lowest energy structure of B20Si-, B20Si0 and B20Si+ clusters is conducted. Structural transitions at different charge states are observed. B20Si- is a 2D planar configuration with no polygonal holes, and Si atom occupies a peripheral position. B20Si+ adopts a 3D tubular shape, and each Si is bonded with four B atoms. But for B20Si0, competition among quasi-planar, tubular and cage like structures is found. These structures differ greatly from that of pure B21 - cluster. The structural transition may result from changes in the framework of bonding, sp 2 hybridization, and structural mechanics. Some of the clusters' properties including frontier molecular orbital, on-site charge on Si atom, electron density, and magnetism are also discussed.

Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

PubMed

Manzoor, Dar; Pal, Sourav

2015-06-18

Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

Metallic-covalent bonding conversion and thermoelectric properties of Al-based icosahedral quasicrystals and approximants.

PubMed

Takagiwa, Yoshiki; Kimura, Kaoru

2014-08-01

In this article, we review the characteristic features of icosahedral cluster solids, metallic-covalent bonding conversion (MCBC), and the thermoelectric properties of Al-based icosahedral quasicrystals and approximants. MCBC is clearly distinguishable from and closely related to the well-known metal-insulator transition. This unique bonding conversion has been experimentally verified in 1/1-AlReSi and 1/0-Al 12 Re approximants by the maximum entropy method and Rietveld refinement for powder x-ray diffraction data, and is caused by a central atom inside the icosahedral clusters. This helps to understand pseudogap formation in the vicinity of the Fermi energy and establish a guiding principle for tuning the thermoelectric properties. From the electron density distribution analysis, rigid heavy clusters weakly bonded with glue atoms are observed in the 1/1-AlReSi approximant crystal, whose physical properties are close to icosahedral Al-Pd-TM (TM: Re, Mn) quasicrystals. They are considered to be an intermediate state among the three typical solids: metals, covalently bonded networks (semiconductor), and molecular solids. Using the above picture and detailed effective mass analysis, we propose a guiding principle of weakly bonded rigid heavy clusters to increase the thermoelectric figure of merit ( ZT ) by optimizing the bond strengths of intra- and inter-icosahedral clusters. Through element substitutions that mainly weaken the inter-cluster bonds, a dramatic increase of ZT from less than 0.01 to 0.26 was achieved. To further increase ZT , materials should form a real gap to obtain a higher Seebeck coefficient.

Planar CoB18- Cluster: a New Motif for - and Metallo-Borophenes

NASA Astrophysics Data System (ADS)

Chen, Teng-Teng; Jian, Tian; Lopez, Gary; Li, Wan-Lu; Chen, Xin; Li, Jun; Wang, Lai-Sheng

2016-06-01

Combined Photoelectron Spectroscopy (PES) and theoretical calculations have found that anion boron clusters (Bn-) are planar and quasi-planar up to B25-. Recent works show that anion pure boron clusters continued to be planar at B27-,B30-,B35- and B36-. B35- and B36- provide the first experimental evidence for the viability of the two-dimensional (2D) boron sheets (Borophene). The 2D to three-dimensional (3D) transitions are shown to happen at B40-,B39- and B28-, which possess cage-like structures. These fullerene-like boron cage clusters are named as Borospherene. Recently, borophenes or similar structures are claimed to be synthesized by several groups. Following an electronic design principle, a series of transition-metal-doped boron clusters (M©Bn-, n=8-10) are found to possess the monocyclic wheel structures. Meanwhile, CoB12- and RhB12- are revealed to adopt half-sandwich-type structures with the quasi-planar B12 moiety similar to the B12- cluster. Very lately, we show that the CoB16- cluster possesses a highly symmetric Cobalt-centered drum-like structure, with a new record of coordination number at 16. Here we report the CoB18- cluster to possess a unique planar structure, in which the Co atom is doped into the network of a planar boron cluster. PES reveals that the CoB18- cluster is a highly stable electronic system with the first adiabatic detachment energy (ADE) at 4.0 eV. Global minimum searches along with high-level quantum calculations show the global minimum for CoB18- is perfectly planar and closed shell (1A1) with C2v symmetry. The Co atom is bonded with 7 boron atoms in the closest coordination shell and the other 11 boron atoms in the outer coordination shell. The calculated vertical detachment energy (VDE) values match quite well with our experimental results. Chemical bonding analysis by the Adaptive Natural Density Partitioning (AdNDP) method shows the CoB18- cluster is π-aromatic with four 4-centered-2-electron (4c-2e) π bonds and one 19-centered-2-electron (19c-2e) π bond, 10 π electrons in total. This perfectly planar structure reveals the viability of creating a new class of hetero-borophenes and metallo-borophenes by doping metal atoms into the plane of monolayer boron atoms. This gives a new approach to design perspective hetero-borophenes and metallo-borophenes materials with tunable chemical, magnetic and optical properties.

A DFT study of pure and lithium doped gold clusters

NASA Astrophysics Data System (ADS)

Rani, Babita

2018-05-01

First principles calculations on Aun and Aun-1Li (n=1-6) clusters are performed to understand the effect of size and composition on their structural and energy parameters. It has been found that binding energy increases continuously with increase in the size of pure Aun and doped Aun-1Li clusters and attains its maximum at n=6. Also, Li doping results in the improvement of relative stabilities of pure gold clusters, owing to higher bond strength (i.e. shorter bond length) of Au- Li bond as compared to Au-Au bonds. Moreover, Aun-1Li clusters are found to be more compact. Structural transformations are observed in case of gold clusters doped with Li atom which may affect their application in the field of catalysis.

Structures and chemical bonding of B{sub 3}O{sub 3}{sup −/0} and B{sub 3}O{sub 3}H{sup −/0}: A combined photoelectron spectroscopy and first-principles theory study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Li-Juan; Xu, Hong-Guang; Feng, Gang

We present a combined photoelectron spectroscopy and first-principles theory study on the structural and electronic properties and chemical bonding of B{sub 3}O{sub 3}{sup −/0} and B{sub 3}O{sub 3}H{sup −/0} clusters. The concerted experimental and theoretical data show that the global-minimum structures of B{sub 3}O{sub 3} and B{sub 3}O{sub 3}H neutrals are very different from those of their anionic counterparts. The B{sub 3}O{sub 3}{sup −} anion is characterized to possess a V-shaped OB–B–BO chain with overall C{sub 2v} symmetry (1A), in which the central B atom interacts with two equivalent boronyl (B≡O) terminals via B–B single bonds as well as withmore » one O atom via a B=O double bond. The B{sub 3}O{sub 3}H{sup −} anion has a C{sub s} (2A) structure, containing an asymmetric OB–B–OBO zig-zag chain and a terminal H atom interacting with the central B atom. In contrast, the C{sub 2v} (1a) global minimum of B{sub 3}O{sub 3} neutral contains a rhombic B{sub 2}O{sub 2} ring with one B atom bonded to a BO terminal and that of neutral B{sub 3}O{sub 3}H (2a) is also of C{sub 2v} symmetry, which is readily constructed from C{sub 2v} (1a) by attaching a H atom to the opposite side of the BO group. The H atom in B{sub 3}O{sub 3}H{sup −/0} (2A and 2a) prefers to interact terminally with a B atom, rather than with O. Chemical bonding analyses reveal a three-center four-electron (3c-4e) π hyperbond in the B{sub 3}O{sub 3}H{sup −} (2A) cluster and a four-center four-electron (4c-4e) π bond (that is, the so-called o-bond) in B{sub 3}O{sub 3} (1a) and B{sub 3}O{sub 3}H (2a) neutral clusters.« less

Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

PubMed

Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

2016-12-28

Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

DFT STUDY OF CO AND NO ADSORPTION ON BORON NITRIDE (BN)n = 3 - 5 NANOCLUSTERS

NASA Astrophysics Data System (ADS)

Zahedi, Ehsan; Pangh, Abdolhakim; Ghorbanpour, Hamed

2015-11-01

Interaction of CO and NO molecules by different orientations on (BN)n=3-5 clusters have been studied at the B3LYP/6-311+G* level of theory. Total electronic energies have been corrected for geometrical counterpoise (gCP) and dispersion (D3) energies at the B3LYP/6-31G* level. Formation of a new sigma bond between the gas and (BN)3 cluster, atom in molecules (AIM) results, density of states spectrums (DOS), molecular electrostatic potential (MEP) surfaces, and visualization of wave function of molecular orbitals in the nearest bonding regions to the Fermi level have confirmed that adsorption of CO by carbon end atom, and NO by nitrogen end atom is covalent in nature, so that the charge transfer is occurred from gas molecule to the cluster.

Electronic structure studies of Ni( 1 0 0 ) surface reconstructions resulting from carbon, nitrogen, or oxygen atom adsorption

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2003-01-01

Solid-state Fenske-Hall band structure calculations have been used to study the different surface structures which result from adsorption of a half monolayer of C, N, or O atoms on the Ni(1 0 0) surface. C or N atoms sit nearly coplanar with the surface Ni atoms and induce the "clock" reconstruction of the surface. In contrast, adsorbed O atoms sit slightly above the Ni(1 0 0) surface plane and have little effect on the overall surface structure. The local environments of the C, N, and O atoms on these surfaces are similar to their environments in a series of late transition metal carbonyl clusters, suggesting that some of the same electronic factors may play a role in favoring the different structures. Results of the calculations indicate that when adsorbates occupy coplanar sites on Ni(1 0 0), much of the Ni-Ni bonding within the surface layer and between the surface- and second-layers is disrupted. On the C- and N-covered surfaces the disruption is more than compensated for by the formation of strong adsorbate-Ni bonds and by new Ni-Ni surface bonds resulting from the clock reconstruction. When O is forced into a coplanar site, however, both the higher electron count and increased electronegativity of the O atoms lead to severe disruption of the surface bonding and weak Ni-O bonds. When O atoms sit above the surface, they form more polar Ni-O bonds, contribute less electron density to the Ni surface bands, and cause less disruption to Ni-Ni surface bonds. These results suggest that, similar to the organometallic clusters, the site preferences of C, N, and O atoms are directly related to their electron count, and in turn to the relative occupation of both Ni-Ni and X-Ni (X=C, N, O) antibonding bands.

Experimental and theoretical study on activation of the C-H bond in pyridine by [M(m)]- (M = Cu, Ag, Au, m = 1-3).

PubMed

Liu, Xiao-Jing; Hamilton, I P; Han, Ke-Li; Tang, Zi-Chao

2010-09-21

Activation of the C-H bond of pyridine by [M(m)](-) (M = Cu, Ag, Au, m = 1-3) is investigated by experiment and theory. Complexes of coinage metal clusters and the pyridyl group, [M(m)-C(5)H(4)N](-), are produced from reactions between metal clusters formed by laser ablation of coinage metal samples and pyridine molecules seeded in argon carrier gas. We examine the structure and formation mechanism of these pyridyl-coinage metal complexes. Our study shows that C(5)H(4)N bonds to the metal clusters through a M-C sigma bond and [M(m)-C(5)H(4)N](-) is produced via a stepwise mechanism. The first step is a direct insertion reaction between [M(m)](-) and C(5)H(5)N with activation of the C-H bond to yield the intermediate [HM(m)-C(5)H(4)N](-). The second step is H atom abstraction by a neutral metal atom to yield [M(m)-C(5)H(4)N](-).

Influence of N-H...O and C-H...O hydrogen bonds on the 17O NMR tensors in crystalline uracil: computational study.

PubMed

Ida, Ramsey; De Clerk, Maurice; Wu, Gang

2006-01-26

We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively.

Tuning optical properties of magic number cluster (SiO2)4O2H4 by substitutional bonding with gold atoms.

PubMed

Cai, Xiulong; Zhang, Peng; Ma, Liuxue; Zhang, Wenxian; Ning, Xijing; Zhao, Li; Zhuang, Jun

2009-04-30

By bonding gold atoms to the magic number cluster (SiO(2))(4)O(2)H(4), two groups of Au-adsorbed shell-like clusters Au(n)(SiO(2))(4)O(2)H(4-n) (n = 1-4) and Au(n)(SiO(2))(4)O(2) (n = 5-8) were obtained, and their spectral properties were studied. The ground-state structures of these clusters were optimized by density functional theory, and the results show that in despite of the different numbers and types of the adsorbed Au atoms, the cluster core (SiO(2))(4)O(2) of T(d) point-group symmetry keeps almost unchanged. The absorption spectra were obtained by time-dependent density functional theory. From one group to the other, an extension of absorption wavelength from the UV-visible to the NIR region was observed, and in each group the absorption strengths vary linearly with the number of Au atoms. These features indicate their advantages for exploring novel materials with easily controlled tunable optical properties. Furthermore, due to the weak electronic charge transfer between the Au atoms, the clusters containing Au(2) dimers, especially Au(8)(SiO(2))(4)O(2), absorb strongly NIR light at 900 approximately 1200 nm. Such strong absorption suggests potential applications of these shell-like clusters in tumor cells thermal therapy, like the gold-coated silica nanoshells with larger sizes.

A DFT investigation on geometry and chemical bonding of isoelectronic Si8N6V-, Si8N6Cr, and Si8N6Mn+ clusters

NASA Astrophysics Data System (ADS)

Tam, Nguyen Minh; Pham, Hung Tan; Cuong, Ngo Tuan; Tung, Nguyen Thanh

2017-10-01

The geometric feature and chemical bonding of isoelectronic systems Si8N6Mq (M = V, Cr, Mn and q = -1, 0, 1, respectively) are investigated by means of density-functional-theory calculations. The encapsulated form is found for all ground-state structures, where the metal atom locates at the central site of the hollow Si8N6 cage. The Si8N6 cage is established by adding two Si atoms to a distorted Si6N6 prism, which is a combination of Si4N2 and Si2N4 strings. Chemical bonding of Si8N6Mq systems is explored by using the electron localization indicator and theory of atom in molecule, revealing the vital role of metal center in stabilizing the clusters.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations.

PubMed

Yin, Shi; Bernstein, Elliot R

2016-10-21

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH) 1-3 - cluster anions are lower than those found for their respective FeS 1-3 - cluster anions. The experimental first VDEs for FeS 1-3 - clusters are observed to increase for the first two S atoms bound to Fe - ; however, due to the formation of an S-S bond for the FeS 3 - cluster, its first VDE is found to be ∼0.41 eV lower than the first VDE for the FeS 2 - cluster. The first VDEs of Fe(SH) 1-3 - cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS 1-3 - and Fe(SH) 1-3 - clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH) - is lower than that for FeS 2 - , but higher than that for Fe(SH) 2 - ; the first VDEs for FeS 2 (SH) - and FeS(SH) 2 - are close to that for FeS 3 - , but higher than that for Fe(SH) 3 - . The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Yin, Shi; Bernstein, Elliot R.

2016-10-01

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH)1-3- cluster anions are lower than those found for their respective FeS1-3- cluster anions. The experimental first VDEs for FeS1-3- clusters are observed to increase for the first two S atoms bound to Fe-; however, due to the formation of an S-S bond for the FeS3- cluster, its first VDE is found to be ˜0.41 eV lower than the first VDE for the FeS2- cluster. The first VDEs of Fe(SH)1-3- cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS1-3- and Fe(SH)1-3- clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH)- is lower than that for FeS2-, but higher than that for Fe(SH)2-; the first VDEs for FeS2(SH)- and FeS(SH)2- are close to that for FeS3-, but higher than that for Fe(SH)3-. The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

PubMed

Fanfrlík, Jindřich; Holub, Josef; Růžičková, Zdeňka; Řezáč, Jan; Lane, Paul D; Wann, Derek A; Hnyk, Drahomír; Růžička, Aleš; Hobza, Pavel

2016-11-04

Halogen bonds are a subset of noncovalent interactions with rapidly expanding applications in materials and medicinal chemistry. While halogen bonding is well known in organic compounds, it is new in the field of boron cluster chemistry. We have synthesized and crystallized carboranes containing Br atoms in two different positions, namely, bound to C- and B-vertices. The Br atoms bound to the C-vertices have been found to form halogen bonds in the crystal structures. In contrast, Br atoms bound to B-vertices formed hydrogen bonds. Quantum chemical calculations have revealed that halogen bonding in carboranes can be much stronger than in organic architectures. These findings open new possibilities for applications of carboranes, both in materials and medicinal chemistry. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metal-metal bond lengths in complexes of transition metals.

PubMed

Pauling, L

1976-12-01

In complexes of the transition metals containing clusters of metal atoms the cobalt-cobalt bond lengths are almost always within 1 pm of the single-bond value 246 pm given by the enneacovalent radius of cobalt, whereas most of the observed iron-iron bond lengths are significantly larger than the single-bond value 248 pm, the mean being 264 pm, which corresponds to a half-bond. A simple discussion of the structures of these complexes based on spd hybrid orbitals, the electroneutrality principle, and the partial ionic character of bonds between unlike atoms leads to the conclusion that resonance between single bonds and no-bonds would occur for iron and its congeners but not for cobalt and its congeners, explaining the difference in the bond lengths.

Electronic levels and charge distribution near the interface of nickel

NASA Technical Reports Server (NTRS)

Waber, J. T.

1982-01-01

The energy levels in clusters of nickel atoms were investigated by means of a series of cluster calculations using both the multiple scattering and computational techniques (designated SSO) which avoids the muffin-tin approximation. The point group symmetry of the cluster has significant effect on the energy of levels nominally not occupied. This influences the electron transfer process during chemisorption. The SSO technique permits the approaching atom or molecule plus a small number of nickel atoms to be treated as a cluster. Specifically, molecular levels become more negative in the O atom, as well as in a CO molecule, as the metal atoms are approached. Thus, electron transfer from the nickel and bond formation is facilitated. This result is of importance in understanding chemisorption and catalytic processes.

Factors driving stable growth of He clusters in W: first-principles study

NASA Astrophysics Data System (ADS)

Feng, Y. J.; Xin, T. Y.; Xu, Q.; Wang, Y. X.

2018-07-01

The evolution of helium (He) bubbles is responsible for the surface morphology variation and subsequent degradation of the properties of plasma-facing materials (PFMs) in nuclear fusion reactors. These severe problems unquestionably trace back to the behavior of He in PFMs, which is closely associated with the interaction between He and the matrix. In this paper, we decomposed the binding energy of the He cluster into three parts, those from W–W, W–He, and He–He interactions, using density functional theory. As a result, we clearly identified the main factors that determine a steplike decrease in the binding energy with increasing number of He atoms, which explains the process of self-trapping and athermal vacancy generation during He cluster growth in the PFM tungsten. The three interactions were found to synergetically shape the features of the steplike decrease in the binding energy. Fairly strong He–He repulsive forces at a short distance, which stem from antibonding states between He atoms, need to be released when additional He atoms are continuously bonded to the He cluster. This causes the steplike feature in the binding energy. The bonding states between W and He atoms in principle facilitate the decreasing trend of the binding energy. The decrease in binding energy with increasing number of He atoms implies that He clusters can grow stably.

Metal-metal bond lengths in complexes of transition metals*

PubMed Central

Pauling, Linus

1976-01-01

In complexes of the transition metals containing clusters of metal atoms the cobalt-cobalt bond lengths are almost always within 1 pm of the single-bond value 246 pm given by the enneacovalent radius of cobalt, whereas most of the observed iron-iron bond lengths are significantly larger than the single-bond value 248 pm, the mean being 264 pm, which corresponds to a half-bond. A simple discussion of the structures of these complexes based on spd hybrid orbitals, the electroneutrality principle, and the partial ionic character of bonds between unlike atoms leads to the conclusion that resonance between single bonds and no-bonds would occur for iron and its congeners but not for cobalt and its congeners, explaining the difference in the bond lengths. PMID:16592368

A density functional study of second-row dicarbides C2X (X = Na-Cl) with carbon monosulfide molecule: molecular structure and bonding mechanism

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Sahu, Sridhar

2018-05-01

In present work, a systematic study regarding molecular structure, and bonding mechanism of carbon monosulfide (CS) on second-row dicarbides C2X with (X = Na-Cl) has been investigated within the framework of density functional theory (DFT). In presence of carbon monosulfide molecule, the structures of C2Na, C2Mg, C2Al, and C2Si are found be changed from cyclic to linear, whereas geometries of C2P, C2S, and C2Cl clusters are almost remain unchanged. Interestingly, the bare carbon monosulfide molecule is attached with carbon site of bare C2X clusters rather than the second-row elements (X = Na-Cl). Furthermore, the nature of bonding in C2XCS clusters has been studiedthrough Bader's topological analysis of the electron charge density distribution ρ(r), Laplacian ∇2 ρ(r) and total energy density H BCP at the bond critical points (BCPs) of the clusters within the framework of the atoms in molecules theory (AIM). In C2XCS clusters, electron density at the bond critical point ρ(r) > 0.30 a.u. with negative values of Laplacian ∇2 ρ(r) indicates shared-kind of interactions between both the carbon atoms of C2X and CS molecule. In addition, we also analyze IR spectra that could assist for the experimental detection.

Origins of hole traps in hydrogenated nanocrystalline and amorphous silicon revealed through machine learning

NASA Astrophysics Data System (ADS)

Mueller, Tim; Johlin, Eric; Grossman, Jeffrey C.

2014-03-01

Genetic programming is used to identify the structural features most strongly associated with hole traps in hydrogenated nanocrystalline silicon with very low crystalline volume fraction. The genetic programming algorithm reveals that hole traps are most strongly associated with local structures within the amorphous region in which a single hydrogen atom is bound to two silicon atoms (bridge bonds), near fivefold coordinated silicon (floating bonds), or where there is a particularly dense cluster of many silicon atoms. Based on these results, we propose a mechanism by which deep hole traps associated with bridge bonds may contribute to the Staebler-Wronski effect.

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

Equilibrium structure and atomic vibrations of Nin clusters

NASA Astrophysics Data System (ADS)

Borisova, Svetlana D.; Rusina, Galina G.

2017-12-01

The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

Interatomic scattering in energy dependent photoelectron spectra of Ar clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patanen, M.; Benkoula, S.; Nicolas, C.

2015-09-28

Soft X-ray photoelectron spectra of Ar 2p levels of atomic argon and argon clusters are recorded over an extended range of photon energies. The Ar 2p intensity ratios between atomic argon and clusters’ surface and bulk components reveal oscillations similar to photoelectron extended X-ray absorption fine structure signal (PEXAFS). We demonstrate here that this technique allows us to analyze separately the PEXAFS signals from surface and bulk sites of free-standing, neutral clusters, revealing a bond contraction at the surface.

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality.

PubMed

Sergeeva, Alina P; Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Romanescu, Constantin; Wang, Lai-Sheng; Boldyrev, Alexander I

2014-04-15

Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron, atomic boron clusters are found to have planar or quasi-planar structures, stabilized by localized two-center-two-electron (2c-2e) σ bonds on the periphery and delocalized multicenter-two-electron (nc-2e) bonds in both σ and π frameworks. Electron delocalization is a result of boron's electron deficiency and leads to fluxional behavior, which has been observed in B13(+) and B19(-). A unique capability of the in-plane rotation of the inner atoms against the periphery of the cluster in a chosen direction by employing circularly polarized infrared radiation has been suggested. Such fluxional behaviors in boron clusters are interesting and have been proposed as molecular Wankel motors. The concepts of aromaticity and antiaromaticity have been extended beyond organic chemistry to planar boron clusters. The validity of these concepts in understanding the electronic structures of boron clusters is evident in the striking similarities of the π-systems of planar boron clusters to those of polycyclic aromatic hydrocarbons, such as benzene, naphthalene, coronene, anthracene, or phenanthrene. Chemical bonding models developed for boron clusters not only allowed the rationalization of the stability of boron clusters but also lead to the design of novel metal-centered boron wheels with a record-setting planar coordination number of 10. The unprecedented highly coordinated borometallic molecular wheels provide insights into the interactions between transition metals and boron and expand the frontier of boron chemistry. Another interesting feature discovered through cluster studies is boron transmutation. Even though it is well-known that B(-), formed by adding one electron to boron, is isoelectronic to carbon, cluster studies have considerably expanded the possibilities of new structures and new materials using the B(-)/C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors' laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.

Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sergeeva, Alina P.; Popov, Ivan A.; Piazza, Zachary A.

Conspectus Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron, atomic boron clusters are found to have planar or quasi-planar structures, stabilized by localized two-center–two-electron (2c–2e) σ bonds on the periphery and delocalized multicenter–two-electron (nc–2e) bonds in both σ and π frameworks. Electron delocalization is a result of boron’s electron deficiency and leads to fluxional behavior, which has been observed in B13+ and B19–. A unique capability of the in-plane rotation of the inner atoms against the periphery of the cluster in a chosen direction by employing circularly polarized infrared radiationmore » has been suggested. Such fluxional behaviors in boron clusters are interesting and have been proposed as molecular Wankel motors. The concepts of aromaticity and antiaromaticity have been extended beyond organic chemistry to planar boron clusters. The validity of these concepts in understanding the electronic structures of boron clusters is evident in the striking similarities of the π-systems of planar boron clusters to those of polycyclic aromatic hydrocarbons, such as benzene, naphthalene, coronene, anthracene, or phenanthrene. Chemical bonding models developed for boron clusters not only allowed the rationalization of the stability of boron clusters but also lead to the design of novel metal-centered boron wheels with a record-setting planar coordination number of 10. The unprecedented highly coordinated borometallic molecular wheels provide insights into the interactions between transition metals and boron and expand the frontier of boron chemistry. Another interesting feature discovered through cluster studies is boron transmutation. Even though it is well-known that B–, formed by adding one electron to boron, is isoelectronic to carbon, cluster studies have considerably expanded the possibilities of new structures and new materials using the B–/C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors’ laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.« less

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework.

PubMed

Kim, In Soo; Li, Zhanyong; Zheng, Jian; Platero-Prats, Ana E; Mavrandonakis, Andreas; Pellizzeri, Steven; Ferrandon, Magali; Vjunov, Aleksei; Gallington, Leighanne C; Webber, Thomas E; Vermeulen, Nicolaas A; Penn, R Lee; Getman, Rachel B; Cramer, Christopher J; Chapman, Karena W; Camaioni, Donald M; Fulton, John L; Lercher, Johannes A; Farha, Omar K; Hupp, Joseph T; Martinson, Alex B F

2018-01-22

Single atoms and few-atom clusters of platinum are uniformly installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 °C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and X-ray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novel catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent induced temperature dependencies of NMR parameters of hydrogen bonded anionic clusters

NASA Astrophysics Data System (ADS)

Golubev, Nikolai S.; Shenderovich, Ilja G.; Tolstoy, Peter M.; Shchepkin, Dmitry N.

2004-07-01

The solvent induced temperature dependence of NMR parameters (proton and fluorine chemical shifts, the two-bond scalar spin coupling constant across the hydrogen bridge, 2hJFF) for dihydrogen trifluoride anion, (FH) 2F -, in a polar aprotic solvent, CDF 3/CDF 2Cl, is reported and discussed. The results are interpreted in terms of a simple electrostatic model, accounting a decrease of electrostatic repulsion of two negatively charged fluorine atoms on placing into a dielectric medium. The conclusion is drawn that polar medium causes some contraction of hydrogen bonds in ionic clusters combined with a decrease of hydrogen bond asymmetry.

Titanium Insertion into CO Bonds in Anionic Ti-CO2 Complexes.

PubMed

Dodson, Leah G; Thompson, Michael C; Weber, J Mathias

2018-03-22

We explore the structures of [Ti(CO 2 ) y ] - cluster anions using infrared photodissociation spectroscopy and quantum chemistry calculations. The existence of spectral signatures of metal carbonyl CO stretching modes shows that insertion of titanium atoms into C-O bonds represents an important reaction during the formation of these clusters. In addition to carbonyl groups, the infrared spectra show that the titanium center is coordinated to oxalato, carbonato, and oxo ligands, which form along with the metal carbonyls. The presence of a metal oxalato ligand promotes C-O bond insertion in these systems. These results highlight the affinity of titanium for C-O bond insertion processes.

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Melting of size-selected gallium clusters with 60-183 atoms.

PubMed

Pyfer, Katheryne L; Kafader, Jared O; Yalamanchali, Anirudh; Jarrold, Martin F

2014-07-10

Heat capacities have been measured as a function of temperature for size-selected gallium cluster cations with between 60 and 183 atoms. Almost all clusters studied show a single peak in the heat capacity that is attributed to a melting transition. The peaks can be fit by a two-state model incorporating only fully solid-like and fully liquid-like species, and hence no partially melted intermediates. The exceptions are Ga90(+), which does not show a peak, and Ga80(+) and Ga81(+), which show two peaks. For the clusters with two peaks, the lower temperature peak is attributed to a structural transition. The melting temperatures for clusters with less than 50 atoms have previously been shown to be hundreds of degrees above the bulk melting point. For clusters with more than 60 atoms the melting temperatures decrease, approaching the bulk value (303 K) at around 95 atoms, and then show several small upward excursions with increasing cluster size. A plot of the latent heat against the entropy change for melting reveals two groups of clusters: the latent heats and entropy changes for clusters with less than 94 atoms are distinct from those for clusters with more than 93 atoms. This observation suggests that a significant change in the nature of the bonding or the structure of the clusters occurs at 93-94 atoms. Even though the melting temperatures are close to the bulk value for the larger clusters studied here, the latent heats and entropies of melting are still far from the bulk values.

Ferromagnetic bond of Li{sub 10} cluster: An alternative approach in terms of effective ferromagnetic sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donoso, Roberto; Fuentealba, Patricio, E-mail: pfuentea@hotmail.es, E-mail: cardena@macul.ciencias.uchile.cl; Cárdenas, Carlos, E-mail: pfuentea@hotmail.es, E-mail: cardena@macul.ciencias.uchile.cl

In this work, a model to explain the unusual stability of atomic lithium clusters in their highest spin multiplicity is presented and used to describe the ferromagnetic bonding of high-spin Li{sub 10} and Li{sub 8} clusters. The model associates the (lack of-)fitness of Heisenberg Hamiltonian with the degree of (de-)localization of the valence electrons in the cluster. It is shown that a regular Heisenberg Hamiltonian with four coupling constants cannot fully explain the energy of the different spin states. However, a more simple model in which electrons are located not at the position of the nuclei but at the positionmore » of the attractors of the electron localization function succeeds in explaining the energy spectrum and, at the same time, explains the ferromagnetic bond found by Shaik using arguments of valence bond theory. In this way, two different points of view, one more often used in physics, the Heisenberg model, and the other in chemistry, valence bond, come to the same answer to explain those atypical bonds.« less

UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6}: A ribbon structure containing a heterobimetallic 5d-5f M{sub 3} cluster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wells, Daniel M.; Chan, George H.; Ellis, Donald E.

2010-02-15

A new solid-state compound containing a heterobimetallic cluster of U and Ta, UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6}, has been synthesized and its structure has been characterized by single-crystal X-ray diffraction methods. UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6} was synthesized from UCl{sub 4} and Ta{sub 1.2}S{sub 2} at 883 K. The O is believed to have originated in the Ta{sub 1.2}S{sub 2} reactant. The compound crystallizes in the space group P1-bar of the triclinic system. The structure comprises a UTa{sub 2} unit bridged by mu{sub 2}-S{sub 2} and mu{sub 3}-O groups. Each Ta atom bonds to two mu{sub 2}-S{sub 2}, the mu{submore » 3}-O, and two terminal Cl atoms. Each U atom bonds to two mu{sub 2}-S{sub 2}, the mu{sub 3}-O, and four Cl atoms. The Cl atoms bridge in pairs to neighboring U atoms to form a ribbon structure. The bond distances are normal and are consistent with formal oxidation states of +IV/+V/-II/-I/-I for U/Ta/O/S/Cl, respectively. The optical absorbance spectrum displays characteristic transition peaks near the absorption edge. Density functional theory was used to assign these peaks to transitions between S{sup 1-} valence-band states and empty U 5f-6d hybrid bands. Density-of-states analysis shows overlap between Ta 5d and U bands, consistent with metal-metal interactions. - The UTa2O(S2)3Cl6 cluster with completed coordination sphere around uranium« less

Mixed-metal cluster chemistry. 28. Core enlargement of tungsten-iridium clusters with alkynyl, ethyndiyl, and butadiyndiyl reagents.

PubMed

Dalton, Gulliver T; Viau, Lydie; Waterman, Susan M; Humphrey, Mark G; Bruce, Michael I; Low, Paul J; Roberts, Rachel L; Willis, Anthony C; Koutsantonis, George A; Skelton, Brian W; White, Allan H

2005-05-02

Reaction of [WIr3(mu-CO)3(CO)8(eta-C5Me5)] (1c) with [W(C[triple bond]CPh)(CO)3(eta-C5H5)] afforded the edge-bridged tetrahedral cluster [W2Ir3(mu4-eta2-C2Ph)(mu-CO)(CO)9(eta-C5H5)(eta-C5Me5)] (3) and the edge-bridged trigonal-bipyramidal cluster [W3Ir3(mu4-eta2-C2Ph)(mu-eta2-C=CHPh)(Cl)(CO)8(eta-C5Me5)(eta-C5H5)2] (4) in poor to fair yield. Cluster 3 forms by insertion of [W(C[triple bond]CPh)(CO)3(eta-C5H5)] into Ir-Ir and W-Ir bonds, accompanied by a change in coordination mode from a terminally bonded alkynyl to a mu4-eta2 alkynyl ligand. Cluster 4 contains an alkynyl ligand interacting with two iridium atoms and two tungsten atoms in a mu4-eta2 fashion, as well as a vinylidene ligand bridging a W-W bond. Reaction of [WIr3(CO)11(eta-C5H5)] (1a) or 1c with [(eta-C5H5)(CO)2 Ru(C[triple bond]C)Ru(CO)2(eta-C5H5)] afforded [Ru2WIr3(mu5-eta2-C2)(mu-CO)3(CO)7(eta-C5H5)2(eta-C5R5)] [R = H (5a), Me (5c)] in low yield, a structural study of 5a revealing a WIr3 butterfly core capped and spiked by Ru atoms; the diruthenium ethyndiyl precursor has undergone Ru-C scission, with insertion of the C2 unit into a W-Ir bond of the cluster precursor. Reaction of [W2Ir2(CO)10(eta-C5H5)2] with the diruthenium ethyndiyl reagent gave [RuW2Ir2{mu4-eta2-(C2C[triple bond]C)Ru(CO)2(eta-C5H5)}(mu-CO)2(CO)6(eta-C5H5)3] (6) in low yield, a structural study of 6 revealing a butterfly W2Ir2 unit capped by a Ru(eta-C5H5) group resulting from Ru-C scission; the terminal C2 of a new ruthenium-bound butadiyndiyl ligand has been inserted into the W-Ir bond. Reaction between 1a, [WIr3(CO)11(eta-C5H4Me)] (1b), or 1c and [(eta-C5H5)(CO)3W(C[triple bond]CC[triple bond]C)W(CO)3(eta-C5H5)] afforded [W2Ir3{mu4-eta2-(C2C[triple bond]C)W(CO)3(eta-C5H5)}(mu-CO)2(CO)2(eta-C5H5)(eta-C5R5)] [R = H (7a), Me (7c); R5 = H4Me (7b)] in good yield, a structural study of 7c revealing it to be a metallaethynyl analogue of 3.

Structural Study of Liquid Lithium Niobate by Neutron Diffraction Role of the Li Atom in the Clustering Near Solidification

NASA Astrophysics Data System (ADS)

Andonov, P.; Fischer, H. E.; Palleau, P.; Kimura, S.

2001-05-01

The structure of liquid LiNbO3 has been investigated by neutron diffraction using samples with different isotopic composition of lithium. The intensity scattered by these samples has been measured for momentum transfers 0.4 Å-1 T> 1500 K, which include the undercooling domain. From an analysis of the correlation functions Gij(r) of the atomic pairs Li-Li, Li-Nb, Li-O and their structural evolutions, given by Δ Gi-j (r) = Gi-j(r)1500 -Gi-j(r)1550 made with reference to the crystalline LiNbO3 ferroelectric structure, it was possible to confirm a local ordering similar to that of the crystal. The presence of clusters (groupings of NbO3 octahedra) is confirmed. Both regular and irregular N b06 octahedra are observed in the liquid near solidification. With its high mobil­ity in the melt, the Li atom plays an important role in the clustering: the Li-O and Li-Nb bonds make possible the staking of four octahedra groups into clusters of eight octahedra or more. The Li-Li bonds join these groups. The diameter of the clusters is a least 22 Å in the undercooling regime.

Nanostructural characterization of amorphous diamondlike carbon films

DOE Office of Scientific and Technical Information (OSTI.GOV)

SIEGAL,MICHAEL P.; TALLANT,DAVID R.; MARTINEZ-MIRANDA,L.J.

2000-01-27

Nanostructural characterization of amorphous diamondlike carbon (a-C) films grown on silicon using pulsed-laser deposition (PLD) is correlated to both growth energetic and film thickness. Raman spectroscopy and x-ray reflectivity probe both the topological nature of 3- and 4-fold coordinated carbon atom bonding and the topographical clustering of their distributions within a given film. In general, increasing the energetic of PLD growth results in films becoming more ``diamondlike'', i.e. increasing mass density and decreasing optical absorbance. However, these same properties decrease appreciably with thickness. The topology of carbon atom bonding is different for material near the substrate interface compared to materialmore » within the bulk portion of an a-C film. A simple model balancing the energy of residual stress and the free energies of resulting carbon topologies is proposed to provide an explanation of the evolution of topographical bonding clusters in a growing a-C film.« less

Density functional study on structure and stability of bimetallic AuNZn (N<=6) clusters and their cations

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Neukermans, Sven; Janssens, Ewald; Silverans, Roger E.; Lievens, Peter

2003-10-01

A systematic study on the structure and stability of zinc doped gold clusters has been performed by density functional theory calculations. All the lowest-energy isomers found have a planar structure and resemble pure gold clusters in shape. Stable isomers tend to equally delocalize valence s electrons of the constituent atoms over the entire structure and maximize the number of Au-Zn bonds in the structure. This is because the Au-Zn bond is stronger than the Au-Au bond and gives an extra σ-bonding interaction by the overlap between vacant Zn 4p and valence Au 6s(5d) orbitals. No three-dimensional isomers were found for Au5Zn+ and Au4Zn clusters containing six delocalized valence electrons. This result reflects that these clusters have a magic number of delocalized electrons for two-dimensional systems. Calculated vertical ionization energies and dissociation energies as a function of the cluster size show odd-even behavior, in agreement with recent mass spectrometric observations [Tanaka et al., J. Am. Chem. Soc. 125, 2862 (2003)].

Formation, structure and bond dissociation thresholds of gas-phase vanadium oxide cluster ions

NASA Astrophysics Data System (ADS)

Bell, R. C.; Zemski, K. A.; Justes, D. R.; Castleman, A. W.

2001-01-01

The formation and structure of gas-phase vanadium oxide cluster anions are examined using a guided ion beam mass spectrometer coupled with a laser vaporization source. The dominant peaks in the anion total mass distribution correspond to clusters having stoichiometries of the form (VO2)n(VO3)m(O2)q-. Collision-induced dissociation studies of the vanadium oxide species V2O4-6-, V3O6-9-, V4O8-10-, V5O11-13-, V6O13-15-, and V7O16-18- indicate that VO2, VO3, and V2O5 units are the main building blocks of these clusters. There are many similarities between the anion mass distribution and that of the cation distribution studied previously. The principal difference is a shift to higher oxygen content by one additional oxygen atom for the stoichiometric anions (VxOy-) as compared to the cations with the same number of vanadium atoms, which is attributed to the extra pair of electrons of the anionic species. The oxygen-rich clusters, VxOy(O2)-, are shown to more tightly adsorb molecular oxygen than those of the corresponding cationic clusters. In addition, the bond dissociation thresholds for the vanadium oxide clusters ΔE(V+-O)=6.09±0.28 eV, ΔE(OV+-O)=3.51±0.36 eV, and ΔE(O2V--O)=5.43±0.31 eV are determined from the energy-dependent collision-induced dissociation cross sections with Xe as the collision partner. To the best of our knowledge, this is the first bond dissociation energy reported for the breaking of the V-O bond of a vanadium oxide anion.

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

A photoelectron spectroscopy and quantum chemical study on ternary Al-B-O clusters: AlnBO2- and AlnBO2 (n = 2, 3).

PubMed

Ou, Ting; Feng, Yuan; Tian, Wen-Juan; Zhao, Li-Juan; Kong, Xiang-Yu; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin

2018-02-14

Both B and Al have high oxygen affinity and their oxidation processes are highly exothermic, hinting at intriguing physical chemistry in ternary Al-B-O clusters. We report a combined photoelectron spectroscopy and density-functional study on the structural, electronic, and bonding properties of Al n BO 2 - and Al n BO 2 (n = 2, 3) clusters. Ground-state vertical detachment energies (VDEs) are measured to be 2.83 and 2.24 eV for Al 2 BO 2 - and Al 3 BO 2 - , respectively. A weak isomer is also observed for Al 3 BO 2 - with a VDE of 1.31 eV. Coalescence-kick global searches allow the identification of candidate structures, confirmed via comparisons with experiment. The Al 2 BO 2 - anion is V-shaped in geometry, C s ( 1 A'), with an Al center connecting to OB and OAl terminals. It can be viewed alternatively as the fusion of BOAl and AlOAl by sharing an Al atom. Al 3 BO 2 - has a C s ( 2 A'') global minimum in which an Al 2 dimer interacts with bridging boronyl (BO) and an OAl unit, as well as a low-lying C 2v ( 2 B 2 ) isomer consisting of boronyl and OAl that are doubly bridged by two Al atoms. The BO 2 block (linear O[double bond, length as m-dash]B[double bond, length as m-dash]O chain) is nonexistent in any of the anion and neutral species. Chemical bonding in these Al-B-O clusters is elucidated via canonical molecular orbitals and adaptive natural density partitioning. The cluster structures are also rationalized using the concept of sequential and competitive oxidation of B versus Al centers in Al n B. The first O atom prefers to oxidize B and form BO, whereas the second O atom has options to interact with a fresh Al/Al n /Al n B unit or a BO group. The former route wins thermodynamically, leading to the observed geometries.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

Nature's polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo-O clusters.

PubMed

Kowalewski, Björn; Poppe, Juliane; Demmer, Ulrike; Warkentin, Eberhard; Dierks, Thomas; Ermler, Ulrich; Schneider, Klaus

2012-06-13

Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo(8), three Mo(5-7), and one Mo(3) clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)(3) protein complex. The structurally identical Mo(8) clusters (three layers of two, four, and two MoO(n) octahedra) are distinguishable from the [Mo(8)O(26)](4-) cluster formed in acidic solutions by two displaced MoO(n) octahedra implicating three kinetically labile terminal ligands. Stabilization in the covalent Mo(8) cluster is achieved by Mo bonding to Hisα156-N(ε2) and Gluα129-O(ε1). The absence of covalent protein interactions in the noncovalent Mo(8) cluster is compensated by a more extended hydrogen-bond network involving three pronounced histidines. One displaced MoO(n) octahedron might serve as nucleation site for an inhomogeneous Mo(5-7) cluster largely surrounded by bulk solvent. In the Mo(3) cluster located on the 3-fold axis, the three accurately positioned His140-N(ε2) atoms of the α subunits coordinate to the Mo atoms. The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host-guest system. Template, nucleation/protection, and catalyst functions of the polypeptide as well as perspectives for designing new clusters are discussed.

A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms.

PubMed

Albertí, Margarita; Huarte-Larrañaga, Fermín; Aguilar, Antonio; Lucas, José M; Pirani, Fernando

2011-05-14

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.

Spin-orbit coupling effect on structural and magnetic properties of ConRh13-n (n = 0-13) clusters

NASA Astrophysics Data System (ADS)

Bai, Xi; Lv, Jin; Zhang, Fu-Qiang; Jia, Jian-Feng; Wu, Hai-Shun

2018-04-01

The effect of spin-orbit interaction on the structures and magnetism of ConRh13-n (n = 0-13) clusters have been systematically investigated by using the spin-orbit coupling (SOC) implementation of the density functional theory (DFT). The results calculated without SOC (NSOC) show that Rh13 prefers the double simple-cubic configuration, and icosahedron is the favorable structure for n = 1-9, while n ≥ 10, clusters favor the hexagonal bilayer structure. The inclusion of SOC in calculation does not change the geometries of clusters. Compared with that in NSOC calculation, although the binding energy per atom in clusters with same composition decreases in SOC calculation, the relative stability of clusters with different compositions does not change. An interesting result is that the spin moments of clusters for n = 1-9 are almost constant (21 μB). Spin-orbit interaction recovers orbital moment and its anisotropy by removing crystal-field effect in calculation. The destruction of bonding symmetry and relaxation of bonding account for high anisotropies of orbital moments in Co11Rh2 and CoRh12 clusters. With atomic composition (Co/Rh) around 4/9-5/8 and 9/4, the Co-Rh clusters exhibit high magnetic anisotropy energies.

Theoretical study of negatively charged Fe(-)-(H2O)(n ≤ 6) clusters.

PubMed

Castro, Miguel

2012-06-14

Interactions of a singly negatively charged iron atom with water molecules, Fe(-)-(H(2)O)(n≤6), in the gas phase were studied by means of density functional theory. All-electron calculations were performed using the B3LYP functional and the 6-311++G(2d,2p) basis set for the Fe, O, and H atoms. In the lowest total energy states of Fe(-)-(H(2)O)(n), the metal-hydrogen bonding is stronger than the metal-oxygen one, producing low-symmetry structures because the water molecules are directly attached to the metal by basically one of their hydrogen atoms, whereas the other ones are involved in a network of hydrogen bonds, which together with the Fe(δ-)-H(δ+) bonding accounts for the nascent hydration of the Fe(-) anion. For Fe(-)-(H(2)O)(3≤n), three-, four-, five-, and six-membered rings of water molecules are bonded to the metal, which is located at the surface of the cluster in such a way as to reduce the repulsion with the oxygen atoms. Nevertheless, internal isomers appear also, lying less than 3 or 5 kcal/mol for n = 2-3 or n = 4-6. These results are in contrast with those of classical TM(+)-(H(2)O)(n) complexes, where the direct TM(+)-O bonding usually produces high symmetry structures with the metal defining the center of the complex. They show also that the Fe(-) anions, as the TM(+) ions, have great capability for the adsorption of water molecules, forming Fe(-)-(H(2)O)(n) structures stabilized by Fe(δ-)-H(δ+) and H-bond interactions.

TiO(2) doping by hydroxyurea at the nucleation stage: towards a new photocatalyst in the visible spectral range.

PubMed

Azouani, R; Tieng, S; Chhor, K; Bocquet, J-F; Eloy, P; Gaigneaux, E M; Klementiev, K; Kanaev, A V

2010-10-07

We report an original method of preparation of OCN-doped TiO(2) for photocatalysis in the visible spectral range. The preparation is achieved by a sol-gel route using titanium tetraisopropoxide precursor. Special attention was paid to fluid micromixing, which enables homogeneous reaction conditions in the reactor bulk and monodispersity of the produced clusters/nanoparticles. The dopant hydroxyurea (HyU, CH(4)N(2)O(2)) is injected into the reactive fluid at the nucleation stage, which lasts tens of milliseconds. The doping results in a strong yellow coloration of the nanocolloids due to the absorption band in the spectral range 380-550 nm and accelerates the aggregation kinetics of both nuclei at the induction stage and sub-nuclei units (clusters) at the nucleation stage. FTIR, Raman and UV-visible absorption analyses show the formation of a stable HyU-TiO(2) complex. EXAFS spectra indicate no appreciable changes of the first-shell Ti atom environment. The doping agent takes available surface sites of TiO(2) clusters/nanoparticles attaining ∼10% molar loading. The reaction kinetics then accelerates due to a longer collisional lifetime between nanoparticles induced by the formation of a weak [double bond, length as m-dash]OTi bond. The OCN-group bonding to titanium atoms produces a weakening of the C[double bond, length as m-dash]O double bond and a strengthening of the C-N and N-O bonds.

Theoretical and experimental insights into the origin of the catalytic activity of subnanometric gold clusters: attempts to predict reactivity with clusters and nanoparticles of gold.

PubMed

Boronat, Mercedes; Leyva-Pérez, Antonio; Corma, Avelino

2014-03-18

Particle size is one of the key parameters determining the unexpected catalytic activity of gold, with reactivity improving as the particle gets smaller. While this is valid in the 1-5 nm range, chemists are now investigating the influence of particle size in the subnanometer regime. This is due to recent advances in both characterization techniques and synthetic routes capable of stabilizing these size-controlled gold clusters. Researchers reported in early studies that small clusters or aggregates of a few atoms can be extremely active in some reactions, while 1-2 nm nanoparticles are catalytically more efficient for other reactions. Furthermore, the possibility that small gold clusters generated in situ from gold salts or complexes could be the real active species in homogeneous gold-catalyzed organic reactions should be considered. In this Account, we address two questions. First, what is the origin of the enhanced reactivity of gold clusters on the subnanometer scale? And second, how can we predict the reactions where small clusters should work better than larger nanoparticles? Both geometric factors and electronic or quantum size effects become important in the subnanometer regime. Geometric reasons play a key role in hydrogenation reactions, where only accessible low coordinated neutral Au atoms are needed to dissociate H2. The quantum size effects of gold clusters are important as well, as clusters formed by only a few atoms have discrete molecule-like electronic states and their chemical reactivity is related to interactions between the cluster's frontier molecular orbitals and those of the reactant molecules. From first principles calculations, we predict an enhanced reactivity of small planar clusters for reactions involving activation of CC multiple bonds in alkenes and alkynes through Lewis acid-base interactions, and a better catalytic performance of 3D gold nanoparticles in redox reactions involving bond dissociation by oxidative addition and new bond formation by reductive elimination. In oxidation reactions with molecular O2, initial dissociation of O2 into basic oxygen atoms would be more effectively catalyzed by gold nanoparticles of ∼1 nm diameter. In contrast, small planar clusters should be more active for reactions following a radical pathway involving peroxo or hydroperoxo intermediates. We have experimentally confirmed these predictions for a series of Lewis acid and oxidation reactions catalyzed by gold clusters and nanoparticles either in solution or supported on solid carriers.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Room-temperature bonding of epitaxial layer to carbon-cluster ion-implanted silicon wafers for CMOS image sensors

NASA Astrophysics Data System (ADS)

Koga, Yoshihiro; Kadono, Takeshi; Shigematsu, Satoshi; Hirose, Ryo; Onaka-Masada, Ayumi; Okuyama, Ryousuke; Okuda, Hidehiko; Kurita, Kazunari

2018-06-01

We propose a fabrication process for silicon wafers by combining carbon-cluster ion implantation and room-temperature bonding for advanced CMOS image sensors. These carbon-cluster ions are made of carbon and hydrogen, which can passivate process-induced defects. We demonstrated that this combination process can be used to form an epitaxial layer on a carbon-cluster ion-implanted Czochralski (CZ)-grown silicon substrate with a high dose of 1 × 1016 atoms/cm2. This implantation condition transforms the top-surface region of the CZ-grown silicon substrate into a thin amorphous layer. Thus, an epitaxial layer cannot be grown on this implanted CZ-grown silicon substrate. However, this combination process can be used to form an epitaxial layer on the amorphous layer of this implanted CZ-grown silicon substrate surface. This bonding wafer has strong gettering capability in both the wafer-bonding region and the carbon-cluster ion-implanted projection range. Furthermore, this wafer inhibits oxygen out-diffusion to the epitaxial layer from the CZ-grown silicon substrate after device fabrication. Therefore, we believe that this bonding wafer is effective in decreasing the dark current and white-spot defect density for advanced CMOS image sensors.

Structural, electronic and vibrational properties of GexCy (x+y=2-5) nanoclusters: A B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Goswami, Sohini; Saha, Sushmita; Yadav, R. K.

2015-11-01

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2-5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C-C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO-LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO-LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

Electronic and molecular structure of carbon grains

NASA Technical Reports Server (NTRS)

Almloef, Jan; Luethi, Hans-Peter

1990-01-01

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Conformational Properties, Spectroscopy and Structure of ISATIN-(WATER)_{n=1-3} Clusters

NASA Astrophysics Data System (ADS)

Singh, Milind K.; Upadhya, D. M.; Singh, Vipin B.

2009-06-01

The structure, stability and vibrational characteristics of Isatin-(Water)_n clusters with n=1=3 have been investigated using second order Moller-Plesset (MP2) perturbation tehory and Density Functional Theory (with B3LYP) methods employing the basis set 6-31+G(d). The vertical excitation energies for these complexes have been also computed using the time-dependent density functional theory. The three stable conformational isomers, each for Isatin-(Water)_1 and Isatin-(Water)_2 clusters were obtained. It is shown that in the most stable isomer of Isatin-(Water)_1 cluster hydrogen bond between amide hydrogen and oxygen of water is found stronger as compared to the H-bond in Indole-(Water)_1 cluster. For a particular position of complexation of water, between the carbonyl oxygen's, results an unusual increase in the dipole moment due to an electronic charge displacement from the N atom to the C atom of the neighboring carbonyl bond. This causes a large separation between the effective charges forming the dipole. The complexes involving this position of water are expected to show a small charge transfer character. The experimentally observed electronic absorption peaks are reasonably reproduced by the TD-DFT calculations and it is found that the longest wavelength absorption peak of isatin at 406 nm is significantly red shifted after addition of a water molecule.

Electronic structures and thermochemical properties of the small silicon-doped boron clusters B(n)Si (n=1-7) and their anions.

PubMed

Tai, Truong Ba; Kadłubański, Paweł; Roszak, Szczepan; Majumdar, Devashis; Leszczynski, Jerzy; Nguyen, Minh Tho

2011-11-18

We perform a systematic investigation on small silicon-doped boron clusters B(n)Si (n=1-7) in both neutral and anionic states using density functional (DFT) and coupled-cluster (CCSD(T)) theories. The global minima of these B(n)Si(0/-) clusters are characterized together with their growth mechanisms. The planar structures are dominant for small B(n)Si clusters with n≤5. The B(6)Si molecule represents a geometrical transition with a quasi-planar geometry, and the first 3D global minimum is found for the B(7)Si cluster. The small neutral B(n)Si clusters can be formed by substituting the single boron atom of B(n+1) by silicon. The Si atom prefers the external position of the skeleton and tends to form bonds with its two neighboring B atoms. The larger B(7)Si cluster is constructed by doping Si-atoms on the symmetry axis of the B(n) host, which leads to the bonding of the silicon to the ring boron atoms through a number of hyper-coordination. Calculations of the thermochemical properties of B(n)Si(0/-) clusters, such as binding energies (BE), heats of formation at 0 K (ΔH(f)(0)) and 298 K (ΔH(f)([298])), adiabatic (ADE) and vertical (VDE) detachment energies, and dissociation energies (D(e)), are performed using the high accuracy G4 and complete basis-set extrapolation (CCSD(T)/CBS) approaches. The differences of heats of formation (at 0 K) between the G4 and CBS approaches for the B(n)Si clusters vary in the range of 0.0-4.6 kcal mol(-1). The largest difference between two approaches for ADE values is 0.15 eV. Our theoretical predictions also indicate that the species B(2)Si, B(4)Si, B(3)Si(-) and B(7)Si(-) are systems with enhanced stability, exhibiting each a double (σ and π) aromaticity. B(5)Si(-) and B(6)Si are doubly antiaromatic (σ and π) with lower stability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

UTa 2O(S 2) 3Cl 6: A ribbon structure containing a heterobimetallic 5 d-5 f M 3 cluster

NASA Astrophysics Data System (ADS)

Wells, Daniel M.; Chan, George H.; Ellis, Donald E.; Ibers, James A.

2010-02-01

A new solid-state compound containing a heterobimetallic cluster of U and Ta, UTa 2O(S 2) 3Cl 6, has been synthesized and its structure has been characterized by single-crystal X-ray diffraction methods. UTa 2O(S 2) 3Cl 6 was synthesized from UCl 4 and Ta 1.2S 2 at 883 K. The O is believed to have originated in the Ta 1.2S 2 reactant. The compound crystallizes in the space group P1¯ of the triclinic system. The structure comprises a UTa 2 unit bridged by μ 2-S 2 and μ 3-O groups. Each Ta atom bonds to two μ 2-S 2, the μ 3-O, and two terminal Cl atoms. Each U atom bonds to two μ 2-S 2, the μ 3-O, and four Cl atoms. The Cl atoms bridge in pairs to neighboring U atoms to form a ribbon structure. The bond distances are normal and are consistent with formal oxidation states of +IV/+V/-II/-I/-I for U/Ta/O/S/Cl, respectively. The optical absorbance spectrum displays characteristic transition peaks near the absorption edge. Density functional theory was used to assign these peaks to transitions between S 1- valence-band states and empty U 5 f-6 d hybrid bands. Density-of-states analysis shows overlap between Ta 5 d and U bands, consistent with metal-metal interactions.

Unified mechanism of alkali and alkaline earth catalyzed gasification reactions of carbon by CO2 and H2O

USGS Publications Warehouse

Chen, S.G.; Yang, R.T.

1997-01-01

From molecular orbital calculations, a unified mechanism is proposed for the gasification reactions of graphite by CO2 and H2O, both uncatalyzed and catalyzed by alkali and alkaline earth catalysts. In this mechanism, there are two types of oxygen intermediates that are bonded to the active edge carbon atoms: an in-plane semiquinone type, Cf(O), and an off-plane oxygen bonded to two saturated carbon atoms that are adjacent to the semiquinone species, C(O)Cf(O). The rate-limiting step is the decomposition of these intermediates by breaking the C-C bonds that are connected to Cf(O). A new rate equation is derived for the uncatalyzed reactions, and that for the catalyzed reactions is readily available from the proposed mechanism. The proposed mechanism can account for several unresolved experimental observations: TPD and TK (transient kinetics) desorption results of the catalyzed systems, the similar activation energies for the uncatalyzed and catalyzed reactions, and the relative activities of the alkali and alkaline earth elements. The net charge of the edge carbon active site is substantially changed by gaining electron density from the alkali or alkaline earth element (by forming C-O-M, where M stands for metal). The relative catalytic activities of these elements can be correlated with their abilities of donating electrons and changing the net charge of the edge carbon atom. As shown previously (Chen, S. G.; Yang, R. T. J. Catal. 1993, 141, 102), only clusters of the alkali compounds are active. This derives from the ability of the clusters to dissociate CO2 and H2O to form O atoms and the mobility of the dissociated O atoms facilitated by the clusters.

Probing the structural and electronic properties of cationic rubidium-gold clusters: [AunRb]+ (n = 1-10)

NASA Astrophysics Data System (ADS)

Zhao, Ya-Ru; Zhang, Hai-Rong; Qian, Yu; Duan, Xu-Chao; Hu, Yan-Fei

2016-03-01

Density functional theory has been applied to study the geometric structures, relative stabilities, and electronic properties of cationic [AunRb]+ and Aun + 1+ (n = 1-10) clusters. For the lowest energy structures of [AunRb]+ clusters, the planar to three-dimensional transformation is found to occur at cluster size n = 4 and the Rb atoms prefer being located at the most highly coordinated position. The trends of the averaged atomic binding energies, fragmentation energies, second-order difference of energies, and energy gaps show pronounced even-odd alternations. It indicated that the clusters containing odd number of atoms maintain greater stability than the clusters in the vicinity. In particular, the [Au6Rb]+ clusters are the most stable isomer for [AunRb]+ clusters in the region of n = 1-10. The charges in [AunRb]+ clusters transfer from the Rb atoms to Aun host. Density of states revealed that the Au-5d, Au-5p, and Rb-4p orbitals hardly participated in bonding. In addition, it is found that the most favourable channel of the [AunRb]+ clusters is Rb+ cation ejection. The electronic localisation function (ELF) analysis of the [AunRb]+ clusters shown that strong interactions are not revealed in this study.

Effects of carbonyl bond, metal cluster dissociation, and evaporation rates on predictions of nanotube production in high-pressure carbon monoxide

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Smalley, Richard E.

2003-01-01

The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNTs) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the conformation of CO2. It is shown that the production of CO2 is significantly greater for FeCO because of its lower bond energy as compared with that of NiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

Effects of Carbonyl Bond and Metal Cluster Dissociation and Evaporation Rates on Predictions of Nanotube Production in HiPco

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Smalley, Richard E.

2002-01-01

The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNT) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the co-formation of CO2. It is shown that the production of CO2 is significantly greater for FeCO due to its lower bond energy as compared with that ofNiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

NASA Technical Reports Server (NTRS)

Walch, S.

1984-01-01

The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

Probing C-O bond activation on gas-phase transition metal clusters: Infrared multiple photon dissociation spectroscopy of Fe, Ru, Re, and W cluster CO complexes

NASA Astrophysics Data System (ADS)

Lyon, Jonathan T.; Gruene, Philipp; Fielicke, André; Meijer, Gerard; Rayner, David M.

2009-11-01

The binding of carbon monoxide to iron, ruthenium, rhenium, and tungsten clusters is studied by means of infrared multiple photon dissociation spectroscopy. The CO stretching mode is used to probe the interaction of the CO molecule with the metal clusters and thereby the activation of the C-O bond. CO is found to adsorb molecularly to atop positions on iron clusters. On ruthenium and rhenium clusters it also binds molecularly. In the case of ruthenium, binding is predominantly to atop sites, however higher coordinated CO binding is also observed for both metals and becomes prevalent for rhenium clusters containing more than nine atoms. Tungsten clusters exhibit a clear size dependence for molecular versus dissociative CO binding. This behavior denotes the crossover to the purely dissociative CO binding on the earlier transition metals such as tantalum.

Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

PubMed

Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

2007-10-31

The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt cluster size, because small clusters, with more coordinatively unsaturated surface atoms, bind oxygen atoms more strongly than larger clusters and exhibit lower steady-state vacancy concentrations and a consequently smaller number of adsorbed DME intermediates involved in kinetically relevant steps. These effects of cluster size and metal-oxygen bond energies on reactivity are ubiquitous in oxidation reactions requiring vacancies on surfaces nearly saturated with intermediates derived from O2.

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

PubMed

Parnis, J Mark; Escobar-Cabrera, Eric; Thompson, Matthew G K; Jacula, J Paul; Lafleur, Rick D; Guevara-García, Alfredo; Martínez, Ana; Rayner, David M

2005-08-18

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Molecular interaction of (ethanol)2-water heterotrimers.

PubMed

Mejía, Sol M; Espinal, Juan F; Restrepo, Albeiro; Mondragón, Fanor

2007-08-23

The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.

Potential of transition metal atoms embedded in buckled monolayer g-C3N4 as single-atom catalysts.

PubMed

Li, Shu-Long; Yin, Hui; Kan, Xiang; Gan, Li-Yong; Schwingenschlögl, Udo; Zhao, Yong

2017-11-15

We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C 3 N 4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C 3 N 4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C 3 N 4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C 3 N 4 gives rise to promising single-atom catalysts at low temperature.

Binding of dinitrogen to an iron-sulfur-carbon site

NASA Astrophysics Data System (ADS)

Čorić, Ilija; Mercado, Brandon Q.; Bill, Eckhard; Vinyard, David J.; Holland, Patrick L.

2015-10-01

Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron-molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe-S bond and binds N2. The product is the first synthetic Fe-N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe-S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.

Rhodium clustering process on defective (8,0) SWCNT: Analysis of chemical and physical properties using density functional theory

NASA Astrophysics Data System (ADS)

Ambrusi, Ruben E.; Luna, C. Romina; Sandoval, Mario G.; Bechthold, Pablo; Pronsato, M. Estela; Juan, Alfredo

2017-12-01

The Spin-polarized density functional theory is used to study the effect of a single vacancy in a (8,0) single-walled carbon nanotube (SWCNT) on the Rh clustering process. The vacancy is considered oxygenated and non-oxygenated and, in each case, different Rhn cluster sizes (n = 1-4) are taken into account. For the analysis of these systems some physical and chemical properties are calculated, such as binding energy (Eb), work function (WF), magnetic moment, charge transfer, bond length, band gap (Eg), and density of state (DOS). From this analysis it can be concluded that: a single Rh atom and Rh2 dimer are adsorbed on vacancy without oxygen, whereas Rh3 and Rh4 clusters prefer to be adsorbed on oxygenated vacancy. In all cases, Rh adsorption induces a magnetic moment. When the Rh atom and Rh2 dimer are bonded to the defective SWCNT, it has been found that they show a semiconductor behavior that could be interesting to use in the spintronic area. In the case of Rh3 and Rh4 clusters our results show a metallic behavior suggesting that these systems are good candidates for nanotube contact.

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Oxygen adsorption onto pure and doped Al surfaces--the role of surface dopants.

PubMed

Lousada, Cláudio M; Korzhavyi, Pavel A

2015-01-21

Using density functional theory (DFT) with the PBE0 density functional we investigated the role of surface dopants in the molecular and dissociative adsorption of O2 onto Al clusters of types Al50, Al50Alad, Al50X and Al49X, where X represents a dopant atom of the following elements Si, Mg, Cu, Sc, Zr, and Ti. Each dopant atom was placed on the Al(111) surface as an adatom or as a substitutional atom, in the last case replacing a surface Al atom. We found that for the same dopant geometry, the closer is the ionization energy of the dopant element to that of elemental Al, the more exothermic is the dissociative adsorption of O2 and the stronger are the bonds between the resulting O atoms and the surface. Additionally we show that the Mulliken concept of electronegativity can be applied in the prediction of the dissociative adsorption energy of O2 on the doped surfaces. The Mulliken modified second-stage electronegativity of the dopant atom is proportional to the exothermicity of the dissociative adsorption of O2. For the same dopant element in an adatom position the dissociation of O2 is more exothermic when compared to the case where the dopant occupies a substitutional position. These observations are discussed in view of the overlap population densities of states (OPDOS) computed as the overlap between the electronic states of the adsorbate O atoms and the clusters. It is shown that a more covalent character in the bonding between the Al surface and the dopant atom causes a more exothermic dissociation of O2 and stronger bonding with the O atoms when compared to a more ionic character in the bonding between the dopant and the Al surface. The extent of the adsorption site reconstruction is dopant atom dependent and is an important parameter for determining the mode of adsorption, adsorption energy and electronic structure of the product of O2 adsorption. The PBE0 functional could predict the existence of the O2 molecular adsorption product for many of the cases investigated here.

Partial Ionic Character beyond the Pauling Paradigm: Metal Nanoparticles

DOE PAGES

Duanmu, Kaining; Truhlar, Donald G.

2014-11-12

A canonical perspective on the chemical bond is the Pauling paradigm: a bond in a molecule containing only identical atoms has no ionic character. However, we show that homonuclear silver clusters have very uneven charge distributions (for example, the C 2v structure of Ag 4 has a larger dipole moment than formaldehyde or acetone), and we show how to predict the charge distribution from coordination numbers and Hirshfeld charges. The new charge model is validated against Kohn–Sham calculations of dipole moments with four approximations for the exchange–correlation functional. We report Kohn–Sham studies of the binding energies of CO on silvermore » monomer and silver clusters containing 2–18 atoms. We also find that an accurate charge model is essential for understanding the site dependence of binding. In particular we find that atoms with more positive charges tend to have higher binding energies, which can be used for guidance in catalyst modeling and design. Furthermore, the nonuniform charge distribution of silver clusters predisposes the site preference of binding of carbon monoxide, and we conclude that nonuniform charge distributions are an important property for understanding binding of metal nanoparticles in general.« less

Classification of ligand molecules in PDB with graph match-based structural superposition.

PubMed

Shionyu-Mitsuyama, Clara; Hijikata, Atsushi; Tsuji, Toshiyuki; Shirai, Tsuyoshi

2016-12-01

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.

Reversing Conventional Reactivity of Mixed Oxo/Alkyl Rare-Earth Complexes: Non-Redox Oxygen Atom Transfer.

PubMed

Hong, Jianquan; Tian, Haiwen; Zhang, Lixin; Zhou, Xigeng; Del Rosal, Iker; Weng, Linhong; Maron, Laurent

2018-01-22

The preferential substitution of oxo ligands over alkyl ones of rare-earth complexes is commonly considered as "impossible" due to the high oxophilicity of metal centers. Now, it has been shown that simply assembling mixed methyl/oxo rare-earth complexes to a rigid trinuclear cluster framework cannot only enhance the activity of the Ln-oxo bond, but also protect the highly reactive Ln-alkyl bond, thus providing a previously unrecognized opportunity to selectively manipulate the oxo ligand in the presence of numerous reactive functionalities. Such trimetallic cluster has proved to be a suitable platform for developing the unprecedented non-redox rare-earth-mediated oxygen atom transfer from ketones to CS 2 and PhNCS. Controlled experiments and computational studies shed light on the driving force for these reactions, emphasizing the importance of the sterical accessibility and multimetallic effect of the cluster framework in promoting reversal of reactivity of rare-earth oxo complexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of the bond-valence method for calculating (29) Si and (31) P magnetic shielding in covalent network solids.

PubMed

Holmes, Sean T; Alkan, Fahri; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2016-07-05

(29) Si and (31) P magnetic-shielding tensors in covalent network solids have been evaluated using periodic and cluster-based calculations. The cluster-based computational methodology employs pseudoatoms to reduce the net charge (resulting from missing co-ordination on the terminal atoms) through valence modification of terminal atoms using bond-valence theory (VMTA/BV). The magnetic-shielding tensors computed with the VMTA/BV method are compared to magnetic-shielding tensors determined with the periodic GIPAW approach. The cluster-based all-electron calculations agree with experiment better than the GIPAW calculations, particularly for predicting absolute magnetic shielding and for predicting chemical shifts. The performance of the DFT functionals CA-PZ, PW91, PBE, rPBE, PBEsol, WC, and PBE0 are assessed for the prediction of (29) Si and (31) P magnetic-shielding constants. Calculations using the hybrid functional PBE0, in combination with the VMTA/BV approach, result in excellent agreement with experiment. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, In Soo; Li, Zhanyong; Zheng, Jian

Installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 degrees C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and Xray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novelmore » catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support.« less

Atomic and electronic basis for the serrations of refractory high-entropy alloys

NASA Astrophysics Data System (ADS)

Wang, William Yi; Shang, Shun Li; Wang, Yi; Han, Fengbo; Darling, Kristopher A.; Wu, Yidong; Xie, Xie; Senkov, Oleg N.; Li, Jinshan; Hui, Xi Dong; Dahmen, Karin A.; Liaw, Peter K.; Kecskes, Laszlo J.; Liu, Zi-Kui

2017-06-01

Refractory high-entropy alloys present attractive mechanical properties, i.e., high yield strength and fracture toughness, making them potential candidates for structural applications. Understandings of atomic and electronic interactions are important to reveal the origins for the formation of high-entropy alloys and their structure-dominated mechanical properties, thus enabling the development of a predictive approach for rapidly designing advanced materials. Here, we report the atomic and electronic basis for the valence-electron-concentration-categorized principles and the observed serration behavior in high-entropy alloys and high-entropy metallic glass, including MoNbTaW, MoNbVW, MoTaVW, HfNbTiZr, and Vitreloy-1 MG (Zr41Ti14Cu12.5Ni10Be22.5). We find that the yield strengths of high-entropy alloys and high-entropy metallic glass are a power-law function of the electron-work function, which is dominated by local atomic arrangements. Further, a reliance on the bonding-charge density provides a groundbreaking insight into the nature of loosely bonded spots in materials. The presence of strongly bonded clusters and weakly bonded glue atoms imply a serrated deformation of high-entropy alloys, resulting in intermittent avalanches of defects movement.

Ab initio studies on the solvation, electronic structures and intracluster reactions in M(+)L(n), with M(+)=magnesium and calcium singly-charged ions, L=water, methanol, ammonia, and n=1-6, and the elimination of a hydrogen atom in H atom in hydrated sodium clusters

NASA Astrophysics Data System (ADS)

Chan, Ka Wai

The solvation and electronic structures of M+Ln, with M+ = Mg+ and Cat, L = H2O, CH 3OH and NH3, n=1-6 were investigated by ab initio calculations using G03 package and density functional theory based ab initio molecular dynamics (AIMD) simulations with projector augmented-wave (PAW) method and a planewave basis set using Vienna Ab initio Simulation Package (VASP). Furthermore, ab initio studies on the intracluster reactions of Mg+ and Ca+ ions with different solvent molecules, H2O, CH3OH and NH3, were also done using G03 package. Finally, the elimination of a H atom in Na(H2O)n was studied. Such studies on the interactions and reactivity in gas clusters can provide insights into their analogies existing in condense phase. Interactions of Mg+ and Ca+ ions in different solvent molecules, H2O, CH3OH and NH3, were calculated with B3LYP and MP2 methods with basis sets 6-31+g** and 6-311+g**. A systematic comparison on the structures and reactivities of these clusters should provide a better understanding on the interplay of the ion-solvent, solvent-solvent, and electron-solvent interactions. It can provide a better understanding on the structures and bonding of complexes having analogies to those existing in condense phase. For Mg+(CH3OH)n and Ca+(CH 3OH)n, both H-elimination from OH/CH bond and CH3-elimination were investigated. H-elimination from O---H bond becomes more accessible for large cluster due to the diffusion of electron density to O---H bond. Studies on the H-elimination in Mg+(NH3)n and H-elimination from C---H bond in Mg+(CH3OH) n show that the reaction barriers flatten above 20 kcal/mol as n reaches 4 and above. These calculation results prove that the source of loss of H atom in ground state Mg+(CH3OH)n should be through the O---H bond rather than through the C---H bond. Compared to Mg+(CH3OH)n, the reaction barriers for H-elimination in Mg+(NH3)n is much larger, which is in consistent with the experimental observation of little H-elimination for Mg+(NH3)n unless it's photo-excited. The examination of neutral Na(H2O)n clusters, n=4~15 for H-elimination was carried out. The reaction profile for H-elimination was obtained by energy minimization at constrained O---H distance which was successively increased. There was a general trend of decreasing reaction barrier, as the cluster size grows. In contrast to Mg+(H 2O)n, the expected switch-off of H-elimination as in Mg +(H2O)n cannot be observed.

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Density functional theory study of small X-doped Mg(n) (X = Fe, Co, Ni, n = 1-9) bimetallic clusters: equilibrium structures, stabilities, electronic and magnetic properties.

PubMed

Kong, Fanjie; Hu, Yanfei

2014-03-01

The geometries, stabilities, and electronic and magnetic properties of Mg(n) X (X = Fe, Co, Ni, n = 1-9) clusters were investigated systematically within the framework of the gradient-corrected density functional theory. The results show that the Mg(n)Fe, Mg(n)Co, and Mg(n)Ni clusters have similar geometric structures and that the X atom in Mg(n)X clusters prefers to be endohedrally doped. The average atomic binding energies, fragmentation energies, second-order differences in energy, and HOMO-LUMO gaps show that Mg₄X (X = Fe, Co, Ni) clusters possess relatively high stability. Natural population analysis was performed and the results showed that the 3s and 4s electrons always transfer to the 3d and 4p orbitals in the bonding atoms, and that electrons also transfer from the Mg atoms to the doped atoms (Fe, Co, Ni). In addition, the spin magnetic moments were analyzed and compared. Several clusters, such as Mg₁,₂,₃,₄,₅,₆,₈,₉Fe, Mg₁,₂,₄,₅,₆,₈,₉Co, and Mg₁,₂,₅,₆,₇,₉Ni, present high magnetic moments (4 μ(B), 3 μ(B), and 2 μ(B), respectively).

Dynamics behavior of lithium in graphite lattice: MD calculation approach

NASA Astrophysics Data System (ADS)

Shimizu, A.; Tachikawa, H.

2000-12-01

In order to investigate the diffusion process of Li atom in graphite, molecular dynamics simulation was achieved on the basis of molecular mechanics 2 (MM2) method using four layers cluster model one of which is composed of C150H30 with terminating hydrogen atoms. According to the simulations at 500 K, Li atom stabilizes initially around the center of mass, gets out of the graphite layers after 3.0 ps through diffusion, which is different from the movement of Li+ ion captured by the dangling bonds of the edge carbon atoms. The diffusion process of Li atom is found to be composed of following four steps in series: (1) vibration around the stabilization point; (2) bulk diffusion; (3) vibration under influence of the dangling bonds of edge carbon atoms; and (4) escape from the graphite layers. The diffusivity for step (3) is smaller than that for step (2).

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

First-principles melting of gallium clusters down to nine atoms: structural and electronic contributions to melting.

PubMed

Steenbergen, Krista G; Gaston, Nicola

2013-10-07

First-principles Born-Oppenheimer molecular dynamics simulations of small gallium clusters, including parallel tempering, probe the distinction between cluster and molecule in the size range of 7-12 atoms. In contrast to the larger sizes, dynamic measures of structural change at finite temperature demonstrate that Ga7 and Ga8 do not melt, suggesting a size limit to melting in gallium exists at 9 atoms. Analysis of electronic structure further supports this size limit, additionally demonstrating that a covalent nature cannot be identified for clusters larger than the gallium dimer. Ga9, Ga10 and Ga11 melt at greater-than-bulk temperatures, with no evident covalent character. As Ga12 represents the first small gallium cluster to melt at a lower-than-bulk temperature, we examine the structural properties of each cluster at finite temperature in order to probe both the origins of greater-than-bulk melting, as well as the significant differences in melting temperatures induced by a single atom addition. Size-sensitive melting temperatures can be explained by both energetic and entropic differences between the solid and liquid phases for each cluster. We show that the lower-than-bulk melting temperature of the 12-atom cluster can be attributed to persistent pair bonding, reminiscent of the pairing observed in α-gallium. This result supports the attribution of greater-than-bulk melting in gallium clusters to the anomalously low melting temperature of the bulk, due to its dimeric structure.

Atomic-Level Properties of Thermal Barrier Coatings: Characterization of Metal-Ceramic Interfaces

DTIC Science & Technology

2001-01-01

these cases metal - metal bonds were stronger than metal - substrate bonds, thus predicting a 3D (cluster) growth mode as opposed to layer-by-layer...coat layer must be deposited. The top coat serves as the insulator and the bond coat mediates contact between the top coat and metal alloy substrate ...in thermomechanical properties between a YSZ top coat and a metal -alloy substrate is enough to require the introduction of an intermediate layer. This

First-Principles Study of Structural, Electronic and Magnetic Properties of Metal-Centered Tetrahexahedral V15+ Cluster

PubMed Central

Ren, Hongjiang; Huang, Xinwei; Li, Shuna

2017-01-01

The V-centered bicapped hexagonal antiprism structure (A), as the most stable geometry of the cationic V15+ cluster, is determined by using infrared multiple photo dissociation (IR-MPD) in combination with density functional theory computations. It is found that the A structure can be stabilized by 18 delocalized 3c-2e σ-bonds on outer V3 triangles of the bicapped hexagonal antiprism surface and 12 delocalized 4c-2e σ-bonds on inner trigonal pyramidal V4 moiety, and the features are related to the strong p-d hybridization of the cluster. The total magnetic moments on the cluster are predicted to be 2.0 µB, which come mainly from the central vanadium atom. PMID:28665337

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Carbon-tuned bonding method significantly enhanced the hydrogen storage of BN-Li complexes.

PubMed

Deng, Qing-ming; Zhao, Lina; Luo, You-hua; Zhang, Meng; Zhao, Li-xia; Zhao, Yuliang

2011-11-01

Through first-principles calculations, we found doping carbon atoms onto BN monolayers (BNC) could significantly strengthen the Li bond on this material. Unlike the weak bond strength between Li atoms and the pristine BN layer, it is observed that Li atoms are strongly hybridized and donate their electrons to the doped substrate, which is responsible for the enhanced binding energy. Li adsorbed on the BNC layer can serve as a high-capacity hydrogen storage medium, without forming clusters, which can be recycled at room temperature. Eight polarized H(2) molecules are attached to two Li atoms with an optimal binding energy of 0.16-0.28 eV/H(2), which results from the electrostatic interaction of the polarized charge of hydrogen molecules with the electric field induced by positive Li atoms. This practical carbon-tuned BN-Li complex can work as a very high-capacity hydrogen storage medium with a gravimetric density of hydrogen of 12.2 wt%, which is much higher than the gravimetric goal of 5.5 wt % hydrogen set by the U.S. Department of Energy for 2015.

Theoretical studies on structural, magnetic, and spintronic characteristics of sandwiched Eu(n)COT(n+1) (n = 1-4) clusters.

PubMed

Zhang, Xiuyun; Ng, Man-Fai; Wang, Yanbiao; Wang, Jinlan; Yang, Shuo-Wang

2009-09-22

Europium (Eu)-cyclootetatrene (COT = C(8)H(8)) multidecker clusters (Eu(n)COT(n+1), n = 1-4) are studied by relativistic density functional theory calculations. These clusters are found to be thermodynamically stable with freely rotatable COT rings, and their total magnetic moments (MMs) increase linearly along with the number of Eu atoms. Each Eu atom contributes about 7 mu(B) to the cluster. Meanwhile, the internal COT rings have little MM contribution while the external COT rings have about 1 mu(B) MM aligned in opposite direction to that of the Eu atoms. The total MM of the Eu(n)COT(n+1) clusters can thus be generalized as 7n - 2 mu(B) where n is the number of Eu atoms. Besides, the ground states of these clusters are ferromagnetic and energetically competitive with the antiferromagnetic states, meaning that their spin states are very unstable, especially for larger clusters. More importantly, we uncover an interesting bonding characteristic of these clusters in which the interior ionic structure is capped by two hybrid covalent-ionic terminals. We suggest that such a characteristic makes the Eu(n)COT(n+1) clusters extremely stable. Finally, we reveal that for the positively charged clusters, the hybrid covalent-ionic terminals will tip further toward the interior part of the clusters to form deeper covalent-ionic caps. In contrast, the negatively charged clusters turn to pure ionic structures.

Deep eutectic solvents: similia similibus solvuntur?

PubMed

Zahn, Stefan

2017-02-01

Deep eutectic solvents, mixtures of an organic compound and a salt with a deep eutectic melting point, are promising cheap and eco-friendly alternatives to ionic liquids. Ab initio molecular dynamics simulations of reline, a mixture consisting of urea and choline chloride, reveal that not solely hydrogen bonds allow similar interactions between both constituents. The chloride anion and the oxygen atom of urea also show a similar spatial distribution close to the cationic core of choline due to a similar charge located on both atoms. As a result of multiple similar interactions, clusters migrating together cannot be observed in reline which supports the hypothesis similia similibus solvuntur. In contrast to previous suggestions, the interaction of the hydroxyl group of choline with a hydrogen bond acceptor is overall rigid. Fast hydrogen bond acceptor dynamics is facilitated by the hydrogen atoms in the trans position to the carbonyl group of urea which contributes to the low melting point of reline.

The adsorption of Run (n = 1-4) on γ-Al2O3 Surface: A DFT study

NASA Astrophysics Data System (ADS)

Liu, Zhe; Guo, Yafei; Chen, Yu; Shen, Rong

2018-05-01

The density functional theory (DFT) was adopted to study the adsorption and growth of Run (n = 1-4) clusters on γ-Al2O3 surface, which is of great significances for the design of many important catalysts, especially for carbon dioxide methanation. It is found that both the Rusbnd Ru bond length and adsorption energy Eads of Ru clusters with the surface increase with the Run clusters increasing. The growth ability of the supported Run cluster is weaker than the gas phase Run clusters through comparing their respective growth process, which ascribes to the stabilization of γ-Al2O3 support. An interesting discovery is that the basin structure was supposed to be the most favorable adsorption geometry for Run clusters. Additionally, the distances between Ru atoms in the adsorbed clusters are longer than that in their isolated counterparts. Bader charge analysis was conducted for the most stable configurations of Run (n = 1-4) clusters on γ-Al2O3 surface as well. And the results suggest that Run (n = 1-4) clusters serve as the electron donators. The result of projected density of states (PDOS) shows that strong adsorption of Ru atom on the γ-Al2O3 surface correlates with strong interaction between d orbital of Ru atom and p orbital of Al or O atom of the Al2O3 support.

Photodissociation Studies of Metal-Containing Clusters and Complexes

NASA Astrophysics Data System (ADS)

Pilgrim, Jeffrey Scott

1995-01-01

There have been two major areas of investigation for researchers working with laser ablation in molecular beams. The first area is the study of weakly-bound complexes. These complexes are bound by electrostatic interactions. In the present study the weakly bound interactions of the rare gases with the magnesium ion are investigated with electronic spectroscopy. The second major area is the study of metal and metal-containing clusters. Examples of previous investigations are the alkali metal clusters and the fullerenes. The present investigation is on metal -carbon clusters. The so-called metallo-carbohedrenes and metal-carbon nanocrystals are studied. Resonance enhanced photodissociation spectroscopy is used to obtain electronic excitation spectra of the Mg^+-rare gas species in the ultraviolet region. This investigation is facilitated by a reflectron time-of-flight mass spectrometer. The interaction of the rare gas with the metal ion is attributed to a "solvation" of the atomic ion transition. Simple bonding arguments predict that the excited state is more bound than the ground state for these complexes. This will result in a shift of the complex vibronic origin to lower energy from the atomic ion transition. This is exactly what is observed in the experiment with progressively larger shifts for the heavier rare gases. The electronic excitation spectra allow the vibrational frequencies and anharmonicities for these complexes to be obtained for the excited state. In turn, the excited state bond dissociation energies can be determined. Finally, conservation of energy allows calculation of the ground state bond dissociation energies. In the metal-carbon systems the stability of the metallo-carbohedrene, met-car, stoichiometry is shown to extend into the transition period at least to the iron group. Photodissociation with a 532 nm laser causes a loss of metal atoms for met-cars formed with first row transition metals and a loss of metal-carbon units for met-cars formed from second-row transition metal atoms. Larger metal-carbon clusters are found to be face-centered-cubic nanocrystals. Photodissociation of these nanocrystals causes fragmentation into smaller nanocrystals. In addition, nanocrystals also dissociatively rearrange into the met -car structure. Two of the metal-carbon nanocrystals ( rm Ti_{14}C_{13 }^+ and rm V_{14 }C_{13}^+) fragment into the met-car with a trapped carbon atom.

Detonation of Meta-stable Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.

2008-05-31

We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetahmore » code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.« less

Structure and Bonding in CE5- (E=Al-Tl) Clusters: Planar Tetracoordinate Carbon versus Pentacoordinate Carbon.

PubMed

Ravell, Estefanía; Jalife, Said; Barroso, Jorge; Orozco-Ic, Mesías; Hernández-Juárez, Gerardo; Ortiz-Chi, Filiberto; Pan, Sudip; Cabellos, José Luis; Merino, Gabriel

2018-03-24

The structure, bonding, and stability of clusters with the empirical formula CE 5 - (E=Al-Tl) have been analyzed by means of high-level computations. The results indicate that, whereas aluminum and gallium clusters have C 2v structures with a planar tetracoordinate carbon (ptC), their heavier homologues prefer three-dimensional C 4v forms with a pentacoordinate carbon center over the ptC one. The reason for such a preference is a delicate balance between the interaction energy of the fifth E atom with CE 4 and the distortion energy. Moreover, bonding analysis shows that the ptC systems can be better described as CE 4 - , with 17-valence electrons interacting with E. The ptC core in these systems exhibits double aromatic (both σ and π) behavior, but the σ contribution is dominating. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

O2 adsorbed on Ptn clusters: Structure and optical absorption

NASA Astrophysics Data System (ADS)

Wang, Ruiying; Zhao, Liang; Jia, Jianfeng; Wu, Hai-Shun

2018-03-01

The interaction of O2 with Ptn and the optical absorption properties of PtnO2 were explored under the framework of density functional theory. The Ptn (n= 2, 4, 6, 9, 10, 14, 18, 22, and 27) clusters were selected, which were reported as magnetic number Ptn clusters in reference (V. Kumar and Y. Kawazoe, Phys. Rev. B 77(20), 205418 (2008)). The single Pt atom was also considered. The longest O2 bonds were found for Pt27O2, Pt6O2 and Pt14O2, while PtO2 and Pt2O2 have the shortest O2 bonds. This result showed that the single Pt atom was not preferred for O2 activation. The O2 bond length was closely related to the electron transfer from Ptn to O2. The optical absorptions of PtnO2 were investigated with time-dependent density functional theory method. A new term of charge transfer strength was defined to estimate the further electron transfer from Ptn to O2 caused by the optical absorption in the visible light range. Our calculations showed that with the increasing n, the further electron transfer from Ptn to O2 caused by optical absorption will become very weak.

Synthesis, structures, and solution dynamics of tetrasubstituted nine-atom germanium deltahedral clusters.

PubMed

Li, Feng; Sevov, Slavi C

2014-08-27

Reported are the rational synthesis, structures, and solution dynamics of three tetrasubstituted and neutral Ge9-based deltahedral clusters [Ge9R3R'](0), where R = Si(SiMe3)3 and R' = Et (1), Sn(n)Bu3 (2), or Tl (3). The first step of the synthesis is a reaction of an acetonitrile suspension of the intermetallic precursor compound K4Ge9 with {Si(SiMe3)3}Cl which produces the trisubstituted monoanions [Ge9{Si(SiMe3)3}](-). A benzene suspension of the latter is then reacted with Sn(n)Bu3Cl or TlCp to produce 2 and 3, respectively, while the same acetonitrile solution is reacted with EtBr in order to produce 1. All three structures can be viewed as tricapped trigonal prisms of Ge9 with the three "hypersilyl" substituents, Si(SiMe3)3, exo-bonded to the capping atoms. The fourth substituent in 1, the ethyl group, is exo-bonded to one of the six available Ge atoms with the Ge-C bond positioned radially to the Ge9 core. In the case of 2, on the other hand, the tin fragment is found above one of the triangular bases of the prism interacting with one or more Ge atoms in three crystallographically different molecules in the structure. Lastly, the Tl atom in the structure of 3 is found capping a pseudosquare face between two hypersilyl substituents. NMR spectroscopy indicates that all three compounds are dynamic at room temperature. Variable-temperature studies suggest that the process in 1 and 2 is intramolecular while the process in 3 involves dissociation of the Tl(+) ion from the molecule followed by association at the same or another equivalent pseudosquare face of the molecule. Thus, the latter compound may be considered to a large extent to be ionic as it is made of a thallium cation and a trisubstituted cluster anion.

CO adsorption on (111) and (100) surfaces of the Pt sub 3 Ti alloy. Evidence for parallel binding and strong activation of CO

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.; Ross, P. N.

1985-01-01

The CO adsorption on a 40 atom cluster model of the (111) surface and a 36 atom cluster model of the (100) surface of the Pt3Ti alloy was studied. Parallel binding to high coordinate sites associated with Ti and low CO bond scission barriers are predicted for both surfaces. The binding of CO to Pt sites occurs in an upright orientation. These orientations are a consequence of the nature of the CO pi donation interactions with the surface. On the Ti sites the orbitals donate to the nearly empty Ti 3d band and the antibonding counterpart orbitals are empty. On the Pt sites, however, they are in the filled Pt 5d region of the alloy band, which causes CO to bond in a vertical orientation by 5 delta donation from the carbon end.

Al6H18: A baby crystal of γ-AlH3

NASA Astrophysics Data System (ADS)

Kiran, B.; Kandalam, Anil K.; Xu, Jing; Ding, Y. H.; Sierka, M.; Bowen, K. H.; Schnöckel, H.

2012-10-01

Using global-minima search methods based on the density functional theory calculations of (AlH3)n (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring structures of AlH3 were predicted to be the preferred structures in which the Al atoms can have a maximum of five-fold coordination. Our calculations also reveal that the Al6H18 cluster, with its hexa-coordination of the Al atoms, resembles the unit-cell of γ-AlH3, thus Al6H18 is designated as the "baby crystal." The fragmentation energies of the (AlH3)n (n = 2-8) along with the dimerization energies for even n clusters indicate an enhanced stability of the Al6H18 cluster. Both covalent (hybridization) and ionic (charge) contribution to the bonding are the driving factors in stabilizing the isomers containing hexa-coordinated Al atoms.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Theoretical investigation of M@Pb122- and M@Sn122- Zintl clusters (M = Lrn+, Lun+, La3+, Ac3+ and n = 0, 1, 2, 3).

PubMed

Joshi, Meenakshi; Chandrasekar, Aditi; Ghanty, Tapan K

2018-06-06

The positions of lawrencium (Lr), lutetium (Lu), actinium (Ac) and lanthanum (La) in the periodic table have been a controversial topic for quite some time. According to studies carried out by different groups with their justifications, these elements may potentially be placed in the d-block, p-block or all four in a 15 element f-block. The present work looks into this issue from a new perspective, which involves encapsulation of these four elements into Zintl ion clusters, Pb122- and Sn122-, followed by the determination of the structural, thermodynamic and electronic properties of these endohedral M@Pb122- and M@Sn122- clusters (M = Lrn+, Lun+ with n = 0, 1, 2, 3) using first principles based density functional theory (DFT). These parameters are compared with similar clusters encapsulated La3+ and Ac3+ ions in order to seek out similarities and differences to draw conclusions about their placement in the periodic table. For the first time the structural, energetic, and electronic properties of these metal atom/ion encapsulated Pb122- and Sn122- clusters have been investigated thoroughly. Structural parameters such as bond distances, geometry and symmetry, electronic properties viz. the density of states, the molecular orbital ordering, the electron localization function, bond critical point properties and charge distributions have been analyzed. Additionally, the thermodynamic property of the binding energy during the encapsulation process has also been calculated. All M@Pb12+ and M@Sn12+ (M = Lr and Lu) clusters form stable 18 bonding electron magic number systems with shell closing. They show negative values of binding energy and relatively large HOMO-LUMO energy gaps indicating the stability of such clusters. All the calculated parameters for Lr encapsulated clusters closely match with the corresponding calculated parameters of Lu encapsulated clusters, confirming the similarity between Lr and Lu metal atoms in various oxidation states, though their atomic ground state valence electronic configurations are different. The effect of spin orbit coupling has also been investigated using the ZORA approach. It is interesting to discover that La and Ac showed striking similarities to Lr and Lu with respect to all the properties investigated and have formed a stable 18-electron system.

Application of the bond valence method in the non-isovalent semiconductor alloy (GaN) 1–x (ZnO) x

DOE PAGES

Liu, Jian

2016-09-29

This paper studies the bond valence method (BVM) and its application in the non-isovalent semiconductor alloy (GaN) 1-x(ZnO) x. Particular attention is paid to the role of short-range order (SRO). A physical interpretation based on atomic orbital interaction is proposed and examined by density-functional theory (DFT) calculations. Combining BVM with Monte-Carlo simulations and a DFT-based cluster expansion model, bond-length distributions and bond-angle variations are predicted. The correlation between bond valence and bond stiffness is also revealed. Lastly the concept of bond valence is extended into the modelling of an atomistic potential.

Bonding properties of FCC-like Au 44 (SR) 28 clusters from X-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Rui; Chevrier, Daniel M.; Zeng, Chenjie

Thiolate-protected gold clusters with precisely controlled atomic composition have recently emerged as promising candidates for a variety of applications because of their unique optical, electronic, and catalytic properties. The recent discovery of the Au44(SR)28 total structure is considered as an interesting finding in terms of the face-centered cubic (FCC)-like core structure in small gold-thiolate clusters. Herein, the unique bonding properties of Au44(SR)28 is analyzed using temperature-dependent X-ray absorption spectroscopy (XAS) measurements at the Au L3-edge and compared with other FCC-like clusters such as Au36(SR)24 and Au28(SR)20. A negative thermal expansion was detected for the Au–Au bonds of the metal coremore » (the first Au–Au shell) and was interpreted based on the unique Au core structure consisting of the Au4 units. EXAFS fitting results from Au28(SR)20, Au36(SR)24, and Au44(SR)28 show a size-dependent negative thermal expansion behavior in the first Au–Au shell, further highlighting the importance of the Au4 units in determining the Au core bonding properties and shedding light on the growth mechanism of these FCC-like Au clusters.« less

Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

Fundamental Studies and Isolation Strategies for Metal Compound Nanoclusters

DTIC Science & Technology

2009-02-28

probe nanocluster structure, bonding and stability, metal oxide, carbide and silicide clusters with up to 50 atoms were investigated with mass...transition metal compounds (carbides, oxides, silicides ) that are expected to have high stability, an essential property for their isolation...Metal carbide, oxide and silicide nanoclusters are studied in the size range from a few up to about 300 atoms. New infrared laser spectroscopy

Topological reaction coordinates to explore the structure of atomic clusters and organic molecule isomers from first principles

NASA Astrophysics Data System (ADS)

Pietrucci, Fabio; Andreoni, Wanda

2011-03-01

We introduce a simple reaction coordinate based on spectral graph theory which describes the topology of the network of chemical bonds around a given atom. We employ the reaction coordinate in combination with DFT-based first-principles metadynamics to systematically explore the possible structures of silicon and carbon clusters (including fullerene-like cages) for sizes of tens of atoms. From our extensive exploration we are able to estimate the fractal dimension of the configuration space, which both for silicon and carbon clusters turns out to be quite low. Using the same approach we simulate the interconversion among a large number of chemically relevant organic molecules which are isomers of the C4 H5 N formula unit, and we demonstrate the possibility of automatically exploring isomerisation, association, and decomposition reactions without prior knowledge of the products involved.

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Qian, Ping

2006-08-14

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

2006-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+n, MNO+, and MCO+2. The DFT works well for frequencies and geometries, even in case with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of successes as well as failures of DFT will be given.

IR signature of the photoionization-induced hydrophobic-->hydrophilic site switching in phenol-Arn clusters

NASA Astrophysics Data System (ADS)

Ishiuchi, Shun-ichi; Sakai, Makoto; Tsuchida, Yuji; Takeda, Akihiro; Kawashima, Yasutake; Dopfer, Otto; Müller-Dethlefs, Klaus; Fujii, Masaaki

2007-09-01

IR spectra of phenol-Arn (PhOH-Arn) clusters with n =1 and 2 were measured in the neutral and cationic electronic ground states in order to determine the preferential intermolecular ligand binding motifs, hydrogen bonding (hydrophilic interaction) versus π bonding (hydrophobic interaction). Analysis of the vibrational frequencies of the OH stretching motion, νOH, observed in nanosecond IR spectra demonstrates that neutral PhOH-Ar and PhOH -Ar2 as well as cationic PhOH +-Ar have a π-bound structure, in which the Ar atoms bind to the aromatic ring. In contrast, the PhOH +-Ar2 cluster cation is concluded to have a H-bound structure, in which one Ar atom is hydrogen-bonded to the OH group. This π →H binding site switching induced by ionization was directly monitored in real time by picosecond time-resolved IR spectroscopy. The π-bound νOH band is observed just after the ionization and disappears simultaneously with the appearance of the H-bound νOH band. The analysis of the picosecond IR spectra demonstrates that (i) the π →H site switching is an elementary reaction with a time constant of ˜7ps, which is roughly independent of the available internal vibrational energy, (ii) the barrier for the isomerization reaction is rather low(<100cm-1), (iii) both the position and the width of the H-bound νOH band change with the delay time, and the time evolution of these spectral changes can be rationalized by intracluster vibrational energy redistribution occurring after the site switching. The observation of the ionization-induced switch from π bonding to H bonding in the PhOH +-Ar2 cation corresponds to the first manifestation of an intermolecular isomerization reaction in a charged aggregate.

Sulfur Adsorption on the Goethite (110) Surface

NASA Astrophysics Data System (ADS)

Simonetti, S.; Damiani, D.; Brizuela, G.; Juan, A.

The electronic structure of S adsorption on goethite (110) surface has been studied by ASED-MO cluster calculations. For S location, the most exposed surface atoms of goethite surface were selected. The calculations show that the surface offers several places for S adsorption. The most energetically stable system corresponds to S location above H atom. We studied in detail the configurations that correspond to the higher OP values. For these configurations, the H-S and Fe-S computed distances are 2.1 and 3.7 Å, respectively. The H-S and Fe-S are mainly bonding interaction with OP values of 0.156 and 0.034, respectively. The Fe-S interaction mainly involves Fe 3dx2-y2 atomic orbitals with lesser participation of Fe 4py and Fe 3dyz atomic orbitals. The O-S interaction shows the same bonding and antibonding contributions giving a small OP value. The O-S interaction involves O 2p orbitals. There is an electron transfer to the Fe atom from the S atom. On the other hand, there is an electron transfer to S atom from the H and O atoms, respectively.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexandrova, Anastassia N.; Nayhouse, Michael J.; Huynh, Mioy T.

CAl₄²-/- (D₄h, ¹A₁g) is is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al₄, facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl₄²-/- (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, evenmore » though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al₄. From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn₄²-/-.« less

Experimental study of the effect of local atomic ordering on the energy band gap of melt grown InGaAsN alloys

NASA Astrophysics Data System (ADS)

Milanova, M.; Donchev, V.; Kostov, K. L.; Alonso-Álvarez, D.; Valcheva, E.; Kirilov, K.; Asenova, I.; Ivanov, I. G.; Georgiev, S.; Ekins-Daukes, N.

2017-08-01

We present a study of melt grown dilute nitride InGaAsN layers by x-ray photoelectron spectroscopy (XPS), Raman and photoluminescence (PL) spectroscopy. The purpose of the study is to determine the degree of atomic ordering in the quaternary alloy during the epitaxial growth at near thermodynamic equilibrium conditions and its influence on band gap formation. Despite the low In concentration (˜3%) the XPS data show a strong preference toward In-N bonding configuration in the InGaAsN samples. Raman spectra reveal that most of the N atoms are bonded to In instead of Ga atoms and the formation of N-centred In3Ga1 clusters. PL measurements reveal smaller optical band gap bowing as compared to the theoretical predictions for random alloy and localised tail states near the conduction band minimum.

A screened independent atom model for the description of ion collisions from atomic and molecular clusters

NASA Astrophysics Data System (ADS)

Lüdde, Hans Jürgen; Horbatsch, Marko; Kirchner, Tom

2018-05-01

We apply a recently introduced model for an independent-atom-like calculation of ion-impact electron transfer and ionization cross sections to proton collisions from water, neon, and carbon clusters. The model is based on a geometrical interpretation of the cluster cross section as an effective area composed of overlapping circular disks that are representative of the atomic contributions. The latter are calculated using a time-dependent density-functional-theory-based single-particle description with accurate exchange-only ground-state potentials. We find that the net capture and ionization cross sections in p-X n collisions are proportional to n α with 2/3 ≤ α ≤ 1. For capture from water clusters at 100 keV impact energy α is close to one, which is substantially different from the value α = 2/3 predicted by a previous theoretical work based on the simplest-level electron nuclear dynamics method. For ionization at 100 keV and for capture at lower energies we find smaller α values than for capture at 100 keV. This can be understood by considering the magnitude of the atomic cross sections and the resulting overlaps of the circular disks that make up the cluster cross section in our model. Results for neon and carbon clusters confirm these trends. Simple parametrizations are found which fit the cross sections remarkably well and suggest that they depend on the relevant bond lengths.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Structural and electronic properties of U{sub n}O{sub m} (n=1-3,m=1-3n) clusters: A theoretical study using screened hybrid density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yu; Liu, Haitao; Zhang, Ping, E-mail: zhang-ping@iapcm.ac.cn

The structural and electronic properties of small uranium oxide clusters U{sub n}O{sub m} (n=1-3, m=1-3n) are systematically studied within the screened hybrid density functional theory. It is found that the formation of U–O–U bondings and isolated U–O bonds are energetically more stable than U–U bondings. As a result, no uranium cores are observed. Through fragmentation studies, we find that the U{sub n}O{sub m} clusters with the m/n ratio between 2 and 2.5 are very stable, hinting that UO{sub 2+x} hyperoxides are energetically stable. Electronically, we find that the O-2p states always distribute in the deep energy range, and the U-5fmore » states always distribute at the two sides of the Fermi level. The U-6d states mainly hybridize with the U-5f states in U-rich clusters, while hybridizing with O-2p states in O-rich clusters. Our work is the first one on the screened hybrid density functional theory level studying the atomic and electronic properties of the actinide oxide clusters.« less

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization.

PubMed

Lin, Qisheng; Miller, Gordon J

2018-01-16

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e - /atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Therefore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate. During our efforts to find quasicrystals and crystalline approximants by valence electron tuning near 2.0 e - /atom, we observed that compositions close to those of quasicrystals are exceptional sources for unprecedented valence electron-poor polar intermetallics, e.g., Ca 4 Au 10 In 3 containing (Au 10 In 3 ) wavy layers, Li 14.7 Mg 36.8 Cu 21.5 Ga 66 adopting a type IV clathrate framework, and Sc 4 Mg x Cu 15-x Ga 7.5 that is incommensurately modulated. In particular, exploratory syntheses of AAu 3 T (A = Ca, Sr, Ba and T = Ge, Sn) phases led to interesting bonding features for Au, such as columns, layers, and lonsdaleite-type tetrahedral frameworks. Overall, the breadth of Au-rich polar intermetallics originates, in part, from significant relativistics effect on the valence electrons of Au, effects which result in greater 6s/5d orbital mixing, a small effective metallic radius, and an enhanced Mulliken electronegativity, all leading to ultimate enhanced binding with nearly all metals including itself. Two other successful strategies to mine electron-poor polar intermetallics include lithiation and "cation-rich" phases. Along these lines, we have studied lithiated Zn-rich compounds in which structural complexity can be realized by small amounts of Li replacing Zn atoms in the parent binary compounds CaZn 2 , CaZn 3 , and CaZn 5 ; their phase formation and bonding schemes can be rationalized by Fermi surface-Brillouin zone interactions between nearly free-electron states. "Cation-rich", electron-poor polar intermetallics have emerged using rare earth metals as the electropositive ("cationic") component together metal/metalloid clusters that mimic the backbones of aromatic hydrocarbon molecules, which give evidence of extensive electronic delocalization and multicenter bonding. Thus, we can identify three distinct, valence electron-poor, polar intermetallic systems that have yielded unprecedented phases adopting novel structures containing complex clusters and intriguing bonding characteristics. In this Account, we summarize our recent specific progress in the developments of novel Au-rich BaAl 4 -type related structures, shown in the "gold-rich grid", lithiation-modulated Ca-Li-Zn phases stabilized by different bonding characteristics, and rare earth-rich polar intermetallics containing unprecedented hydrocarbon-like planar Co-Ge metal clusters and pronounced delocalized multicenter bonding. We will focus mainly on novel structural motifs, bonding analyses, and the role of valence electrons for phase stability.

Photoelectron spectroscopy and density functional theory studies of (FeS)mH- (m = 2-4) cluster anions: effects of the single hydrogen.

PubMed

Yin, Shi; Bernstein, Elliot R

2017-12-20

Single hydrogen containing iron hydrosulfide cluster anions (FeS) m H - (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS) m H - (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS) m H - (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS) m - clusters, the first VDE trend of the diverse type (FeS) m H 0,1 - (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally affect their VDEs: a more negative or less positive localized charge distribution is correlated with a lower first VDE. The single hydrogen in these (FeS) m H - (m = 2-4) cluster anions is suggested to affect their first VDEs through the different structure types (SH- or FeH-), the nature of the NBO/HSOMOs at the local site, and the value of partial charge number at the local site of the NBO/HSOMO.

Reactions of Metal-Metal Multiple Bonds. 14. Synthesis and Characterization of Triangulo-W3 and Mo2W-oxo Capped Alkoxide Clusters. Comproportionation of M-M Triple Bonds, sigma(2)pi(4) and d(o) Metal-oxo Groups: M Triple Bond M + M Triple Bond O Yields M3(micron 3-O).

DTIC Science & Technology

1984-05-02

the syntheses of dinuclear and trinuclear complexes employing metal -alkylidyne or -alkylidene fragments.8 Reaction 1 also has a parallel with the...1 0 which was previously examined. The mixed metal complex is undoubtedly disordered with respect to the disposition of molybdenum and tungsten atoms...than for the analogous Mo3 complex suggests greater metal - metal overlap and possibly stronger bonding interactions in the W3 complex which would not

Photoelectron spectroscopy of B4O4-: Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters

NASA Astrophysics Data System (ADS)

Tian, Wen-Juan; Zhao, Li-Juan; Chen, Qiang; Ou, Ting; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin; Li, Si-Dian

2015-04-01

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B4O40/- clusters. The measured PES spectra of B4O4- exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDE of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of Cs B4O4- (2A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D2h B4O4- (2B2g) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B2O2 core bonded with terminal BO and/or BO2 groups. The same Y-shaped and rhombic structures are also located for the B4O4 neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B4O40/- clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B4O40/- clusters. This work is the first experimental study on a molecular system with an o-bond.

An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

NASA Astrophysics Data System (ADS)

Schailey, Ronald

1999-11-01

Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

Accelerated Oxygen Atom Transfer and C-H Bond Oxygenation by Remote Redox Changes in Fe 3Mn-Iodosobenzene Adducts

DOE PAGES

de Ruiter, Graham; Carsch, Kurtis M.; Gul, Sheraz; ...

2017-03-24

In this paper, we report the synthesis, characterization, and reactivity of [LFe 3(PhPz) 3OMn( sPhIO)][OTf] x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene–metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, 57Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe III 2Fe IIMn II vs. Fe III 3Mn II) influence oxygen atom transfer in tetranuclear Fe 3Mn clusters. Finally, in particular, a one-electron redox change atmore » a distal metal site leads to a change in oxygen atom transfer reactivity by ca. two orders of magnitude.« less

Accelerated Oxygen Atom Transfer and C-H Bond Oxygenation by Remote Redox Changes in Fe3 Mn-Iodosobenzene Adducts.

PubMed

de Ruiter, Graham; Carsch, Kurtis M; Gul, Sheraz; Chatterjee, Ruchira; Thompson, Niklas B; Takase, Michael K; Yano, Junko; Agapie, Theodor

2017-04-18

We report the synthesis, characterization, and reactivity of [LFe 3 (PhPz) 3 OMn( s PhIO)][OTf] x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene-metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, 57 Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe III 2 Fe II Mn II vs. Fe III 3 Mn II ) influence oxygen atom transfer in tetranuclear Fe 3 Mn clusters. In particular, a one-electron redox change at a distal metal site leads to a change in oxygen atom transfer reactivity by ca. two orders of magnitude. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Qisheng; Miller, Gordon J.

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e –/atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Furthermore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization

DOE PAGES

Lin, Qisheng; Miller, Gordon J.

2017-12-18

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e –/atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Furthermore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate.

CO oxidation on Alsbnd Au nano-composite systems

NASA Astrophysics Data System (ADS)

Rajesh, C.; Majumder, C.

2018-03-01

Using first principles method we report the CO oxidation behaviour of Alsbnd Au nano-composites in three different size ranges: Al6Au8, Al13Au42 and a periodic slab of Alsbnd Au(1 1 1) surface. The clusters prefer enclosed structures with alternating arrangement of Al and Au atoms, maximising Auδ-sbnd Alδ+ bonds. Charge distribution analysis suggests the charge transfer from Al to Au atoms, corroborated by the red shift in the density of states spectrum. Further, CO oxidation on these nano-composite systems was investigated through both Eley - Rideal and Langmuir Hinshelwood mechanism. While, these clusters interact with O2 non-dissociatively with an elongation of the Osbnd O bond, further interaction with CO led to formation of CO2 spontaneously. On contrary, the CO2 evolution by co-adsorption of O2 and CO molecules has a transition state barrier. On the basis of the results it is inferred that nano-composite material of Alsbnd Au shows significant promise toward effective oxidative catalysis.

A comparative DFT study of interactions of Au and small gold clusters Aun (n = 2-4) with CH3S and CH2 radicals

NASA Astrophysics Data System (ADS)

Blaško, Martin; Rajský, Tomáš; Urban, Miroslav

2017-03-01

We compare DFT binding energies (BEs) of Au and small gold clusters interacting with CH3S and CH2 ligands (Aun-L complexes, n = 1-4). The spin state and the binding mechanism in Aun-L varies with the participation of singly occupied non-bonding orbitals or doubly occupied lone-pair orbitals of a ligand and on the number of atoms (even or odd) of Aun. The highest BE, 354 kJ/mol, exhibits the Au3-CH2 complex with the covalent bond in which participate two singly occupied orbitals of the triplet state of CH2. With CH3S the highest BE (277 kJ/mol) is calculated for Au3-SCH3 with the single Au-S bond.

Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Kurban, Mustafa; Erkoç, Şakir

2017-04-01

Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

Catalyst Architecture for Stable Single Atom Dispersion Enables Site-Specific Spectroscopic and Reactivity Measurements of CO Adsorbed to Pt Atoms, Oxidized Pt Clusters, and Metallic Pt Clusters on TiO2.

PubMed

DeRita, Leo; Dai, Sheng; Lopez-Zepeda, Kimberly; Pham, Nicholas; Graham, George W; Pan, Xiaoqing; Christopher, Phillip

2017-10-11

Oxide-supported precious metal nanoparticles are widely used industrial catalysts. Due to expense and rarity, developing synthetic protocols that reduce precious metal nanoparticle size and stabilize dispersed species is essential. Supported atomically dispersed, single precious metal atoms represent the most efficient metal utilization geometry, although debate regarding the catalytic activity of supported single precious atom species has arisen from difficulty in synthesizing homogeneous and stable single atom dispersions, and a lack of site-specific characterization approaches. We propose a catalyst architecture and characterization approach to overcome these limitations, by depositing ∼1 precious metal atom per support particle and characterizing structures by correlating scanning transmission electron microscopy imaging and CO probe molecule infrared spectroscopy. This is demonstrated for Pt supported on anatase TiO 2 . In these structures, isolated Pt atoms, Pt iso , remain stable through various conditions, and spectroscopic evidence suggests Pt iso species exist in homogeneous local environments. Comparing Pt iso to ∼1 nm preoxidized (Pt ox ) and prereduced (Pt metal ) Pt clusters on TiO 2 , we identify unique spectroscopic signatures of CO bound to each site and find CO adsorption energy is ordered: Pt iso ≪ Pt metal < Pt ox . Pt iso species exhibited a 2-fold greater turnover frequency for CO oxidation than 1 nm Pt metal clusters but share an identical reaction mechanism. We propose the active catalytic sites are cationic interfacial Pt atoms bonded to TiO 2 and that Pt iso exhibits optimal reactivity because every atom is exposed for catalysis and forms an interfacial site with TiO 2 . This approach should be generally useful for studying the behavior of supported precious metal atoms.

Ionic bonding of lanthanides, as influenced by d- and f-atomic orbitals, by core-shells and by relativity.

PubMed

Ji, Wen-Xin; Xu, Wei; Schwarz, W H Eugen; Wang, Shu-Guang

2015-03-15

Lanthanide trihalide molecules LnX3 (X = F, Cl, Br, I) were quantum chemically investigated, in particular detail for Ln = Lu (lutetium). We applied density functional theory (DFT) at the nonrelativistic and scalar and SO-coupled relativistic levels, and also the ab initio coupled cluster approach. The chemically active electron shells of the lanthanide atoms comprise the 5d and 6s (and 6p) valence atomic orbitals (AO) and also the filled inner 4f semivalence and outer 5p semicore shells. Four different frozen-core approximations for Lu were compared: the (1s(2) -4d(10) ) [Pd] medium core, the [Pd+5s(2) 5p(6) = Xe] and [Pd+4f(14) ] large cores, and the [Pd+4f(14) +5s(2) 5p(6) ] very large core. The errors of LuX bonding are more serious on freezing the 5p(6) shell than the 4f(14) shell, more serious upon core-freezing than on the effective-core-potential approximation. The LnX distances correlate linearly with the AO radii of the ionic outer shells, Ln(3+) -5p(6) and X(-) -np(6) , characteristic for dominantly ionic Ln(3+) -X(-) binding. The heavier halogen atoms also bind covalently with the Ln-5d shell. Scalar relativistic effects contract and destabilize the LuX bonds, spin orbit coupling hardly affects the geometries but the bond energies, owing to SO effects in the free atoms. The relativistic changes of bond energy BE, bond length Re , bond force k, and bond stretching frequency vs do not follow the simple rules of Badger and Gordy (Re ∼BE∼k∼vs ). The so-called degeneracy-driven covalence, meaning strong mixing of accidentally near-degenerate, nearly nonoverlapping AOs without BE contribution is critically discussed. © 2015 Wiley Periodicals, Inc.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

1997-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+(sub n), MNO+, and MCO+(sub 2). The DFT works well for frequencies and geometries, even in cases with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of the successes as well as failures of DFT will be given.

Structures and mechanical behaviors of Zr55Cu35Al10 bulk amorphous alloys at ambient and cryogenic temperatures

NASA Astrophysics Data System (ADS)

Fan, Cang; Liaw, P. K.; Haas, V.; Wall, J. J.; Choo, H.; Inoue, A.; Liu, C. T.

2006-07-01

Based on a systematic study of pair distribution functions, carried out at cryogenic and ambient temperatures, on as-cast and crystallized ternary Zr-based bulk amorphous alloys (BAAs), we found that the atoms in BAAs are inhomogenously distributed at a local atomic level. They exist as different clusters with significantly shorter bond lengths than their crystallized counterpart structures—intermetallic compounds, and these structures exist stably in the amorphous state. This results in additional free volume, which is about ˜7% larger than that measured by the Archimedes method. The compressive strength measured at ˜77K was found to be ˜16% larger than that measured at 298K . In this study, an amorphous structural model is proposed, in which strongly bonded clusters acting as units are randomly distributed and strongly correlated to one another, as the free volume forms between clusters. Simulations with reverse Monte Carlo were performed by combining icosehadral and cubic structures as the initial structures for the BAA. The simulations show results consistent with our model. An attempt has been made to connect the relationship between amorphous structures and their mechanical properties.

The cluster model of a hot dense vapor

NASA Astrophysics Data System (ADS)

Zhukhovitskii, D. I.

2015-04-01

We explore thermodynamic properties of a vapor in the range of state parameters where the contribution to thermodynamic functions from bound states of atoms (clusters) dominates over the interaction between the components of the vapor in free states. The clusters are assumed to be light and sufficiently "hot" for the number of bonds to be minimized. We use the technique of calculation of the cluster partition function for the cluster with a minimum number of interatomic bonds to calculate the caloric properties (heat capacity and velocity of sound) for an ideal mixture of the lightest clusters. The problem proves to be exactly solvable and resulting formulas are functions solely of the equilibrium constant of the dimer formation. These formulas ensure a satisfactory correlation with the reference data for the vapors of cesium, mercury, and argon up to moderate densities in both the sub- and supercritical regions. For cesium, we extend the model to the densities close to the critical one by inclusion of the clusters of arbitrary size. Knowledge of the cluster composition of the cesium vapor makes it possible to treat nonequilibrium phenomena such as nucleation of the supersaturated vapor, for which the effect of the cluster structural transition is likely to be significant.

Seventeen-Coordinate Actinide Helium Complexes.

PubMed

Kaltsoyannis, Nikolas

2017-06-12

The geometries and electronic structures of molecular ions featuring He atoms complexed to actinide cations are explored computationally using density functional and coupled cluster theories. A new record coordination number is established, as AcHe 17 3+ , ThHe 17 4+ , and PaHe 17 4+ are all found to be true geometric minima, with the He atoms clearly located in the first shell around the actinide. Analysis of AcHe n 3+ (n=1-17) using the quantum theory of atoms in molecules (QTAIM) confirms these systems as having closed shell, charge-induced dipole bonding. Excellent correlations (R 2 >0.95) are found between QTAIM metrics (bond critical point electron densities and delocalization indices) and the average Ac-He distances, and also with the incremental He binding energies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A pseudoatom in a cage: trimetallofullerene Y(3)@C(80) mimics y(3)n@c(80) with nitrogen substituted by a pseudoatom.

PubMed

Popov, Alexey A; Zhang, Lin; Dunsch, Lothar

2010-02-23

Y(3)C(80) obtained in the synthesis of nitride clusterfullerenes Y(3)N@C(2n) (2n = 80-88) by the reactive atmosphere method is found to be a genuine trimetallofullerene, Y(3)@C(80), with low ionization potential and divalent state of yttrium atoms. DFT studies of the electronic structure of Y(3)@C(80) show that this molecule mimics Y(3)N@C(80) with the pseudoatom (PA) instead of the nitrogen atom. Topology analysis of the electron density and electron localization function show that yttrium atoms form Y-PA bonds rather than direct Y-Y bonds. Molecular dynamics simulations show that the Y(3)PA cluster is as rigid as Y(3)N and rotates inside the fullerene cage as a single entity.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arslan, Ilke; Dixon, David A.; Gates, Bruce C.

2015-09-30

To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-themore » art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify ligands on the metals and their reactions; EXAFS spectroscopy and high-resolution STEM to determine cluster framework structures and changes resulting from reactant treatment and locations of metal atoms on support surfaces; X-ray diffraction crystallography to determine full structures of cluster-ligand combinations in the absence of a support, and TEM with tomographic methods to observe individual metal atoms and determine three-dimensional structures of catalysts. Electronic structure calculations were used to verify and interpret spectra and extend the understanding of reactivity beyond what is measurable experimentally.« less

Tuning of Terahertz Resonances of Pyridyl Benzamide Derivatives by Electronegative Atom Substitution

NASA Astrophysics Data System (ADS)

Dash, Jyotirmayee; Ray, Shaumik; Devi, Nirmala; Basutkar, Nitin; Gonnade, Rajesh G.; Ambade, Ashootosh V.; Pesala, Bala

2018-05-01

N-(pyridin-2-yl) benzamide (Ph2AP)-based organic molecules with prominent terahertz (THz) signatures (less than 5 THz) have been synthesized. The THz resonances are tuned by substituting the most electronegative atom, fluorine, at ortho (2F-Ph2AP), meta (3F-Ph2AP), and para (4F-Ph2AP) positions in a Ph2AP molecule. Substitution of fluorine helps in varying the charge distribution of the atoms forming hydrogen bond and hence strength of the hydrogen bond is varied which helps in tuning the THz resonances. The tuning of lower THz resonances of 2F-Ph2AP, 3F-Ph2AP, and 4F-Ph2AP has been explained in terms of compliance constant (relaxed force constant). Four-molecule cluster simulations have been carried out using Gaussian09 software to calculate the compliance constant of the hydrogen bonds. Crystal structure simulations of the above molecules using CRYSTAL14 software have been carried out to understand the origin of THz resonances. It has been observed that THz resonances are shifted to higher frequencies with stronger hydrogen bonds. The study shows that 3F-Ph2AP and 4F-Ph2AP have higher hydrogen bond strength and hence the THz resonances originating due to stretching of intermolecular hydrogen bonds have been shifted to higher frequencies compared to 2F-Ph2AP. The methodology presented here will help in designing novel organic molecules by substituting various electronegative atoms in order to achieve prominent THz resonances.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Adsorption of beryllium atoms and clusters both on graphene and in a bilayer of graphite investigated by DFT.

PubMed

Ferro, Yves; Fernandez, Nicolas; Allouche, Alain; Linsmeier, Christian

2013-01-09

We herein investigate the interaction of beryllium with a graphene sheet and in a bilayer of graphite by means of periodic DFT calculations. In all cases, we find the beryllium atoms to be more weakly bonded on graphene than in the bilayer. Be(2) forms both magnetic and non-magnetic structures on graphene depending on the geometrical configuration of adsorption. We find that the stability of the Be/bilayer system increases with the size of the beryllium clusters inserted into the bilayer of graphite. We also find a charge transfer from beryllium to the graphite layers. All these results are analysed in terms of electronic structure.

Atomic-scale distortion of optically activated Sm dopants identified with site-selective X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Ishii, Masashi; Crowe, Iain F.; Halsall, Matthew P.; Hamilton, Bruce; Hu, Yongfeng; Sham, Tsun-Kong; Harako, Susumu; Zhao, Xin-Wei; Komuro, Shuji

2013-10-01

The local structure of luminescent Sm dopants was investigated using an X-ray absorption fine-structure technique with X-ray-excited optical luminescence. Because this technique evaluates X-ray absorption from luminescence, only optically active sites are analyzed. The Sm L3 near-edge spectrum contains split 5d states and a shake-up transition that are specific to luminescent Sm. Theoretical calculations using cluster models identified an atomic-scale distortion that can reproduce the split 5d states. The model with C4v local symmetry and compressive bond length of Sm-O of a six-fold oxygen (SmO6) cluster is most consistent with the experimental results.

The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology.

PubMed

Mejía, Sol M; Mills, Matthew J L; Shaik, Majeed S; Mondragon, Fanor; Popelier, Paul L A

2011-05-07

Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen. This journal is © the Owner Societies 2011

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Qisheng; Aguirre, Kaiser; Saunders, Scott M.

Planar hydrocarbon-like metal clusters may foster new insights linking organic molecules with conjugated π-π bonding interactions and inorganic structures in terms of their bonding characteristics. However, such clusters are uncommon in polar intermetallics. Herein, we report two polar intermetallic phases, Pr 5Co 2Ge 3 and Pr 7Co 2Ge 4, both of which feature such planar metal clusters, viz., ethylene-like [Co 2Ge 4] clusters plus the concatenated forms and polyacene-like [Co 2Ge 2] n ribbons in Pr 5Co 2Ge 3, and 1,2,4,5-tetramethylbenzene-like [Co4Ge6] cluster in Pr 7Co 2Ge 4. Just as in the related planar organic structures, these metal-metalloid species aremore » dominated by covalent bonding interactions. Both compounds magnetically order at low temperature with net ferromagnetic components: Pr 5Co 2Ge 3 via a series of transitions below 150 K; and Pr 7Co 2Ge 4 via a single ferromagnetic transition at 19 K. Spin-polarized electronic structure calculations for Pr 7Co 2Ge 4 reveal strong spin-orbit coupling within Pr and considerable magnetic contributions from Co atoms. This work suggests that similar structural chemistry can emerge for other rare earth-late transition metal-main group systems.« less

Effect of cutting temperature on hardness of SiC and diamond in the nano-cutting process of monocrystalline silicon

NASA Astrophysics Data System (ADS)

Wang, Jiachun; Li, Yuntao; Liu, Xiaoxuan; Lv, Maoqiang

2016-10-01

In the process of cutting silicon by natural diamond tools, groove wear happens on the flank face of cutting tool frequently.Scholars believe that one of the wear reasons is mechanical scratching effect by hard particles like SiC. To reveal the mechanical scratching mechanism, it is essential to study changes in the mechanical properties of hard particles and diamond, especially the effect of cutting temperature on hardness of diamond and hard particles. Molecular dynamics (MD) model that contact-zone temperature between tool and workpiece was calculated by dividing zone while nano-cutting monocrystalline silicon was established, cutting temperature values in different regions were computed as the simulation was carried out.On this basis, the models of molecular dynamics simulation of SiC and diamond were established separately with setting the initial temperature to room temperature. The laws of length change of C-C bond and Si-C bond varing with increase of simulation temperature were studied. And drawing on predecessors' research on theoretical calculation of hardness of covalent crystals and the relationship between crystal valence electron density and bond length, the curves that the hardness of diamond and SiC varing with bond length were obtained. The effect of temperature on the hardness was calculated. Results show that, local cutting temperature can reach 1300K.The rise in cutting temperature leaded to a decrease in the diamond local atomic clusters hardness,SiC local atomic clusters hardness increased. As the cutting temperature was more than 1100K,diamond began to soften, the local clusters hardness was less than that of SiC.

Temperature and composition dependence of short-range order and entropy, and statistics of bond length: the semiconductor alloy (GaN)(1-x)(ZnO)(x).

PubMed

Liu, Jian; Pedroza, Luana S; Misch, Carissa; Fernández-Serra, Maria V; Allen, Philip B

2014-07-09

We present total energy and force calculations for the (GaN)1-x(ZnO)x alloy. Site-occupancy configurations are generated from Monte Carlo (MC) simulations, on the basis of a cluster expansion model proposed in a previous study. Local atomic coordinate relaxations of surprisingly large magnitude are found via density-functional calculations using a 432-atom periodic supercell, for three representative configurations at x = 0.5. These are used to generate bond-length distributions. The configurationally averaged composition- and temperature-dependent short-range order (SRO) parameters of the alloys are discussed. The entropy is approximated in terms of pair distribution statistics and thus related to SRO parameters. This approximate entropy is compared with accurate numerical values from MC simulations. An empirical model for the dependence of the bond length on the local chemical environments is proposed.

Reactivity of chemisorbed oxygen atoms and their catalytic consequences during CH4-O2 catalysis on supported Pt clusters.

PubMed

Chin, Ya-Huei Cathy; Buda, Corneliu; Neurock, Matthew; Iglesia, Enrique

2011-10-12

Kinetic and isotopic data and density functional theory treatments provide evidence for the elementary steps and the active site requirements involved in the four distinct kinetic regimes observed during CH(4) oxidation reactions using O(2), H(2)O, or CO(2) as oxidants on Pt clusters. These four regimes exhibit distinct rate equations because of the involvement of different kinetically relevant steps, predominant adsorbed species, and rate and equilibrium constants for different elementary steps. Transitions among regimes occur as chemisorbed oxygen (O*) coverages change on Pt clusters. O* coverages are given, in turn, by a virtual O(2) pressure, which represents the pressure that would give the prevalent steady-state O* coverages if their adsorption-desorption equilibrium was maintained. The virtual O(2) pressure acts as a surrogate for oxygen chemical potentials at catalytic surfaces and reflects the kinetic coupling between C-H and O═O activation steps. O* coverages and virtual pressures depend on O(2) pressure when O(2) activation is equilibrated and on O(2)/CH(4) ratios when this step becomes irreversible as a result of fast scavenging of O* by CH(4)-derived intermediates. In three of these kinetic regimes, C-H bond activation is the sole kinetically relevant step, but occurs on different active sites, which evolve from oxygen-oxygen (O*-O*), to oxygen-oxygen vacancy (O*-*), and to vacancy-vacancy (*-*) site pairs as O* coverages decrease. On O*-saturated cluster surfaces, O*-O* site pairs activate C-H bonds in CH(4) via homolytic hydrogen abstraction steps that form CH(3) groups with significant radical character and weak interactions with the surface at the transition state. In this regime, rates depend linearly on CH(4) pressure but are independent of O(2) pressure. The observed normal CH(4)/CD(4) kinetic isotope effects are consistent with the kinetic-relevance of C-H bond activation; identical (16)O(2)-(18)O(2) isotopic exchange rates in the presence or absence of CH(4) show that O(2) activation steps are quasi-equilibrated during catalysis. Measured and DFT-derived C-H bond activation barriers are large, because of the weak stabilization of the CH(3) fragments at transition states, but are compensated by the high entropy of these radical-like species. Turnover rates in this regime decrease with increasing Pt dispersion, because low-coordination exposed Pt atoms on small clusters bind O* more strongly than those that reside at low-index facets on large clusters, thus making O* less effective in H-abstraction. As vacancies (*, also exposed Pt atoms) become available on O*-covered surfaces, O*-* site pairs activate C-H bonds via concerted oxidative addition and H-abstraction in transition states effectively stabilized by CH(3) interactions with the vacancies, which lead to much higher turnover rates than on O*-O* pairs. In this regime, O(2) activation becomes irreversible, because fast C-H bond activation steps scavenge O* as it forms. Thus, O* coverages are set by the prevalent O(2)/CH(4) ratios instead of the O(2) pressures. CH(4)/CD(4) kinetic isotope effects are much larger for turnovers mediated by O*-* than by O*-O* site pairs, because C-H (and C-D) activation steps are required to form the * sites involved in C-H bond activation. Turnover rates for CH(4)-O(2) reactions mediated by O*-* pairs decrease with increasing Pt dispersion, as in the case of O*-O* active structures, because stronger O* binding on small clusters leads not only to less reactive O* atoms, but also to lower vacancy concentrations at cluster surfaces. As O(2)/CH(4) ratios and O* coverages become smaller, O(2) activation on bare Pt clusters becomes the sole kinetically relevant step; turnover rates are proportional to O(2) pressures and independent of CH(4) pressure and no CH(4)/CD(4) kinetic isotope effects are observed. In this regime, turnover rates become nearly independent of Pt dispersion, because the O(2) activation step is essentially barrierless. In the absence of O(2), alternate weaker oxidants, such as H(2)O or CO(2), lead to a final kinetic regime in which C-H bond dissociation on *-* pairs at bare cluster surfaces limit CH(4) conversion rates. Rates become first-order in CH(4) and independent of coreactant and normal CH(4)/CD(4) kinetic isotope effects are observed. In this case, turnover rates increase with increasing dispersion, because low-coordination Pt atoms stabilize the C-H bond activation transition states more effectively via stronger binding to CH(3) and H fragments. These findings and their mechanistic interpretations are consistent with all rate and isotopic data and with theoretical estimates of activation barriers and of cluster size effects on transition states. They serve to demonstrate the essential role of the coverage and reactivity of chemisorbed oxygen in determining the type and effectiveness of surface structures in CH(4) oxidation reactions using O(2), H(2)O, or CO(2) as oxidants, as well as the diversity of rate dependencies, activation energies and entropies, and cluster size effects that prevail in these reactions. These results also show how theory and experiments can unravel complex surface chemistries on realistic catalysts under practical conditions and provide through the resulting mechanistic insights specific predictions for the effects of cluster size and surface coordination on turnover rates, the trends and magnitude of which depend sensitively on the nature of the predominant adsorbed intermediates and the kinetically relevant steps.

Carbon Fibers Conductivity Studies

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Butkus, A. M.

1980-01-01

In an attempt to understand the process of electrical conduction in polyacrylonitrile (PAN)-based carbon fibers, calculations were carried out on cluster models of the fiber consisting of carbon, nitrogen, and hydrogen atoms using the modified intermediate neglect of differential overlap (MINDO) molecular orbital (MO) method. The models were developed based on the assumption that PAN carbon fibers obtained with heat treatment temperatures (HTT) below 1000 C retain nitrogen in a graphite-like lattice. For clusters modeling an edge nitrogen site, analysis of the occupied MO's indicated an electron distribution similar to that of graphite. A similar analysis for the somewhat less stable interior nitrogen site revealed a partially localized II electron distribution around the nitrogen atom. The differences in bonding trends and structural stability between edge and interior nitrogen clusters led to a two-step process proposed for nitrogen evolution with increasing HTT.

Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, X. J.; Xue, X. L.; Guo, Z. X.

Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal Pt N nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for Pt N, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D 6h symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). But, the magic number of Pt Nmore » clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt-57 motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d 96s 1) of Pt, which result in a delicate balance between the enhanced Pt-Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. Our findings about Pt N clusters are also applicable to Ir N clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. Finally, the findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.« less

Electronic Effects on Room-Temperature, Gas-Phase C-H Bond Activations by Cluster Oxides and Metal Carbides: The Methane Challenge.

PubMed

Schwarz, Helmut; Shaik, Sason; Li, Jilai

2017-12-06

This Perspective discusses a story of one molecule (methane), a few metal-oxide cationic clusters (MOCCs), dopants, metal-carbide cations, oriented-electric fields (OEFs), and a dizzying mechanistic landscape of methane activation! One mechanism is hydrogen atom transfer (HAT), which occurs whenever the MOCC possesses a localized oxyl radical (M-O • ). Whenever the radical is delocalized, e.g., in [MgO] n •+ the HAT barrier increases due to the penalty of radical localization. Adding a dopant (Ga 2 O 3 ) to [MgO] 2 •+ localizes the radical and HAT transpires. Whenever the radical is located on the metal centers as in [Al 2 O 2 ] •+ the mechanism crosses over to proton-coupled electron transfer (PCET), wherein the positive Al center acts as a Lewis acid that coordinates the methane molecule, while one of the bridging oxygen atoms abstracts a proton, and the negatively charged CH 3 moiety relocates to the metal fragment. We provide a diagnostic plot of barriers vs reactants' distortion energies, which allows the chemist to distinguish HAT from PCET. Thus, doping of [MgO] 2 •+ by Al 2 O 3 enables HAT and PCET to compete. Similarly, [ZnO] •+ activates methane by PCET generating many products. Adding a CH 3 CN ligand to form [(CH 3 CN)ZnO] •+ leads to a single HAT product. The CH 3 CN dipole acts as an OEF that switches off PCET. [MC] + cations (M = Au, Cu) act by different mechanisms, dictated by the M + -C bond covalence. For example, Cu + , which bonds the carbon atom mostly electrostatically, performs coupling of C to methane to yield ethylene, in a single almost barrier-free step, with an unprecedented atomic choreography catalyzed by the OEF of Cu + .

Anisotropy of atomic bonds formed by p-type dopants in bulk GaN crystals

NASA Astrophysics Data System (ADS)

Lawniczak-Jablonska, K.; Suski, T.; Gorczyca, I.; Christensen, N. E.; Libera, J.; Kachniarz, J.; Lagarde, P.; Cortes, R.; Grzegory, I.

The anisotropy of atomic bonds formed by acceptor dopants with nitrogen in bulk wurtzite GaN crystals was studied by means of linearly polarized synchrotron radiation used in measurements of X-ray-absorption spectra for the K-edgeof Mg and Zn dopants. These spectra correspond to i) a single acceptor N bond along the c-axis and ii) three bonds realized with N atoms occupying the ab-plane perpendicular to the c-axis. The Zn dopant formed resonant spectra similar to that characteristic for Ga cations. In the case of the Mg dopant, similarity to Ga cations was observed for triple bonds in the ab-plane, only. Practically no resonant structure for spectra detected along the c-axis was observed. The absorption spectra were compared with ab initio calculations using the full-potential linear muffin-tin-orbital method. These calculations were also used for determination of the bond length for Mg-N and Zn-N in wurtzite GaN crystals and show that introducing dopants causes an increase of the lengths of the bonds formed by both dopants. Extended X-ray-absorption fine-structure measurements performed for bulk GaN:Zn confirmed the prediction of the theory in the case of the Zn-N bond. Finally, it is suggested that the anisotropy in the length of the Mg-N bonds, related to their larger strength in the case of bonds in the ab-plane, can explain preferential formation of a superlattice consisting of Mg-rich layers arranged in ab-planes of several bulk GaN:Mg crystals observed by transmission electron microscopy. Within the sensitivity of the method used, no parasitic metallic clusters or oxide compounds formed by the considered acceptors in GaN crystals were found.

Star-like superalkali cations featuring planar pentacoordinate carbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Jin-Chang; Tian, Wen-Juan; Zhao, Xue-Feng

Superalkali cations, known to possess low vertical electron affinities (VEAs), high vertical detachment energies, and large highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, are intriguing chemical species. Thermodynamically, such species need to be the global minima in order to serve as the promising targets for experimental realization. In this work, we propose the strategies of polyhalogenation and polyalkalination for designing the superalkali cations. By applying these strategies, the local-minimum planar pentacoordinate carbon (ppC) cluster CBe{sub 5} can be modified to form a series of star-like superalkali ppC or quasi-ppC CBe{sub 5}X{sub 5}{sup +} (X = F,more » Cl, Br, Li, Na, K) cations containing a CBe{sub 5} moiety. Polyhalogenation and polyalkalination on the CBe{sub 5} unit may help eliminate the high reactivity of bare CBe{sub 5} molecule by covering the reactive Be atoms with noble halogen anions and alkali cations. Computational exploration of the potential energy surfaces reveals that the star-like ppC or quasi-ppC CBe{sub 5}X{sub 5}{sup +} (X = F, Cl, Br, Li, Na, K) clusters are the true global minima of the systems. The predicted VEAs for CBe{sub 5}X{sub 5}{sup +} range from 3.01 to 3.71 eV for X = F, Cl, Br and 2.12–2.51 eV for X = Li, Na, K, being below the lower bound of the atomic ionization potential of 3.89 eV in the periodic table. Large HOMO-LUMO energy gaps are also revealed for the species: 10.76–11.07 eV for X = F, Cl, Br and 4.99–6.91 eV for X = Li, Na, K. These designer clusters represent the first series of superalkali cations with a ppC center. Bonding analyses show five Be–X–Be three-center two-electron (3c-2e) σ bonds for the peripheral bonding, whereas the central C atom is associated with one 6c-2e π bond and three 6c-2e σ bonds, rendering (π and σ) double aromaticity. Born-Oppenheimer molecular dynamics simulations indicate that the CBe{sub 5} motif is robust in the clusters. As planar hypercoordination carbon species are often thermodynamically unstable and highly reactive, the superalkali cation characters of these ppC species should be highlighted, which may be suitable for experimental realization.« less

Polar Intermetallics Pr 5Co 2Ge 3 and Pr 7Co 2Ge 4 With Planar Hydrocarbon-Like Metal Clusters

DOE PAGES

Lin, Qisheng; Aguirre, Kaiser; Saunders, Scott M.; ...

2017-06-19

Planar hydrocarbon-like metal clusters may foster new insights linking organic molecules with conjugated π-π bonding interactions and inorganic structures in terms of their bonding characteristics. However, such clusters are uncommon in polar intermetallics. Herein, we report two polar intermetallic phases, Pr 5Co 2Ge 3 and Pr 7Co 2Ge 4, both of which feature such planar metal clusters, viz., ethylene-like [Co 2Ge 4] clusters plus the concatenated forms and polyacene-like [Co 2Ge 2] n ribbons in Pr 5Co 2Ge 3, and 1,2,4,5-tetramethylbenzene-like [Co4Ge6] cluster in Pr 7Co 2Ge 4. Just as in the related planar organic structures, these metal-metalloid species aremore » dominated by covalent bonding interactions. Both compounds magnetically order at low temperature with net ferromagnetic components: Pr 5Co 2Ge 3 via a series of transitions below 150 K; and Pr 7Co 2Ge 4 via a single ferromagnetic transition at 19 K. Spin-polarized electronic structure calculations for Pr 7Co 2Ge 4 reveal strong spin-orbit coupling within Pr and considerable magnetic contributions from Co atoms. This work suggests that similar structural chemistry can emerge for other rare earth-late transition metal-main group systems.« less

Efficient electrocatalytic conversion of CO.sub.2 to CO using ligand-protected Au.sub.25 clusters

DOEpatents

Kauffman, Douglas; Matranga, Christopher; Qian, Huifeng; Jin, Rongchao; Alfonso, Dominic R.

2015-09-22

An apparatus and method for CO.sub.2 reduction using an Au.sub.25 electrode. The Au.sub.25 electrode is comprised of ligand-protected Au.sub.25 having a structure comprising an icosahedral core of 13 atoms surrounded by a shell of six semi-ring structures bonded to the core of 13 atoms, where each semi-ring structure is typically --SR--Au--SR--Au--SR or --SeR--Au--SeR--Au--SeR. The 12 semi-ring gold atoms within the six semi-ring structures are stellated on 12 of the 20 faces of the icosahedron of the Au.sub.13 core, and organic ligand --SR or --SeR groups are bonded to the Au.sub.13 core with sulfur or selenium atoms. The Au.sub.25 electrode and a counter-electrode are in contact with an electrolyte comprising CO.sub.2 and H+, and a potential of at least -0.1 volts is applied from the Au.sub.25 electrode to the counter-electrode.

Theoretical prediction of novel ultrafine nanowires formed by Si12C12 cage-like clusters

NASA Astrophysics Data System (ADS)

Yong, Yongliang; Song, Bin; He, Pimo

2014-02-01

Using density functional theory calculations, we predict that novel SiC ultrafine nanowires can be produced via the coalescence of stable Si12C12 clusters. For the isolated Si12C12 clusters, we find that the cage-like structure with a distinct segregation between Si and C atoms is energetically more favourable than the fullerene-like structure with alternating Si-C bonds. Via the coalescence of Si12C12 clusters, three novel stable nanowires have been characterised. The band structure reveals that these nanowires are semiconductors with narrow gap, indicating that they may be used as infrared detectors and thermoelectrics.

Analyzing ZnO clusters through the density-functional theory.

PubMed

Zaragoza, Irineo-Pedro; Soriano-Agueda, Luis-Antonio; Hernández-Esparza, Raymundo; Vargas, Rubicelia; Garza, Jorge

2018-06-16

The potential energy surface of Zn n O n clusters (n = 2, 4, 6, 8) has been explored by using a simulated annealing method. For n = 2, 4, and 6, the CCSD(T)/TZP method was used as the reference, and from here it is shown that the M06-2X/TZP method gives the lowest deviations over PBE, PBE0, B3LYP, M06, and MP2 methods. Thus, with the M06-2X method we predict isomers of Zn n O n clusters, which coincide with some isomers reported previously. By using the atoms in molecules analysis, possible contacts between Zn and O atoms were found for all structures studied in this article. The bond paths involved in several clusters suggest that Zn n O n clusters can be obtained from the zincite (ZnO crystal), such an observation was confirmed for clusters with n = 2 - 9,18 and 20. The structure with n = 23 was obtained by the procedure presented here, from crystal information, which could be important to confirm experimental data delivered for n = 18 and 23.

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Theoretical investigation of stabilities and optical properties of Si12C12 clusters

NASA Astrophysics Data System (ADS)

Duan, Xiaofeng F.; Burggraf, Larry W.

2015-01-01

By sorting through hundreds of globally stable Si12C12 isomers using a potential surface search and using simulated annealing, we have identified low-energy structures. Unlike isomers knit together by Si-C bonds, the lowest energy isomers have segregated carbon and silicon regions that maximize stronger C-C bonding. Positing that charge separation between the carbon and silicon regions would produce interesting optical absorption in these cluster molecules, we used time-dependent density functional theory to compare the calculated optical properties of four isomers representing structural classes having different types of silicon and carbon segregation regions. Absorptions involving charge transfer between segregated carbon and silicon regions produce lower excitation energies than do structures having alternating Si-C bonding for which frontier orbital charge transfer is exclusively from separated carbon atoms to silicon atoms. The most stable Si12C12 isomer at temperatures below 1100 K is unique as regards its high symmetry and large optical oscillator strength in the visible blue. Its high-energy and low-energy visible transitions (1.15 eV and 2.56 eV) are nearly pure one-electron silicon-to-carbon transitions, while an intermediate energy transition (1.28 eV) is a nearly pure carbon-to-silicon one-electron charge transfer.

Simulating structure and dynamics in small droplets of 1-ethyl-3-methylimidazolium acetate

NASA Astrophysics Data System (ADS)

Brehm, Martin; Sebastiani, Daniel

2018-05-01

To investigate the structure and dynamics of small ionic liquid droplets in gas phase, we performed a DFT-based ab initio molecular dynamics study of several 1-ethyl-3-methylimidazolium acetate clusters in vacuum as well as a bulk phase simulation. We introduce an unbiased criterion for average droplet diameter and density. By extrapolation of the droplet densities, we predict the experimental bulk phase density with a deviation of only a few percent. The hydrogen bond geometry between cations and anions is very similar in droplets and bulk, but the hydrogen bond dynamics is significantly slower in the droplets, becoming slower with increasing system size, with hydrogen bond lifetimes up to 2000 ps. From a normal mode analysis of the trajectories, we identify the modes of the ring proton C-H stretching, which are strongly affected by hydrogen bonding. From analyzing these, we find that the hydrogen bond becomes weaker with increasing system size. The cations possess an increased concentration inside the clusters, whereas the anions show an excess concentration on the outside. Almost all anions point towards the droplet center with their carboxylic groups. Ring stacking is found to be a very important structural motif in the droplets (as in the bulk), but side chain interactions are only of minor importance. By using Voronoi tessellation, we define the exposed droplet surface and find that it consists mainly of hydrogen atoms from the cation's and anion's methyl and ethyl groups. Polar atoms are rarely found on the surface, such that the droplets appear completely hydrophobic on the outside.

Novel silicon-carbon fullerene-like nanostructures: an Ab initio study on the stability of Si54C6 and Si60C6 clusters.

PubMed

Srinivasan, Aravind; Ray, Asok K

2006-01-01

Silicon fullerene like nanostructures with six carbon atoms on the surface of Si60 cages by substitution, as well as inside the cage at various symmetry orientations have been studied within the generalized gradient approximation to density functional theory. Full geometry optimizations have been performed without any symmetry constraints using the Gaussian 03 suite of programs and the LANL2DZ basis set. Thus, for the silicon atom, the Hay-Wadt pseudopotential with the associated basis set are used for the core electrons and the valence electrons, respectively. For the carbon atom, the Dunning/Huzinaga double zeta basis set is employed. Electronic and geometric properties of the nanostructures are presented and discussed in detail. It was found that optimized silicon-carbon fullerene like nanostructures have increased stability compared to bare Si60 cage and the stability depends on the orientation of carbon atoms, as well as on the nature of bonding between silicon and carbon atoms and also on the carbon-carbon bonding.

The cluster model of a hot dense vapor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhukhovitskii, D. I., E-mail: dmr@ihed.ras.ru

2015-04-28

We explore thermodynamic properties of a vapor in the range of state parameters where the contribution to thermodynamic functions from bound states of atoms (clusters) dominates over the interaction between the components of the vapor in free states. The clusters are assumed to be light and sufficiently “hot” for the number of bonds to be minimized. We use the technique of calculation of the cluster partition function for the cluster with a minimum number of interatomic bonds to calculate the caloric properties (heat capacity and velocity of sound) for an ideal mixture of the lightest clusters. The problem proves tomore » be exactly solvable and resulting formulas are functions solely of the equilibrium constant of the dimer formation. These formulas ensure a satisfactory correlation with the reference data for the vapors of cesium, mercury, and argon up to moderate densities in both the sub- and supercritical regions. For cesium, we extend the model to the densities close to the critical one by inclusion of the clusters of arbitrary size. Knowledge of the cluster composition of the cesium vapor makes it possible to treat nonequilibrium phenomena such as nucleation of the supersaturated vapor, for which the effect of the cluster structural transition is likely to be significant.« less

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and ferromagnetism. Considering the diversity of their composition, their distinct electronic structures, and the disparate coordination behaviors of the different metal elements, these materials suggest abundant opportunities for designing multifunctional materials with varied structures. The third type of clusters that we discuss are based on polyoxometalates, in particular those containing pentagonal units. However, unlike in fullerene chemistry, which does not allow the use of discrete pentagonal building blocks, the metal oxide-based pentagonal units can be used as fundamental building blocks for constructing various Keplerate structures. These structures also have a variety of functions, including intriguing magnetic properties in some cases. Coupled with different linking groups, such pentagonal units can be used for the assembly of a large number of spherical molecules whose properties can be tuned and optimized. Although this Account focuses on the topological aspects of fullerene-like metal clusters, we hope that this topical review will stimulate more efforts in the exploratory synthesis of new fullerene-like clusters. More importantly, we hope that further study of the bonding interactions and properties of these molecules will lead to the development of new functional materials.

Photoelectron spectroscopy of B4O4 (-): Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters.

PubMed

Tian, Wen-Juan; Zhao, Li-Juan; Chen, Qiang; Ou, Ting; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin; Li, Si-Dian

2015-04-07

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B4O4 (0/-) clusters. The measured PES spectra of B4O4 (-) exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDE of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of Cs B4O4 (-) ((2)A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D2h B4O4 (-) ((2)B2g) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B2O2 core bonded with terminal BO and/or BO2 groups. The same Y-shaped and rhombic structures are also located for the B4O4 neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B4O4 (0/-) clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B4O4 (0/-) clusters. This work is the first experimental study on a molecular system with an o-bond.

An intermetallic Au24Ag20 superatom nanocluster stabilized by labile ligands.

PubMed

Wang, Yu; Su, Haifeng; Xu, Chaofa; Li, Gang; Gell, Lars; Lin, Shuichao; Tang, Zichao; Häkkinen, Hannu; Zheng, Nanfeng

2015-04-08

An intermetallic nanocluster containing 44 metal atoms, Au24Ag20(2-SPy)4(PhC≡C)20Cl2, was successfully synthesized and structurally characterized by single-crystal analysis and density funtional theory computations. The 44 metal atoms in the cluster are arranged as a concentric three-shell Au12@Ag20@Au12 Keplerate structure having a high symmetry. For the first time, the co-presence of three different types of anionic ligands (i.e., phenylalkynyl, 2-pyridylthiolate, and chloride) was revealed on the surface of metal nanoclusters. Similar to thiolates, alkynyls bind linearly to surface Au atoms using their σ-bonds, leading to the formation of two types of surface staple units (PhC≡C-Au-L, L = PhC≡C(-) or 2-pyridylthiolate) on the cluster. The co-presence of three different surface ligands allows the site-specific surface and functional modification of the cluster. The lability of PhC≡C(-) ligands on the cluster was demonstrated, making it possible to keep the metal core intact while removing partial surface capping. Moreover, it was found that ligand exchange on the cluster occurs easily to offer various derivatives with the same metal core but different surface functionality and thus different solubility.

Insights into the catalysis of a lysine-tryptophan bond in bacterial peptides by a SPASM domain radical S-adenosylmethionine (SAM) peptide cyclase.

PubMed

Benjdia, Alhosna; Decamps, Laure; Guillot, Alain; Kubiak, Xavier; Ruffié, Pauline; Sandström, Corine; Berteau, Olivier

2017-06-30

Radical S -adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to C α atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus , and a reaction mechanism has been proposed. By combining site-directed mutagenesis, biochemical assays, and spectroscopic analyses, we show here that this enzyme, belonging to the emerging family of SPASM domain radical SAM enzymes, likely contains three [4Fe-4S] clusters. Notably, our data support that the seven conserved cysteine residues, present within the SPASM domain, are critical for enzyme activity. In addition, we uncovered the minimum substrate requirements and demonstrate that KW cyclic peptides are more widespread than anticipated, notably in pathogenic bacteria. Finally, we show a strict specificity of the enzyme for lysine and tryptophan residues and the dependence of an eight-amino acid leader peptide for activity. Altogether, our study suggests novel mechanistic links among SPASM domain radical SAM enzymes and supports the involvement of non-cysteinyl ligands in the coordination of auxiliary clusters. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Catalysis by Atomic-Sized Centers: Methane Activation for Partial Oxidation and Combustion

DTIC Science & Technology

2015-07-21

example, H adsorbed alone on an oxide surface will bind to oxygen to form a hydroxide . However, if a Lewis base (e.g. any electron donor) is...that on a gold surface, which is not surprising considering the bonding character between the cluster and metal surfaces. The high mobility verifies

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong

2015-07-29

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. Themore » higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.« less

Facile O-atom insertion into CC and CH bonds by a trinuclear copper complex designed to harness a singlet oxene

PubMed Central

Chen, Peter P.-Y.; Yang, Richard B.-G.; Lee, Jason C.-M.; Chan, Sunney I.

2007-01-01

Two trinuclear copper [CuICuICuI(L)]1+ complexes have been prepared with the multidentate ligands (L) 3,3′-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-Me) and (3,3′-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-Et) as models for the active site of the particulate methane monooxygenase (pMMO). The ligands were designed to form the proper spatial and electronic geometry to harness a “singlet oxene,” according to the mechanism previously suggested by our laboratory. Consistent with the design strategy, both [CuICuICuI(L)]1+ reacted with dioxygen to form a putative bis(μ3-oxo)CuIICuIICuIII species, capable of facile O-atom insertion across the central CC bond of benzil and 2,3-butanedione at ambient temperature and pressure. These complexes also catalyze facile O-atom transfer to the CH bond of CH3CN to form glycolonitrile. These results, together with our recent biochemical studies on pMMO, provide support for our hypothesis that the hydroxylation site of pMMO contains a trinuclear copper cluster that mediates CH bond activation by a singlet oxene mechanism. PMID:17804786

Theoretical studies on the electronic structures and photoelectron spectra of tri-rhenium oxide clusters: Re3O(n)(-) and Re3O(n) (n=1-6).

PubMed

Zhou, Qi; Gong, Wei-Chao; Xie, Lu; Zheng, Cun-Gong; Zhang, Wei; Wang, Bin; Zhang, Yong-Fan; Huang, Xin

2014-01-03

Density functional theory (DFT) calculations are performed to study the structural and electronic properties of tri-rhenium oxide clusters Re3On(-/0) (n=1-6). Generalized Koopmans' theorem is applied to predict the vertical detachment energies (VDEs) and simulate the photoelectron spectra (PES). Theoretical calculations at the B3LYP level are carried out to search for the global minima for both the anions and the neutrals. For the anions, the first two O atoms prefer the same corner position of a Re3 triangle. Whereas, Re3O3(-) possesses a C2v symmetry with one bridging and two terminal O atoms. The next three O atoms (n=4-6) are adding sequentially on the basis of Re3O3(-) motif, i.e., adding one terminal O atom for Re3O4(-), one terminal and one bridging O atoms for Re3O5(-), and one terminal and two bridging O atoms for Re3O6(-), respectively. Their corresponding neutral species are similar to the anions in geometry except Re3O4 and Re3O5. Molecular orbital analyses are employed to investigate the chemical bonding and structural evolution in these tri-rhenium oxide clusters. Copyright © 2013 Elsevier B.V. All rights reserved.

Internal and external atomic steps in graphite exhibit dramatically different physical and chemical properties.

PubMed

Lee, Hyunsoo; Lee, Han-Bo-Ram; Kwon, Sangku; Salmeron, Miquel; Park, Jeong Young

2015-04-28

We report on the physical and chemical properties of atomic steps on the surface of highly oriented pyrolytic graphite (HOPG) investigated using atomic force microscopy. Two types of step edges are identified: internal (formed during crystal growth) and external (formed by mechanical cleavage of bulk HOPG). The external steps exhibit higher friction than the internal steps due to the broken bonds of the exposed edge C atoms, while carbon atoms in the internal steps are not exposed. The reactivity of the atomic steps is manifested in a variety of ways, including the preferential attachment of Pt nanoparticles deposited on HOPG when using atomic layer deposition and KOH clusters formed during drop casting from aqueous solutions. These phenomena imply that only external atomic steps can be used for selective electrodeposition for nanoscale electronic devices.

Lasagna-type arrays with halide-nitromethane cluster filling. The first recognition of the Hal(-)···HCH2NO2 (Hal = Cl, Br, I) hydrogen bonding.

PubMed

Gushchin, Pavel V; Kuznetsov, Maxim L; Wang, Qian; Karasik, Andrey A; Haukka, Matti; Starova, Galina L; Kukushkin, Vadim Yu

2012-06-21

The previously predicted ability of the methyl group of nitromethane to form hydrogen bonding with halides is now confirmed experimentally based on X-ray data of novel nitromethane solvates followed by theoretical ab initio calculations at the MP2 level of theory. The cationic (1,3,5-triazapentadiene)Pt(II) complexes [Pt{HN=C(NC(5)H(10))N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [1](Hal)(2) (Hal = Cl, Br, I), and [Pt{HN=C(NC(4)H(8)O)N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [2](Cl)(2), were crystallized from MeNO(2)-containing systems providing nitromethane solvates studied by X-ray diffraction. In the crystal structure of [1][(Hal)(2)(MeNO(2))(2)] (Hal = Cl, Br, I) and [2][(Cl)(2)(MeNO(2))(2)], the solvated MeNO(2) molecules occupy vacant spaces between lasagna-type layers and connect to the Hal(-) ion through a weak hydrogen bridge via the H atom of the methyl thus forming, by means of the Hal(-)···HCH(2)NO(2) contact, the halide-nitromethane cluster "filling". The quantum-chemical calculations demonstrated that the short distance between the Hal(-) anion and the hydrogen atom of nitromethane in clusters [1][(Hal)(2)(MeNO(2))(2)] and [2][(Cl)(2)(MeNO(2))(2)] is not just a consequence of the packing effect but a result of the moderately strong hydrogen bonding.

Intriguing structures and magic sizes of heavy noble metal nanoclusters around size 55 governed by relativistic effect and covalent bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, X. J.; Xue, X. L.; Jia, Yu

Nanoclusters usually display exotic physical and chemical properties due to their intriguing geometric structures in contrast to their bulk counterparts. By means of first-principles calculations within density functional theory, we find that heavy noble metal Pt{sub N} nanoclusters around the size N = 55 begin to prefer an open configuration, rather than previously reported close-packed icosahedron or core-shell structures. Particularly, for Pt{sub N}, the widely supposed icosahedronal magic cluster is changed to a three-atomic-layered structure with D{sub 6h} symmetry, which can be well addressed by our recently established generalized Wulff construction principle (GWCP). However, the magic number of Pt{sub N}more » clusters around 55 is shifted to a new odd number of 57. The high symmetric three-layered Pt{sub 57} motif is mainly stabilized by the enhanced covalent bonding contributed by both spin-orbital coupling effect and the open d orbital (5d{sup 9}6s{sup 1}) of Pt, which result in a delicate balance between the enhanced Pt–Pt covalent bonding of the interlayers and negligible d dangling bonds on the cluster edges. These findings about Pt{sub N} clusters are also applicable to Ir{sub N} clusters, but qualitatively different from their earlier neighboring element Os and their later neighboring element Au. The magic numbers for Os and Au are even, being 56 and 58, respectively. The findings of the new odd magic number 57 are the important supplementary of the recently established GWCP.« less

Surface Modification of Silicone Rubber for Adhesion Patterning of Mesenchymal Stem Cells by Water Cluster Ion Beam

NASA Astrophysics Data System (ADS)

Sommani, Piyanuch; Ichihashi, Gaku; Ryuto, Hiromichi; Tsuji, Hiroshi; Gotoh, Yasuhito; Takaoka, Gikan H.

2011-01-01

Biocompatibility of silicone rubber sheet (SR) was improved by the water cluster ion irradiation for adhesion patterning of mesenchymal stem cells (MSCs). The water cluster ions were irradiated at acceleration voltage of 6 kV and doses of 1014-1016 ions/cm2. The effect of ion dose on changes in wettability and surface atomic bonding state was observed. Compared to the unirradiated SR, about four-time smoother surface on the irradiated one was observed. Water contact angle decreased with an increase in the ion dose up to 1×1015 ions/cm2. With an increase in ion dose, XPS showed decrease of atomic carbon due to lateral sputtering effect and increase of atomic oxygen due to surface oxidation. After 7 days in vitro culture, the complete adhesion pattern of the rat MSCs was obtained on the irradiated SR at dose of 1×1015 ions/cm2, corresponding to the low contact angle of 87°. At low dose, the partial pattern on the irradiated region was observed instead.

The role of charge transfer in the oxidation state change of Ce atoms in the TM13-CeO2(111) systems (TM = Pd, Ag, Pt, Au): a DFT + U investigation.

PubMed

Tereshchuk, Polina; Freire, Rafael L H; Ungureanu, Crina G; Seminovski, Yohanna; Kiejna, Adam; Da Silva, Juarez L F

2015-05-28

Despite extensive studies of transition metal (TM) clusters supported on ceria (CeO2), fundamental issues such as the role of the TM atoms in the change in the oxidation state of Ce atoms are still not well understood. In this work, we report a theoretical investigation based on static and ab initio molecular dynamics density functional theory calculations of the interaction of 13-atom TM clusters (TM = Pd, Ag, Pt, Au) with the unreduced CeO2(111) surface represented by a large surface unit cell and employing Hubbard corrections for the strong on-site Coulomb correlation in the Ce f-electrons. We found that the TM13 clusters form pyramidal-like structures on CeO2(111) in the lowest energy configurations with the following stacking sequence, TM/TM4/TM8/CeO2(111), while TM13 adopts two-dimensional structures at high energy structures. TM13 induces a change in the oxidation state of few Ce atoms (3 of 16) located in the topmost Ce layer from Ce(IV) (itinerant Ce f-states) to Ce(III) (localized Ce f-states). There is a charge flow from the TM atoms to the CeO2(111) surface, which can be explained by the electronegativity difference between the TM (Pd, Ag, Pt, Au) and O atoms, however, the charge is not uniformly distributed on the topmost O layer due to the pressure induced by the TM13 clusters on the underlying O ions, which yields a decrease in the ionic charge of the O ions located below the cluster and an increase in the remaining O ions. Due to the charge flow mainly from the TM8-layer to the topmost O-layer, the charge cannot flow from the Ce(IV) atoms to the O atoms with the same magnitude as in the clean CeO2(111) surface. Consequently, the effective cationic charge decreases mainly for the Ce atoms that have a bond with the O atoms not located below the cluster, and hence, those Ce atoms change their oxidation state from IV to III. This increases the size of the Ce(III) compared with the Ce(IV) cations, which builds-in a strain within the topmost Ce layer, and hence, also affecting the location of the Ce(III) cations and the structure of the TM13 clusters.

Size and Site Dependence of the Catalytic Activity of Iridium Clusters toward Ethane Dehydrogenation.

PubMed

Ge, Yingbin; Jiang, Hao; Kato, Russell; Gummagatta, Prasuna

2016-12-01

This research focuses on optimizing transition metal nanocatalyst immobilization and activity to enhance ethane dehydrogenation. Ethane dehydrogenation, catalyzed by thermally stable Ir n (n = 8, 12, 18) atomic clusters that exhibit a cuboid structure, was studied using the B3LYP method with triple-ζ basis sets. Relativistic effects and dispersion corrections were included in the calculations. In the dehydrogenation reaction Ir n + C 2 H 6 → H-Ir n -C 2 H 5 → (H) 2 -Ir n -C 2 H 4 , the first H-elimination is the rate-limiting step, primarily because the reaction releases sufficient heat to facilitate the second H-elimination. The catalytic activity of the Ir clusters strongly depends on the Ir cluster size and the specific catalytic site. Cubic Ir 8 is the least reactive toward H-elimination in ethane: Ir 8 + C 2 H 6 → H-Ir 8 -C 2 H 5 has a large (65 kJ/mol) energy barrier, whereas Ir 12 (3 × 2 × 2 cuboid) and Ir 18 (3 × 3 × 2 cuboid) lower this energy barrier to 22 and 3 kJ/mol, respectively. The site dependence is as prominent as the size effect. For example, the energy barrier for the Ir 18 + C 2 H 6 → H-Ir 18 -C 2 H 5 reaction is 3, 48, and 71 kJ/mol at the corner, edge, or face-center sites of the Ir 18 cuboid, respectively. Energy release due to Ir cluster insertion into an ethane C-H bond facilitates hydrogen migration on the Ir cluster surface, and the second H-elimination of ethane. In an oxygen-rich environment, oxygen molecules may be absorbed on the Ir cluster surface. The oxygen atoms bonded to the Ir cluster surface may slightly increase the energy barrier for H-elimination in ethane. However, the adsorption of oxygen and its reaction with H atoms on the Ir cluster releases sufficient heat to yield an overall thermodynamically favored reaction: Ir n + C 2 H 6 + 1 / 2 O 2 → Ir n + C 2 H 4 + H 2 O. These results will be useful toward reducing the energy cost of ethane dehydrogenation in industry.

Experimental and theoretical study on Raman spectra of magnesium fluoride clusters and solids.

PubMed

Neelamraju, S; Bach, A; Schön, J C; Fischer, D; Jansen, M

2012-11-21

In this study, the Raman and IR spectra of a large number of isomers of MgF(2) clusters and of possible bulk polymorphs of MgF(2) are calculated and compared with experimental data observed using a low-temperature atom beam deposition. The bulk polymorphs were taken from earlier work, while the cluster modifications for the neutral (MgF(2))(n) (n = 1-10) clusters and charged clusters (up to the trimer anion and cation, (Mg(3)F(7))(-) and (Mg(3)F(5))(+), respectively) are determined in the present work by global energy landscape explorations using simulated annealing. These theoretical calculations are complemented by an experimental study on both the vapor phase and the deposited films of MgF(2), which are generated in a low-temperature atom beam deposition setup for the synthesis of MgF(2) bulk phases. The MgF(2) vapor and film are characterized via Raman spectroscopy of the MgF(2) gas phase species embedded in an Ar-matrix and of the MgF(2)-films deposited onto a cooled substrate, respectively. We find that, in the vapor phase, there are monomers and dimers and charged species to be present in our experimental setup. Furthermore, the results suggest that in the amorphous bulk MgF(2), rutile-like domains are present and MgF(2) clusters similar to those in the matrix. Finally, peaks at about 800 cm(-1), which are in the same range as the A(g) modes of clusters with dangling fluorine atoms connected to three-coordinated Mg atoms, indicate that such dangling bonds are also present in amorphous MgF(2).

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters.

PubMed

Pathak, A K; Mukherjee, T; Maity, D K

2007-07-28

We report vertical detachment energy (VDE) and IR spectra of Br2.-.(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2.-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150 K. A linear relationship is obtained for VDE versus (n+3)(-1/3) and bulk VDE of Br2.- aqueous solution is calculated as 10.01 eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by approximately 0.5 eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by approximately 6.4 eV. Calculated IR spectra show that the formation of Br2.--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2.-.(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters

NASA Astrophysics Data System (ADS)

Pathak, A. K.; Mukherjee, T.; Maity, D. K.

2007-07-01

We report vertical detachment energy (VDE) and IR spectra of Br2•-•(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2•-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150K. A linear relationship is obtained for VDE versus (n+3)-1/3 and bulk VDE of Br2•- aqueous solution is calculated as 10.01eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by ˜0.5eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by ˜6.4eV. Calculated IR spectra show that the formation of Br2•--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2•-•(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.

On the performance of large Gaussian basis sets for the computation of total atomization energies

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

Sulfide bonded atomic radii

NASA Astrophysics Data System (ADS)

Gibbs, G. V.; Ross, N. L.; Cox, D. F.

2017-09-01

The bonded radius, r b(S), of the S atom, calculated for first- and second-row non-transition metal sulfide crystals and third-row transition metal sulfide molecules and crystals indicates that the radius of the sulfur atom is not fixed as traditionally assumed, but that it decreases systematically along the bond paths of the bonded atoms with decreasing bond length as observed in an earlier study of the bonded radius of the oxygen atom. When bonded to non-transition metal atoms, r b(S) decreases systematically with decreasing bond length from 1.68 Å when the S atom is bonded to the electropositive VINa atom to 1.25 Å when bonded to the more electronegative IVP atom. In the case of transition metal atoms, rb(S) likewise decreases with decreasing bond length from 1.82 Å when bonded to Cu and to 1.12 Å when bonded to Fe. As r b(S) is not fixed at a given value but varies substantially depending on the bond length and the field strength of the bonded atoms, it is apparent that sets of crystal and atomic sulfide atomic radii based on an assumed fixed radius for the sulfur atom are satisfactory in that they reproduce bond lengths, on the one hand, whereas on the other, they are unsatisfactory in that they fail to define the actual sizes of the bonded atoms determined in terms of the minima in the electron density between the atoms. As such, we urge that the crystal chemistry and the properties of sulfides be studied in terms of the bond lengths determined by adding the radii of either the atomic and crystal radii of the atoms but not in terms of existing sets of crystal and atomic radii. After all, the bond lengths were used to determine the radii that were experimentally determined, whereas the individual radii were determined on the basis of an assumed radius for the sulfur atom.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

PubMed

Fox, Naomi; Streinu, Ileana

2013-01-01

Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

PubMed Central

2013-01-01

Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu. PMID:24564209

Investigations into the mechanism of material removal and surface modification at atomic scale on stainless steel using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ranjan, Prabhat; Balasubramaniam, R.; Jain, V. K.

2018-06-01

A molecular dynamics simulation (MDS) has been carried out to investigate the material removal phenomenon of chemo-mechanical magnetorheological finishing (CMMRF) process. To understand the role of chemical assisted mechanical abrasion in CMMRF process, material removal phenomenon is subdivided into three different stages. In the first stage, new atomic bonds viz. Fe-O-Si is created on the surface of the workpiece (stainless steel). The second stage deals with the rupture of parent bonds like Fe-Fe on the workpiece. In the final stage, removal of material from the surface in the form of dislodged debris (cluster of atoms) takes place. Effects of process parameters like abrasive particles, depth of penetration and initial surface condition on finishing force, potential energy (towards secondary phenomenon such as chemical instability of the finished surface) and material removal at atomic scale have been investigated. It was observed that the type of abrasive particle is one of the important parameters to produce atomically smooth surface. Experiments were also conducted as per the MDS to generate defect-free and sub-nanometre-level finished surface (Ra value better than 0.2 nm). The experimental results reasonably agree well with the simulation results.

Cooperativity of hydrogen-bonded networks in 7-azaindole(CH3OH)n (n=2,3) clusters evidenced by IR-UV ion-dip spectroscopy and natural bond orbital analysis.

PubMed

Sakota, Kenji; Kageura, Yutaka; Sekiya, Hiroshi

2008-08-07

IR-UV ion-dip spectra of the 7-azaindole (7AI)(CH(3)OH)(n) (n=1-3) clusters have been measured in the hydrogen-bonded NH and OH stretching regions to investigate the stable structures of 7AI(CH(3)OH)(n) (n=1-3) in the S(0) state and the cooperativity of the H-bonding interactions in the H-bonded networks. The comparison of the IR-UV ion-dip spectra with IR spectra obtained by quantum chemistry calculations shows that 7AI(CH(3)OH)(n) (n=1-3) have cyclic H-bonded structures, where the NH group and the heteroaromatic N atom of 7AI act as the proton donor and proton acceptor, respectively. The H-bonded OH stretch fundamental of 7AI(CH(3)OH)(2) is remarkably redshifted from the corresponding fundamental of (CH(3)OH)(2) by 286 cm(-1), which is an experimental manifestation of the cooperativity in H-bonding interaction. Similarly, two localized OH fundamentals of 7AI(CH(3)OH)(3) also exhibit large redshifts. The cooperativity of 7AI(CH(3)OH)(n) (n=2,3) is successfully explained by the donor-acceptor electron delocalization interactions between the lone-pair orbital in the proton acceptor and the antibonding orbital in the proton donor in natural bond orbital (NBO) analyses.

Nanostructures nucleation in carbon-metal gaseous phase: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.

2018-01-01

We perform nonequilibrium molecular dynamics simulation of carbon nanoclusters nucleation and early stages of growth from the gaseous phase. We analyze the catalytic effect of iron atoms on the nucleation kinetics and structure of the resultant nanoparticles. Reactive Force Field (ReaxFF) is used in the simulations for the description of bond formation and dissociation during the nucleation process at the nanoscale. The catalytic effect of iron reveals itself even on nanosecond simulation times: iron atoms accelerate the process of clustering but result in less graphitized carbon structures.

Ti12Xe: A twelve-coordinated Xe-containing molecule

NASA Astrophysics Data System (ADS)

Miao, Junjian; Xu, Wenwu; Zhu, Beien; Gao, Yi

2017-08-01

A twelve-coordinated Xe-containing molecule Ti12Xe has been predicted by DFT calculations with quasi-icosahedral symmetry. Structural and NBO analyses show the chemical bonding exists between the central Xe atom and peripheral Ti atoms, which leads to the high stability of the molecule to a considerable degree. First principle molecular dynamics simulations further reveal the particularly high thermal stability of Ti12Xe up to 1500 K. This unique species may disclose new physics and chemistry of xenon element and stir interest in the Xe-transition metal cluster physics and chemistry.

Thermodynamics of confined gallium clusters.

PubMed

Chandrachud, Prachi

2015-11-11

We report the results of ab initio molecular dynamics simulations of Ga13 and Ga17 clusters confined inside carbon nanotubes with different diameters. The cluster-tube interaction is simulated by the Lennard-Jones (LJ) potential. We discuss the geometries, the nature of the bonding and the thermodynamics under confinement. The geometries as well as the isomer spectra of both the clusters are significantly affected. The degree of confinement decides the dimensionality of the clusters. We observe that a number of low-energy isomers appear under moderate confinement while some isomers seen in the free space disappear. Our finite-temperature simulations bring out interesting aspects, namely that the heat capacity curve is flat, even though the ground state is symmetric. Such a flat nature indicates that the phase change is continuous. This effect is due to the restricted phase space available to the system. These observations are supported by the mean square displacement of individual atoms, which are significantly smaller than in free space. The nature of the bonding is found to be approximately jellium-like. Finally we note the relevance of the work to the problem of single file diffusion for the case of the highest confinement.

A systemic investigation of hydrogen peroxide clusters (H2O2)n (n = 1-6) and liquid-state hydrogen peroxide: based on atom-bond electronegativity equalization method fused into molecular mechanics and molecular dynamics.

PubMed

Yu, Chun-Yang; Yang, Zhong-Zhi

2011-03-31

Hydrogen peroxide (HP) clusters (H(2)O(2))(n) (n = 1-6) and liquid-state HP have been systemically investigated by the newly constructed ABEEM/MM fluctuating charge model. Because of the explicit description of charge distribution and special treatment of the hydrogen-bond interaction region, the ABEEM/MM potential model gives reasonable properties of HP clusters, including geometries, interaction energies, and dipole moments, when comparing with the present ab initio results. Meanwhile, the average dipole moment, static dielectric constant, heats of vaporization, radial distribution function, and diffusion constant for the dynamic properties of liquid HP at 273 K and 1 atm are fairly consistent with the available experimental data. To the best of our knowledge, this is the first theoretical investigation of condensed HP. The properties of HP monomer are studied in detail involving the structure, torsion potentials, molecular orbital analysis, charge distribution, dipole moment, and vibrational frequency.

Selected AB4 2−/− (A = C, Si, Ge; B = Al, Ga, In) ions: a battle between covalency and aromaticity, and prediction of square planar Si in SiIn4 2−/−†

PubMed Central

Alexandrova, Anastassia N.; Nayhouse, Michael J.; Huynh, Mioy T.; Kuo, Jonathan L.; Melkonian, Arek V.; Chavez, Gerardo; Hernando, Nina M.; Kowal, Matthew D.; Liu, Chi-Ping

2012-01-01

CAl4 2−/− (D4h, 1A1g) is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al4, facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl4 2−/− (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, even though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al4. From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn4 2−/−. PMID:22868353

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Structure of fluorescent metal clusters on a DNA template.

NASA Astrophysics Data System (ADS)

Vdovichev, A. A.; Sych, T. S.; Reveguk, Z. V.; Smirnova, A. A.; Maksimov, D. A.; Ramazanov, R. R.; Kononov, A. I.

2016-08-01

Luminescent metal clusters are a subject of growing interest in recent years due to their bright emission from visible to near infrared range. Detailed structure of the fluorescent complexes of Ag and other metal clusters with ligands still remains a challenging task. In this joint experimental and theoretical study we synthesized Ag-DNA complexes on a DNA oligonucleotide emitting in violet- green spectral range. The structure of DNA template was determined by means of various spectral measurements (CD, MS, XPS). Comparison of the experimental fluorescent excitation spectra and calculated absorption spectra for different QM/MM optimized structures allowed us to determine the detailed structure of the green cluster containing three silver atoms in the stem of the DNA hairpin structure stabilized by cytosine-Ag+-cytosine bonds.

Effects of Al addition on atomic structure of Cu-Zr metallic glass

NASA Astrophysics Data System (ADS)

Li, Feng; Zhang, Huajian; Liu, Xiongjun; Dong, Yuecheng; Yu, Chunyan; Lu, Zhaoping

2018-02-01

The atomic structures of Cu52Zr48 and Cu45Zr48Al7 metallic glasses (MGs) have been studied by molecular dynamic simulations. The results reveal that the molar volume of the Cu45Zr48Al7 MG is smaller than that of the Cu52Zr48 MG, although the size of the Al atom is larger than that of the Cu atom, implying an enhanced atomic packing density achieved by introducing Al into the ternary MG. Bond shortening in unlike atomic pairs Zr-Al and Cu-Al is observed in the Cu45Zr48Al7 MG, which is attributed to strong interactions between Al and (Zr, Cu) atoms. Meanwhile, the atomic packing efficiency is enhanced by the minor addition of Al. Compared with the Cu52Zr48 binary MG, the potential energy of the ternary MG decreases and the glass transition temperature increases. Structural analyses indicate that more Cu- and Al-centered full icosahedral clusters emerge in the Cu45Zr48Al7 MG as some Cu atoms are substituted by Al. Furthermore, the addition of Al leads to more icosahedral medium-range orders in the ternary MG. The increase of full icosahedral clusters and the enhancement of the packing density are responsible for the improved glass-forming ability of Cu45Zr48Al7.

Photoelectron spectroscopy of B{sub 4}O{sub 4}{sup −}: Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Wen-Juan; Chen, Qiang; Ou, Ting

2015-04-07

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B{sub 4}O{sub 4}{sup 0/−} clusters. The measured PES spectra of B{sub 4}O{sub 4}{sup −} exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDEmore » of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of C{sub s} B{sub 4}O{sub 4}{sup −} ({sup 2}A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D{sub 2h} B{sub 4}O{sub 4}{sup −} ({sup 2}B{sub 2g}) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B{sub 2}O{sub 2} core bonded with terminal BO and/or BO{sub 2} groups. The same Y-shaped and rhombic structures are also located for the B{sub 4}O{sub 4} neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B{sub 4}O{sub 4}{sup 0/−} clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B{sub 4}O{sub 4}{sup 0/−} clusters. This work is the first experimental study on a molecular system with an o-bond.« less

Catalytic hydrolysis of carbonyl sulphide and carbon disulphide over Fe2O3 cluster: Competitive adsorption and reaction mechanism.

PubMed

Ning, Ping; Song, Xin; Li, Kai; Wang, Chi; Tang, Lihong; Sun, Xin

2017-10-31

The competitive adsorption and reaction mechanism for the catalytic hydrolysis of carbonyl sulphide (COS) and carbon disulphide (CS 2 ) over Fe 2 O 3 cluster was investigated. Compared with experimental results, the theoretical study was used to further investigate the competitive adsorption and effect of H 2 S in the hydrolysis reaction of COS and CS 2 . Experimental results showed that Fe 2 O 3 cluster enhanced the catalytic hydrolysis effect. Meanwhile, H 2 S was not conducive to the hydrolysis of COS and CS 2 . Theoretical calculations indicated that the order of competitive adsorption on Fe 2 O 3 is as follows: H 2 O (strong) >CS 2 (medium) >COS (weak). In the hydrolysis process, the C=S bond cleavage occurs easier than C=O bond cleavage. The hydrolysis reaction is initiated via the migration of an H-atom, which triggers C=S bond cleavage and S-H bond formation. Additionally, we find the first step of CS 2 hydrolysis to be rate limiting. The presence of H 2 S increases the reaction energy barrier, which is not favourable for COS hydrolysis. Fe 2 O 3 can greatly decrease the maximum energy barrier, which decreases the minimum energy required for hydrolysis, making it relatively facile to occur. In general, the theoretical results were consistent with experimental results, which proved that the theoretical study was reliable.

Evaluation of optical and electronic properties of silicon nano-agglomerates embedded in SRO: applying density functional theory

PubMed Central

2014-01-01

In systems in atomic scale and nanoscale such as clusters or agglomerates constituted by particles from a few to less than 100 atoms, quantum confinement effects are very important. Their optical and electronic properties are often dependent on the size of the systems and the way in which the atoms in these clusters are bonded. Generally, these nanostructures display optical and electronic properties significantly different to those found in corresponding bulk materials. Silicon agglomerates embedded in silicon rich oxide (SRO) films have optical properties, which have been reported to be directly dependent on silicon nanocrystal size. Furthermore, the room temperature photoluminescence (PL) of SRO has repeatedly generated a huge interest due to its possible applications in optoelectronic devices. However, a plausible emission mechanism has not been widely accepted in the scientific community. In this work, we present a short review about the experimental results on silicon nanoclusters in SRO considering different techniques of growth. We focus mainly on their size, Raman spectra, and photoluminescence spectra. With this as background, we employed the density functional theory with a functional B3LYP and a basis set 6-31G* to calculate the optical and electronic properties of clusters of silicon (constituted by 15 to 20 silicon atoms). With the theoretical calculation of the structural and optical properties of silicon clusters, it is possible to evaluate the contribution of silicon agglomerates in the luminescent emission mechanism, experimentally found in thin SRO films. PMID:25276105

Clustering/anticlustering effects on the GeSi Raman spectra at moderate (Ge,Si) contents: Percolation scheme vs. ab initio calculations

NASA Astrophysics Data System (ADS)

Torres, V. J. B.; Hajj Hussein, R.; Pagès, O.; Rayson, M. J.

2017-02-01

We test a presumed ability behind the phenomenological percolation scheme used for the basic description of the multi-mode Raman spectra of mixed crystals at one dimension along the linear chain approximation, to determine, via the Raman intensities, the nature of the atom substitution, as to whether this is random or due to local clustering/anticlustering. For doing so, we focus on the model percolation-type GeySi1-y system characterized by six oscillators { 1 × ( G e - G e ) , 3 × ( G e - S i ) , 2 × ( S i - S i ) } and place the study around the critical compositions y ˜ (0.16, 0.71, and 0.84) corresponding to nearly matching of intensities between the like Raman modes from a given multiplet ( G e - S i triplet or S i - S i doublet). The interplay between the GeySi1-y Raman intensities predicted by the percolation scheme depending on a suitable order parameter κ of local clustering/anticlustering is found to be consistent with ab initio calculations of the GeySi1-y Raman spectra done with the Ab Initio Modeling PROgram code using large (64-, 216-, and 512-atoms) disordered cubic supercells matching the required ( y , κ ) values. The actual "percolation vs. ab initio" comparative insight at moderate/dilute-(Ge,Si) limits, with an emphasis on the κ -induced intra-bond transfer of oscillator strength, extends a pioneering one earlier achieved at an intermediate composition ( y ˜ 0.50) by using small (32-atom) supercells [O. Pagès et al., J. Appl. Phys. 114, 033513 (2013)], mainly concerned with the inter-bond transfer of oscillator strength, providing altogether a complete picture.

Methane Activation Mediated by a Series of Cerium-Vanadium Bimetallic Oxide Cluster Cations: Tuning Reactivity by Doping.

PubMed

Ma, Jia-Bi; Meng, Jing-Heng; He, Sheng-Gui

2016-04-18

The reactions of cerium-vanadium cluster cations Cex Vy Oz (+) with CH4 are investigated by time-of-flight mass spectrometry and density functional theory calculations. (CeO2 )m (V2 O5 )n (+) clusters (m=1,2, n=1-5; m=3, n=1-4) with dimensions up to nanosize can abstract one hydrogen atom from CH4 . The theoretical study indicates that there are two types of active species in (CeO2 )m (V2 O5 )n (+) , V[(Ot )2 ](.) and [(Ob )2 CeOt ](.) (Ot and Ob represent terminal and bridging oxygen atoms, respectively); the former is less reactive than the latter. The experimentally observed size-dependent reactivities can be rationalized by considering the different active species and mechanisms. Interestingly, the reactivity of the (CeO2 )m (V2 O5 )n (+) clusters falls between those of (CeO2 )2-4 (+) and (V2 O5 )1-5 (+) in terms of C-H bond activation, thus the nature of the active species and the cluster reactivity can be effectively tuned by doping. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study of electron correlation effects in transition metal dimers

NASA Technical Reports Server (NTRS)

Das, G. P.; Jaffe, R. L.

1984-01-01

Introduction of partially localized orbitals is shown to reduce the number of terms needed to describe the bonding in transition metal clusters. Using this formalism, it is possible to compute the various intra- and inter-atomic electron correlation contributions to the bond energy. Calculations demonstrate the relative importance of several kinds of electron correlation terms involving the 3p, 3d, and 4s electrons. Improved interaction potentials are obtained for the dimers V(2) and Cr(2) when additional correlation is added to the CAS SCF results of Walch, Bauschlicher, Roos, and Nelin (1983).

Mechanical properties of Fe rich Fe-Si alloys: ab initio local bulk-modulus viewpoint

NASA Astrophysics Data System (ADS)

Bhattacharya, Somesh Kr; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori; Saengdeejing, Arkapol; Chen, Ying; Mohri, Tetsuo

2017-11-01

Fe-rich Fe-Si alloys show peculiar bulk-modulus changes depending on the Si concentration in the range of 0-15 at.%Si. In order to clarify the origin of this phenomenon, we have performed density-functional theory calculations of supercells of Fe-Si alloy models with various Si concentrations. We have applied our recent techniques of ab initio local energy and local stress, by which we can obtain a local bulk modulus of each atom or atomic group as a local constituent of the cell-averaged bulk modulus. A2-phase alloy models are constructed by introducing Si substitution into bcc Fe as uniformly as possible so as to prevent mutual neighboring, while higher Si concentrations over 6.25 at.%Si lead to contacts between SiFe8 cubic clusters via sharing corner Fe atoms. For 12.5 at.%Si, in addition to an A2 model, we deal with partial D03 models containing local D03-like layers consisting of edge-shared SiFe8 cubic clusters. For the cell-averaged bulk modulus, we have successfully reproduced the Si-concentration dependence as a monotonic decrease until 11.11 at.%Si and a recovery at 12.5 at.%Si. The analysis of local bulk moduli of SiFe8 cubic clusters and Fe regions is effective to understand the variations of the cell-averaged bulk modulus. The local bulk moduli of Fe regions become lower for increasing Si concentration, due to the suppression of bulk-like d-d bonding states in narrow Fe regions. For higher Si concentrations till 11.11 at.%Si, corner-shared contacts or 1D chains of SiFe8 clusters lead to remarkable reduction of local bulk moduli of the clusters. At 12 at.%Si, on the other hand, two- or three-dimensional arrangements of corner- or edge-shared SiFe8 cubic clusters show greatly enhanced local bulk moduli, due to quite different bonding nature with much stronger p-d hybridization. The relation among the local bulk moduli, local electronic and magnetic structures, and local configurations such as connectivity of SiFe8 clusters and Fe-region sizes has been analyzed. The ab initio local stress has opened the way for obtaining accurate local elastic properties reflecting local valence-electron behaviors.

Water-soluble Au13 clusters protected by binary thiolates: Structural accommodation and the use for chemosensing

NASA Astrophysics Data System (ADS)

Ding, Weihua; Huang, Chuanqi; Guan, Lingmei; Liu, Xianhu; Luo, Zhixun; Li, Weixue

2017-05-01

Here we report a successful synthesis of water-soluble 13-atoms gold clusters under the monolayer protection of binary thiolates, glutathione and penicillamine, under a molecular formula of Au13(SG)5(PA)7. This monolayer-protected cluster (MPC) finds decent stability and is demonstrated to possess an icosahedral geometry pertaining to structural accommodation in contrast to a planar bare Au13 of local minima energy. Natural bond orbital (NBO) analysis depicts the interaction patterns between gold and the ligands, enlightening to understand the origin of enhanced stability of the Au13 MPCs. Further, the water-soluble Au13 MPCs are found to be a decent candidate for chemosensing and bioimaging.

Density Functional Investigation of the Inclusion of Gold Clusters on a CH 3 S Self-Assembled Lattice on Au(111)

DOE PAGES

Allen, Darnel J.; Archibald, Wayne E.; Harper, John A.; ...

2016-01-01

We employ first-principles density functional theoretical calculations to address the inclusion of gold (Au) clusters in a well-packed CH 3 S self-assembled lattice. We compute CH 3 S adsorption energies to quantify the energetic stability of the self-assembly and gold adsorption and dissolution energies to characterize the structural stability of a series of Au clusters adsorbed at the SAM-Au interface. Our results indicate that the inclusion of Au clusters with less than four Au atoms in the SAM-Au interface enhances the binding of CH 3 S species. In contrast, larger Au clusters destabilize the self-assembly. We attribute this effect tomore » the low-coordinated gold atoms in the cluster. For small clusters, these low-coordinated sites have significantly different electronic properties compared to larger islands, which makes the binding with the self-assembly energetically more favorable. Our results further indicate that Au clusters in the SAM-Au interface are thermodynamically unstable and they will tend to dissolve, producing Au adatoms incorporated in the self-assembly in the form of CH 3 S-Au-SCH 3 species. This is due to the strong S-Au bond which stabilizes single Au adatoms in the self-assembly. Our results provide solid insight into the impact of adatom islands at the CH 3 S-Au interface.« less

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

DOE PAGES

Vukmirovic, Miomir B.; Teeluck, Krishani M.; Liu, Ping; ...

2017-08-08

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogenmore » oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.« less

Cooperativity of halogen, chalcogen, and pnictogen bonds in infinite molecular chains by electronic structure theory.

PubMed

George, Janine; Deringer, Volker L; Dronskowski, Richard

2014-05-01

Halogen bonds (XBs) are intriguing noncovalent interactions that are frequently being exploited for crystal engineering. Recently, similar bonding mechanisms have been proposed for adjacent main-group elements, and noncovalent "chalcogen bonds" and "pnictogen bonds" have been identified in crystal structures. A fundamental question, largely unresolved thus far, is how XBs and related contacts interact with each other in crystals; similar to hydrogen bonding, one might expect "cooperativity" (bonds amplifying each other), but evidence has been sparse. Here, we explore the crucial step from gas-phase oligomers to truly infinite chains by means of quantum chemical computations. A periodic density functional theory (DFT) framework allows us to address polymeric chains of molecules avoiding the dreaded "cluster effects" as well as the arbitrariness of defining a "large enough" cluster. We focus on three types of molecular chains that we cut from crystal structures; furthermore, we explore reasonable substitutional variants in silico. We find evidence of cooperativity in chains of halogen cyanides and also in similar chalcogen- and pnictogen-bonded systems; the bonds, in the most extreme cases, are amplified through cooperative effects by 79% (I···N), 90% (Te···N), and 103% (Sb···N). Two experimentally known organic crystals, albeit with similar atomic connectivity and XB characteristics, show signs of cooperativity in one case but not in another. Finally, no cooperativity is observed in alternating halogen/acetone and halogen/1,4-dioxane chains; in fact, these XBs weaken each other by up to 26% compared to the respective gas-phase dimers.

Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

Compositional effects on Si–OH bond length in hydrous silicates with implications for trends in the SiOH acidity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zarubin, Dmitri P., E-mail: dmitri.zarubin@mtu-net.ru

2014-04-01

Theoretical calculations of the structure and Brønsted acidity of SiOH groups in silica clusters have never addressed the question if these vary with the degree of SiOH deprotonation. In this connection, a statistical analysis is presented of Si–OH bond lengths in crystalline hydrogen silicates with well-determined structures with a special emphasis placed on effects of the silicate composition. It is found that among hydrogen silicates of large cations with low charges the Si–OH bonds are always longer than terminal Si–O bonds in the same anion and correlate in length with the anionic charge per tetrahedron. The findings are explained bymore » steric limitations on charge balancing at oxygen atoms by hydrogen bonds and/or cations. It is suggested that similar limitations and imbalances may underlie the well-known trends in the Brønsted acidity of silicic acids and silicas in aqueous media: decreased acidity with increased SiOH deprotonation and increased acidity with increased tetrahedra connectivity. - Graphical abstract: Si–OH bonds in crystalline silicates lengthen with the anionic charge per tetrahedron, which is in parallel with the well-known trend of decreased acidity of silicic acids and silicas in solution with increased degree of deprotonation. - Highlights: • Si–OH bonds in alkali hydrogen silicates are always longer than terminal Si–O bonds. • Si–OH bonds in silicates lengthen with the anionic charge per tetrahedron. • The Si–OH bond elongation results from inherent underbonding of terminal O atoms. • The longer the Si–OH bond, the less acidic the OH group is.« less

The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Xu, Jian; Huai, Ping; Deng, Huiqiu; Hu, Wangyu

2016-02-01

Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the HeN and HeNV1SIA1 clusters, the average length of He-He bonds shortens, but it elongates for the HeNV1 clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of HeNVM cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

Comparison of S-adsorption on (111) and (100) facets of Cu nanoclusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boschen, Jeffery S.; Lee, Jiyoung; Windus, Theresa L.

2016-10-31

In order to gain insight into the nature of chemical bonding of sulfur atoms on coinage metal surfaces, we compare the adsorption energy and structural parameters for sulfur at four-fold hollow (4fh) sites on (100) facets and at three-fold hollow (3fh) sites on (111) facets of Cu nanoclusters. Consistent results are obtained from localized atomic orbital and plane-wave based density functional theory using the same functionals. PBE and its hybrid counterpart (PBE0 or HSE06) also give similar results. 4fh sites are preferred over 3fh sites with stronger bonding by ~0.6 eV for nanocluster sizes above ~280 atoms. However, for smallermore » sizes there are strong variations in the binding strength and the extent of the binding site preference. In addition, we show that suitable averaging over clusters of different sizes, or smearing the occupancy of orbitals, provide useful strategies to aid assessment of the behavior in extended surface systems. From site-projected density of states analysis using the smearing technique, we show that S adsorbed on a 4fh site has similar bonding interactions with the substrate as that on a 3fh site, but with much weaker antibonding interactions.« less

Martensitic transformations in Ag-Au bimetallic core-shell nanoalloys

NASA Astrophysics Data System (ADS)

Chen, Fuyi; Johnston, Roy L.

2008-01-01

Combining the Gupta potential and bond order analysis in a molecular dynamics simulation, a martensitic transformation is observed in the 147-atom AucoreAgshell nanostructure at 328K. The response time for this transformation is about 7ps at 350K. In pure gold clusters, it was previously thought that a similar solid-to-solid transformation is a prelude to melting transitions. In the present case, atomic pathway snapshots show that the heating energy is used to overcome the energy barrier for initiating the spontaneous process. The subsequent twist-deformation propagation and termination are clearly observed.

On the nature of the {SO2-4}/{Ag(111) } and {SO2-4}/{Au(111) } surface bonding

NASA Astrophysics Data System (ADS)

Patrito, E. M.; Olivera, P. Paredes; Sellers, Harrell

1997-05-01

The nature of sulfate-Ag(111) and sulfate-Au(111) surface bonding has been investigated at the SCF + MP2 level of theory. Convergence of binding energy with cluster size is investigated and, unlike neutral adsorbates, large clusters are required in order to obtain reliable binding energies. In the most stable adsorption mode, sulfate binds to the surface via three oxygen atoms (C 3v symmetry) with a binding energy of 159.3 kcal/mol on Ag(111) and 143.9 kcal/mol on Au(111). The geometry of adsorbed sulfate was optimized at the SCF level. While the bond length between sulfur and the oxygens coordinated to the surface increases, the sulfur-uncoordinated oxygen bond length decreases. This weakening and strengthening of the bonds, respectively, is consistent with bond order conservation in adsorbates on metal surfaces. Although a charge transfer of 0.4 electrons towards the metal is observed, the adsorbate remains very much sulfate-like. The molecular orbital analysis indicates that there is also some charge back-donation towards unoccupied orbitals of sulfate. This results in an increased electron density around sulfur as revealed in the electron density difference maps. Analysis of the Laplacian of the charge density of free sulfate provides a suitable framework to understand the nature of the different charge transfer processes and allows us to establish some similarities with the CO- and SO 2-metal bondings.

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.

PubMed

Suga, Michihiro; Akita, Fusamichi; Sugahara, Michihiro; Kubo, Minoru; Nakajima, Yoshiki; Nakane, Takanori; Yamashita, Keitaro; Umena, Yasufumi; Nakabayashi, Makoto; Yamane, Takahiro; Nakano, Takamitsu; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Kimura, Tetsunari; Nomura, Takashi; Yonekura, Shinichiro; Yu, Long-Jiang; Sakamoto, Tomohiro; Motomura, Taiki; Chen, Jing-Hua; Kato, Yuki; Noguchi, Takumi; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Nango, Eriko; Tanaka, Rie; Naitow, Hisashi; Matsuura, Yoshinori; Yamashita, Ayumi; Yamamoto, Masaki; Nureki, Osamu; Yabashi, Makina; Ishikawa, Tetsuya; Iwata, So; Shen, Jian-Ren

2017-03-02

Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn 4 CaO 5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the Q B /non-haem iron and the Mn 4 CaO 5 cluster. The changes around the Q B /non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn 4 CaO 5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ 4 -oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.

Theoretical studies of large water clusters: (H2O)28, (H2O)29, (H2O)30, and (H2O)31 hexakaidecahedral structures

NASA Astrophysics Data System (ADS)

Khan, Arshad

1997-04-01

The 28, 29, 30, and 31 mer hexakaidecahedral water clusters were studied by applying the intermediate neglect of differential overlap self-consistent field restricted Hartree-Fock method (INDO SCF RHF) after parametrization for H and O atoms. The most stable 29 and 30 mer clusters have one and two water molecules, respectively within the cavity of the distorted hexakaidecahedral cage with stabilization energy/monomer values of around 10.9 and 11.0 kcal, respectively. The 31 mer cluster with three water molecules within the cavity is less stable than the isomer with two molecules within the cavity and the third one bonded outside of the cage by around 3 kcal/mol.

Interaction of TGA with CdSe nanoparticles

NASA Astrophysics Data System (ADS)

Bharti, Shivani; Singh, Satvinder; Jain, Shikshita; Kaur, Gurvir; Gupta, Shikha; Tripathi, S. K.

2018-05-01

In this paper, the interaction of thioglycolic acid (TGA) with CdSe atomic cluster have been studied using first principle calculations and experimentally synthesized using chemical route method. Density Functional Theory (DFT) have been used for all the calculations. Structural and electronic properties have been studied theorectically and results have been compared to the experimentally obtained micrographs from TEM microscopy. The most stable interaction of CdSe cluster is obtained with thiol group of TGA due to the high bond dissiciation energy between Cd-S than Cd-O. Theoretical calculations have been performed using Gaussian basis set approach.

Rapid reversible borane to boryl hydride exchange by metal shuttling on the carborane cluster surface† †Electronic supplementary information (ESI) available. CCDC 1545735 and 1545736. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01846k

PubMed Central

Eleazer, Bennett J.; Smith, Mark D.

2017-01-01

In this work, we introduce a novel concept of a borane group vicinal to a metal boryl bond acting as a supporting hemilabile ligand in exohedrally metalated three-dimensional carborane clusters. The (POBOP)Ru(Cl)(PPh3) pincer complex (POBOP = 1,7-OP(i-Pr)2-m-2-carboranyl) features extreme distortion of the two-center-two-electron Ru–B bond due to the presence of a strong three-center-two-electron B–H···Ru vicinal interaction. Replacement of the chloride ligand with a hydride afforded the (POBOP)Ru(H)(PPh3) pincer complex, which possesses B–Ru, B–H···Ru, and Ru–H bonds. This complex was found to exhibit a rapid exchange between hydrogen atoms of the borane and the terminal hydride through metal center shuttling between two boron atoms of the carborane cage. This exchange process, which involves sequential cleavage and formation of strong covalent metal–boron and metal–hydrogen bonds, is unexpectedly facile at temperatures above –50 °C corresponding to an activation barrier of 12.2 kcal mol–1. Theoretical calculations suggested two equally probable pathways for the exchange process through formally Ru(0) or Ru(iv) intermediates, respectively. The presence of this hemilabile vicinal B–H···Ru interaction in (POBOP)Ru(H)(PPh3) was found to stabilize a latent coordination site at the metal center promoting efficient catalytic transfer dehydrogenation of cyclooctane under nitrogen and air at 170 °C. PMID:28970919

Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

PubMed

Neumann, Piotr; Tittmann, Kai

2014-12-01

Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Destructive Clustering of Metal Nanoparticles in Chalcogenide and Oxide Glassy Matrices.

PubMed

Shpotyuk, M V; Shpotyuk, O I; Cebulski, J; Kozyukhin, S

2016-12-01

The energetic χ-criterion is developed to parameterize difference in the origin of high-order optical non-linearity associated with metallic atoms (Cu, Ag, Au) embedded destructively in oxide- and chalcogenide glasses. Within this approach, it is unambiguously proved that covalent-bonded networks of soft semiconductor chalcogenides exemplified by binary As(Ge)-S(Se) glasses differ essentially from those typical for hard dielectric oxides like vitreous silica by impossibility to accommodate pure agglomerates of metallic nanoparticles. In an excellence according to known experimental data, it is suggested that destructive clustering of nanoparticles is possible in Cu-, Ag-, and Au-ion-implanted dielectric oxide glass media, possessing a strongly negative χ-criterion. Some recent speculations trying to ascribe equally this ability to soft chalcogenide glasses despite an obvious difference in the corresponding bond dissociation energies have been disclosed and criticized as inconclusive.

The structural study of acetohydroxamic and oxalodihydroxamic acids in DMSO solution based on the DFT calculations of NMR spectra

NASA Astrophysics Data System (ADS)

Kaczor, Agnieszka; Proniewicz, Leonard M.

2004-10-01

The 1H and 13C NMR spectra of acetohydroxamic (aha) and oxalodihydroxamic (oxha) acids were measured in DMSO- d6 solution. The atoms chemical shifts of chosen stable entgegen and zusammen conformers of monomeric acids were computed along with some clusters of the compounds with the solvent molecules [B3LYP/6-311++G(d,p), GIAO]. The latter were proposed to explain the differences between the theoretical and experimental resonances of the protons of the N-H and O-H groups. The computed chemical shifts of aha-(DMSO) 2 and oxha-(DMSO) 2 models are in good agreement with experimental data proving that the compounds existing in solution form aggregates with DMSO. The acids are H-bonded via all the labile protons to the oxygen atoms of the solvent molecules. aha exists in the zusammen and entgegen (relative to C-N bond) forms with the relative intensities of 8:1 while the sole z, E, z-conformers (notation refers to C-N, C-C and C-N bonds, respectively) were found for oxha.

Formation rates, stability and reactivity of sulfuric acid - amine clusters predicted by computational chemistry

NASA Astrophysics Data System (ADS)

Kurtén, Theo; Ortega, Ismael; Kupiainen, Oona; Olenius, Tinja; Loukonen, Ville; Reiman, Heidi; McGrath, Matthew; Vehkamäki, Hanna

2013-04-01

Despite the importance of atmospheric particle formation for both climate and air quality, both experiments and non-empirical models using e.g. sulfuric acid, ammonia and water as condensing vapors have so far been unable to reproduce atmospheric observations using realistic trace gas concentrations. Recent experimental and theoretical evidence has shown that this mystery is likely resolved by amines. Combining first-principles evaporation rates for sulfuric acid - dimethylamine clusters with cluster kinetic modeling, we show that even sub-ppt concentrations of amines, together with atmospherically realistic concentrations of sulfuric acid, result in formation rates close to those observed in the atmosphere. Our simulated cluster formation rates are also close to, though somewhat larger than, those measured at the CLOUD experiment in CERN for both sulfuric acid - ammonia and sulfuric acid - dimethylamine systems. A sensitivity analysis indicates that the remaining discrepancy for the sulfuric acid - amine particle formation rates is likely caused by steric hindrances to cluster formation (due to alkyl groups of the amine molecules) rather than by significant errors in the evaporation rates. First-principles molecular dynamic and reaction kinetic modeling shed further light on the microscopic physics and chemistry of sulfuric acid - amine clusters. For example, while the number and type of hydrogen bonds in the clusters typically reach their equilibrium values on a picosecond timescale, and the overall bonding patterns predicted by traditional "static" quantum chemical calculations seem to be stable, the individual atoms participating in the hydrogen bonds continuously change at atmospherically realistic temperatures. From a chemical reactivity perspective, we have also discovered a surprising phenomenon: clustering with sulfuric acid molecules slightly increases the activation energy required for the abstraction of alkyl hydrogens from amine molecules. This implies that the oxidation rate of amines by OH and possibly other oxidants may be decreased by clustering, thus prolonging the chemical lifetime of amines in the air.

Tantalum induced butterfly-like clusters on Si (111)-7 × 7 surface: STM/STS study at low coverage

NASA Astrophysics Data System (ADS)

Shukrynau, Pavel; Mutombo, Pingo; Švec, Martin; Hietschold, Michael; Cháb, Vladimír

2012-02-01

The adsorption of the small amounts of tantalum on Si (111)-7 × 7 reconstructed surface is investigated systematically using scanning tunneling microscopy and tunneling spectroscopy combined with first-principles density functional theory calculations. We find out that the moderate annealing of the Ta covered surface results in the formation of clusters of the butterfly-like shape. The clusters are sporadically distributed over the surface and their density is metal coverage dependent. Filled and empty state STM images of the clusters differ strongly suggesting the existence of covalent bonds within the cluster. Tunneling spectroscopy measurements reveal small energy gap, showing semiconductor-like behavior of the constituent atoms. The cluster model based on experimental images and theoretical calculations has been proposed and discussed. Presented results show that Ta joins the family of adsorbates, that are known to form magic clusters on Si (111)-7 × 7, but its magic cluster has the structural and electronic properties that are different from those reported before.

An Investigation of Armenite, BaCa2Al6Si9O302H2O.H2O Molecules and H Bonding in Microporous Silicates

NASA Astrophysics Data System (ADS)

Geiger, C. A.; Gatta, G.; Xue, X.; McIntyre, G.

2012-12-01

The crystal chemistry of armenite, ideally BaCa2Al6Si9O30.2H2O, a double-ring structure belonging to the milarite group, was studied to better understand the nature of extra-framework "Ca-oxygen-anion-H2O-molecule quasi-clusters" and H bonding behavior in microporous silicates. Neutron and X-ray single-crystal diffraction and IR powder and 1H NMR spectroscopic measurements were made. Four crystallographically independent Ca and H2O molecule sites were refined from the diffraction data, whereby both sites appear to have partial occupancies such that locally a Ca atom can have only a single H2O molecule bonded to it through an ion-dipole interaction. The Ca cation is further bonded to six O atoms of the framework forming a quasi cluster around it. The neutron results give the first static description of the protons in armenite, allowing bond distances and angles relating to the H2O molecules and H bonds to be determined. The IR spectrum of armenite is characterized in the OH-stretching region at RT by two broad bands at roughly 3470 and 3410 cm-1 and by a single H2O bending mode at 1654 cm-1. At 10 K four intense OH bands are located at 3479, 3454, 3401 and 3384 cm-1 and two H2O bending modes at 1650 and 1606 cm-1. The 1H MAS NMR spectrum shows a single strong resonance near 5.3 ppm and a smaller one near 2.7 ppm. The former can be assigned to H2O molecules bonded to Ca and the latter to weakly bonded H2O located at a site at the center of the structural double ring and it is partially occupied. The nature of H bonding in the microporous Ca-bearing zeolites scolecite, wairakite and epistilbite are also analyzed. The average OH stretching wavenumber shown by the IR spectra of armenite (~3435 cm-1) and scolecite (~3430 cm-1) are similar, while the average OH wavenumbers for wairakite (~3475 cm-1) and epistilbite (~3500 cm-1) are greater. In all cases the average OH stretching wavenumber is more similar to that of liquid water (~3400 cm-1) than of ice (~3220 cm-1). The strength of hydrogen bonding of the H2O molecules in microporous silicates does not appear to change greatly with decreasing temperatures from 300 K down to 10 K. The reason for this and also understanding better the ion-dipole interaction and its effect on H-bonding strength in Ca-quasi clusters need further study. The crystal structure of armenite viewed down [001] and [010].

Rutile-Deposited Pt–Pd clusters: A Hypothesis Regarding the Stability at 50/50 Ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ha, Mai-Anh; Dadras, Mostafa J.; Alexandrova, Anastassia N.

2014-10-03

Mixed Pt–Pd clusters deposited on oxides have been of great interest to catalysis. Clusters containing Pt and Pd in roughly equal proportions were found to be unusually stable against sintering, one of the major mechanisms of catalyst deactivation. After aging of such catalysts, the 50/50 Pt–Pd and Pd–O clusters appeared to be the two most prevalent phases. The reason for the enhanced stability of these equally proportioned clusters has remained unclear. In the following, sintering of mixed Pt–Pd clusters on TiO2(110) for various initial atomic concentrations of Pt and Pd and at a range of catalytically relevant temperatures was simulated.more » It is confirmed that equally mixed clusters have the relatively highest survival rate. Surprisingly, subnanoclusters containing Pt and Pd in all proportions have very similar geometries and chemical bonding, revealing no apparent explanation for favoring the 1:1 Pt/Pd ratio. However, it was discovered that at high temperatures, the 50/50 clusters have considerably more thermally accessible isomers than clusters containing Pt and Pd in other proportions. Hence, one of the reasons for stability is entropic stabilization. Electrostatics also plays a key role as a subtle charge redistribution, and a shift of electron density to the slightly more electronegative Pt results in the partially charged atoms being further stabilized by intracluster Coulomb attraction; this effect is greatest for 1:1 mixtures.« less

The role of highly oxygenated molecules (HOMs) in determining the composition of ambient ions in the boreal forest

NASA Astrophysics Data System (ADS)

Bianchi, Federico; Garmash, Olga; He, Xucheng; Yan, Chao; Iyer, Siddharth; Rosendahl, Ida; Xu, Zhengning; Rissanen, Matti P.; Riva, Matthieu; Taipale, Risto; Sarnela, Nina; Petäjä, Tuukka; Worsnop, Douglas R.; Kulmala, Markku; Ehn, Mikael; Junninen, Heikki

2017-11-01

In order to investigate the negative ions in the boreal forest we have performed measurements to chemically characterise the composition of negatively charged clusters containing highly oxygenated molecules (HOMs). Additionally, we compared this information with the chemical composition of the neutral gas-phase molecules detected in the ambient atmosphere during the same period. The chemical composition of the ions was retrieved using an atmospheric pressure interface time-of-flight mass spectrometer (APi-TOF-MS) while the gas-phase neutral molecules (mainly sulfuric acid and HOMs) were characterised using the same mass spectrometer coupled to a nitrate-based chemical ionisation unit (CI-APi-TOF). Overall, we divided the identified HOMs in two classes: HOMs containing only carbon, hydrogen and oxygen and nitrogen-containing HOMs or organonitrates (ONs). During the day, among the ions, in addition to the well-known pure sulfuric acid clusters, we found a large number of HOMs clustered with nitrate (NO3-) or bisulfate (HSO4-), with the first one being more abundant. During the night, the distribution of ions, mainly composed of HOM clustered with NO3-, was very similar to the neutral compounds that are detected in the CI-APi-TOF as adducts with the artificially introduced primary ion (NO3-). For the first time, we identified several clusters containing up to 40 carbon atoms. These ions are formed by up to four oxidised α-pinene units clustered with NO3-. While we know that dimers (16-20 carbon atoms) are probably formed by a covalent bond between two α-pinene oxidised units, it is still unclear what bonding formed larger clusters. Finally, diurnal profiles of the negative ions were consistent with the neutral compounds revealing that ONs peak during the day while HOMs are more abundant at night-time. However, during the day, a large fraction of the negative charge is taken up by the pure sulfuric acid clusters causing differences between ambient ions and neutral compounds (i.e. less available charge for HOM and ON).

Formation of C-C and C-O bonds and oxygen removal in reactions of alkanediols, alkanols, and alkanals on copper catalysts.

PubMed

Sad, María E; Neurock, Matthew; Iglesia, Enrique

2011-12-21

This study reports evidence for catalytic deoxygenation of alkanols, alkanals, and alkanediols on dispersed Cu clusters with minimal use of external H(2) and with the concurrent formation of new C-C and C-O bonds. These catalysts selectively remove O-atoms from these oxygenates as CO or CO(2) through decarbonylation or decarboxylation routes, respectively, that use C-atoms present within reactants or as H(2)O using H(2) added or formed in situ from CO/H(2)O mixtures via water-gas shift. Cu catalysts fully convert 1,3-propanediol to equilibrated propanol-propanal intermediates that subsequently form larger oxygenates via aldol-type condensation and esterification routes without detectable involvement of the oxide supports. Propanal-propanol-H(2) equilibration is mediated by their chemisorption and interconversion at surfaces via C-H and O-H activation and propoxide intermediates. The kinetic effects of H(2), propanal, and propanol pressures on turnover rates, taken together with measured selectivities and the established chemical events for base-catalyzed condensation and esterification reactions, indicate that both reactions involve kinetically relevant bimolecular steps in which propoxide species, acting as the base, abstract the α-hydrogen in adsorbed propanal (condensation) or attack the electrophilic C-atom at its carbonyl group (esterification). These weakly held basic alkoxides render Cu surfaces able to mediate C-C and C-O formation reactions typically catalyzed by basic sites inherent in the catalyst, instead of provided by coadsorbed organic moieties. Turnover rates for condensation and esterification reactions decrease with increasing Cu dispersion, because low-coordination corner and edge atoms prevalent on small clusters stabilize adsorbed intermediates and increase the activation barriers for the bimolecular kinetically relevant steps required for both reactions. © 2011 American Chemical Society

Bonded Radii and the Contraction of the Electron Density of the Oxygen Atom by Bonded Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2013-02-21

The bonded radii for more than 550 bonded pairs of atoms, comprising more than 50 crystals, determined from experimental and theoretical electron density distributions, are compared with the effective ionic, ri(M), and crystal radii, rc(M), for metal atoms, M, bonded to O atoms. At odds with the fixed ionic radius of 1.40 Å, assumed for the O atom in the compilation of the ionic radii, the bonded radius for the atom, rb(O), is not fixed but displays a relatively wide range of values as the O atom is progressively polarized by the M-O bonded interactions: as such, rb(O) decreases systematicallymore » from 1.40 Å (the Pauling radius of the oxide anion) as bond lengths decrease when bonded to an electropositive atom like sodium, to 0.64 Å (Bragg’s atomic radius of the O atom) when bonded to an electronegative atom like nitrogen. Both rb(M) and rb(O) increase in tandum with the increasing coordination number of the M atom. The bonded radii of the M atoms are highly correlated with both ri(M) and rc(M), but they both depart systematically from rb(M) and become smaller as the electronegativity of the M atom increases and the M-O bond length decreases. The well-developed correlations between both sets of radii and rb(M) testifies to the relative precision of both sets of radii and the fact that both sets are highly correlated the M-O bond 1 lengths. On the other hand, the progressive departure of rb(O) from the fixed ionic radius of the O atom with the increasing electronegativity of the bonded M atom indicates that any compilation of sets of ionic radii, assuming that the radius for the oxygen atom is fixed in value, is problematical and impacts on the accuracy of the resulting sets of ionic and crystal radii thus compiled. The assumption of a fixed O atom radius not only results in a negative ionic radii for several atoms, but it also results in values of rb(M) that are much as ~ 0.6 Å larger than the ri(M) and rc(M) values, respectively, particularly for the more electronegative M atoms. On the other hand, the ionic radii are in closer agreement with rb(M) for the more electropositive atoms. Notwithstanding that ionic radii are typically smaller than bonded radii, particularly for the more electronegative atoms, they have been used with considerable success in understanding and rationalizing problems and properties in crystal chemistry primarily because both ionic and crystal radii are highly correlated on a one-to-one basis with both the bonded radii and the associated M-O bond lengths. The lack of agreement between the effective ionic and crystal radii and the bonded radii for the more shared bonded interactions is ascribed to the progressive increase in the polarization of the O atom by the bonded atoms with a concomitant decrease in its radius, a factor that was neglected in the compilation of ionic and crystal radii for fluorides, oxides, sulfides and nitrides. This accounts for ionic radii for these materials being smaller than the bonded radii for the more electronegative atoms.« less

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

Structural and electronic properties of copper-doped chalcogenide glasses

NASA Astrophysics Data System (ADS)

Guzman, David M.; Strachan, Alejandro

2017-10-01

Using ab initio molecular dynamics based on density functional theory, we study the atomic and electronic structure, and transport properties of copper-doped germanium-based chalcogenide glasses. These mixed ionic-electronic conductor materials exhibit resistance or threshold switching under external electric field depending on slight variations of chemical composition. Understanding the origin of the transport character is essential for the functionalization of glassy chalcogenides for nanoelectronics applications. To this end, we generated atomic structures for GeX3 and GeX6 (X = S, Se, Te) at different copper concentrations and characterized the atomic origin of electronic states responsible for transport and the tendency of copper clustering as a function of metal concentration. Our results show that copper dissolution energies explain the tendency of copper to agglomerate in telluride glasses, consistent with filamentary conduction. In contrast, copper is less prone to cluster in sulfides and selenides leading to hysteresisless threshold switching where the nature of transport is dominated by electronic midgap defects derived from polar chalcogen bonds and copper atoms. Simulated I -V curves show that at least 35% by weight of copper is required to achieve the current demands of threshold-based devices for memory applications.

Global optimization of small bimetallic Pd-Co binary nanoalloy clusters: a genetic algorithm approach at the DFT level.

PubMed

Aslan, Mikail; Davis, Jack B A; Johnston, Roy L

2016-03-07

The global optimisation of small bimetallic PdCo binary nanoalloys are systematically investigated using the Birmingham Cluster Genetic Algorithm (BCGA). The effect of size and composition on the structures, stability, magnetic and electronic properties including the binding energies, second finite difference energies and mixing energies of Pd-Co binary nanoalloys are discussed. A detailed analysis of Pd-Co structural motifs and segregation effects is also presented. The maximal mixing energy corresponds to Pd atom compositions for which the number of mixed Pd-Co bonds is maximised. Global minimum clusters are distinguished from transition states by vibrational frequency analysis. HOMO-LUMO gap, electric dipole moment and vibrational frequency analyses are made to enable correlation with future experiments.

Photochemistry of 1- and 2-Naphthols and Their Water Clusters: The Role of 1 ππ*(La ) Mediated Hydrogen Transfer to Carbon Atoms.

PubMed

Novak, Jurica; Prlj, Antonio; Basarić, Nikola; Corminboeuf, Clémence; Došlić, Nađa

2017-06-16

The computational analysis of the isomer- and conformer-dependent photochemistry of 1- and 2-naphthols and their microsolvated water clusters is motivated by their very different excited state reactivities. We present evidence that 1- and 2-naphthol follow distinct excited state deactivation pathways. The deactivation of 2-naphthols, 2-naphthol water clusters, as well as of the anti conformer of 1-naphthol is mediated by the optically dark 1 πσ* state. The dynamics of the 1 πσ* surface leads to the homolytic cleavage of the OH bond. On the contrary, the excited state deactivation of syn 1-naphthol and 1-naphthol water clusters follows an uncommon reaction pathway. Upon excitation to the bright 1 ππ*(L a ) state, a highly specific excited state hydrogen transfer (ESHT) to carbon atoms C8 and C5 takes place, yielding 1,8- and 1,5-naphthoquinone methides. The ESHT pathway arises from the intrinsic electronic properties of the 1 ππ*(L a ) state of 1-naphthols. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trends in hydrogen chemisorption on transition metals

NASA Astrophysics Data System (ADS)

Muscat, J. P.

1981-10-01

A systematic study of H adsorption on the close-packed surfaces of the transition metals in the 3d and 4d series is presented. The effect of the TM d band on the chemisorption bond is investigated, by embedding a cluster of TM muffin tins at the surface of an effective jellium-like medium. It is found that the broad and incomplete H/jellium resonance is narrowed, shifted down and made to contain more electrons as a result of hybridization with the TM d states. These effects are larger in the case of the 4d metals, thus indicating a greater participation in the chemisorption bond of the d electrons for these metals than for the 3d metals. Calculation of one-electron energy differences on going from the H on jellium system to that of H on the TM cluster are presented. Trends for the one-electron energy differences are compared to trends in experimental chemisorption energy. H adsorption in the three-fold hollow site with no secondlayer TM atom below the H site is favoured for the hcp metals, while no discernible preference between the two hollow sites is recorded for the fcc metals, with the exception of Rh where the site with no second-layer TM atom below is preferred.

A Triatomic Silicon(0) Cluster Stabilized by a Cyclic Alkyl(amino) Carbene.

PubMed

Mondal, Kartik Chandra; Roy, Sudipta; Dittrich, Birger; Andrada, Diego M; Frenking, Gernot; Roesky, Herbert W

2016-02-24

Reduction of the neutral carbene tetrachlorosilane adduct (cAAC)SiCl4 (cAAC=cyclic alkyl(amino) carbene :C(CMe2)2 (CH2)N(2,6-iPr2C6H3) with potassium graphite produces stable (cAAC)3Si3, a carbene-stabilized triatomic silicon(0) molecule. The Si-Si bond lengths in (cAAC)3Si3 are 2.399(8), 2.369(8) and 2.398(8) Å, which are in the range of Si-Si single bonds. Each trigonal pyramidal silicon atom of the triangular molecule (cAAC)3Si3 possesses a lone pair of electrons. Its bonding, stability, and electron density distributions were studied by quantum chemical calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lam, Royce K.; Smith, Jacob W.; Saykally, Richard J., E-mail: saykally@berkeley.edu

While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure.more » The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility.« less

Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

NASA Astrophysics Data System (ADS)

Hamid, Ahmed M.; El-Shall, M. Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G.

2014-08-01

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N+.(HCN)n and C4H4N2+.(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH+(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CHδ+⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH+⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH+⋯NCH..NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CHδ+⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CHδ+⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CHδ+ centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

Unconventional hydrogen bonding to organic ions in the gas phase: stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine.

PubMed

Hamid, Ahmed M; El-Shall, M Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G

2014-08-07

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N(+·)(HCN)n and C4H4N2 (+·)(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH(+)(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH(δ+)⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH(+)⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH(+)⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH(δ+)⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CH(δ+)⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH(δ+) centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

Ion collision-induced chemistry in pure and mixed loosely bound clusters of coronene and C60 molecules.

PubMed

Domaracka, Alicja; Delaunay, Rudy; Mika, Arkadiusz; Gatchell, Michael; Zettergren, Henning; Cederquist, Henrik; Rousseau, Patrick; Huber, Bernd A

2018-05-23

Ionization, fragmentation and molecular growth have been studied in collisions of 22.5 keV He2+- or 3 keV Ar+-projectiles with pure loosely bound clusters of coronene (C24H12) molecules or with loosely bound mixed C60-C24H12 clusters by using mass spectrometry. The heavier and slower Ar+ projectiles induce prompt knockout-fragmentation - C- and/or H-losses - from individual molecules and highly efficient secondary molecular growth reactions before the clusters disintegrate on picosecond timescales. The lighter and faster He2+ projectiles have a higher charge and the main reactions are then ionization by ions that are not penetrating the clusters. This leads mostly to cluster fragmentation without molecular growth. However, here penetrating collisions may also lead to molecular growth but to a much smaller extent than with 3 keV Ar+. Here we present fragmentation and molecular growth mass distributions with 1 mass unit resolution, which reveals that the same numbers of C- and H-atoms often participate in the formation and breaking of covalent bonds inside the clusters. We find that masses close to those with integer numbers of intact coronene molecules, or with integer numbers of both intact coronene and C60 molecules, are formed where often one or several H-atoms are missing or have been added on. We also find that super-hydrogenated coronene is formed inside the clusters.

Crystal structure of tetra-kis-(μ3-2-{[1,1-bis-(hy-droxy-meth-yl)-2-oxidoeth-yl]imino-meth-yl}-6-meth-oxy-phenolato)tetra-kis-[aqua-copper(II)]: a redetermination at 200 K.

PubMed

Buvaylo, Elena A; Vassilyeva, Olga Yu; Skelton, Brian W

2015-10-01

The crystal structure of the tetra-nuclear title compound, [Cu4(C12H15NO5)4(H2O)4], has been previously reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem. (2015), 641, 941-947], based on room-temperature data. In the previously published structure, no standard uncertainties are recorded for the deprotonated hy-droxy-methyl group and water mol-ecule O atoms coordinating to the metal atom indicating that they were not refined; furthermore, the H atoms of some OH groups and water mol-ecules have not been positioned accurately. Since the current structure was determined at a lower temperature, all atoms, including the H atoms of these hy-droxy groups and the water mol-ecule, have been determined more accurately resulting in improved standard uncertainties in the bond lengths and angles. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. In addition, it is now possible to report intra- and inter-molecular O-H⋯O inter-actions. In the title complex molecule, which has crystallographic -4 symmetry, the Cu(II) ions are coordinated by the tridentate Schiff base ligands and water mol-ecules, forming a tetra-nuclear Cu4O4 cubane-like core. The Cu(II) ion adopts a CuNO5 elongated octa-hedral environment. The coordination environment of Cu(II) at 200 K displays a small contraction of the Cu-N/O bonds, compared with the room-temperature structure. In the crystal lattice, the neutral clusters are linked by inter-molecular O-H⋯O hydrogen bonds into a one-dimensional hydrogen-bonding network propagating along the b axis.

Facile synthesis of novel two- and three-dimensional coordination polymers containing dialkyltin phosphonate-based tri/tetra-nuclear clusters with appended sulfonate groups.

PubMed

Shankar, Ravi; Jain, Archana; Singh, Atul Pratap; Kociok-Köhn, Gabriele; Molloy, Kieran C

2009-04-20

The coordination-driven self-assemblies of mixed-ligand dialkyltin derivatives, [(Et(2)Sn)(4) (O(2)P(OH)Me)(2)(O(3)PMe)(2)(OSO(2)Et)(2) x 2 H(2)O](n) 1, [(Et(2)Sn)(3)(O(3)PMe)(2)(OSO(2)Me)(2) x CHCl(3)](n) 2, and [(Me(2)Sn)(3)(O(3)PBu(t))(2)(OSO(2)Me)(2) x 2 CHCl(3)](n) 3 have been achieved by reacting the tin precursors, [R(2)Sn(OR(1))(OSO(2)R(1))](n) (R = Et, R(1) = Et (1a), Me (2a); R = Me, R(1) = Me (3a)) with an equimolar amount of methylphosphonic/t-butylphosphonic acid under mild conditions (rt, 8 h, CH(2)Cl(2)). These have been characterized by IR and multinuclear ((1)H, (13)C, (31)P, and (119)Sn) NMR spectroscopy as well as single crystal X-ray diffraction. The asymmetric unit of 1 is composed of a tetranuclear, Sn(4)(mu(2)-PO(2))(2)(mu(3)-PO(3))(2) core bearing an appended ethanesulfonate group on each terminal tin (Sn2) atom and two P(OH)...O hydrogen bonded water molecules. The ladder-like structural motif thus formed is extended into one-dimensional polymeric chains by virtue of bridging bidentate mode of the sulfonate groups. These chains are linked by O-H...O(S) hydrogen bonds involving H(2)O molecules and oxygen atoms of the sulfonate groups. The asymmetric units of 2 and 3 are composed of trinuclear tin clusters with a Sn(3)(mu(3)-PO(3))(2) core and two dangling methanesulfonate groups which are covalently bonded to the tin centers. The construction of three-dimensional self-assemblies is effected by variable bonding modes (mu(2), mu(3) in 2; mu(2) in 3) of the methanesulfonate groups. Both the structural motifs possess five- and six-coordinated tin atoms and form rectangular channels which are occupied by CHCl(3) molecules.

Computational quest for spherical C12B68 fullerenes with "magic" π-electrons and quasi-planar tetra-coordinated carbon.

PubMed

Li, Fengyu; Jiang, De-en; Chen, Zhongfang

2014-02-01

Inspired by the exciting properties of B80 clusters and the novel chemical bonding of planar tetra-coordinated carbon (ptC), we computationally investigated C12B68 clusters by substituting 12 boron atoms to 12 carbon in the B80 framework. Three types of C12B68 configurations, namely core-shell, boron-trapped and fullerene-like, were examined. The fullerene-like C12B68 clusters are featured with multiple quasi-planar tetra-coordinated carbon moieties; though with "magic" (72) number of electrons, they are not highly aromatic due to the limitations of Hirsch's rule for clusters with more than 50 π electrons. These C12B68 fullerenes are not global minima, but the appreciable HOMO-LUMO gaps, spherical aromaticity, and the thermal stability indicate their reasonable stabilities.

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Insights into the crystal chemistry of Earth materials rendered by electron density distributions: Pauling's rules revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-05-20

Pauling's first two rules are examined in terms of the accumulation of the electron density between bonded pairs of atoms for a relatively large number of oxide and silicate crystals and siloxane molecules. The distribution of the electron density shows that the radius of the oxygen atom is not fixed, but that it actually decreases systematically from ~1.40 Å to ~ 0.65 Å as the polarizing power and the electronegativity of the bonded metal atoms increase and the distribution of the O atom is progressively polarized and contracted along the bond vectors by the impact of the bonded interactions. Themore » contractions result in an aspherical oxygen atom that displays as many different bonded “radii” as it has bonded interactions. The bonded radii for the metal atoms match the Shannon and Prewitt ionic radii for the more electropositive atoms like potassium and sodium, but they are systematically larger for the more electronegative atoms like aluminum, silicon and phosphorous. Pauling's first rule is based on the assumption that the radius of the oxide anion is fixed and that the radii of the cations are such that radius sum of the spherical oxide anion and a cation necessarily equals the separation between the cation-anion bonded pair with the coordination number of the cation being determined by the ratio of the radii of the cation and anion. In the case of the bonded radii, the sum of the bonded radii for the metal atoms and the oxide anion necessarily equals the bond lengths by virtue of the way that the bonded radii were determined in the partitioning of the electron density along the bond path into metal and O atom parts. But, the radius ratio for the O and M atoms is an unsatisfactory rule for determining the coordination number of the metal atom inasmuch as a bonded O atom is not, in general, spherical, and its size varies substantially along its bonded directions. But by counting the number of bond paths that radiate from a bonded atom, the coordination number of the atom is determined uniquely independent of the asphericity and sizes of the atom. A power law connection established between the bond lengths and bond strengths for crystals and molecules is mirrored by a comparable power law connection between bond length and the accumulation of the electron density between bonded pairs of atoms, a connection that is consistent with Pauling's electroneutrality postulate that the charges of the atoms in an oxide are negligibly small. The connection indicates that a one-to-one correspondence exists between the accumulation between a pair of bonded atoms and the Pauling bond strength for M-O bonded interaction for all atoms of the periodic table. The connection provides a common basis for understanding the success of the manifold applications that have been made with the bond valence theory model together with the modeling of crystal structures, chemical zoning, leaching and cation transport in batteries and the like. We believe that the wide spread applications of the model in mineralogy and material science owes much of its success to the direct connection between bond strength and the quantum mechanical observable, the electron density distribution. Comparable power law expressions established for the bonded interactions for both crystals and molecules support Pauling's assertion that his second rule has significance for molecules as well as for crystals. A simple expression is found that provides a one to one connection between the accumulation of the electron density between bonded M and O atoms and the Pauling bond strength for all M atoms of the periodic table with ~ 95 % of the variation of the bond strength being explained in terms of a linear dependence on the accumulated electron density. Compelling evidence is presented that supports the argument that the Si-O bonded interactions for tiny siloxane molecules and silicate crystals are chemically equivalent.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan, T.R.

The cyclo-addition of two Mo/sub 2/Cl/sub 4/(P(C/sub 6/H/sub 5/)/sub 3/)/sub 2/(CH/sub 3/OH)/sub 2/ molecules has produced a new type of tetrameric molybdenum cluster, Mo/sub 4/Cl/sub 8/L/sub 4/. Structural characterization of this dimer revealed weak molybdenum-methanol bonding which was consistent with the observed reactivity of the compound. New synthetic methods were devised for the preparation of Mo/sub 4/X/sub 8/L/sub 4/ clusters where X = Cl, Br, I, and L = PR/sub 3/, PO/sub 3/, RCN, CH/sub 3/OH. A scheme for the metal-metal bonding in these clusters was presented which was in agreement with the known structural features of Mo/sub 4/Cl/sub 8/(PR/submore » 3/)/sub 4/, R = C/sub 2/H/sub 5/, n-C/sub 4/H/sub 9/. The preparation of the analogous W/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/ cluster from WCl/sub 4/ was accomplished by application of techniques used in the molybdenum syntheses. The single crystal x-ray structure revealed slight differences from the molybdenum analog which were rationalized in terms of the known behavior in dimeric tungsten and molybdenum species. The attempted preparation of a tetrameric tungsten cluster from W/sub 2/(mhp)/sub 4/ was unsuccessful (mhp = anion of 2-methyl-6-hydroxypyridine). Instead, the new tungsten dimer, W/sub 2/Cl/sub 2/(mhp)/sub 3/, was isolated which possessed a metal-metal bond order of 3.5. The x-ray crystal structure of the dimer revealed that the chlorine atoms was situated cis, one bound to each tungsten. Cyclic voltammetry showed that the compound could be reversibly reduced, presumably to a W/sub 2//sup 4 +/ dimer containing a quadruple metal-metal bond.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan, T.R.

The cyclo-addition of two Mo/sub 2/Cl/sub 4/(P(C/sub 6/H/sub 5/)/sub 3/)/sub 2/(CH/sub 3/OH)/sub 2/ molecules has produced a new type of tetrameric molybdenum cluster, Mo/sub 4/Cl/sub 8/L/sub 4/. Structural characterization of this dimer revealed weak molybdenum-methanol bonding which was consistent with the observed reactivity of the compound. New synthetic methods were devised for the preparation of Mo/sub 4/X/sub 8/L/sub 4/ clusters where X = Cl, Br, I and L = PR/sub 3/, Po/sub 3/, RCN, CH/sub 3/OH. A scheme for the metal-metal bonding in these clusters was presented which was in agreement with the known structural features of Mo/sub 4/Cl/sub 8/(PR/submore » 3/)/sub 4/, R = C/sub 2/H/sub 5/, n-C/sub 4/H/sub 9/. The preparation of the analogous W/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/ cluster from WCl/sub 4/ was accomplished by application of techniques used in the molybdenum syntheses. The single crystal x-ray structure revealed slight differences from the molybdenum analog which were rationalized in terms of the known behavior in dimeric tungsten and molybdenum species. The attempted preparation of a tetrameric tungsten cluster from W/sub 2/(mhp)/sub 4/ was unsuccessful (mhp = anion of 2-methyl-6-hydroxypyridine). Instead, the new tungsten dimer, W/sub 2/Cl/sub 2/(mhp)/sub 3/, was isolated which possessed a metal-metal bond order of 3.5. The x-ray crystal structure of the dimer revealed that the chlorine atoms were situated cis, one bound to each tungsten. Cyclic voltammetry showed that the compound could be reversibly reduced, presumably to a W/sub 2//sup 4 +/ dimer containing a quadruple metal-metal bond.« less

Structural building principles of complex face-centered cubic intermetallics.

PubMed

Dshemuchadse, Julia; Jung, Daniel Y; Steurer, Walter

2011-08-01

Fundamental structural building principles are discussed for all 56 known intermetallic phases with approximately 400 or more atoms per unit cell and space-group symmetry F43m, Fd3m, Fd3, Fm3m or Fm3c. Despite fundamental differences in chemical composition, bonding and electronic band structure, their complex crystal structures show striking similarities indicating common building principles. We demonstrate that the structure-determining elements are flat and puckered atomic {110} layers stacked with periodicities 2p. The atoms on this set of layers, which intersect each other, form pentagon face-sharing endohedral fullerene-like clusters arranged in a face-centered cubic packing (f.c.c.). Due to their topological layer structure, all these crystal structures can be described as (p × p × p) = p(3)-fold superstructures of a common basic structure of the double-diamond type. The parameter p, with p = 3, 4, 7 or 11, is determined by the number of layers per repeat unit and the type of cluster packing, which in turn are controlled by chemical composition.

Site specific interaction between ZnO nanoparticles and tyrosine: A density functional theory study

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Janpreet; Singh, Baljinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-05-01

First Principles Calculations have been performed on ZnO/Tyrosine atomic complex to study site specific interaction of Tyrosine and ZnO nanoparticles. Calculated results shows that -COOH group present in Tyrosine is energetically more favorable than -NH2 group. Interactions show ionic bonding between ZnO and Tyrosine. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/Tyrosine complex have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations.

Computational study of the electronic structure and magnetic properties of the Ni-C state in [NiFe] hydrogenases including the second coordination sphere.

PubMed

Kampa, Mario; Lubitz, Wolfgang; van Gastel, Maurice; Neese, Frank

2012-12-01

[NiFe] hydrogenases catalyze the reversible formation of H(2). The [NiFe] heterobimetallic active site is rich in redox states. Here, we investigate the key catalytic state Ni-C of Desulfovibrio vulgaris Miyazaki F hydrogenase using a cluster model that includes the truncated amino acids of the entire second coordination sphere of the enzyme. The optimized geometries, computed g tensors, hyperfine coupling constants, and IR stretching frequencies all agree well with experimental values. For the hydride in the bridging position, only a single minimum on the potential energy surface is found, indicating that the hydride bridges and binds to both nickel and iron. The influence of the second coordination sphere on the electronic structure is investigated by comparing results from the large cluster models with truncated models. The largest interactions of the second coordination sphere with the active site concern the hydrogen bonds with the cyanide ligands, which modulate the bond between iron and these ligands. Secondly, the electronic structure of the active site is found to be sensitive to the protonation state of His88. This residue forms a hydrogen bond with the spin-carrying sulfur atom of Cys549, which in turn tunes the spin density at the nickel and coordinating sulfur atoms. In addition, the unequal distribution of spin density over the equatorial cysteine residues results from different orientations of the cysteine side chains, which are kept in their particular orientation by the secondary structure of the protein.

Absorption spectroscopy of heavy alkaline earth metals Ba and Sr in rare gas matrices—CCSD(T) calculations and atomic site occupancies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, Barry M.; McCaffrey, John G., E-mail: john.mccaffrey@nuim.ie

2016-01-28

Isolation of the heavier alkaline earth metals Ba and Sr in the solid rare gases (RGs) Ar, Kr, and Xe is analysed with absorption spectroscopy and interpreted partly with the assistance of ab initio calculations of the diatomic M ⋅ RG ground state interaction potentials. The y{sup 1}P←a{sup 1}S resonance transitions in the visible spectral region are used to compare the isolation conditions of these two metal atom systems and calcium. Complex absorption bands were recorded in all three metal atom systems even after extensive sample annealing. Coupled cluster calculations conducted on the ground states of the nine M ⋅more » RG diatomics (M = Ca, Sr, and Ba; RG = Ar, Kr, and Xe) at the coupled cluster single, double, and non-iterative triple level of theory revealed long bond lengths (>5 Å) and shallow bound regions (<130 cm{sup −1}). All of the M ⋅ RG diatomics have bond lengths considerably longer than those of the rare gas dimers, with the consequence that isolation of these metal atoms in a single substitutional site of the solid rare gas is unlikely, with the possible exception of Ca/Xe. The luminescence of metal dimer bands has been recorded for Ba and Sr revealing very different behaviours. Resonance fluorescence with a lifetime of 15 ns is observed for the lowest energy transition of Sr{sub 2} while this transition is quenched in Ba{sub 2}. This behaviour is consistent with the absence of vibrational structure on the dimer absorption band in Ba{sub 2} indicating lifetime broadening arising from efficient relaxation to low-lying molecular states. More extensive 2D excitation-emission data recorded for the complex site structures present on the absorption bands of the atomic Ba and Sr systems will be presented in future publications.« less

Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.

PubMed

Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick

2016-09-19

The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Di-μ3-chlorido-tetra-μ2-chlorido-dichloridobis(dimethyl­formamide-κO)hexa­kis­(1H-imidazole-κN 3)tetra­cadmium

PubMed Central

Zhu, Run-Qiang

2011-01-01

The centrosymmetric mol­ecule of the title complex, [Cd4Cl8(C3H4N2)6(C3H7NO)2], contains four CdII atoms, six imidazole, two dimethyl­formamide and eight chloride ligands. The structure shows a novel chloride-bridged tetra­nuclear cadmium quasi-cubane cluster. The coordination geometry of all CdII atoms is distorted octa­hedral, with the two metal atoms in the asymmetric unit in different coordination environments. One of the Cd2+ ions is coordinated by five Cl− ions and by one N atom from an imidazole ligand, while the second is coordinated by three chloride ligands, two N atoms from two imidazole ligands and one O atom from a dimethyl­formamide mol­ecule. Inter­molecular N—H⋯Cl hydrogen bonds link the mol­ecules into a two-dimensional polymeric structure parallel to the ab plane. PMID:22058708

Gold as hydrogen: Structural and electronic properties and chemical bonding in Si3Au3+/0/- and comparisons to Si3H3+/0/-

NASA Astrophysics Data System (ADS)

Kiran, Boggavarapu; Li, Xi; Zhai, Hua-Jin; Wang, Lai-Sheng

2006-10-01

A single Au atom has been shown to behave like H in its bonding to Si in several mono- and disilicon gold clusters. In the current work, we investigate the Au /H analogy in trisilicon gold clusters, Si3Au3+/0/-. Photoelectron spectroscopy and density functional calculations are combined to examine the geometric and electronic structure of Si3Au3-. We find that there are three isomers competing for the ground state of Si3Au3- as is the case for Si3H3-. Extensive structural searches show that the potential energy surfaces of the trisilicon gold clusters (Si3Au3-, Si3Au3, and Si3Au3+) are similar to those of the corresponding silicon hydrides. The lowest energy isomers for Si3Au3- and Si3Au3 are structurally similar to a Si3Au four-membered ring serving as a common structural motif. For Si3Au3+, the 2π aromatic cyclotrisilenylium auride ion, analogous to the aromatic cyclotrisilenylium ion (Si3H3+), is the most stable species. Comparison of the structures and chemical bonding between Si3Au3+/0/- and the corresponding silicon hydrides further extends the isolobal analogy between Au and H.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

The formal combination of three singlet biradicaloid entities to a singlet hexaradicaloid metalloid Ge14[Si(SiMe3)3]5[Li(THF)2]3 cluster.

PubMed

Schenk, Christian; Kracke, Andreas; Fink, Karin; Kubas, Adam; Klopper, Wim; Neumaier, Marco; Schnöckel, Hansgeorg; Schnepf, Andreas

2011-03-02

The reaction of GeBr with LiSi(SiMe(3))(3) leads to the metalloid cluster compound [(THF)(2)Li](3)Ge(14)[Si(SiMe(3))(3)](5) (1). After the introduction of a first cluster of this type, in which 14 germanium atoms form an empty polyhedron, [(THF)(2)Li](3)Ge(14)[Ge(SiMe(3))(3)](5) (2), we present here further investigations on 1 to obtain preliminary insight into its chemical and bonding properties. The molecular structure of 1 is determined via X-ray crystal structure solution using synchrotron radiation. The electronic structure of the Ge(14) polyhedron is further examined by quantum chemical calculations, which indicate that three singlet biradicaloid entities formally combine to yield the singlet hexaradicaloid character of 1. Moreover, the initial reactions of 1 after elimination of the [Li(THF)(2)](+) groups by chelating ligands (e.g., TMEDA or 12-crown-4) are presented. Collision induced dissociation experiments in the gas phase, employing FT-ICR mass spectrometry, lead to the elimination of the singlet biradicaloid Ge(5)H(2)[Si(SiMe(3))(3)](2) cluster. The unique multiradicaloid bonding character of the metalloid cluster 1 might be used as a model for reactions and properties in the field of surface science and nanotechnology.

Efficient Decarbonylation of Furfural to Furan Catalyzed by Zirconia-Supported Palladium Clusters with Low Atomicity.

PubMed

Ishida, Tamao; Kume, Kurumi; Kinjo, Kota; Honma, Tetsuo; Nakada, Kengo; Ohashi, Hironori; Yokoyama, Takushi; Hamasaki, Akiyuki; Murayama, Haruno; Izawa, Yusuke; Utsunomiya, Masaru; Tokunaga, Makoto

2016-12-20

Decarbonylation of furfural to furan was efficiently catalyzed by ZrO 2 -supported Pd clusters in the liquid phase under a N 2 atmosphere without additives. Although Pd/C and Pd/Al 2 O 3 have frequently been used for decarbonylation, Pd/ZrO 2 exhibited superior catalytic performance compared with these conventional catalysts. Transmission electron microscopy and X-ray absorption fine structure measurements revealed that the size of the Pd particles decreased with an increase in the specific surface area of ZrO 2 . ZrO 2 with a high surface area immobilized Pd as clusters consisting of several (three to five) Pd atoms, whereas Pd aggregated to form nanoparticles on other supports such as carbon and Al 2 O 3 despite their high surface areas. The catalytic activity of Pd/ZrO 2 was enhanced with a decrease in particle size, and the smallest Pd/ZrO 2 was the most active catalyst for decarbonylation. When CeO 2 was used as the support, a decrease in Pd particle size with an increase in surface area was also observed. Single Pd atoms were deposited on CeO 2 with a high surface area, with a strong interaction through the formation of a Pd-O-Ce bond, which led to a lower catalytic activity than that of Pd/ZrO 2 . This result suggests that zero-valent small Pd clusters consisting of more than one Pd atom are the active species for the decarbonylation reaction. Recycling tests proved that Pd/ZrO 2 maintained its catalytic activity until its sixth use. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids.

PubMed

Wu, Yang; Li, Yao; Hu, Na; Hong, Mei

2014-02-14

Recently, experimental and theoretical studies on amino acid ionic liquid (AAIL) systems have attracted much attention. A transferable intermolecular potential approach that includes fluctuating charges and a flexible body based on a combination of the electronegativity equalization method and molecular mechanics (EEM/MM), and its application to an AAIL system containing 1-ethyl-3-methylimidazolium ([Emim](+)) and glycine ([Gly](-)) are explored and tested in this study. A consistent integration of EEM with MM requires the input of the EEM charges of all atoms into the MM intermolecular electrostatic interaction term. Compared with ionic liquid (IL) force fields, the EEM/MM model has an outstanding feature: the EEM/MM model not only presents the electrostatic interaction of atoms and their changes in response to different ambient environments but also introduces "the H-bond interaction region" in which a new parameter kHB(RHB) is used to describe the electrostatic interaction of hydrogen atoms in [Emim](+) and oxygen atoms in [Gly](-), which can form hydrogen bonds. The EEM/MM model gives quite accurate predictions for gas-phase state properties of [Emim](+), [Gly](-), and ion pairs, such as optimized geometries, dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and hydrogen bonds, the EEM/MM model also performs well for the liquid-phase properties of [Emim][Gly] under ambient conditions. The calculated properties, such as density, heat of vaporization, the self-diffusion coefficient, and ionic conductivity, are fairly consistent with available experimental results.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Al4H7− is a resilient building block for aluminum hydrogen cluster materials

PubMed Central

Roach, P. J.; Reber, A. C.; Woodward, W. H.; Khanna, S. N.; Castleman, A. W.

2007-01-01

The formation and oxygen etching of AlnHm− clusters are characterized in a flow reactor experiment with first-principles theoretical investigations to demonstrate the exceptional stability of Al4H7−. The origin of the preponderance of Al4H7− in the mass spectra of hydrogenated aluminum anions and its resistance to O2 etching are discussed. Al4H7− is shown to have the ability to bond with ionic partners to form stable hydrides through addition of an alkali atom [XAl4H7 (X = Li-Cs)]. An intuitive model that can predict the existence of stable hydrogenated cluster species is proposed. The potential synthetic utility of the superatom assemblies built on these units is addressed. PMID:17823245

A new hexanuclear iron-selenium nitrosyl cluster: primary exploration of the preparation methods, structure, and spectroscopic and electrochemical properties.

PubMed

Wang, Rongming; Xu, Wei; Zhang, Jian; Li, Lijuan

2010-06-07

A new hexanuclear iron-selenium nitrosyl cluster, [(n-Bu)(4)N](2)[Fe(6)Se(6)(NO)(6)] (1), and a hexanuclear iron-sulfur nitrosyl cluster, [(n-Bu)(4)N](2)[Fe(6)S(6)(NO)(6)] (2), were synthesized by the solvent-thermal reactions of [(n-Bu)(4)N][Fe(CO)(3)NO] with selenium or sulfur in methanol, while a tetranuclear iron-sulfur nitrosyl cluster, (Me(4)N)[Fe(4)S(3)(NO)(7)] (3), was also prepared by the solvent-thermal reaction of FeCl(2).4H(2)O with thiourea in the presence of (CH(3))(4)NCl, NaNO(2), and methanol. Complexes 1-3 were characterized by IR, UV-vis, (1)H NMR, electrochemistry, and single-crystal X-ray diffraction analysis. IR spectra of complexes 1 and 2 show the characteristic NO stretching frequencies at 1694 and 1698 cm(-1), respectively, while the absorptions of complex 3 appear at 1799, 1744, and 1710 cm(-1). The UV-vis spectra of complexes 1-3 show different bands in the range of 259-562 nm, which are assigned to the transitions between orbitals delocalized over the Fe-S cluster, the ligand-to-metal charge transfer, pi*(NO)-d(Fe), and the metal-to-ligand charge transfer, d(Fe)-pi*(NO). Single-crystal X-ray structural analysis reveals that complex 1 crystallizes in the monoclinic P2(1)/n space group with two molecules per unit cell. Two parallel "chair-shaped" structures, consisting of three iron and three selenium atoms, are connected by Fe-Se bonds with an average distance of 2.341 A; each iron center is bonded to three selenium atoms and a nitrogen atom from the nitrosyl ligand with a pseudotetrahedral center geometry. Cyclic voltammograms of complexes 1 and 2 display two cathodic and three anodic current peaks with an unusually strong cathodic peak. Further electrochemical investigations demonstrated that the intensity of the unusually strong peak is a result of at least three processes. One is the quasi-reversible reduction, and the other two are from an irreversible electrochemical process, in which the compound goes through a typical electron transfer and chemical reaction mechanism. Compound 3 shows three quasi-reversible reductions.

Theoretical investigation of HNgNH{sub 3}{sup +} ions (Ng = He, Ne, Ar, Kr, and Xe)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Kunqi; Sheng, Li, E-mail: shengli@hit.edu.cn

2015-04-14

The equilibrium geometries, harmonic frequencies, and dissociation energies of HNgNH{sub 3}{sup +} ions (Ng = He, Ne, Ar, Kr, and Xe) were investigated using the following method: Becke-3-parameter-Lee-Yang-Parr (B3LYP), Boese-Matrin for Kinetics (BMK), second-order Møller-Plesset perturbation theory (MP2), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The results indicate that HHeNH{sub 3}{sup +}, HArNH{sub 3}{sup +}, HKrNH{sub 3}{sup +}, and HXeNH{sub 3}{sup +} ions are metastable species that are protected from decomposition by high energy barriers, whereas the HNeNH{sub 3}{sup +} ion is unstable because of its relatively small energy barrier for decomposition.more » The bonding nature of noble-gas atoms in HNgNH{sub 3}{sup +} was also analyzed using the atoms in molecules approach, natural energy decomposition analysis, and natural bond orbital analysis.« less

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

Expanded Definition of the Oxidation State

ERIC Educational Resources Information Center

Loock, Hans-Peter

2011-01-01

A proposal to define the oxidation state of an atom in a compound as the hypothetical charge of the corresponding atomic ion that is obtained by heterolytically cleaving its bonds such that the atom with the higher electronegativity in a bond is allocated all electrons in the bond. Bonds between like atoms are cleaved homolytically. This…

Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses.

PubMed

Kumagai, Yoshiaki; Jurek, Zoltan; Xu, Weiqing; Fukuzawa, Hironobu; Motomura, Koji; Iablonskyi, Denys; Nagaya, Kiyonobu; Wada, Shin-Ichi; Mondal, Subhendu; Tachibana, Tetsuya; Ito, Yuta; Sakai, Tsukasa; Matsunami, Kenji; Nishiyama, Toshiyuki; Umemoto, Takayuki; Nicolas, Christophe; Miron, Catalin; Togashi, Tadashi; Ogawa, Kanade; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Son, Sang-Kil; Ziaja, Beata; Santra, Robin; Ueda, Kiyoshi

2018-06-01

We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses

NASA Astrophysics Data System (ADS)

Kumagai, Yoshiaki; Jurek, Zoltan; Xu, Weiqing; Fukuzawa, Hironobu; Motomura, Koji; Iablonskyi, Denys; Nagaya, Kiyonobu; Wada, Shin-ichi; Mondal, Subhendu; Tachibana, Tetsuya; Ito, Yuta; Sakai, Tsukasa; Matsunami, Kenji; Nishiyama, Toshiyuki; Umemoto, Takayuki; Nicolas, Christophe; Miron, Catalin; Togashi, Tadashi; Ogawa, Kanade; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Son, Sang-Kil; Ziaja, Beata; Santra, Robin; Ueda, Kiyoshi

2018-06-01

We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

Photoelectron Spectroscopic and Theoretical Study of B-16(-) and B-16(2-): An All-Boron Naphthalene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sergeeva, Alina P.; Zubarev, Dmitry Y.; Zhai, Hua Jin

Although boron clusters were experimentally studied shortly after the discovery of the fullerenes, their structural characterization was only possible fairly recently when we combined photoelectron spectroscopy (PES) and theoretical calculations to investigate the structures and bonding of boron clusters. Early theoretical studies indicated that small boron clusters do not assume cage-like structures, which are common in bulk boron and compounds; instead, planar or quasi-planar structures were suggested. The combined PES and theoretical studies show indeed boron clusters with up to 15 atom are planar, and only at B20 does a three-dimensional (3D) structure (double ring) become energetically competitive, whereas B20-more » still remains planar. A recent ion mobility and theoretical study showed that for Bn + the doublering 3D structure becomes competitive at B16 +7.« less

The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO 2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO 2 photoreduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.

2015-09-04

In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO 2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO 2 photoreduction reaction (bent CO 2 –), we find that flatter (2D-like) Pt clusters that “wet” the TiO 2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO 2 interfacial sites with geometries that can aid CO 2 bond bendingmore » and charge transfer processes. Second, binding competition among each Pt–CO 2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO 2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO 2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO 2 surfaces for CO 2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO 2 on TiO 2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.« less

Geometry-dependent distributed polarizability models for the water molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.

2016-01-21

Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successivelymore » occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.« less

Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.

PubMed

Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

2018-05-30

Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

Thermal and adsorbate effects on the activity and morphology of size-selected Pdn/TiO2 model catalysts

NASA Astrophysics Data System (ADS)

Kaden, William E.; Kunkel, William A.; Roberts, F. Sloan; Kane, Matthew; Anderson, Scott L.

2014-03-01

Model catalysts containing size-selected Pdn (n = 1,2,4,7,10,16,20,25) deposited on rutile TiO2(110) deactivate during repeated CO oxidation temperature-programmed reaction (TPR) cycles, and the deactivation process has been probed using a combination of X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), low-energy ion scattering (ISS), temperature-dependent ion scattering (TD-ISS), annealing experiments, and temperature-programmed desorption following exposure to CO and O2 reactants. Results from such experiments suggest the cluster deactivation proceeds via an alloy-like, strong metal-support interaction (SMSI) effect that chemically modifies the clusters via electronic interactions between the supported metal atoms and Ti from the support. Threshold measurements show that this effect detrimentally affects CO-oxidation activity prior to the formation of an encapsulating overlayer by severely weakening the COPd bond strengths for binding configurations on top of the clusters. Oxidation appears to provide means of partially restoring the clusters to their initial state, but after sufficient exposure to reducing environments and elevated temperatures, all Pdn become covered by an overlayer and begin to electronically and chemically resemble freshly deposited atoms, which are completely inactive towards the probe reaction. In addition, we find evidence of oxygen spillover induced by co-adsorbed CO during TPRs for all active Pdn clusters.

Multiple Aromaticity and Antiaromaticity in Silicon Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Hua JIN.; Kuznetsov, A E.; Boldyrev, Alexander I.

A series of silicon clusters containing four atoms but with different charge states (Si{sub 4}{sup 2+}, Si{sub 4}, Si{sub 4}{sup 2-}, and NaSi{sub 4}{sup -}) were studied by photoelectron spectroscopy and ab initio calculations. Structure evolution and chemical bonding in this series were interpreted in terms of aromaticity and antiaromaticity, which allowed the prediction of how structures of the four-atom silicon clusters change upon addition or removal of two electrons. It is shown that Si{sub 4}{sup 2+} is square-planar, analogous to the recently discovered aromatic Al{sub 4}{sup 2-} cluster. Upon addition of two electrons, neutral Si{sub 4} becomes {sigma}-antiaromatic andmore » exhibits a rhombus distortion. Adding two more electrons to Si{sub 4} leads to two energetically close structures of Si{sub 4}{sup 2-}: either a double antiaromatic parallelogram structure or an aromatic system with a butterfly distortion. Because of the electronic instability of doubly charged Si{sub 4}{sup 2-}, a stabilizing cation (Na{sup +}) was used to produce Si{sub 4}{sup 2-} in the gas phase in the form of Na{sup +}[Si{sub 4}{sup 2-}], which was characterized experimentally by photoelectron spectroscopy. Multiple antiaromaticity in the parallelogram Na{sup +}[Si{sub 4}{sup 2-}] species is highly unusual.« less

Atomic and electronic structure of Pd40Ni40P20 bulk metallic glass from ab initio simulations

NASA Astrophysics Data System (ADS)

Kumar, Vijay; Fujita, T.; Konno, K.; Matsuura, M.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2011-10-01

The atomic structure of Pd40Ni40P20 bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

Electronic structure of the alkyne-bridged dicobalt hexacarbonyl complex Co(2) micro-C(2)H(2) (CO)(6): evidence for singlet diradical character and implications for metal-metal bonding.

PubMed

Platts, James A; Evans, Gareth J S; Coogan, Michael P; Overgaard, Jacob

2007-08-06

A series of ab initio calculations are presented on the alkyne-bridged dicobalt hexacarbonyl cluster Co2 micro-C2H2 (CO)6, indicating that this compound has substantial multireference character, which we interpret as evidence of singlet diradical behavior. As a result, standard theoretical methods such as restricted Hartree-Fock (RHF) or Kohn-Sham (RKS) density functional theory cannot properly describe this compound. We have therefore used complete active space (CAS) methods to explore the bonding in and spectroscopic properties of Co2 micro-C2H2 (CO)6. CAS methods identify significant population of a Co-Co antibonding orbital, along with Co-pi* back-bonding, and a relatively large singlet-triplet energy splitting. Analysis of the electron density and related quantities, such as energy densities and atomic overlaps, indicates a small but significant amount of covalent bonding between cobalt centers.

New Theoretical Developments in Exploring Electronically Excited States: Including Localized Configuration Interaction Singles and Application to Large Helium Clusters

NASA Astrophysics Data System (ADS)

Closser, Kristina Danielle

This thesis presents new developments in excited state electronic structure theory. Contrasted with the ground state, the electronically excited states of atoms and molecules often are unstable and have short lifetimes, exhibit a greater diversity of character and are generally less well understood. The very unusual excited states of helium clusters motivated much of this work. These clusters consist of large numbers of atoms (experimentally 103--109 atoms) and bands of nearly degenerate excited states. For an isolated atom the lowest energy excitation energies are from 1s → 2s and 1s → 2 p transitions, and in clusters describing the lowest energy band minimally requires four states per atom. In the ground state the clusters are weakly bound by van der Waals interactions, however in the excited state they can form well-defined covalent bonds. The computational cost of quantum chemical calculations rapidly becomes prohibitive as the size of the systems increase. Standard excited-state methods such as configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) can be used with ≈100 atoms, and are optimized to treat only a few states. Thus, one of our primary aims is to develop a method which can treat these large systems with large numbers of nearly degenerate excited states. Additionally, excited states are generally formed far from their equilibrium structures. Vertical excitations from the ground state induce dynamics in the excited states. Thus, another focus of this work is to explore the results of these forces and the fate of the excited states. Very little was known about helium cluster excited states when this work began, thus we first investigated the excitations in small helium clusters consisting of 7 or 25 atoms using CIS. The character of these excited states was determined using attachment/detachment density analysis and we found that in the n = 2 manifold the excitations could generally be interpreted as superpositions of atomic states with surface states appearing close to the atomic excitation energies and interior states being blue shifted by up to ≈2 eV. The dynamics resulting from excitation of He_7 were subsequently explored using ab initio molecular dynamics (AIMD). These simulations were performed with classical adiabatic dynamics coupled to a new state-following algorithm on CIS potential energy surfaces. Most clusters were found to completely dissociate and resulted in a single excited atomic state (90%), however, some trajectories formed bound, He*2 (3%), and a few yielded excited trimers (<0.5%). Comparisons were made with available experimental information on much larger clusters. Various applications of this state following algorithm are also presented. In addition to AIMD, these include excited-state geometry optimization and minimal energy path finding via the growing string method. When using state following we demonstrate that more physical results can be obtained with AIMD calculations. Also, the optimized geometries of three excited states of cytosine, two of which were not found without state following, and the minimal energy path between the lowest two singlet excited states of protonated formaldimine are offered as example applications. Finally, to address large clusters, a local variation of CIS was developed. This method exploits the properties of absolutely localized molecular orbitals (ALMOs) to limit the total number of excitations to scaling only linearly with cluster size, which results in formal scaling with the third power of the system size. The derivation of the equations and design of the algorithm are discussed in detail, and computational timings as well as a pilot application to the size dependence of the helium cluster spectrum are presented.

Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals

NASA Astrophysics Data System (ADS)

Liu, Junzi; Shen, Yue; Asthana, Ayush; Cheng, Lan

2018-01-01

A novel implementation of the two-component spin-orbit (SO) coupled-cluster singles and doubles (CCSD) method and the CCSD augmented with the perturbative inclusion of triple excitations [CCSD(T)] method using mean-field SO integrals is reported. The new formulation of SO-CCSD(T) features an atomic-orbital-based algorithm for the particle-particle ladder term in the CCSD equation, which not only removes the computational bottleneck associated with the large molecular-orbital integral file but also accelerates the evaluation of the particle-particle ladder term by around a factor of 4 by taking advantage of the spin-free nature of the instantaneous electron-electron Coulomb interaction. Benchmark calculations of the SO splittings for the thallium atom and a set of diatomic 2Π radicals as well as of the bond lengths and harmonic frequencies for a set of closed-shell diatomic molecules are presented. The basis-set and core-correlation effects in the calculations of these properties have been carefully analyzed.

Basic Equations Interrelate Atomic and Nuclear Properties to Patterns at the Size Scales of the Cosmos, Extended Clusters of Galaxies, Galaxies, and Nebulae

NASA Astrophysics Data System (ADS)

Allen, Rob

2016-09-01

Structures within molecules and nuclei have relationships to astronomical patterns. The COBE cosmic scale plots, and large scale surveys of galaxy clusters have patterns also repeating and well known at atomic scales. The Induction, Strong Force, and Nuclear Binding Energy Periods within the Big Bang are revealed to have played roles in the formation of these large scale distributions. Equations related to the enormous patterns also model chemical bonds and likely nucleus and nucleon substructures. ratios of the forces that include gravity are accurately calculated from the distributions and shapes. In addition, particle masses and a great many physical constants can be derived with precision and accuracy from astrophysical shapes. A few very basic numbers can do modelling from nucleon internals to molecules to super novae, and up to the Visible Universe. Equations are also provided along with possible structural configurations for some Cold Dark Matter and Dark Energy.

A bronze matryoshka: the discrete intermetalloid cluster [Sn@Cu12@Sn20](12-) in the ternary phases A12Cu12Sn21 (A = Na, K).

PubMed

Stegmaier, Saskia; Fässler, Thomas F

2011-12-14

The synthesis and crystal structure of the first ternary A-Cu-Sn intermetallic phases for the heavier alkali metals A = Na to Cs is reported. The title compounds A(12)Cu(12)Sn(21) show discrete 33-atom intermetalloid Cu-Sn clusters {Sn@Cu(12)@Sn(20)}, which are composed of {Sn(20)} pentagonal dodecahedra surrounding {Cu(12)} icosahedra with single Sn atoms at the center. Na(12)Cu(12)Sn(21) and K(12)Cu(12)Sn(21) were characterized by single-crystal XRD studies, and the successful synthesis of analogous A-Cu-Sn compounds with A = Rb and Cs is deduced from powder XRD data. The isotypic A(12)Cu(12)Sn(21) phases crystallize in the cubic space group Pn ̅3m (No. 224), with the Cu-Sn clusters adopting a face centered cubic arrangement. A formal charge of 12- can be assigned to the {Sn@Cu(12)@Sn(20)} cluster unit, and the interpretation of the title compounds as salt-like intermetallic phases featuring discrete anionic intermetalloid [Sn@Cu(12)@Sn(20)](12-) clusters separated by alkali metal cations is supported by electronic structure calculations. For both Na(12)Cu(12)Sn(21) and K(12)Cu(12)Sn(21), DFT band structure calculations (TB-LMTO-ASA) reveal a band gap. The discrete [Sn@Cu(12)@Sn(20)](12-) cluster is analyzed in consideration of the molecular orbitals obtained from hybrid DFT calculations (Gaussian 09) for the cluster anion. The [Sn@Cu(12)@Sn(20)](12-) cluster MOs can be classified with labels indicating the numbers of radial and angular nodes, in the style of spherical shell models of cluster bonding. © 2011 American Chemical Society

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

DOE PAGES

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; ...

2015-10-13

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

Tungsten Hydride Phosphorus- and Arsenic-Bearing Molecules with Double and Triple W-P and W-As Bonds.

PubMed

Andrews, Lester; Cho, Han-Gook; Fang, Zongtang; Vasiliu, Monica; Dixon, David A

2018-05-07

Laser ablation of tungsten metal provides W atoms which react with phosphine and arsine during condensation in excess argon and neon, leading to major new infrared (IR) absorptions. Annealing, UV irradiation, and deuterium substitution experiments coupled with electronic structure calculations at the density functional theory level led to the assignment of the observed IR absorptions to the E≡WH 3 and HE═WH 2 molecules for E = P and As. The potential energy surfaces for hydrogen transfer from PH 3 to the W were calculated at the coupled-cluster CCSD(T)/complete basis set level. Additional weak bands in the phosphide and arsenide W-H stretching region are assigned to the molecules with loss of H from W, E≡WH 2 . The electronic structure calculations show that the E≡WH 3 molecules have a W-E triple bond, the HE═WH 2 molecules have a W-E double bond, and the H 2 E-WH molecules have a W-E single bond. The formation of multiple E-W bonds leads to increasing stability for the isomers.

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

Competing 1πσ* mediated dynamics in mequinol: O-H versus O-CH3 photodissociation pathways.

PubMed

Hadden, David J; Roberts, Gareth M; Karsili, Tolga N V; Ashfold, Michael N R; Stavros, Vasilios G

2012-10-14

Deactivation of excited electronic states through coupling to dissociative (1)πσ* states in heteroaromatic systems has received considerable attention in recent years, particularly as a mechanism that contributes to the ultraviolet (UV) photostability of numerous aromatic biomolecules and their chromophores. Recent studies have expanded upon this work to look at more complex species, which involves understanding competing dynamics on two different (1)πσ* potential energy surfaces (PESs) localized on different heteroatom hydride coordinates (O-H and N-H bonds) within the same molecule. In a similar spirit, the work presented here utilizes ultrafast time-resolved velocity map ion imaging to study competing dissociation pathways along (1)πσ* PESs in mequinol (p-methoxyphenol), localized at O-H and O-CH(3) bonds yielding H atoms or CH(3) radicals, respectively, over an excitation wavelength range of 298-238 nm and at 200 nm. H atom elimination is found to be operative via either tunneling under a conical intersection (CI) (298 ≥ λ ≥ 280 nm) or ultrafast internal conversion through appropriate CIs (λ ≤ 245 nm), both of which provide mechanisms for coupling onto the dissociative state associated with the O-H bond. In the intermediate wavelength range of 280 ≥ λ ≥ 245 nm, mediated H atom elimination is not observed. In contrast, we find that state driven CH(3) radical elimination is only observed in the excitation range 264 ≥ λ ≥ 238 nm. Interpretation of these experimental results is guided by: (i) high level complete active space with second order perturbation theory (CASPT2) calculations, which provide 1-D potential energy cuts of the ground and low lying singlet excited electronic states along the O-H and O-CH(3) bond coordinates; and (ii) calculated excitation energies using CASPT2 and the equation-of-motion coupled cluster with singles and doubles excitations (EOM-CCSD) formalism. From these comprehensive studies, we find that the dynamics along the O-H coordinate generally mimic H atom elimination previously observed in phenol, whereas O-CH(3) bond fission in mequinol appears to present notably different behavior to the CH(3) elimination dynamics previously observed in anisole (methoxybenzene).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Jia, E-mail: jia-zhu@jxnu.edu.cn, E-mail: zhangyf@fzu.edu.cn; Zhang, Hui; Tong, Yawen

The structures and electronic properties of bimetallic oxide CrW{sub 2}O{sub 9} clusters supported on the perfect and defective MgO(001) surfaces with three different color centers, F{sub S}{sup 0}, F{sub S}{sup +}, and F{sub S}{sup 2+} centers, respectively, have been investigated by density functional theory calculations. Our results show that the configurations, adsorption energies, charge transfers, and bonding modes of dispersed CrW{sub 2}O{sub 9} clusters are sensitive to the charge states of the F{sub S} centers. Compared with the gas-phase configuration, the CrW{sub 2}O{sub 9} clusters supported on the defective surfaces are distorted dramatically, which exhibit different chain structures. On themore » perfect MgO surface, the depositions of clusters do not involve obvious charge transfer, while the situation is quite different on the defective MgO(001) surfaces in which significant electron transfer occurs from the surface to the cluster. Interestingly, this effect becomes more remarkable for electron-rich oxygen vacancies (F{sub S}{sup 0} center) than that for electron-poor oxygen vacancies (F{sub S}{sup +} and F{sub S}{sup 2+} centers). Furthermore, our work reveals a progressive Brønsted acid sites where spin density preferentially localized around the Cr atoms not the W atoms for all kinds of F{sub S}-centers, indicating the better catalytic activities can be expected for CrW{sub 2}O{sub 9} cluster on defective MgO(001) surfaces with respect to the W{sub 3}O{sub 9} cluster.« less

Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamid, Ahmed M.; El-Shall, M. Samy, E-mail: mselshal@vcu.edu; Hilal, Rifaat

2014-08-07

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C{sub 5}H{sub 5}N{sup +·}(HCN){sub n} and C{sub 4}H{sub 4}N{sub 2}{sup +·}(HCN){sub n} clusters, respectively, with n = 1–4. For comparison, the binding of 1–4 HCN molecules to the protonated pyridine C{sub 5}H{sub 5}NH{sup +}(HCN){sub n} has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than themore » HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH{sup δ+}⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH{sup +}⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH{sup +}⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH{sup δ+}⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11–12 kcal/mol) are stronger than the similar (CH{sup δ+}⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH{sup δ+} centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.« less

Structural, energetic, and electronic trends in low-dimensional late-transition-metal systems

NASA Astrophysics Data System (ADS)

Hu, C. H.; Chizallet, C.; Toulhoat, H.; Raybaud, P.

2009-05-01

Using first-principles calculations, we present a comprehensive investigation of the structural trends of low dimensionality late 4d (from Tc to Ag) and 5d (from Re to Au) transition-metal systems including 13-atom clusters. Energetically favorable clusters not being reported previously are discovered by molecular-dynamics simulation based on the simulated annealing method. They allow a better agreement between experiments and theory for their magnetic properties. The structural periodic trend exhibits a nonmonotonic variation of the ratio of square to triangular facets for the two rows, with a maximum for Rh13 and Ir13 . By a comparative analysis of the relevant energetic and electronic properties performed on other metallic systems with reduced dimensionalities such as four-atom planar clusters, one-dimensional (1D) scales, double scales, 1D cylinders, monatomic films, two and seven layer slabs, we highlight that this periodic trend can be generalized. Hence, it appears that 1D-metallic nanocylinders or 1D-double nanoscales (with similar binding energies as TM13 ) also favor square facets for Rh and Ir. We finally propose an interpretation based on the evolution of the width of the valence band and of the Coulombic repulsions of the bonding basins.

The Electronic Structure of Transition Metal Coated Fullerenes

NASA Astrophysics Data System (ADS)

Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

1998-03-01

Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

The role of OH…O and CH…O hydrogen bonds and H…H interactions in ethanol/methanol-water heterohexamers.

PubMed

Mejía, Sol M; Espinal, Juan F; Mills, Matthew J L; Mondragón, Fanor

2016-08-01

Bioethanol is one of the world's most extensively produced biofuels. However, it is difficult to purify due to the formation of the ethanol-water azeotrope. Knowledge of the azeotrope structure at the molecular level can help to improve existing purification methods. In order to achieve a better understanding of this azeotrope structure, the characterization of (ethanol)5-water heterohexamers was carried out by analyzing the results of electronic structure calculations performed at the B3LYP/6-31+G(d) level. Hexamerization energies were found to range between -36.8 and -25.8 kcal/mol. Topological analysis of the electron density confirmed the existence of primary (OH…O) hydrogen bonds (HBs), secondary (CH…O) HBs, and H…H interactions in these clusters. Comparison with three different solvated alcohol systems featuring the same types of atom-atom interactions permitted the following order of stability to be determined: (methanol)5-water > (methanol)6 > (ethanol)5-water > (ethanol)6. These findings, together with accompanying geometric and spectroscopic analyses, show that similar cooperative effects exist among the primary HBs for structures with the same arrangement of primary HBs, regardless of the nature of the molecules involved. This result provides an indication that the molecular ratio can be considered to determine the unusual behavior of the ethanol-water system. The investigation also highlights the presence of several types of weak interaction in addition to primary HBs. Graphical Abstract Water-ethanol clusters exhibit a variety of interaction types between their atoms, such as primary OH...O (blue), secondary CH...O (green) and H...H (yellow) interactions as revealed by Quantum Chemical Topology.

(Carbonyl-1κC)bis-[2,3(η)-cyclo-penta-dien-yl][μ(3)-(S-methyl trithio-carbonato)methylidyne-1:2:3κC,S'':C:C](triphenyl-phosphine-1κP)(μ(3)-sulfido-1:2:3κS)dicobalt(II)iron(II) trifluoro-methane-sulfonate.

PubMed

Manning, Anthony R; McAdam, C John; Palmer, Anthony J; Simpson, Jim

2008-04-10

The asymmetric unit of the title compound, [FeCo(2)(C(5)H(5))(2)(C(3)H(3)S(3))S(C(18)H(15)P)(CO)]CF(3)SO(3), consists of a triangular irondicobalt cluster cation and a trifluoro-methane-sulfonate anion. In the cation, the FeCo(2) triangle is symmetrically capped on one face by an S atom and on the other by a C atom linked to a methyl trithio-carbonate residue that bridges the Fe-C bond. Each Co atom carries a cyclo-penta-dienyl ligand while the Fe atom coordinates to one carbonyl and one triphenyl-phosphine ligand. In the crystal structure, the cation is linked to the anion by a number of weak non-classical C-H⋯O and C-H⋯F hydrogen bonds and weak S⋯O (3.317 Å) and S⋯F (3.198 Å) inter-actions. The structure is further stabilized by additional inter-molecular C-H⋯O, C-H⋯F and O⋯O (2.942 Å) contacts, together with an unusual S⋯π(Cp) inter-action (S⋯centroid distance = 3.385 Å), generating an extended network.

Density functional study of hypophosphite adsorption on Ni (1 1 1) and Cu (1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Zeng, Yue; Liu, Shubin; Ou, Lihui; Yi, Jianlong; Yu, Shanci; Wang, Huixian; Xiao, Xiaoming

2006-02-01

Surface structures and electronic properties of hypophosphite, H 2PO 2-, molecularly adsorbed on Ni(1 1 1) and Cu(1 1 1) surfaces are investigated in this work by density functional theory at B3LYP/6-31++g(d, p) level. We employ a four-metal-atom cluster as the simplified model for the surface and have fully optimized the geometry and orientation of H 2PO 2- on the metal cluster. Six stable orientations have been discovered on both Ni (1 1 1) and Cu (1 1 1) surfaces. The most stable orientation of H 2PO 2- was found to have its two oxygen atoms interact the surface with two P sbnd O bonds pointing downward. Results of the Mulliken population analysis showed that the back donation from 3d orbitals of the transition metal substrate to the unfilled 3d orbital of the phosphorus atom in H 2PO 2- and 4s orbital's acceptance of electron donation from one lone pair of the oxygen atom in H 2PO 2- play very important roles in the H 2PO 2- adsorption on the transition metals. The averaged electron configuration of Ni in Ni 4 cluster is 4s 0.634p 0.023d 9.35 and that of Cu in Cu 4 cluster is 4s 1.004p 0.033d 9.97. Because of this subtle difference of electron configuration, the adsorption energy is larger on the Ni surface than on the Cu surface. The amount of charge transfers due to above two donations is larger from H 2PO 2- to the Ni surface than to the Cu surface, leading to a more positively charged P atom in Ni nH 2PO 2- than in Cu nH 2PO 2-. These results indicate that the phosphorus atom in Ni nH 2PO 2- complex is easier to be attacked by a nucleophile such as OH - and subsequent oxidation of H 2PO 2- can take place more favorably on Ni substrate than on Cu substrate.

Electronic structures of AlMoO(y)(-) (y = 1-4) determined by photoelectron spectroscopy and density functional theory calculations.

PubMed

Waller, Sarah E; Mann, Jennifer E; Hossain, Ekram; Troyer, Mary; Jarrold, Caroline C

2012-07-14

Vibrationally-resolved photoelectron spectra of AlMoO(y)(-) (y = 1-4) are presented and analyzed in conjunction with density functional theory computational results. The structures determined for the AlMoO(y) anion and neutral clusters suggest ionic bonding between Al(+) and a MoO(y)(-) or MoO(y)(-2) moiety, and point to the relative stability of Mo=O versus Al=O bonds. The highest occupied and partially occupied orbitals in the anions and neutrals can be described as Mo atomic-like orbitals, so while the Mo is in a higher oxidation state than Al, the most energetically accessible electrons are localized on the molybdenum center.

Oxygen adsorption on the Al₉Co₂(001) surface: first-principles and STM study.

PubMed

Villaseca, S Alarcón; Loli, L N Serkovic; Ledieu, J; Fournée, V; Gille, P; Dubois, J-M; Gaudry, E

2013-09-04

Atomic oxygen adsorption on a pure aluminum terminated Al9Co2(001) surface is studied by first-principle calculations coupled with STM measurements. Relative adsorption energies of oxygen atoms have been calculated on different surface sites along with the associated STM images. The local electronic structure of the most favourable adsorption site is described. The preferential adsorption site is identified as a 'bridge' type site between the cluster entities exposed at the (001) surface termination. The Al-O bonding between the adsorbate and the substrate presents a covalent character, with s-p hybridization occurring between the states of the adsorbed oxygen atom and the aluminum atoms of the surface. The simulated STM image of the preferential adsorption site is in agreement with experimental observations. This work shows that oxygen adsorption generates important atomic relaxations of the topmost surface layer and that sub-surface cobalt atoms strongly influence the values of the adsorption energies. The calculated Al-O distances are in agreement with those reported in Al2O and Al2O3 oxides and for oxygen adsorption on Al(111).

The Hydrogen Abstraction from A Diamond(111) Surface in A Uniform Electric Field

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Kang, Jeung Ku.; Musgrave, Charles B.; Arnold, James O. (Technical Monitor)

1998-01-01

Bond breaking in a strong electric field is shown to arise from a crossing of the ionic and covalent asymptotes. The specific example of hydrogen abstraction from a diamond(111) surface is studied using a cluster model. The addition of nearby atoms in both the parallel and perpendicular direction to the electric field are found to have an effect. It is also shown that the barrier is not only related to the position of the ionic and covalent asymptotes.

Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

PubMed

Kildgaard, Jens; Mikkelsen, Kurt V; Bilde, Merete; Elm, Jonas

2018-05-09

We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algo- rithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in 9 different orientations. To allow the sam- pling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond and a water molecule is placed in between in three different ori- entations. Generated redundant structures are eliminated based on minimizing the root mean square distance (RMSD) of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density func- tional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm we study the hydration of sulfuric acid with up to 15 water molecules. We find that the additions of the first four water molecules "saturate" the sulfuric acid molecule and are more thermodynamically favourable than the addition of water molecule 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91 and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimates the binding energies compared to cou- pled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.

Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation.

PubMed

Koua, Faisal Hammad Mekky; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren

2013-03-05

Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 Å, and compared it with the 1.9 Å structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca(2+), resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca(2+), W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr(2+)-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 Å structure of native PSII, was found in the Sr-PSII structure.

Quantum chemistry of the minimal CdSe clusters

NASA Astrophysics Data System (ADS)

Yang, Ping; Tretiak, Sergei; Masunov, Artëm E.; Ivanov, Sergei

2008-08-01

Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd2Se2, which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd2Se2 at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface Cd/Se atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand binding energies are systematically examined. The role played by positive charges on ligand binding is also explored. The calculated binding energies for various ligands L are found to decrease in the order OPMe3>OPH3>NH2Me>=NH3>=NMe3>PMe3>PH3 for neutral clusters and OPMe3>OPH3>PMe3>=NMe3>=NH2Me>=NH3>PH3 and OPMe3>OPH3>NH2Me>=NMe3>=PMe3>=NH3>PH3 for single and double ligations of positively charged Cd2Se22+ cluster, respectively.

Alchemical and structural distribution based representation for universal quantum machine learning

NASA Astrophysics Data System (ADS)

Faber, Felix A.; Christensen, Anders S.; Huang, Bing; von Lilienfeld, O. Anatole

2018-06-01

We introduce a representation of any atom in any chemical environment for the automatized generation of universal kernel ridge regression-based quantum machine learning (QML) models of electronic properties, trained throughout chemical compound space. The representation is based on Gaussian distribution functions, scaled by power laws and explicitly accounting for structural as well as elemental degrees of freedom. The elemental components help us to lower the QML model's learning curve, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training. This point is demonstrated for the prediction of covalent binding in single, double, and triple bonds among main-group elements as well as for atomization energies in organic molecules. We present numerical evidence that resulting QML energy models, after training on a few thousand random training instances, reach chemical accuracy for out-of-sample compounds. Compound datasets studied include thousands of structurally and compositionally diverse organic molecules, non-covalently bonded protein side-chains, (H2O)40-clusters, and crystalline solids. Learning curves for QML models also indicate competitive predictive power for various other electronic ground state properties of organic molecules, calculated with hybrid density functional theory, including polarizability, heat-capacity, HOMO-LUMO eigenvalues and gap, zero point vibrational energy, dipole moment, and highest vibrational fundamental frequency.

Thermal decomposition of 1,3,3-trinitroazetidine (TNAZ): A density functional theory and ab initio study

NASA Astrophysics Data System (ADS)

Veals, Jeffrey D.; Thompson, Donald L.

2014-04-01

Density functional theory and ab initio methods are employed to investigate decomposition pathways of 1,3,3-trinitroazetidine initiated by unimolecular loss of NO2 or HONO. Geometry optimizations are performed using M06/cc-pVTZ and coupled-cluster (CC) theory with single, double, and perturbative triple excitations, CCSD(T), is used to calculate accurate single-point energies for those geometries. The CCSD(T)/cc-pVTZ energies for NO2 elimination by N-N and C-N bond fission are, including zero-point energy (ZPE) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can occur by a concerted H-atom and nitramine NO2 group elimination or by a concerted H-atom and nitroalkyl NO2 group elimination via barriers (at the CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of these four decomposition steps from energetically most favored to least favored is: NO2 elimination by N-N bond fission, HONO elimination involving the nitramine NO2 group, HONO elimination involving a nitroalkyl NO2 group, and finally NO2 elimination by C-N bond fission.

Absolute surface energy calculations of Wurtzite (0001)/(000-1): a study of ZnO and GaN

NASA Astrophysics Data System (ADS)

Zhang, Jingzhao; Zhang, Yiou; Tse, Kinfai; Deng, Bei; Xu, Hu; Zhu, Junyi

The accurate absolute surface energies of (0001)/(000-1) surfaces of wurtzite structures are crucial in determining the thin film growth mode of important energy materials. However, the surface energies still remain to be solved due to the intrinsic difficulty of calculating dangling bond energy of asymmetrically bonded surface atoms. We used a pseudo-hydrogen passivation method to estimate the dangling bond energy and calculate the polar surfaces of ZnO and GaN. The calculations were based on the pseudo chemical potentials obtained from a set of tetrahedral clusters or simple pseudo-molecules, using density functional theory approaches, for both GGA and HSE. And the surface energies of (0001)/(000-1) surfaces of wurtzite ZnO and GaN we obtained showed relatively high self-consistencies. A wedge structure calculation with a new bottom surface passivation scheme of group I and group VII elements was also proposed and performed to show converged absolute surface energy of wurtzite ZnO polar surfaces. Part of the computing resources was provided by the High Performance Cluster Computing Centre, Hong Kong Baptist University. This work was supported by the start-up funding and direct Grant with the Project code of 4053134 at CUHK.

Maximum-valence radii of transition metals

PubMed Central

Pauling, Linus

1975-01-01

In many of their compounds the transition metals have covalence 9, forming nine bonds with use of nine hybrid spd bond orbitals. A set of maximum-valence single-bond radii is formulated for use in these compounds. These radii are in reasonably good agreement with observed bond lengths. Quadruple bonds between two transition metal atoms are about 50 pm (iron-group atoms) or 55 pm (palladium and platinum-group atoms) shorter than single bonds. This amount of shortening corresponds to four bent single bonds with the best set of bond angles, 79.24° and 128.8°. PMID:16578730

Bias in bonding behavior among boron, carbon, and nitrogen atoms in ion implanted a-BN, a-BC, and diamond like carbon films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genisel, Mustafa Fatih; Uddin, Md. Nizam; Say, Zafer

2011-10-01

In this study, we implanted N{sup +} and N{sub 2}{sup +} ions into sputter deposited amorphous boron carbide (a-BC) and diamond like carbon (DLC) thin films in an effort to understand the chemical bonding involved and investigate possible phase separation routes in boron carbon nitride (BCN) films. In addition, we investigated the effect of implanted C{sup +} ions in sputter deposited amorphous boron nitride (a-BN) films. Implanted ion energies for all ion species were set at 40 KeV. Implanted films were then analyzed using x-ray photoelectron spectroscopy (XPS). The changes in the chemical composition and bonding chemistry due to ion-implantationmore » were examined at different depths of the films using sequential ion-beam etching and high resolution XPS analysis cycles. A comparative analysis has been made with the results from sputter deposited BCN films suggesting that implanted nitrogen and carbon atoms behaved very similar to nitrogen and carbon atoms in sputter deposited BCN films. We found that implanted nitrogen atoms would prefer bonding to carbon atoms in the films only if there is no boron atom in the vicinity or after all available boron atoms have been saturated with nitrogen. Implanted carbon atoms also preferred to either bond with available boron atoms or, more likely bonded with other implanted carbon atoms. These results were also supported by ab-initio density functional theory calculations which indicated that carbon-carbon bonds were energetically preferable to carbon-boron and carbon-nitrogen bonds.« less

Energetics of a Li Atom adsorbed on B/N doped graphene with monovacancy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rani, Babita, E-mail: babitabaghla15@gmail.com; Department of Physics, Punjabi University, Patiala 147002; Jindal, V.K.

We use density functional theory (DFT) to study the adsorption properties and diffusion of Li atom across B/N-pyridinic graphene. Regardless of the dopant type, B atoms of B-pyridinic graphene lose electron density. On the other hand, N atoms (p-type dopants) have tendency to gain electron density in N-pyridinic graphene. Higher chemical reactivity and electronic conductivity of B/N-pyridinic graphene are responsible for stronger binding of Li with the substrates as compared to pristine graphene. The binding energy of Li with B/N-pyridinic graphene exceeds the cohesive energy of bulk Li, making it energetically unfavourable for Li to form clusters on these substrates.more » Li atom gets better adsorbed on N-pyridinic graphene due to an additional p-p hybridization of the orbitals while Li on B-pyridinic prefers the ionic bonding. Also, significant distortion of N-pyridinic graphene upon Li adsorption is a consequence of the change in bonding mechanism between Li atom and the substrate. Our results show that bonding character and hence binding energies between Li and graphene can be tuned with the help of B/N doping of monovacancy defects. Further, the sites for most stable adsorption are different for the two types of doped and defective graphene, leading to greater Li uptake capacity of B-pyridinic graphene near the defect. In addition, B-pyridinic graphene offering lower diffusion barrier, ensures better Li kinetics. Thus, B-pyridinic graphene presents itself as a better anode material for LIBs as compared to N-pyridinic graphene. - Graphical abstract: Adsorption and diffusion of Li atom across the B/N doped monovacancy graphene is studied using ab-initio DFT calculations. Our results show that bonding mechanism and binding of Li with graphene can be tuned with the help of N/B doping of defects. Also, B-pyridinic graphene presents itself as a better anode material for lithium ion batteries as compared to N-pyridinic graphene. Display Omitted - Highlights: • Density functional theory (DFT) calculations are employed to study the effect of B/N doping of monovacancy graphene on the adsorption and diffusion of Li atom across the sheet using VASP. • Higher chemical reactivity and electronic conductivity of B/N-pyridinic graphene (p-type semiconductors) as compared to pristine graphene lead to stronger binding of Li. It also exceeds the cohesive energy of bulk Li. Thus, uniform distribution of Li atoms is possible on both substrates. • Li gets adsorbed stably at centre of defect in N-pyridinic graphene. B-pyridinic graphene has stable adsorption of Li at hollow site of hexagon, neighboring the defect, having only one boron atom. It leads to maximum Li uptake capacity of B-pyridinic graphene. • Li gets better adsorbed on N-pyridinic graphene due to an additional p-p hybridization of the orbitals. This change in bonding mechanism causes significant distortion of the substrate. On the other hand, Li on B-pyridinic graphene shows ionic bonding character. • B-pyridinic graphene offers lower energy barrier for Li to diffuse across the substrate in comparison to N-pyridinic graphene. Thus, B-pyridinic graphene presents itself as a better anode material for lithium ion batteries due to optimal Li adsorption and better diffusion kinetics.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano

Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer overmore » the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.« less

Electronic structure of trioxide, oxoperoxide, oxosuperoxide, and ozonide clusters of the 3d elements: density functional theory study.

PubMed

Uzunova, Ellie L

2011-03-03

The trioxide clusters with stoichiometry MO3, and the structural isomers with side-on and end-on bonded oxygen atoms, are studied by DFT with the B1LYP functional. For the first half of the 3d elements row (Sc to Cr), pyramidal or distorted pyramidal structures dominate among the trioxide and oxoperoxide ground states, while the remaining elements form planar trioxides, oxoperoxides, oxosuperoxides, and ozonides. Low-lying trioxide clusters are formed by Ti, V, Cr, and Mn, among which the distorted pyramidal VO3 in the (2)A'' state, the pyramidal CrO3 in the (1)A1 state, and the planar MnO3 in the (2)A1' state are global minima. With the exception of the middle-row elements Mn, Fe, and Co, the magnetic moment of the ground-state clusters is formed with a major contribution from unpaired electrons located at the oxygen atoms. The stability of trioxides and oxoperoxides toward release of molecular oxygen is significantly higher for Sc, Ti, and V than for the remaining elements of the row. A trend of increasing the capability to dissociate one oxygen molecule is observed from Cr to Cu, with the exception of OFe(O2) being more reactive than OCo(O2). A gradual increase of reactivity from Ti to Cu is observed for the complete fragmentation reaction M + O + O2.

DNA-nanoparticle superlattices formed from anisotropic building blocks

NASA Astrophysics Data System (ADS)

Jones, Matthew R.; Macfarlane, Robert J.; Lee, Byeongdu; Zhang, Jian; Young, Kaylie L.; Senesi, Andrew J.; Mirkin, Chad A.

2010-11-01

Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions on the nanoscale, both through face-selective functionalization of the particle with recognition elements to introduce the concept of valency, and through anisotropic interactions resulting from particle shape. In this work, we examine the concept of inherent shape-directed crystallization in the context of DNA-mediated nanoparticle assembly. Importantly, we show how the anisotropy of these particles can be used to synthesize one-, two- and three-dimensional structures that cannot be made through the assembly of spherical particles.

Enzymatically Controlled Vacancies in Nanoparticle Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnaby, Stacey N.; Ross, Michael B.; Thaner, Ryan V.

In atomic systems, the mixing of metals results in distinct phase behavior that depends on the identity and bonding characteristics of the atoms. In nanoscale systems, the use of oligonucleotides as programmable “bonds” that link nanoparticle “atoms” into superlattices allows for the decoupling of atom identity and bonding. While much research in atomic systems is dedicated to understanding different phase behavior of mixed metals, it is not well understood on the nanoscale how changes in the nanoscale “bond” affect the phase behavior of nanoparticle crystals. In this work, the identity of the atom is kept the same but the chemicalmore » nature of the bond is altered, which is not possible in atomic systems, through the use of DNA and RNA bonding elements. These building blocks assemble into single crystal nanoparticle superlattices with mixed DNA and RNA bonding elements throughout. The nanoparticle crystals can be dynamically changed through the selective and enzymatic hydrolysis of the RNA bonding elements, resulting in superlattices that retain their crystalline structure and habit, while incorporating up to 35% random vacancies generated from the nanoparticles removed. Therefore, the bonding elements of nanoparticle crystals can be enzymatically and selectively addressed without affecting the nature of the atom.« less

SFG experiment and ab initio study of the chemisorption of CN - on low-index platinum surfaces

NASA Astrophysics Data System (ADS)

Tadjeddine, M.; Flament, J.-P.; Le Rille, A.; Tadjeddine, A.

2006-05-01

A dual analysis is proposed in order to have a better understanding of the adsorption of the cyanide ions on a platinum electrode. The SFG (Sum Frequency Generation) spectroscopy allows the in situ vibrational study and the SFG spectra of the CN - species adsorbed on single crystal Pt electrode allow a systematic study of the low-index platinum surfaces. This experimental work is supported by ab initio calculations using density functional theory and cluster models. For each surface orientation and each geometry, a cluster model of 20-30 Pt atoms has been built in order to interpret the chemisorption of the CN - ions through four kinds of adsorption geometry: on-top or bridge site, bonding via C or N atoms. Geometries have been optimized and adsorption energies, electronic properties and vibrational frequencies have been computed. From the electronic properties, we can propose an analysis of the bonding mechanism for each studied kind of adsorption. The SFG spectra of the CN -/Pt(1 1 1) system present an unique resonance owing to the top C adsorption. It is mainly the same for the CN -/Pt(1 0 0) system. It is also the case for the SFG spectra of the CN -/Pt(1 1 0) system recorded at negative electrochemical voltage; at more positive voltage, a second resonance appears at a lower frequency, owing to the top N adsorption. Experimental and theoretical values of the C-N stretching frequencies are in excellent agreement.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

Resonance of an unshared electron pair between two atoms connected by a single bond

PubMed Central

Pauling, Linus

1983-01-01

The reported structure of the dimer of a compound of bicovalent tin indicates that the tin-tin bond is of a new type. It can be described as involving resonance between two structures in which there is transfer of an electron pair from one tin atom to the other. The tin atoms are connected by a single covalent bond (each also forms two covalent bonds with carbon atoms), and an unshared electron pair resonates between the fourth sp3 orbitals of the two atoms. Similar structures probably occur in digermene and distannene. PMID:16593329

Effects of dilute aqueous NaCl solution on caffeine aggregation

NASA Astrophysics Data System (ADS)

Sharma, Bhanita; Paul, Sandip

2013-11-01

The effect of salt concentration on association properties of caffeine molecule was investigated by employing molecular dynamics simulations in isothermal-isobaric ensemble of eight caffeine molecules in pure water and three different salt (NaCl) concentrations, at 300 K temperature and 1 atm pressure. The concentration of caffeine was taken almost at the solubility limit. With increasing salt concentration, we observe enhancement of first peak height and appearance of a second peak in the caffeine-caffeine distribution function. Furthermore, our calculated solvent accessible area values and cluster structure analyses suggest formation of higher order caffeine cluster on addition of salt. The calculated hydrogen bond properties reveal that there is a modest decrease in the average number of water-caffeine hydrogen bonds on addition of NaCl salt. Also observed are: (i) decrease in probability of salt contact ion pair as well as decrease in the solvent separated ion pair formation with increasing salt concentration, (ii) a modest second shell collapse in the water structure, and (iii) dehydration of hydrophobic atomic sites of caffeine on addition of NaCl.

Effects of dilute aqueous NaCl solution on caffeine aggregation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Bhanita; Paul, Sandip, E-mail: sandipp@iitg.ernet.in

The effect of salt concentration on association properties of caffeine molecule was investigated by employing molecular dynamics simulations in isothermal-isobaric ensemble of eight caffeine molecules in pure water and three different salt (NaCl) concentrations, at 300 K temperature and 1 atm pressure. The concentration of caffeine was taken almost at the solubility limit. With increasing salt concentration, we observe enhancement of first peak height and appearance of a second peak in the caffeine-caffeine distribution function. Furthermore, our calculated solvent accessible area values and cluster structure analyses suggest formation of higher order caffeine cluster on addition of salt. The calculated hydrogenmore » bond properties reveal that there is a modest decrease in the average number of water-caffeine hydrogen bonds on addition of NaCl salt. Also observed are: (i) decrease in probability of salt contact ion pair as well as decrease in the solvent separated ion pair formation with increasing salt concentration, (ii) a modest second shell collapse in the water structure, and (iii) dehydration of hydrophobic atomic sites of caffeine on addition of NaCl.« less

Isotopic equilibria in aqueous clusters at low temperatures: Insights from the MB-pol many-body potential

NASA Astrophysics Data System (ADS)

Videla, Pablo E.; Rossky, Peter J.; Laria, Daniel

2018-02-01

By combining path-integrals molecular dynamics simulations with the accurate MB-pol potential energy surface, we investigate the role of alternative potential models on isotopic fractionation ratios between H and D atoms at dangling positions in water clusters at low temperatures. Our results show clear stabilizations of the lighter isotope at dangling sites, characterized by free energy differences ΔG that become comparable to or larger than kBT for temperatures below ˜75 K. The comparison between these results to those previously reported using the empirical q-TIP4P/F water model [P. E. Videla et al., J. Phys. Chem. Lett. 5, 2375 (2014)] reveals that the latter Hamiltonian overestimates the H stabilization by ˜25%. Moreover, predictions from the MB-pol model are in much better agreement with measured results reported for similar isotope equilibria at ice surfaces. The dissection of the quantum kinetic energies into orthogonal directions shows that the dominant differences between the two models are to be found in the anharmonic characteristics of the potential energy surfaces along OH bond directions involved in hydrogen bonds.

A comparison of the bonding in organoiron clusters

NASA Astrophysics Data System (ADS)

Buhl, Margaret L.; Long, Gary J.

1994-12-01

The Mössbauer effect hyperfine parameters and the results of the Fenske-Hall molecular orbit (mo) calculations have been used to study the electronic properties of trinuclear iron, tetranuclear iron butterfly, Fe-Co, and Fe-Cu carbonyl clusters. The more negative Fe charge and the larger Fe 4s population in an Fe(CO)4 fragment as compared with that in an Fe(CO)3 or an Fe(CO)2 fragment is a result of the CO ligands rather than the near-neighbor metals. The clusters which contain heterometals have more negative isomer shifts. The isomer shift correlated well with the sum of the Fe 4s orbital population and the Zeff these electrons experience. The mo wave functions and the atomic charges generally give a larger calculated Δ E Q than is observed, indicating the need to include Sternheimer factors in the calculation. The valence contribution dominates the EFG.

Bond-length relaxation in crystalline Si1-xGex alloys: An extended x-ray-absorption fine-structure study

NASA Astrophysics Data System (ADS)

Kajiyama, Hiroshi; Muramatsu, Shin-Ichi; Shimada, Toshikazu; Nishino, Yoichi

1992-06-01

Extended x-ray-absorption fine-structure spectra for crystalline Si1-xGex alloys, measured at the K edge of Ge at room temperature, are analyzed with a curve-fitting method based on the spherical-wave approximation. The Ge-Ge and Ge-Si bond lengths, coordination numbers of Ge and Si atoms around a Ge atom, and Debye-Waller factors of Ge and Si atoms are obtained. It is shown that Ge-Ge and Ge-Si bonds relax completely, for all Ge concentrations of their study, while the lattice constant varies monotonically, following Vegard's law. As noted by Bragg and later by Pauling and Huggins, the Ge-Ge and Ge-Si bond lengths are close to the sum of their constituent-element atomic radii: nearly 2.45 Å for Ge-Ge bonds and 2.40 Å for Ge-Si bonds. A study on the coordination around a Ge atom in the alloys revealed that Ge and Si atoms mix randomly throughout the compositional range studied.

Convenient Relations for the Estimation of Bond Ionicity in A-B Type Compounds.

ERIC Educational Resources Information Center

Barbe, Jacques

1983-01-01

Bond character is directly conditioned by the peculiar capacity of bonded atoms to exchange electrons; such a capacity is clearly illustrated by electronegativity. The determination of bond character using the electronegativity difference between the bonded atoms is discussed and an equation focusing on relationships between bonds is provided. (JN)

Nucleophilic ring opening of bridging thietanes in open triosmium cluster complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, R.D.; Belinski, J.A.

1992-07-01

The complexes Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}] (1) and Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}] (2) were obtained from the reactions of Os{sub 3}(CO){sub 10}({mu}{sub 3}-S) with 3,3-dimethylthietane (DMT) and thietane, respectively, at -42 {degree}C in the presence of Me{sub 3}NO. Compound 1 was characterized by a single-crystal X-ray diffraction analysis and was found to contain a DMT group bridging two of the nonbonded metal atoms in the open cluster of three metal atoms by using both lone pairs of electrons on the sulfur atom. Compound 1 reacted with bis(triphenylphosphine)nitrogen(1+) chloride ([PPN]Cl) at 25 {degrees}C tomore » yield the salt [PPN][Os{sub 3}-(CO){sub 9}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}Cl)({mu}{sub 3}-S)] (3; 76%), in which the chloride ion was added to one of the methylene groups of the DMT ring in a process that caused the ring to open by cleavage of one of the carbon-sulfur bonds. A 4-chloro-3,3-dimethylpropanethiolate ligand bridges the open edge of the anionic triosmium cluster. Compound 3 was converted to the neutral complex Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (4) by reaction with HCl at 25 {degrees}C. Compound 4 is structurally similar to 3, except that is contains a hydride ligand bridging one of the two metal-metal bonds. Compounds 1 and 2 react with HCl in CH{sub 2}Cl{sub 2} solvent to yield the neutral compounds 4 and Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (5) in 89% and 90% yields, respectively, in one step. 11 refs., 3 figs., 10 tabs.« less

Resonance bonding in XNgY (X = F, Cl, Br, I; Ng = Kr or Xe; Y = CN or NC) molecules: an NBO/NRT investigation.

PubMed

Song, Junjie; Su, Yue; Jia, Yanping; Chen, Lusheng; Zhang, Guiqiu

2018-05-07

Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY molecules should be better described as a resonance hybrid of ω-bonding and [Formula: see text]-type long-bonding structures: X: - Ng +  - Y, X - Ng + : Y - , and X ^ Y. The ω-bonding and long-bonding make competing contributions to the composite resonance hybrid due to the accurately preserved bond order conservation principle. We find that the resonance bonding is highly tunable for these noble-gas-containing molecules due to its dependence on the nature of the halogen X or the central noble-gas atoms Ng. When the molecule XNgY consists of a relatively lighter Ng atom, a relatively low-electronegative X atom, and the CN fragment rather than NC, the long-bonding structure X ^ Y tends to be highlighted. In contrast, the heavy Ng atom and high-electronegative X atom will enhance the ω-bonding structure. Overall, the present work provides electronic principles and chemical insights that help understand the bonding in these XNgY species.

Probing plasma fluorinated graphene via spectromicroscopy.

PubMed

Struzzi, C; Scardamaglia, M; Reckinger, N; Sezen, H; Amati, M; Gregoratti, L; Colomer, J-F; Ewels, C; Snyders, R; Bittencourt, C

2017-11-29

Plasma fluorination of graphene is studied using a combination of spectroscopy and microscopy techniques, giving insight into the yield and fluorination mechanism for functionalization of supported graphene with both CF 4 and SF 6 gas precursors. Ion acceleration during fluorination is used to probe the effect on grafting functionalities. Adatom clustering, which occurs with CF 4 plasma treatment, is suppressed when higher kinetic energy is supplied to the ions. During SF 6 plasma functionalization, the sulfur atoms tend to bond to bare copper areas instead of affecting the graphene chemistry, except when the kinetic energy of the ions is restricted. Using scanning photoelectron microscopy, with a 100 nm spatial resolution, the chemical bonding environment is evaluated in the fluorinated carbon network at selected regions and the functionalization homogeneity is controlled in individual graphene flakes.

Density functional study of the structural, electronic, and magnetic properties of Mo n and Mo n S ( n = 1 - 10) clusters

NASA Astrophysics Data System (ADS)

Ziane, M.; Amitouche, F.; Bouarab, S.; Vega, A.

2017-12-01

Structural and electronic properties of pure molybdenum Mo n and molybdenum-sulfide Mo n S ( n = 1 - 10) clusters were investigated in the framework of the density functional theory within the generalized gradient approximation to exchange and correlation with the aim of addressing how doping with a single S atom affects the geometries, magnetic properties, and reactivity of pure molybdenum clusters. These clusters exhibit a less marked tendency to dimerization than their isoelectronic Cr counterparts despite sharing their half-filled valence shell configuration. Doping with a single S impurity is enough to change the structure of the host molybdenum cluster to a large extent, as well as to modify the bonding pattern, the magnetic state and the magnetic moment distribution in the Mo host. Vertical ionization potentials and electron affinities are calculated to determine global reactivity indicators like the electronegativity and the chemical hardness. The results are discussed in terms of the thermodynamical and relative stabilities, charge transfer effects, and spin-polarized densities of electronic states.

Peculiar bonding associated with atomic doping and hidden honeycombs in borophene

NASA Astrophysics Data System (ADS)

Lee, Chi-Cheng; Feng, Baojie; D'angelo, Marie; Yukawa, Ryu; Liu, Ro-Ya; Kondo, Takahiro; Kumigashira, Hiroshi; Matsuda, Iwao; Ozaki, Taisuke

2018-02-01

Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly perfect electron donors for filling the graphitic σ bonding states without forming additional in-plane bonds by first-principles calculations. The dilute electron density distribution owing to the weak bonding surrounding the center atoms provides easier atomic-scale engineering and is highly tunable via in-plane strain, promising for practical applications, such as modulating the extraordinarily high thermal conductance that exceeds the reported value in graphene. The hidden honeycomb bonding structure suggests an unusual energy sequence of core electrons that has been verified by our high-resolution core-level photoelectron spectroscopy measurements. With the experimental and theoretical evidence, we demonstrate that borophene exhibits a peculiar bonding structure and is distinctive among two-dimensional materials.

In situ formation of the first proteinogenically functionalized [TeW6O24O2(Glu)]7– structure reveals unprecedented chemical and geometrical features of the Anderson-type cluster† †Electronic supplementary information (ESI) available: Full experimental details and additional figures are provided. See DOI: 10.1039/c6cc07004c Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Molitor, Christian; Bijelic, Aleksandar

2016-01-01

The chemistry of polyoxometalates (POMs) in a protein environment is an almost unexplored but highly relevant research field as important biological and pharmacological attributes of certain POMs are based on their interactions with proteins. We report on the A-type Anderson–Evans polyoxotungstate, [TeW6O24]6– (TEW), mediated crystallization of Coreopsis grandiflora aurone synthase (cgAUS1) using ∼0.24 mM protein and 1.0 mM TEW. The 1.78 Å crystal structure reveals the covalent binding of TEW to the protein under the formation of an unprecedented polyoxotungstate cluster, [TeW6O24O2(Glu)]7– (GluTEW). The polyoxotungstate–protein complex exhibits the first covalent bond between a protein and the A-type Anderson–Evans cluster, an archetype where up to now no hybrid structures exist. The polyoxotungstate is modified at two of its six addenda tungsten atoms, which covalently bind to the carboxylic oxygen atoms of glutamic acid (Glu157), leading to W–O distances of ∼2.35 Å. This ligand substitution reaction is accompanied by a reduction of the coordination number of two μ3 polyoxotungstate oxygen atoms. This is so far unique since all known hybridizations of the Anderson–Evans POM with organic units have been obtained via the functionalization of the B-type Anderson–Evans structure through its bridging oxygen atoms. The structure reported here proves the reactivity of this POM archetype's addenda atoms as it has been administered into the protein solution as a pre-assembled cluster. Moreover, the novel cluster [TeW6O24O2(Glu)]7– displays the great versatility of the Anderson–Evans POM class. PMID:27722437

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Baumann, Robert

1999-01-01

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, R.R.; Baumann, R.

1999-03-30

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Baumann, Robert

2003-08-26

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Bauman, Robert

2006-11-14

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Thermodynamics of hydrogen bond patterns in supramolecular assemblies of water molecules.

PubMed

Henry, Marc

2002-07-02

The PACHA (Partial Atomic Charges and Hardnesses Analysis) formalism is applied to various supramolecular assemblies of water molecules. After a detailed study of all available crystal structures for ice polymorphs, we shown that the hydrogen bond strength is roughly constant below 1 GPa and considerably weakened above that value. New hydrogen bond patterns are proposed for ice IV, V, and VI after (EB) (electrostatic balance) minimization. For other polymorphs, there is an almost perfect coincidence between experimental and predicted hydrogen bond patterns. The evolution of hydrogen bond energy as a function of molecular geometry in water clusters with up to 280 water molecules and in large supramolecular compounds is quantitatively described. Intermolecular hydrogen bonds are found to lie between -9 and -32 kJ mol-1, the stronger interaction occurs within the spherical fully disordered water droplet buried at the heart of Müller's superfullerene keplerate. The weakest one occurs in a chiral molecular snub cube built from six calix[4]resorcinarene and eight water molecules. Intramolecular hydrogen bonds are found in the range -10-100 kJ mol-1 and can thus be considerably stronger than intermolecular bonds. Finally, through the investigation of a clathrate type I compound, it was possible to obtain a deep insight of the host-guest interactions and self-assembly rules of water cages in these materials.

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape

PubMed Central

Manibog, Kristine; Sankar, Kannan; Kim, Sun-Ae; Zhang, Yunxiang; Jernigan, Robert L.; Sivasankar, Sanjeevi

2016-01-01

Classical cadherin cell–cell adhesion proteins are essential for the formation and maintenance of tissue structures; their primary function is to physically couple neighboring cells and withstand mechanical force. Cadherins from opposing cells bind in two distinct trans conformations: strand-swap dimers and X-dimers. As cadherins convert between these conformations, they form ideal bonds (i.e., adhesive interactions that are insensitive to force). However, the biophysical mechanism for ideal bond formation is unknown. Here, we integrate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis for cadherin ideal bond formation. Using simulations, we predict the energy landscape for cadherin adhesion, the transition pathways for interconversion between X-dimers and strand-swap dimers, and the cadherin structures that form ideal bonds. Based on these predictions, we engineer cadherin mutants that promote or inhibit ideal bond formation and measure their force-dependent kinetics using single-molecule force-clamp measurements with an atomic force microscope. Our data establish that cadherins adopt an intermediate conformation as they shuttle between X-dimers and strand-swap dimers; pulling on this conformation induces a torsional motion perpendicular to the pulling direction that unbinds the proteins and forms force-independent ideal bonds. Torsional motion is blocked when cadherins associate laterally in a cis orientation, suggesting that ideal bonds may play a role in mechanically regulating cadherin clustering on cell surfaces. PMID:27621473

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

PubMed Central

Ravindranath, Pradeep Anand; Sanner, Michel F.

2016-01-01

Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

(Carbonyl-1κC)bis­[2,3(η5)-cyclo­penta­dien­yl][μ3-(S-methyl trithio­carbonato)methylidyne-1:2:3κ4 C,S′′:C:C](triphenyl­phosphine-1κP)(μ3-sulfido-1:2:3κ3 S)dicobalt(II)iron(II) trifluoro­methane­sulfonate

PubMed Central

Manning, Anthony R.; McAdam, C. John; Palmer, Anthony J.; Simpson, Jim

2008-01-01

The asymmetric unit of the title compound, [FeCo2(C5H5)2(C3H3S3)S(C18H15P)(CO)]CF3SO3, consists of a triangular irondicobalt cluster cation and a trifluoro­methane­sulfonate anion. In the cation, the FeCo2 triangle is symmetrically capped on one face by an S atom and on the other by a C atom linked to a methyl trithio­carbonate residue that bridges the Fe—C bond. Each Co atom carries a cyclo­penta­dienyl ligand while the Fe atom coordinates to one carbonyl and one triphenyl­phosphine ligand. In the crystal structure, the cation is linked to the anion by a number of weak non-classical C—H⋯O and C—H⋯F hydrogen bonds and weak S⋯O (3.317 Å) and S⋯F (3.198 Å) inter­actions. The structure is further stabilized by additional inter­molecular C—H⋯O, C—H⋯F and O⋯O (2.942 Å) contacts, together with an unusual S⋯π(Cp) inter­action (S⋯centroid distance = 3.385 Å), generating an extended network. PMID:21202187

Ligand induced ferromagnetism in ZnO nanostructures.

PubMed

Wang, Qian; Sun, Qiang; Jena, P

2008-10-28

Complementary to the experimental finding that ZnO nanoparticles become ferromagnetic when coated with N and S containing ligands such as dodecylamine and dodecanethiol [Garcia et al., Nano Lett. 7, 1489 (2007)], we provide the first theoretical understanding of the origin of magnetism in ligated ZnO nanoparticles as well as the structural properties of the ligated systems by using density functional theory and generalized gradient approximation for exchange and correlation, and a cluster model for the nanoparticles. We show that N or S atoms of the ligand bind to the Zn sites. The accompanying changes in the Zn-O bond length, hybridization between Zn 4s orbitals with N 2p or S 3p orbitals, and consequently the redistribution of charges between Zn and O atoms result in a magnetic system where the 2p electrons in O and N, and 3p electrons in S sites are spin polarized. Furthermore, the sites nearest to the Zn atom attached to the ligand carry bulk of the magnetic moment. Studies, as a function of cluster size, also illustrate that magnetism resides only on the surface. Our results confirm that the use of ligands can pave a new way for introducing magnetism in ZnO nanostructures, which can be used to develop magnetic sensors to detect N and S containing molecules.

Metal cluster chemistry: Structure and stereochemistry in the polynuclear rhodium hydrides HnRhn[P(OR)3]2n

PubMed Central

Brown, R. K.; Williams, J. M.; Fredrich, M. F.; Day, V. W.; Sivak, A. J.; Muetterties, E. L.

1979-01-01

Crystallographic analyses of x-ray and neutron diffraction data have provided a definitive structural representation of {HRh[P(O-i-C3H7)3]2}2 and {HRh[P(OCH3)3]2}3. These polynuclear hydrides are generated from square planar H2Rh[P(OR)3]2 units by edge (hydrogen atom) sharing and by vertex (hydrogen atom) sharing to form the dimeric and trimeric structures, respectively. The square-planar units are held together through four-center and three-center two-electron Rh—H—Rh bonds in the dimer and trimer, respectively. The dimer and trimer molecules each add one molecule of hydrogen to form H[(i-C3H7O)3P]2RhH3Rh [P(O-i-C3H7)3]2 and H5Rh3[P(OCH3)3]6, respectively. NMR spectral information has served to define the stereochemical features of these polyhydrides. The significance of this chemistry in the metal cluster-metal surface analogy is described. PMID:16592645

AB Initi Molecular Dynamics Simulation of the Amorphous Structure of Ca-Mg-Cu and Ca-Mg-Zn Alloys (Postprint)

DTIC Science & Technology

2012-09-26

characteristic coordination poly- hedra present in an amorphous structure.[23,42] A coor- dination polyhedron is defined as an i-centered cluster with...vertices at the first-shell atom positions and edges coinciding with the interatomic bonds in the first shell.[45] Each coordination polyhedron can be...assigned a Voronoi signature (n3, n4, n5, n6), where nm is the number of vertices common to m polyhedron faces (or edges).[46] m is also called the

Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules

DTIC Science & Technology

2015-01-01

properties into atomic and bonding contributions, continue to be a focus of considerable attention, dating from early studies of Slater [12], Van Vleck [13...theory employing (Eisenschitz-London) spectral products of atomic eigenstates, familiar from early combined studies of covalent and van der Waals...of atoms and bonds in molecules provided by the present study , rather than to report highly accurate potential curves for the H3 molecule obtained

Efficient Nitrogen Fixation via a Redox-Flexible Single-Iron Site with Reverse-Dative Iron → Boron σ Bonding.

PubMed

Lu, Jun-Bo; Ma, Xue-Lu; Wang, Jia-Qi; Liu, Jin-Cheng; Xiao, Hai; Li, Jun

2018-05-10

Model systems of the FeMo cofactor of nitrogenase have been explored extensively in catalysis to gain insights into their ability for nitrogen fixation that is of vital importance to the human society. Here we investigate the trigonal pyramidal borane-ligand Fe complex by first-principles calculations, and find that the variation of oxidation state of Fe along the reaction path correlates with that of the reverse-dative Fe → B bonding. The redox-flexibility of the reverse-dative Fe → B bonding helps to provide an electron reservoir that buffers and stabilizes the evolution of Fe oxidation state, which is essential for forming the key intermediates of N 2 activation. Our work provides insights for understanding and optimizing homogeneous and surface single-atom catalysts with reverse-dative donating ligands for efficient dinitrogen fixation. The extension of this kind of molecular catalytic active center to heterogeneous catalysts with surface single-clusters is also discussed.

Iron Oxide Nanoparticles Employed as Seeds for the Induction of Microcrystalline Diamond Synthesis

PubMed Central

2008-01-01

Iron nanoparticles were employed to induce the synthesis of diamond on molybdenum, silicon, and quartz substrates. Diamond films were grown using conventional conditions for diamond synthesis by hot filament chemical vapor deposition, except that dispersed iron oxide nanoparticles replaced the seeding. X-ray diffraction, visible, and ultraviolet Raman Spectroscopy, energy-filtered transmission electron microscopy , electron energy-loss spectroscopy, and X-ray photoelectron spectroscopy (XPS) were employed to study the carbon bonding nature of the films and to analyze the carbon clustering around the seed nanoparticles leading to diamond synthesis. The results indicate that iron oxide nanoparticles lose the O atoms, becoming thus active C traps that induce the formation of a dense region of trigonally and tetrahedrally bonded carbon around them with the ensuing precipitation of diamond-type bonds that develop into microcrystalline diamond films under chemical vapor deposition conditions. This approach to diamond induction can be combined with dip pen nanolithography for the selective deposition of diamond and diamond patterning while avoiding surface damage associated to diamond-seeding methods.

Free energy landscape from path-sampling: application to the structural transition in LJ38

NASA Astrophysics Data System (ADS)

Adjanor, G.; Athènes, M.; Calvo, F.

2006-09-01

We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q4 bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.

A first-principles study of the influence of helium atoms on the optical response of small silver clusters.

PubMed

Pereiro, M; Baldomir, D; Arias, J E

2011-02-28

Optical excitation spectra of Ag(n) and Ag(n)@He(60) (n = 2, 8) clusters are investigated in the framework of the time-dependent density functional theory (TDDFT) within the linear response regime. We have performed the ab initio calculations for two different exact exchange functionals (GGA-exact and LDA-exact). The computed spectra of Ag(n)@He(60) clusters with the GGA-exact functional accounting for exchange-correlation effects are found to be generally in a relatively good agreement with the experiment. A strategy is proposed to obtain the ground-state structures of the Ag(n)@He(60) clusters and in the initial process of the geometry optimization, the He environment is simulated with buckyballs. A redshift of the silver clusters spectra is observed in the He environment with respect to the ones of bare silver clusters. This observation is discussed and explained in terms of a contraction of the Ag-He bonding length and a consequent confinement of the s valence electrons in silver clusters. Likewise, the Mie-Gans predictions combined with our TDDFT calculations also show that the dielectric effect produced by the He matrix is considerably less important in explaining the redshifting observed in the optical spectra of Ag(n)@He(60) clusters.

Two-leg SU ( 2 n ) spin ladder: A low-energy effective field theory approach

DOE PAGES

Lecheminant, P.; Tsvelik, A. M.

2015-05-07

We present a field-theory analysis of a model of two SU( 2n)-invariant magnetic chains coupled by a generic interaction preserving time reversal and inversion symmetry. Contrary to the SU(2)-invariant case the zero-temperature phase diagram of such two-leg spin ladder does not contain topological phases. Thus, only generalized Valence Bond Solid phases are stabilized when n > 1 with different wave vectors and ground-state degeneracies. In particular, we find a phase which is made of a cluster of 2n spins put in an SU( 2n) singlet state. For n = 3, this cluster phase is relevant to ¹⁷³Yb ultracold atoms, withmore » an emergent SU(6) symmetry, loaded in a double-well optical lattice.« less

Combinatorial Broadening Mechanism of O-H Stretching Bands in H-Bonded Molecular Clusters

NASA Astrophysics Data System (ADS)

Pitsevich, G. A.; Doroshenko, I. Yu.; Pogorelov, V. E.; Pettersson, L. G. M.; Sablinskas, V.; Sapeshko, V. V.; Balevicius, V.

2016-07-01

A new mechanism for combinatorial broadening of donor-OH stretching-vibration absorption bands in molecular clusters with H-bonds is proposed. It enables the experimentally observed increase of the O-H stretching-vibration bandwidth with increasing number of molecules in H-bonded clusters to be explained. Knowledge of the half-width of the OH stretching-vibration absorption band in the dimer and the number of H-bonds in the analyzed cluster is suffi cient in the zeroth-order approximation to estimate the O-H stretching-absorption bands in clusters containing several molecules. Good agreement between the calculated and published experimental half-widths of the OH stretching-vibration absorption bands in MeOH and PrOH clusters was obtained using this approach.

Synthesis of 2H- and 13C-substituted dithanes

DOEpatents

Martinez, Rodolfo A.; Alvarez, Marc A.; Silks, III, Louis A.; Unkefer, Clifford J.

2003-01-01

The present invention is directed to labeled compounds, [2-.sup.13 C]dithiane wherein the .sup.13 C atom is directly bonded to one or two deuterium atoms. The present invention is also directed to processes of preparing [2-.sup.13 C]dithiane wherein the .sup.13 C atom is directly bonded to one or two deuterium atoms. The present invention is also directed to labeled compounds, e.g., [.sup.2 H.sub.1-2, .sup.13 C]methanol (arylthio)-, acetates wherein the .sup.13 C atom is directly bonded to exactly one or two deuterium atoms.

Synthesis Of 2h- And 13c-Substituted Dithanes

DOEpatents

Martinez, Rodolfo A.; Alvarez, Marc A.; Silks, III, Louis A.; Unkefer, Clifford J.

2004-05-04

The present invention is directed to labeled compounds, [2-.sup.13 C]dithane wherein the .sup.13 C atom is directly bonded to one or two deuterium atoms. The present invention is also directed to processes of preparing [2-.sup.13 C]dithane wherein the .sup.13 C atom is directly bonded to one or two deuterium atoms. The present invention is also directed to labeled compounds, e.g., [.sup.2 H.sub.1-2, .sup.13 C]methanol (arylthio)-, acetates wherein the .sup.13 C atom is directly bonded to exactly one or two deuterium atoms.

The Halogen Bond in the Design of Functional Supramolecular Materials: Recent Advances

PubMed Central

2013-01-01

Halogen bonding is an emerging noncovalent interaction for constructing supramolecular assemblies. Though similar to the more familiar hydrogen bonding, four primary differences between these two interactions make halogen bonding a unique tool for molecular recognition and the design of functional materials. First, halogen bonds tend to be much more directional than (single) hydrogen bonds. Second, the interaction strength scales with the polarizability of the bond-donor atom, a feature that researchers can tune through single-atom mutation. In addition, halogen bonds are hydrophobic whereas hydrogen bonds are hydrophilic. Lastly, the size of the bond-donor atom (halogen) is significantly larger than hydrogen. As a result, halogen bonding provides supramolecular chemists with design tools that cannot be easily met with other types of noncovalent interactions and opens up unprecedented possibilities in the design of smart functional materials. This Account highlights the recent advances in the design of halogen-bond-based functional materials. Each of the unique features of halogen bonding, directionality, tunable interaction strength, hydrophobicity, and large donor atom size, makes a difference. Taking advantage of the hydrophobicity, researchers have designed small-size ion transporters. The large halogen atom size provided a platform for constructing all-organic light-emitting crystals that efficiently generate triplet electrons and have a high phosphorescence quantum yield. The tunable interaction strengths provide tools for understanding light-induced macroscopic motions in photoresponsive azobenzene-containing polymers, and the directionality renders halogen bonding useful in the design on functional supramolecular liquid crystals and gel-phase materials. Although halogen bond based functional materials design is still in its infancy, we foresee a bright future for this field. We expect that materials designed based on halogen bonding could lead to applications in biomimetics, optics/photonics, functional surfaces, and photoswitchable supramolecules. PMID:23805801

Methane combustion reactivity during the metal→metallic oxide transformation of Pd-Pt catalysts: Effect of oxygen pressure

NASA Astrophysics Data System (ADS)

Qi, Wenjie; Ran, Jingyu; Zhang, Zhien; Niu, Juntian; Zhang, Peng; Fu, Lijuan; Hu, Bo; Li, Qilai

2018-03-01

Density functional theory combined with kinetic models were used to probe different kinetics consequences by which methane activation on different oxygen chemical potential surfaces as oxygen pressure increased. The metallic oxide → metal transformation temperature of Pd-Pt catalysts increased with the increase of the Pd content or/and O2 pressure. The methane conversion rate on Pt catalyst increased and then decreased to a constant value when increasing the O2 pressure, and Pd catalyst showed a poor activity performance in the case of low O2 pressure. Moreover, its activity increased as the oxygen chemical potential for O2 pressure increased in the range of 2.5-10 KPa. For metal clusters, the Csbnd H bond and Odbnd O bond activation steps occurred predominantly on *-* site pairs. The methane conversion rate was determined by O2 pressure because the adsorbed O atoms were rapidly consumed by other adsorbed species in this kinetic regime. As the O2 pressure increased, the metallic active sites for methane activation were decreased and there was no longer lack of adsorbed O atoms, resulting in the decrease of the methane conversion rate. Furthermore, when the metallic surfaces were completely covered by adsorbed oxygen atoms at higher oxygen chemical potentials, Pt catalyst showed a poor activity due to a high Csbnd H bond activation barrier on O*sbnd O*. In the case of high O2 pressure, Pd atoms preferred to segregate to the active surface of Pd-Pt catalysts, leading to the formation of PdO surfaces. The increase of Pd segregation promoted a subsequent increase in active sites and methane conversion rate. The PdO was much more active than metallic and O* saturated surfaces for methane activation, inferred from the theory and experimental study. Pd-rich bimetallic catalyst (75% molar Pd) showed a dual high methane combustion activity on O2-poor and O2-rich conditions.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Mechanistic Insights into Ring Cleavage and Contraction of Benzene over a Titanium Hydride Cluster.

PubMed

Kang, Xiaohui; Luo, Gen; Luo, Lun; Hu, Shaowei; Luo, Yi; Hou, Zhaomin

2016-09-14

Carbon-carbon bond cleavage of benzene by transition metals is of great fundamental interest and practical importance, as this transformation is involved in the production of fuels and other important chemicals in the industrial hydrocracking of naphtha on solid catalysts. Although this transformation is thought to rely on cooperation of multiple metal sites, molecular-level information on the reaction mechanism has remained scarce to date. Here, we report the DFT studies of the ring cleavage and contraction of benzene by a molecular trinuclear titanium hydride cluster. Our studies suggest that the reaction is initiated by benzene coordination, followed by H2 release, C6H6 hydrometalation, repeated C-C and C-H bond cleavage and formation to give a MeC5H4 unit, and insertion of a Ti atom into the MeC5H4 unit with release of H2 to give a metallacycle product. The C-C bond cleavage and ring contraction of toluene can also occur in a similar fashion, though some details are different due to the presence of the methyl substituent. Obviously, the facile release of H2 from the metal hydride cluster to provide electrons and to alter the charge population at the metal centers, in combination with the flexible metal-hydride connections and dynamic redox behavior of the trimetallic framework, has enabled this unusual transformation to occur. This work has not only provided unprecedented insights into the activation and transformation of benzene over a multimetallic framework but it may also offer help in the design of new molecular catalysts for the activation and transformation of inactive aromatics.

Stability chart of small mixed 4He-3He clusters

NASA Astrophysics Data System (ADS)

Guardiola, R.; Navarro, J.

2003-11-01

A stability chart of mixed 4He and 3He clusters has been obtained by means of the diffusion Monte Carlo method, using both the Aziz HFD-B and the Tang-Toennies-Yiu atom-atom interaction. The investigated clusters contain up to eight 4He atoms and up to 20 3He atoms. One single 4He binds 20 3He atoms, and two 4He bind 1, 2, 8, and more than 14 3He atoms. All clusters with three or more 4He atoms are bound, although the combinations 4He33He9,10,11 and 4He34He9 are metastable. Clusters with 2, 8, and 20 3He atoms are particularly stable and define magic 3He numbers.

Tried and True: The Romance of the Atoms--Animated Atomic Attractions

ERIC Educational Resources Information Center

Hibbitt, Catherine

2010-01-01

Since the formation of atomic bonds is active, the authors sought a way of learning through drama or kinetic activity. To achieve this goal, they developed an activity called Romance of the Atoms. The activity requires students to use computer-animation technology to develop short cartoons that explain atomic classification and bonds. This…

The effect of surface and interface on Neel transition temperature of low-dimensional antiferromagnetic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Wen; Zhou, Zhaofeng, E-mail: zfzhou@xtu.edu.cn; Zhong, Yuan

2015-11-15

Incorporating the bond order-length-strength (BOLS) notion with the Ising premise, we have modeled the size dependence of the Neel transition temperature (T{sub N}) of antiferromagnetic nanomaterials. Reproduction of the size trends reveals that surface atomic undercoordination induces bond contraction, and interfacial hetero-coordination induces bond nature alteration. Both surface and interface of nanomaterials modulate the T{sub N} by adjusting the atomic cohesive energy. The T{sub N} is related to the atomic cohesive/exchange energy that is lowered by the coordination number (CN) imperfection of the undercoordinated atoms near the surface and altered by the changed bond nature of epitaxial interface. A numericalmore » match between predictions and measurements reveals that the T{sub N} of antiferromagnetic nanomaterials declines with reduced size and increases with both the strengthening of heterogeneous bond and the increase of the bond number.« less

Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zarycz, M. Natalia C., E-mail: mnzarycz@gmail.com; Provasi, Patricio F., E-mail: patricio@unne.edu.ar; Sauer, Stephan P. A., E-mail: sauer@kiku.dk

2014-10-21

We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing themore » changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.« less

Platinum clusters with precise numbers of atoms for preparative-scale catalysis.

PubMed

Imaoka, Takane; Akanuma, Yuki; Haruta, Naoki; Tsuchiya, Shogo; Ishihara, Kentaro; Okayasu, Takeshi; Chun, Wang-Jae; Takahashi, Masaki; Yamamoto, Kimihisa

2017-09-25

Subnanometer noble metal clusters have enormous potential, mainly for catalytic applications. Because a difference of only one atom may cause significant changes in their reactivity, a preparation method with atomic-level precision is essential. Although such a precision with enough scalability has been achieved by gas-phase synthesis, large-scale preparation is still at the frontier, hampering practical applications. We now show the atom-precise and fully scalable synthesis of platinum clusters on a milligram scale from tiara-like platinum complexes with various ring numbers (n = 5-13). Low-temperature calcination of the complexes on a carbon support under hydrogen stream affords monodispersed platinum clusters, whose atomicity is equivalent to that of the precursor complex. One of the clusters (Pt 10 ) exhibits high catalytic activity in the hydrogenation of styrene compared to that of the other clusters. This method opens an avenue for the application of these clusters to preparative-scale catalysis.The catalytic activity of a noble metal nanocluster is tied to its atomicity. Here, the authors report an atom-precise, fully scalable synthesis of platinum clusters from molecular ring precursors, and show that a variation of only one atom can dramatically change a cluster's reactivity.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Nitrilotris(methylenephosphonato)potassium K[μ{sup 6}-NH(CH{sub 2}PO{sub 3}){sub 3}H{sub 4}]: Synthesis, structure, and the nature of the K–O chemical bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somov, N. V., E-mail: somov@phys.unn.ru; Chausov, F. F., E-mail: xps@ftiudm.ru; Zakirova, R. M., E-mail: ftt@udsu.ru

2016-07-15

The crystal structure of nitrilotris(methylenephosphonato)potassium K[μ{sup 6}-NH(CH{sub 2}PO{sub 3}){sub 3}H{sub 4}]—a three-dimensional coordination polymer—was determined. The potassium atom is coordinated by seven oxygen atoms belonging to the six nearest ligand molecules, resulting in distorted monocapped octahedral coordination geometry. The complex contains the four-membered chelate ring K–O–P–O. The K–O chemical bond is predominantly ionic. Meanwhile, the bonds of the potassium atom with some oxygen atoms have a noticeable covalent component. In addition to coordination bonds, the molecules in the crystal packing are linked by hydrogen bonds.

Dispersion interactions between neighboring Bi atoms in (BiH3 )2 and Te(BiR2 )2.

PubMed

Haack, Rebekka; Schulz, Stephan; Jansen, Georg

2018-03-13

Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR 2 ) 2 molecules (R = H, Me, Et) and in (BiH 3 ) 2 were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn-syn and syn-anti conformers of Te(BiR 2 ) 2 (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE PAGES

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-24

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Hydrogen bonding between hydrides of the upper-right part of the periodic table

NASA Astrophysics Data System (ADS)

Simončič, Matjaž; Urbic, Tomaz

2018-05-01

One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. The strength of the bond depends on numerous factors, among them the electronegativity of participating atoms. In this work we calculated the strength of hydrogen bonds between hydrides of the upper-right part of the periodic table (C, N, O, F, P, S, Cl, As, Se, Br) using quantum-chemical methods. The aim was to determine what influences the strength of strong and weak hydrogen bonds in simple hydrides. Various relationships were checked. A relation between the strength of the bond and the electronegativity of the participating atoms was found. We also observed a correlation between the strength of hydrogen bonds and the inter-atomic distances, along with the dependence on the charge transfer on the atom of the donor. We also report characteristic geometries of different dimers.

Interfacial structure of two-dimensional epitaxial Er silicide on Si(111)

NASA Astrophysics Data System (ADS)

Tuilier, M. H.; Wetzel, P.; Pirri, C.; Bolmont, D.; Gewinner, G.

1994-07-01

Auger-electron diffraction (AED) and surface-extended x-ray-absorption fine structure (SEXAFS) have been used to obtain a complete description of the atomic structure of a two-dimensional epitaxial Er silicide layer on Si(111). AED reveals that a monolayer of Er is located underneath a buckled Si double layer. The relevant Er-Si interlayer spacings are determined by means of single scattering cluster simulations and a R-factor analysis to be 1.92+/-0.05 Å to the first and 2.70+/-0.05 Å to the second Si top layer. Er near-neighbor bond lengths and coordination numbers are obtained independently from polarization-dependent SEXAFS. The SEXAFS data, when combined with the Si top-layer geometry inferred from AED, permit the determination of the atomic positions at the silicide/Si(111) interface. The Er is found to reside in relaxed T4 sites of Si(111) with a single Er-Si distance of 3.09+/-0.04 Å to the first- and second-layer Si atoms of the substrate.

Adsorption of formamide over pristine and Al-doped boron nitride nanosheets: A dispersion-corrected DFT study.

PubMed

Esrafili, Mehdi D; Mousavian, Parisasadat; Arjomandi Rad, Farzad

2018-06-01

Using the dispersion-corrected DFT calculations, different adsorption modes of formamide molecule are studied over the pristine and Al-doped boron nitride nanosheets (BNNS). It is found that the interaction between the Al atom and its neighboring N atoms in the Al-doped BNNS is very strong, which would hinder the dispersion and clustering of the Al atoms over the BNNS surface. Unlike the pristine nanosheet, the electronic properties of Al-doped BNNS are very sensitive to the formamide adsorption. The adsorption energies of formamide over the Al-doped sheet are in the range of -0.93 to -1.85 eV, which indicates the quite strong interaction of this molecule with the surface. Moreover, the dehydrogenation of formamide over the Al-doped BNNS is examined. According to our results, the N-H bond scission of formamide is more energetically favorable than the C-H one. Copyright © 2018 Elsevier Inc. All rights reserved.

On the nature of bonding in binary Be2O2 and Si2O2 clusters: rhombic four-center four-electron π and σ bonds.

PubMed

Wang, Kang; Wang, Ying-Jin; Li, Da-Zhi; Ou, Ting; Zhao, Xiao-Yun; Zhai, Hua-Jin

2016-04-14

The structural and electronic properties and chemical bonding of binary Be2O2 and Si2O2 clusters have been studied using quantum chemical calculations at the B3LYP level. For the Be2O2 cluster, the potential energy surface is probed by unbiased structural searches and the global-minimum structure was established using the B3LYP calculations, complemented by PBE0 and single-point CCSD(T) calculations for top isomers. The perfectly planar D2h Be2O2 ((1)Ag) global minimum is well defined, being at least 3.64 eV lower in energy than alternative structures at the CCSD(T)//B3LYP/aug-cc-pVTZ level. Chemical bonding analyses show that D2h Be2O2 and Si2O2 clusters possess the rhombic four-center four-electron (4c-4e) π bond, that is, the o-bond, a conception derived from electron-deficient boron oxide clusters lately. Furthermore, the Be2O2 and Si2O2 clusters also exhibit rhombic 4c-4e σ bonds, both for the radial and tangential σ frameworks (σr and σt). The σt framework is classified as an o-bond only formally, due to the secondary contribution from the Be/Si s component. The three-fold (π, σr, and σt) o-bonds in Be2O2 and Si2O2 are considered to resemble the three-fold aromaticity in all-metal Al4(2-) dianions. A 4c-4e o-bond makes use of four O 2p electrons, which would otherwise be two lone-pairs, for a delocalized and completely bonding orbital, as well as a residual nonbonding orbital. Three-fold o-bonds thus greatly stabilize the binary Be2O2 and Si2O2 clusters. We anticipate that the bonding concept should be applicable to additional molecular systems, including those with larger heterocyclic rings.

Electronegativity determination of individual surface atoms by atomic force microscopy.

PubMed

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-04-26

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.

Electronegativity determination of individual surface atoms by atomic force microscopy

PubMed Central

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-01-01

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale. PMID:28443645

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Donghai; Lebarbier, Vanessa M.; Rousseau, Roger

In a combined experimental and first-principles density functional theory (DFT) study, benzene steam reforming (BSR) over MgAl 2O 4 supported Rh and Ir catalysts was investigated. Experimentally, it has been found that both highly dispersed Rh and Ir clusters (1-2 nm) on the MgAl 2O 4 spinel support are stable during the BSR in the temperature range of 700-850°C. Compared to the Ir/MgAl 2O 4 catalyst, the Rh/MgAl 2O 4 catalyst is more active with higher benzene turnover frequency and conversion. At typical steam conditions with the steam-to-carbon ratio > 12, the benzene conversion is only a weak function ofmore » the H 2O concentration in the feed. This suggests that the initial benzene decomposition step rather than the benzene adsorption is most likely the rate-determined step in BSR over supported Rh and Ir catalysts. In order to understand the differences between the two catalysts, we followed with a comparative DFT study of initial benzene decomposition pathways over two representative model systems for each supported metal (Rh and Ir) catalysts. A periodic terrace (111) surface and an amorphous 50-atom metal cluster with a diameter of 1.0 nm were used to represent the two supported model catalysts under low and high dispersion conditions. Our DFT results show that the decreasing catalyst particle size enhances the benzene decomposition on supported Rh catalysts by lowering both C-C and C-H bond scission. The activation barriers of the C-C and the C-H bond scission decrease from 1.60 and 1.61 eV on the Rh(111) surface to 1.34 and 1.26 eV on the Rh50 cluster. For supported Ir catalysts, the decreasing particle size only affects the C-C scission. The activation barrier of the C-C scission of benzene decreases from 1.60 eV on the Ir(111) surface to 1.35 eV on the Ir50 cluster while the barriers of the C-H scission are practically the same. The experimentally measured higher BSR activity on the supported highly dispersed Rh catalyst can be rationalized by the thermodynamic limitation for the very first C-C bond scission of benzene on the small Ir50 catalyst. The C-C bond scission of benzene on the small Ir50 catalyst is highly endothermic although the barrier is competitive with the barriers of both the C-C and the C-H bond-breakings on the small Rh50 catalyst. The calculations also imply that, for the supported Rh catalysts the C-C and C-H bond scissions are competitive, independently of the Rh cluster sizes. After the initial dissociation step via either the C-C or the C-H bond scission, the C-H bond breaking seems to be more favorable rather than the C-C bond breaking on the larger Rh terrace surface. This work was financially supported by the United States Department of Energy’s Office of Biomass Program’s. Computing time was granted by a user project at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Effect of oxygen impurities on properties of the ternary superconductor SnMo/sub 6/S/sub 8/: Extended x-ray-absorption fine-structure determination of bond distances and local-density cluster calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guenzburger, D.; Ellis, D.E.; Montano, P.A.

1985-10-01

Electronic structure calculations were performed for clusters representing the Chevrel-phase SnMo/sub 6/S/sub 8/, with and without oxygen doping. In order to obtain the local structure around the Sn atom, extended x-ray-absorption fine-structure (EXAFS) measurements were made with synchro- tron radiation. The interatomic distances obtained experimentally were used in the calculations. The effect of oxygen doping on the Moessbauer isomer shift and quadrupole splitting values of /sup 119/Sn was investigated theoretically and compared with reported experimental values. The effect of oxygen substitution on the density of states at the Fermi energy of the (Mo/sub 6/S/sub 8/)/sup 2 -/ cluster was alsomore » studied. The results suggest that oxygen doping does not alter significantly the electronic structure of SnMo/sub 6/S/sub 8/.« less

Structural Analysis of Cubane-Type Iron Clusters

PubMed Central

Tan, Lay Ling; Holm, R. H.; Lee, Sonny C.

2013-01-01

The generalized cluster type [M4(μ3-Q)4Ln]x contains the cubane-type [M4Q4]z core unit that can approach, but typically deviates from, perfect Td symmetry. The geometric properties of this structure have been analyzed with reference to Td symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M4, Q4) and the total [M4Q4] core (as a tetracapped M4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe4Q4] (Q = S2−, Se2−, Te2−, [NPR3]−, [NR]2−) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information. PMID:24072952

Structural Analysis of Cubane-Type Iron Clusters.

PubMed

Tan, Lay Ling; Holm, R H; Lee, Sonny C

2013-07-13

The generalized cluster type [M 4 (μ 3 -Q) 4 L n ] x contains the cubane-type [M 4 Q 4 ] z core unit that can approach, but typically deviates from, perfect T d symmetry. The geometric properties of this structure have been analyzed with reference to T d symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M 4 , Q 4 ) and the total [M 4 Q 4 ] core (as a tetracapped M 4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe 4 Q 4 ] (Q = S 2- , Se 2- , Te 2- , [NPR 3 ] - , [NR] 2- ) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information.

Method and apparatus for differential spectroscopic atomic-imaging using scanning tunneling microscopy

DOEpatents

Kazmerski, Lawrence L.

1990-01-01

A Method and apparatus for differential spectroscopic atomic-imaging is disclosed for spatial resolution and imaging for display not only individual atoms on a sample surface, but also bonding and the specific atomic species in such bond. The apparatus includes a scanning tunneling microscope (STM) that is modified to include photon biasing, preferably a tuneable laser, modulating electronic surface biasing for the sample, and temperature biasing, preferably a vibration-free refrigerated sample mounting stage. Computer control and data processing and visual display components are also included. The method includes modulating the electronic bias voltage with and without selected photon wavelengths and frequency biasing under a stabilizing (usually cold) bias temperature to detect bonding and specific atomic species in the bonds as the STM rasters the sample. This data is processed along with atomic spatial topography data obtained from the STM raster scan to create a real-time visual image of the atoms on the sample surface.

Atomic insight into tribochemical wear mechanism of silicon at the Si/SiO2 interface in aqueous environment: Molecular dynamics simulations using ReaxFF reactive force field

NASA Astrophysics Data System (ADS)

Wen, Jialin; Ma, Tianbao; Zhang, Weiwei; Psofogiannakis, George; van Duin, Adri C. T.; Chen, Lei; Qian, Linmao; Hu, Yuanzhong; Lu, Xinchun

2016-12-01

In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO2 interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si-O-Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si-Si bonds in the stretched Si-Si-O-Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si-O-Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si-O-Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.

AceDRG: a stereochemical description generator for ligands

PubMed Central

Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

2017-01-01

The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307

Coexistence of cyclic (CH3OH)2(H2O)8 heterodecamer and acyclic water trimer in the channels of silver-azelate framework

NASA Astrophysics Data System (ADS)

Luo, Geng-Geng; Zhu, Rui-Min; He, Wei-Jun; Li, Ming-Zhi; Zhao, Qing-Hua; Li, Dong-Xu; Dai, Jing-Cao

2012-08-01

Flexible azelaic acid (H2aze) and 1,3-bis(4-pyridyl)propane) (bpp) react ultrasonically with silver(I) oxide, generating a new metal-organic framework [Ag2(bpp)2(aze)·7H2O·CH3OH]n (1) that forms a 3D supramolecular structure through H-bonding interactions between solvent molecules and carboxylate O atoms with void spaces. Two kinds of solvent clusters, discrete cyclic (CH3OH)2(H2O)8 heterodecameric and acyclic water trimeric clusters occupy the channels in the structure. Furthermore, 1 exhibits strong photoluminescence maximized at 500 nm upon 350 nm excitation at room temperature, of which CIE chromaticity ordinate (x = 0.28, y = 0.44) is close to that of edge of green component.

The Crystal Structure of Ba 17Sm 10Cl 64

NASA Astrophysics Data System (ADS)

Liu, Guo; Eick, Harry A.

1999-08-01

The structure of Ba17Sm10Cl64, prepared by solvolytic extraction of a program-cooled 1:1 BaCl2:SmCl3 molar mixture sealed in a quartz tube and heated to 750°C, was determined from single-crystal X-ray diffraction data. The compound exhibits cubic symmetry, space group Pa3 (No. 205) with a=21.366(2) Å and Z=4. Refinement effected with I>2σ(I) yielded R1= 0.0926 and wR2=0.216. One Ba atom is 12-coordinated by Cl atoms in a distorted icosahedral arrangement; the three other Ba atoms are 10-coordinated in a distorted bicapped cubic arrangement. There are two Sm atom sites. The coordination around one Sm atom is best described as square antiprismatic, but one Sm-Cl distance is too long for effective bonding. The other Sm atom site, occupied statistically by {1}/{3}Ba and {2}/{3}Sm atoms, is 9-coordinated by Cl atoms in a monocapped square antiprismatic arrangement. The two types of Sm sites combine to form an M6Cl37 cuboctahedral cluster of the composition BaSm5Cl37. It is shown that the cβ phase identified previously in the Yb-F and related fluoride systems is probably isostructural with Ba17Sm10Cl64.

Application of the Covalent Bond Classification Method for the Teaching of Inorganic Chemistry

ERIC Educational Resources Information Center

Green, Malcolm L. H.; Parkin, Gerard

2014-01-01

The Covalent Bond Classification (CBC) method provides a means to classify covalent molecules according to the number and types of bonds that surround an atom of interest. This approach is based on an elementary molecular orbital analysis of the bonding involving the central atom (M), with the various interactions being classified according to the…

Introducing new reactivity descriptors: "Bond reactivity indices." Comparison of the new definitions and atomic reactivity indices.

PubMed

Sánchez-Márquez, Jesús

2016-11-21

A new methodology to obtain reactivity indices has been defined. This is based on reactivity functions such as the Fukui function or the dual descriptor and makes it possible to project the information of reactivity functions over molecular orbitals instead of the atoms of the molecule (atomic reactivity indices). The methodology focuses on the molecule's natural bond orbitals (bond reactivity indices) because these orbitals (with physical meaning) have the advantage of being very localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region. This methodology gives a reactivity index for every Natural Bond Orbital (NBO), and we have verified that they have equivalent information to the reactivity functions. A representative set of molecules has been used to test the new definitions. Also, the bond reactivity index has been related with the atomic reactivity one, and complementary information has been obtained from the comparison. Finally, a new atomic reactivity index has been defined and compared with previous definitions.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

PubMed

Sugimoto, Yoshiaki; Yurtsever, Ayhan; Hirayama, Naoki; Abe, Masayuki; Morita, Seizo

2014-07-11

Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

Structures of 38-atom gold-platinum nanoalloy clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

A valence bond study of three-center four-electron pi bonding: electronegativity vs electroneutrality.

PubMed

DeBlase, Andrew; Licata, Megan; Galbraith, John Morrison

2008-12-18

Three-center four-electron (3c4e) pi bonding systems analogous to that of the ozone molecule have been studied using modern valence bond theory. Molecules studied herein consist of combinations of first row atoms C, N, and O with the addition of H atoms where appropriate in order to preserve the 3c4e pi system. Breathing orbital valence bond (BOVB) calculations were preformed at the B3LYP/6-31G**-optimized geometries in order to determine structural weights, pi charge distributions, resonance energies, and pi bond energies. It is found that the most weighted VB structure depends on atomic electronegativity and charge distribution, with electronegativity as the dominant factor. By nature, these systems are delocalized, and therefore, resonance energy is the main contributor to pi bond energies. Molecules with a single dominant VB structure have low resonance energies and therefore low pi bond energies.

Crystal structure of N′′-benzyl-N′′-[3-(benzyl­dimethyl­aza­nium­yl)prop­yl]-N,N,N′,N′-tetra­methyl­guanidinium bis­(tetra­phenyl­borate)

PubMed Central

Tiritiris, Ioannis; Kantlehner, Willi

2015-01-01

In the crystal structure of the title salt, C24H38N4 2+·2C24H20B−, the C—N bond lengths in the central CN3 unit of the guanidinium ion are 1.3364 (13), 1.3407 (13) and 1.3539 (13) Å, indicating partial double-bond character. The central C atom is bonded to the three N atoms in a nearly ideal trigonal–planar geometry and the positive charge is delocalized in the CN3 plane. The bonds between the N atoms and the terminal methyl groups of the guanidinium moiety and the four C—N bonds to the central N atom of the (benzyl­dimethyl­aza­nium­yl)propyl group have single-bond character. In the crystal, C—H⋯π inter­actions between the guanidin­ium H atoms and the phenyl C atoms of the tetra­phenyl­borate ions are present, leading to the formation of a two-dimensional supra­molecular pattern parallel to the ac plane. PMID:26870511

Mid-infrared signatures of hydroxyl containing water clusters: Infrared laser Stark spectroscopy of OH–H{sub 2}O and OH(D{sub 2}O){sub n} (n = 1-3)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, Federico J.; INFIQC, Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón, X5000HUA Córdoba; Brice, Joseph T.

2015-10-28

Small water clusters containing a single hydroxyl radical are synthesized in liquid helium droplets. The OH–H{sub 2}O and OH(D{sub 2}O){sub n} clusters (n = 1-3) are probed with infrared laser spectroscopy in the vicinity of the hydroxyl radical OH stretch vibration. Experimental band origins are qualitatively consistent with ab initio calculations of the global minimum structures; however, frequency shifts from isolated OH are significantly over-predicted by both B3LYP and MP2 methods. An effective Hamiltonian that accounts for partial quenching of electronic angular momentum is used to analyze Stark spectra of the OH–H{sub 2}O and OH–D{sub 2}O binary complexes, revealing amore » 3.70(5) D permanent electric dipole moment. Computations of the dipole moment are in good agreement with experiment when large-amplitude vibrational averaging is taken into account. Polarization spectroscopy is employed to characterize two vibrational bands assigned to OH(D{sub 2}O){sub 2}, revealing two nearly isoenergetic cyclic isomers that differ in the orientation of the non-hydrogen-bonded deuterium atoms relative to the plane of the three oxygen atoms. The dipole moments for these clusters are determined to be approximately 2.5 and 1.8 D for “up-up” and “up-down” structures, respectively. Hydroxyl stretching bands of larger clusters containing three or more D{sub 2}O molecules are observed shifted approximately 300 cm{sup −1} to the red of the isolated OH radical. Pressure dependence studies and ab initio calculations imply the presence of multiple cyclic isomers of OH(D{sub 2}O){sub 3}.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations.

PubMed

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J

2018-04-28

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s -1 ) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

NASA Astrophysics Data System (ADS)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-01

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s-1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

PubMed

Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

2018-07-05

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The latent fingerprint in mass transport of polycrystalline materials

NASA Astrophysics Data System (ADS)

Thirunavukarasu, Gopinath; Kundu, Sukumar; Chatterjee, Subrata

2016-02-01

Herein, a systematic investigation was carried out to reach a rational understanding and to provide information concerning the possible causes for a significant influence of pressure variation in the underlying processes of mass transport in polycrystalline materials. The authors focused their research in solid-state diffusion, a part of the subject "Mass Transport in Solids". Theories on diffusion are the subject by itself which exists as a latent fingerprint in every text of higher learning in interdisciplinary science. In this research, authors prepared sandwich samples of titanium alloy and stainless steel using nickel as an intermediate metal. The samples were processed at three different levels of bonding pressure (3, 4 and 5 MPa) while bonding temperature and bonding time was maintained at 750 °C and 1 h, respectively, throughout the experiments. It was observed that the net flux of atomic diffusion of nickel atoms into Ti-alloy at TiA/Ni interface increased by ~63 % with the rise in the bonding pressure from 3 to 4 MPa, but decreased by ~40 % with the rise in the bonding pressure from 4 to 5 MPa. At the same time, the net flux of atomic diffusion of nickel atoms into stainless steel at Ni/SS interface increased by ~19 % with the rise in the bonding pressure from 3 to 4 MPa, but increased by ~17 % with the rise in the bonding pressure from 4 to 5 MPa. Here authors showed that the pressure variations have different effects at the TiA/Ni interface and Ni/SS interface, and tried to explain the explicit mechanisms operating behind them. In general for sandwich samples processed irrespective of bonding pressure chosen, the net flux of Ni-atoms diffused into SS is greater than that of the net flux of Ni-atoms diffused in Ti-alloy matrix by four orders of magnitude. The calculated diffusivity of Ni-atoms into Ti-alloy reaches its highest value of ~5.083 × 10-19 m2/s for the sandwich sample processed using 4-MPa bonding-pressure, whereas the diffusivity of Ni-atoms into SS reaches its peak value of ~1.615 × 10-14 m2/s for the sample bonded using 5-MPa bonding-pressure.

Communication: Surface-to-bulk diffusion of isolated versus interacting C atoms in Ni(111) and Cu(111) substrates: A first principle investigation.

PubMed

Harpale, Abhilash; Panesi, Marco; Chew, Huck Beng

2015-02-14

Using first principle calculations, we study the surface-to-bulk diffusion of C atoms in Ni(111) and Cu(111) substrates, and compare the barrier energies associated with the diffusion of an isolated C atom versus multiple interacting C atoms. We find that the preferential Ni-C bonding over C-C bonding induces a repulsive interaction between C atoms located at diagonal octahedral voids in Ni substrates. This C-C interaction accelerates C atom diffusion in Ni with a reduced barrier energy of ∼1 eV, compared to ∼1.4-1.6 eV for the diffusion of isolated C atoms. The diffusion barrier energy of isolated C atoms in Cu is lower than in Ni. However, bulk diffusion of interacting C atoms in Cu is not possible due to the preferential C-C bonding over C-Cu bonding, which results in C-C dimer pair formation near the surface. The dramatically different C-C interaction effects within the different substrates explain the contrasting growth mechanisms of graphene on Ni(111) and Cu(111) during chemical vapor deposition.

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Origins of IR Intensity in Overtones and Combination Bands in Hydrogen Bonded Systems

NASA Astrophysics Data System (ADS)

Horvath, Samantha; McCoy, Anne B.

2010-06-01

As the infrared spectra of an increasing number of hydrogen bonded and ion/water complexes have been investigated experimentally, we find that they often contain bands with significant intensity that cannot be attributed to fundamental transitions. In this talk, we explore several sources of the intensity of these overtone and combination bands. A common source of intensity is mode-mode coupling, as is often seen between the proton transfer coordinate and the associated heavy atom vibration. A second important mechanism involves large changes in the dipole moment due the loss of a hydrogen bond. This results in intense overtone transitions involving non-totally symmetric vibrations as well as the introduction of intense combination bands involving intramolecular bending coupled to hindered rotations. These effects will be discussed in the context of several systems, including the spectra of complexes of argon atoms with {H}_3{O}^+, F^-\\cdotH_2O, Cl^-\\cdotH_2O, protonated water clusters,^a and HOONO. T. Guasco, S. Olesen and M. A. Johnson, private communication S. Horvath, A. B. McCoy, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 112, 12337-44 (2008) S. Horvath, A. B. McCoy, B. M. Eliot, G. H. Weddle, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 115, 1556-68 (2010). A. B. McCoy, M. K. Sprague and M. Okumura, J. Phys. Chem. A, 115, 1324-33 (2010)

Efficient Organometallic Spin Filter between Single-Wall Carbon Nanotube or Graphene Electrodes

NASA Astrophysics Data System (ADS)

Koleini, Mohammad; Paulsson, Magnus; Brandbyge, Mads

2007-05-01

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green’s function techniques. We consider weak and strong cluster-contact bonds. Depending on the bonding we find from 73% (strong bonds) up to 99% (weak bonds) spin polarization of the electron transmission, and enhanced polarization with increased cluster length.

A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-10-01

The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

Formation of {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]} Dimers Bonded by Single C-C Bonds and Bridging η(2)-Coordinated Cobalt Atoms.

PubMed

Konarev, Dmitri V; Troyanov, Sergey I; Ustimenko, Kseniya A; Nakano, Yoshiaki; Shestakov, Alexander F; Otsuka, Akihiro; Yamochi, Hideki; Saito, Gunzi; Lyubovskaya, Rimma N

2015-05-18

Coordination of two bridging cobalt atoms to fullerenes by the η(2) type in {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]}·3C6H4Cl2 [1; dppe = 1,2-bis(diphenylphosphino)ethane] triggers fullerene dimerization with the formation of two intercage C-C bonds of 1.571(4) Å length. Coordination-induced fullerene dimerization opens a path to the design of fullerene structures bonded by both covalent C-C bonds and η(2)-coordination-bridged metal atoms.

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

PubMed

Zhurova, Elizabeth A; Zhurov, Vladimir V; Pinkerton, A Alan

2007-11-14

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

PubMed

Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

2016-02-18

Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tandy, P.; Yu, Ming; Leahy, C.

2015-03-28

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemicalmore » bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ∼230 compact boron clusters B{sub N} with N in the range from ∼100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B{sub 12} units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.« less

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

NASA Astrophysics Data System (ADS)

Tandy, P.; Yu, Ming; Leahy, C.; Jayanthi, C. S.; Wu, S. Y.

2015-03-01

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemical bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ˜230 compact boron clusters BN with N in the range from ˜100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B12 units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.

Hund’s rule in superatoms with transition metal impurities

PubMed Central

Medel, Victor M.; Reveles, Jose Ulises; Khanna, Shiv N.; Chauhan, Vikas; Sen, Prasenjit; Castleman, A. Welford

2011-01-01

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund’s rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMgn clusters where TM is a 3d atom. The clusters exhibit Hund’s filling, opening the pathway to superatoms with magnetic shells. PMID:21646542

Hund's rule in superatoms with transition metal impurities.

PubMed

Medel, Victor M; Reveles, Jose Ulises; Khanna, Shiv N; Chauhan, Vikas; Sen, Prasenjit; Castleman, A Welford

2011-06-21

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund's rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMg(n) clusters where TM is a 3d atom. The clusters exhibit Hund's filling, opening the pathway to superatoms with magnetic shells.

Ice surfaces in the mesosphere: Absence of dangling bonds in the presence of atomic oxygen

NASA Astrophysics Data System (ADS)

Boulter, James E.; Morgan, Christopher G.; Marschall, Jochen

2005-07-01

Ice deposition experiments in the presence of microwave discharge-dissociated molecular oxygen suggest heterogeneous interactions between dangling OH bonds on the ice surface and atomic oxygen. Ice films deposited on a gold substrate at temperatures of 115, 130, and 140 K from oxygen/water gas mixtures representative of the summertime polar mesosphere exhibit infrared absorption features characteristic of dangling bonds, whereas films grown in the presence of atomic oxygen do not. Dangling bond spectral features are shown to diminish rapidly when the microwave discharge is activated during ice deposition. Similar decreases were not seen when the gas stream was heated or when the ice film was slowly annealed from 130 to 160 K. One interpretation of these results is that atomic oxygen binds to dangling bond sites during ice growth, a phenomenon that may also occur during the formation of ice particles observed just below the cold summertime mesopause.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

A new analysis of charge transfer and polarization for ligand-metal bonding - Model studies of Al4CO and Al4NH3

NASA Technical Reports Server (NTRS)

Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr.

1984-01-01

The nature of the bonding of CO and NH3 ligands to Al is analyzed, and the intra-unit charge polarization and inter-unit donation for the interaction of ligands with metals are studied. The consequences of metal-to-ligand and ligand-to-metal charge transfer are separately considered by performing a constrained space orbital variation (CSOV) with the electrons of the metal member of the complex in the field of frozen ligand. The electrons of the metal atoms are then frozen in the relaxed distribution given by the CSOV SCF wave function and the ligand electrons are allowed to relax. Quantitative measures of the importance of inter-unit charge transfers and intra-unit polarization are obtained using results of SCF studies of Al4CO and Al4NH3 clusters chosen to simulate the adsorption of the ligands at an on-top side of the Al(111) surface. The electrostatic attraction of the effective dipole moments of the metal and ligand units makes an important contribution to the bond.

Poly[[di-μ-aqua-(μ-4-formyl-2-meth­oxy­phenol­ato)disodium] 4-formyl-2-meth­oxy­phenolate

PubMed Central

Asghar, Muhammad Nadeem; Şahin, Onur; Arshad, Muhammad Nadeem; Mazhar, Uzma; Khan, Islam Ullah; Büyükgüngör, Orhan

2010-01-01

In the title coordination polymer, {[Na2(C8H7O3)(H2O)4](C8H7O3)}n, all the non-H atoms except the water O atoms lie on a crystallographic mirror plane. One sodium cation is bonded to four water O atoms and one vanillinate O atom in a distorted square-based pyramidal arrangement; the other Na+ ion is six-coordinated by four water O atoms and two vanillinate O atoms in an irregular geometry. One of the vanillinate anions is directly bonded to two sodium ions, whilst the other only inter­acts with the polymeric network by way of hydrogen bonds. In the crystal, a two-dimensional polymeric array is formed; this is reinforced by O—H⋯O hydrogen bonds, which generate R 2 1(6) and R 2 2(20) loops. PMID:21579628

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Yoder, Bruce L; Maze, Joshua T; Raghavachari, Krishnan; Jarrold, Caroline Chick

2005-03-01

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

The importance of atomic and molecular correlation on the bonding in transition metal compounds

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.

1986-01-01

The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

Crystal structure of tetra­aqua­bis­(pyrimidin-1-ium-4,6-diolato-κO 4)manganese(II)

PubMed Central

Shennara, Khaled A.

2017-01-01

The MnII ion in the structure of the mononuclear title compound, [Mn(C4H3N2O2)2(H2O)4], is situated on an inversion center and is coordinated by two O atoms from two deprotonated 4,6-di­hydroxy­pyrimidine ligands and by four O atoms from water mol­ecules giving rise to a slightly distorted octa­hedral coordination sphere. The complex includes an intra­molecular hydrogen bond between an aqua ligand and the non-protonated N ring atom. The extended structure is stabilized by inter­molecular hydrogen bonds between aqua ligands, by hydrogen bonds between N and O atoms of the ligands of adjacent mol­ecules, and by hydrogen bonds between aqua ligands and the non-coordinating O atom of an adjacent mol­ecule. PMID:28435734

Substrate Effects for Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. For excellent structural stability, we demand chemical bonding between the adatoms and substrate atoms, but then good electronic isolation may not be guaranteed. Conditions are clarified for good isolation. Because of the chemical bonding, fundamental adatom properties are strongly influenced: a chain with group IV adatoms having two chemical bonds, or a chain with group III adatoms having one chemical bond is semiconducting. Charge transfer from or to the substrate atoms brings about unintentional doping, and the electronic properties have to be considered for the entire combination of the adatom and substrate systems even if the adatom modes are well localized at the surface.

Studies of carbon incorporation on the diamond [100] surface during chemical vapor deposition using density functional theory.

PubMed

Cheesman, Andrew; Harvey, Jeremy N; Ashfold, Michael N R

2008-11-13

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the [100] surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (approximately 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of approximately 150 kJ mol (-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

Microsolvation of the 5-hydroxyindole cation (5HI+) with nonpolar and quadrupolar ligands: Infrared photodissociation spectra of 5HI+-Ln clusters with L = Ar and N2 (n ≤ 3)

NASA Astrophysics Data System (ADS)

Klyne, Johanna; Dopfer, Otto

2017-07-01

Solvation of biomolecules and their building blocks has a strong influence on their structure and function. Herein we characterize the initial microsolvation of the 5-hydroxyindole cation (5HI+) in its 2A″ ground electronic state with nonpolar and quadrupolar ligands (L = Ar, N2) by infrared photodissociation (IRPD) spectroscopy of cold and mass-selected 5HI+-Ln (n ≤ 3) clusters in a molecular beam and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). The isomer-selective OH and NH stretch frequency shifts (ΔνOH/NH) disentangle the competition between H-bonding to the acidic OH and NH groups and π-stacking to the conjugated bicyclic aromatic π-electron system, the intermolecular interaction strengths, and the cluster growth sequence. For 5HI+-Arn, H-bonding and π-stacking strongly compete, indicating that dispersion forces are important for the interaction of 5HI+ with nonpolar ligands. In contrast, for 5HI+-(N2)n clusters, the H-bonds are much stronger than the π-bonds and largely determine the initial solvation process. In all clusters, the OH…L bonds are stronger than the NH…L bonds followed by the π-bonds. The interaction of 5HI+ with N2 is roughly twice stronger than with Ar, mainly due to the additional quadrupole moment of N2. The nature and strength of the individual interactions are quantified by the noncovalent interaction approach. Comparison of 5HI+-L with the corresponding neutral clusters reveals the strong impact of ionization on the total and relative interaction strengths of the H-bonds and π-bonds. In addition, comparison of 5HI+-L with corresponding clusters of the phenol, indole, and pyrrole radical cations illustrates the effects of substitution of functional groups and the addition of aromatic rings to the various subunits of 5HI on the intermolecular potential.

Photoionization of rare gas clusters

NASA Astrophysics Data System (ADS)

Zhang, Huaizhen

This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the angular distribution parameter values of the two-spin-orbit components from Ar 2p clusters are slightly different. When comparing the beta values for Ar between atoms and clusters, we found different results between Ar 3s atoms and clusters, and between Ar 3p atoms and clusters. Argon cluster resonance from surface and bulk were also measured. Furthermore, the angular distribution parameters of Ar cluster photoelectrons and Ar atom photoelectrons in the 3s → np ionization region were obtained.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement with that of 7.6(7) found from an X-ray Pt/Pd microanalysis (WDS spectrometer) on three crystals of 1. Our utilization of this site-occupancy (Pt(x)Pd(1-x))-analysis for shells 1-3 originated from the microanalytical results; otherwise, the presumed metal-core composition would have been (mu(12)-Pt)Pd(164). [Alternatively, the (mu(12)-Pt)M(164) core-geometry of 1 may be viewed as a pseudo-Ih Pt-centered six-shell successive nu(1) polyhedral system, each with radially equivalent vertex atoms: Pt@M(12)(icosahedron)@M(30)(icosidodecahedron)@M(12)(icosahedron)@M(60)(rhombicosidodecahedron)@M(30)(icosidodecahedron)@M(20)(pentagonal dodecahedron)]. Completely surprising structural dissimilarities between 1 and 2 are: (1) to date 1 is only reproducibly isolated as a heterometallic Pd-Pt cluster with a central Pt instead of Pd atom; (2) the 50 atoms comprising the outer fourth nu(2) pentagonal dodecahedral shell in 1 are less than the 60 atoms of the inner third shell in 1, in contradistinction to shell-by-shell growth processes in all other known shell-based structures; (3) the 10 fewer PR3 ligands in 1 necessitate larger bulky PPh(3) ligands to protect the Pd-Pt core-geometry; (4) the 72 CO ligands consist of six bridging COs within each of the 12 pentagons in shell 4 that are coordinated to intershell metal atoms. SQUID magnetometry measurements showed a single-crystal sample of 1 to be diamagnetic over the entire temperature range of 10-300 K.

Wigner-Seitz local-environment study of the high-T/sub c/ superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melamud, M.; Bennett, L.H.; Watson, R.E.

The near-neighbor environments and the bonding of atoms in the high-T/sub c/ superconductors are studied using a Wigner-Seitz-cell contruction. Assuming metallic radii for the atoms, it is shown that the Ba, Y, and La atoms have large coordination numbers, implying a three-dimensional bonding scheme. The La-Cu-O type (approx. =40 K) and the Y-Ba-Cu-O type (approx. =90 K) superconductors both display the same bonding characteristics.

Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

PubMed

Li, Lei

2012-11-01

Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. Copyright © 2011 Elsevier B.V. All rights reserved.

Elucidation of metal-ion accumulation induced by hydrogen bonds on protein surfaces by using porous lysozyme crystals containing Rh(III) ions as the model surfaces.

PubMed

Ueno, Takafumi; Abe, Satoshi; Koshiyama, Tomomi; Ohki, Takahiro; Hikage, Tatsuo; Watanabe, Yoshihito

2010-03-01

Metal-ion accumulation on protein surfaces is a crucial step in the initiation of small-metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh(III) ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino-acid residues to capture Rh(III) ions. ii) Water molecules pre-organized by hydrogen bonds can stabilize Rh(III) coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino-acid residues can be replaced by Rh(III) ions to form polynuclear structures with the residues. iv) Rh(III) aqua complexes are retained on amino-acid residues through stabilizing hydrogen bonds even at low pH (approximately 2). These metal-protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.

Multiple valence superatoms.

PubMed

Reveles, J U; Khanna, S N; Roach, P J; Castleman, A W

2006-12-05

We recently demonstrated that, in gas phase clusters containing aluminum and iodine atoms, an Al(13) cluster behaves like a halogen atom, whereas an Al(14) cluster exhibits properties analogous to an alkaline earth atom. These observations, together with our findings that Al(13)(-) is inert like a rare gas atom, have reinforced the idea that chosen clusters can exhibit chemical behaviors reminiscent of atoms in the periodic table, offering the exciting prospect of a new dimension of the periodic table formed by cluster elements, called superatoms. As the behavior of clusters can be controlled by size and composition, the superatoms offer the potential to create unique compounds with tailored properties. In this article, we provide evidence of an additional class of superatoms, namely Al(7)(-), that exhibit multiple valences, like some of the elements in the periodic table, and hence have the potential to form stable compounds when combined with other atoms. These findings support the contention that there should be no limitation in finding clusters, which mimic virtually all members of the periodic table.

Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

PubMed

Cohen, A; Niv, M Y; Gerber, R B

2001-01-01

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.

Structure and property of metal melt I: The number of residual bonds after solid-liquid phase changes

NASA Astrophysics Data System (ADS)

Mi, Guangbao; Li, Peijie; He, Liangju

2010-09-01

Based on the mechanism of metal solid-liquid phase change and the theory of liquid metal’s micro-inhomogeneity, a physical model is established between latent heats of fusion and vaporization and the numbers of residual bonds and short-range ordered atoms at the melting point inside a metal melt. Meanwhile, the mathematical derivation and proof are also offered. This model produces the numbers of residual bonds and short-range ordered atoms after the solid-liquid phase change only by using basic parameters and thermophysical properties of the crystal structure. Therefore, it presents a more effective way to analyze the melt’s structural information. By using this model, this study calculates the numbers of residual bonds and short-range ordered atoms in Al and Ni melts. The calculated results are consistent with the experimental results. Simultaneously, this study discusses the atomic number’s influence on the numbers of residual bonds and short-range ordered atoms in the melts within the first (IA) and second main group (IIA) elements.

An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†.

PubMed

Gatti, Carlo; Macetti, Giovanni; Boyd, Russell J; Matta, Chérif F

2018-07-05

The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Effect of nitrogen plasma afterglow on the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films

NASA Astrophysics Data System (ADS)

Kayed, Kamal

2018-06-01

The aim of this paper is to investigate the relationship between the micro structure and the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films prepared by laser ablation method. The study results show that the charge effect coefficient (E) is not just a correction factor. We found that the changes in this coefficient value due to incorporation of nitrogen atoms into the carbon network are related to the spatial configurations of the sp2 bonded carbon atoms, order degree and sp2 clusters size. In addition, results show that the curve E vs. C(sp3)-N is a characteristic curve of the micro structure. This means that using this curve makes it easy to sorting the samples according to the micro structure (hexagonal rings or chains).

Efficient and accurate treatment of electron correlations with correlation matrix renormalization theory

DOE PAGES

Yao, Y. X.; Liu, J.; Liu, C.; ...

2015-08-28

We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We alsomore » show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.« less

Nature of Bonding in Bowl-Like B36 Cluster Revisited: Concentric (6π+18π) Double Aromaticity and Reason for the Preference of a Hexagonal Hole in a Central Location.

PubMed

Li, Rui; You, Xue-Rui; Wang, Kang; Zhai, Hua-Jin

2018-05-04

The bowl-shaped C 6v B 36 cluster with a central hexagon hole is considered an ideal molecular model for low-dimensional boron-based nanosystems. Owing to the electron deficiency of boron, chemical bonding in the B 36 cluster is intriguing, complicated, and has remained elusive despite a couple of papers in the literature. Herein, a bonding analysis is given through canonical molecular orbitals (CMOs) and adaptive natural density partitioning (AdNDP), further aided by natural bond orbital (NBO) analysis and orbital composition calculations. The concerted computational data establish the idea of concentric double π aromaticity for the B 36 cluster, with inner 6π and outer 18π electron counting, which both conform to the (4n+2) Hückel rule. The updated bonding picture differs from existing knowledge of the system. A refined bonding model is also proposed for coronene, of which the B 36 cluster is an inorganic analogue. It is further shown that concentric double π aromaticity in the B 36 cluster is retained and spatially fixed, irrespective of the migration of the hexagonal hole; the latter process changes the system energetically. The hexagonal hole is a destabilizing factor for σ/π CMOs. The central hexagon hole affects substantially fewer CMOs, thus making the bowl-shaped C 6v B 36 cluster the global minimum. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

Atomic Covalent Functionalization of Graphene

PubMed Central

Johns, James E.; Hersam, Mark C.

2012-01-01

Conspectus Although graphene’s physical structure is a single atom thick, two-dimensional, hexagonal crystal of sp2 bonded carbon, this simple description belies the myriad interesting and complex physical properties attributed to this fascinating material. Because of its unusual electronic structure and superlative properties, graphene serves as a leading candidate for many next generation technologies including high frequency electronics, broadband photodetectors, biological and gas sensors, and transparent conductive coatings. Despite this promise, researchers could apply graphene more routinely in real-world technologies if they could chemically adjust graphene’s electronic properties. For example, the covalent modification of graphene to create a band gap comparable to silicon (~1 eV) would enable its use in digital electronics, and larger band gaps would provide new opportunities for graphene-based photonics. Towards this end, researchers have focused considerable effort on the chemical functionalization of graphene. Due to its high thermodynamic stability and chemical inertness, new methods and techniques are required to create covalent bonds without promoting undesirable side reactions or irreversible damage to the underlying carbon lattice. In this Account, we review and discuss recent theoretical and experimental work studying covalent modifications to graphene using gas phase atomic radicals. Atomic radicals have sufficient energy to overcome the kinetic and thermodynamic barriers associated with covalent reactions on the basal plane of graphene but lack the energy required to break the C-C sigma bonds that would destroy the carbon lattice. Furthermore, because they are atomic species, radicals substantially reduce the likelihood of unwanted side reactions that confound other covalent chemistries. Overall, these methods based on atomic radicals show promise for the homogeneous functionalization of graphene and the production of new classes of two-dimensional materials with fundamentally different electronic and physical properties. Specifically, we focus on recent studies of the addition of atomic hydrogen, fluorine, and oxygen to the basal plane of graphene. In each of these reactions a high energy, activating step initiates the process, breaking the local π structure and distorting the surrounding lattice. Scanning tunneling microscopy experiments reveal that substrate mediated interactions often dominate when the initial binding event occurs. We then compare these substrate effects with the results of theoretical studies that typically assume a vacuum environment. As the surface coverage increases, clusters often form around the initial distortion, and the stoichiometric composition of the saturated end product depends strongly on both the substrate and reactant species. In addition to these chemical and structural observations, we review how covalent modification can extend the range of physical properties that are achievable in two-dimensional materials. PMID:23030800

Photoelectron Spectroscopy Study of [Ta2B6]-: a Hexagonal Bipyramdial Cluster

NASA Astrophysics Data System (ADS)

Jian, Tian; Li, Weili; Romanescu, Constantin; Wang, Lai-Sheng

2014-06-01

It has been a long-sought goal in cluster science to discover stable atomic clusters as building blocks for cluster-assembled nanomaterials, as exemplified by the fullerenes and their subsequent bulk syntheses.[1,2] Clusters have also been considered as models to understand bulk properties, providing a bridge between molecular and solid-state chemistry.[3] Herein we report a joint photoelectron spectroscopy and theoretical study on the [Ta2B6]- and [Ta2B6] clusters.[4] The photoelectron spectrum of [Ta2B6]- displays a simple spectral pattern and a large HOMO-LUMO gap, suggesting its high symmetry. Theoretical calculations show that both the neutral and anion are D6h pyramidal. The chemical bonding analyses for [Ta2B6] revealed the nature of the B6 and Ta interactions and uncovered strong covalent bonding between B6 and Ta. The D6h-[TaB6Ta] gaseous cluster is reminiscent of the structural pattern in the ReB6X6Re core in the [(Cp*Re)2B6H4Cl2] and the TiB6Ti motif in the newly synthesized Ti7Rh4Ir2B8 solid-state compound.[5,6] The current work provides an intrinsic link between a gaseous cluster and motifs for solid materials. Continued investigations of the transition-metal boron clusters may lead to the discovery of new structural motifs involving pure boron clusters for the design of novel boride materials. Reference [1] H.W. Kroto, J. R. Heath, S. C. OBrien, R. F. Curl, R. E. Smalley, Nature 1985, 318, 162 - 163. [2] W. Krtschmer, L. D. Lamb, K. Fostiropoulos, D. R. Huffman, Nature 1990, 347, 354 - 358. [3] T. P. Fehlner, J.-F. Halet, J.-Y. Saillard, Molecular Clusters: A Bridge to Solid-State Chemitry, Cambridge University Press, UK, 2007. [4] W. L. Li, L. Xie, T. Jian, C. Romanescu, X. Huang, L.-S. Wang, Angew. Chem. Int. Ed. 2014, 126, 1312 - 1316. [5] B. Le Guennic, H. Jiao, S. Kahlal, J.-Y. Saillard, J.-F. Halet, S. Ghosh, M. Shang, A. M. Beatty, A. L. Rheingold, T. P. Fehlner, J. Am. Chem. Soc. 2004, 126, 3203 - 3217. [6] B. P. T. Fokwa, M. Hermus, Angew. Chem. 2012, 124, 1734 - 1737; Angew. Chem. Int. Ed. 2012, 51, 1702 - 1705.

Theoretical Study of Diamond-Like Carbons and Nucleation of Diamond

NASA Astrophysics Data System (ADS)

Lee, Choon-Heung

Different forms of amorphous carbon and hydrocarbons with varying elastic and optical properties, hardness, density and hydrogen content exist depending on the preparation technique. The structure can vary from graphitic to diamond -like, i.e., from mainly threefold coordinated to mainly four-fold coordinated. In order to study the properties of such materials, microscopic models must be developed. These studies include the modelling of crosslinked defective graphite, diamond nucleation along the graphite edges, and diamond-like carbons. Tamor's proposed structure for diamondlike carbon consists of crosslinked graphitic regions. We studied a concrete realization of this model in which the cross -links are produced by shortening the interplanar bond lengths. The model study was accomplished with a pure rhombohedral graphite cell. For this study we used a semi-empirical potential based on Tersoff's environment-dependent potential which contains angular terms. It is enhanced by a long-range potential which describes the interplanar interactions. We found a configuration corresponding to a local minimum. More general features such as the randomness of the distribution of cross-links are needed for a realistic model. A model study of diamond/graphite interfaces was motivated by recent observations by Li and Angus. They observed a significant enhancement of diamond nucleation on the graphite edge planes with the preferential orientation relationship: {0001} _{g} | {111 }_{d}, < 1120 >_{g} | < 101>_{d}. Two possible interface structures were studied using the Tersoff potential. We found that the models have comparable low interface energies even if they contain some dangling bonds. Moreover, lower interface energies were found when the dangling bonds of the non-bonded diamond layer were satisfied with hydrogen. We have proposed a growth mechanism based on this study. Finally, we constructed realistic models of dense amorphous carbon. The WWW (introduced earlier for a-Si by Wooten, Winer and Weaire) model was the starting structure. The effects of clustering of the threefold coordinated atoms in pairs, chains, or graphitic (planar hexagonal clusters) were studied. The resulting models were relaxed using the Tersoff potential. Their electronic structures were studied using an empirical tight-binding scheme with parameters adjusted to reproduce the diamond and graphite band-structures. The models were found to have densities of ~ 3 g/cm^3 and bulk moduli of ~3.1 Mbar. Localized dangling bonds and pi - pi^* states were found within the wide gap of the WWW model consistent with optical gaps of the order of 0.5-2 eV. Hydrogen atoms were introduced to remove some of the dangling bonds. The models were found to account for the essential features of ion-beam deposited amorphous carbon and hydrogenated amorphous carbon.

Meta-atom cluster acoustic metamaterial with broadband negative effective mass density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Huaijun; Zhai, Shilong; Ding, Changlin

2014-02-07

We design a resonant meta-atom cluster, via which a two-dimensional (2D) acoustic metamaterial (AM) with broadband negative effective mass density from 1560 Hz to 5580 Hz is fabricated. Experimental results confirm that there is only weak interaction among the meta-atoms in the cluster. And then the meta-atoms in the cluster independently resonate, resulting in the cluster becoming equivalent to a broadband resonance unit. Extracted effective refractive indices from reflection and transmission measurements of the 2D AM appear to be negative from 1500 Hz to 5480 Hz. The broadband negative refraction has also been demonstrated by our further experiments. We expectmore » that this meta-atom cluster AM will significantly contribute to the design of broadband negative effective mass density AM.« less

Formation of Acetylene in the Reaction of Methane with Iron Carbide Cluster Anions FeC3- under High-Temperature Conditions.

PubMed

Li, Hai-Fang; Jiang, Li-Xue; Zhao, Yan-Xia; Liu, Qing-Yu; Zhang, Ting; He, Sheng-Gui

2018-03-01

The underlying mechanism for non-oxidative methane aromatization remains controversial owing to the lack of experimental evidence for the formation of the first C-C bond. For the first time, the elementary reaction of methane with atomic clusters (FeC 3 - ) under high-temperature conditions to produce C-C coupling products has been characterized by mass spectrometry. With the elevation of temperature from 300 K to 610 K, the production of acetylene, the important intermediate proposed in a monofunctional mechanism of methane aromatization, was significantly enhanced, which can be well-rationalized by quantum chemistry calculations. This study narrows the gap between gas-phase and condensed-phase studies on methane conversion and suggests that the monofunctional mechanism probably operates in non-oxidative methane aromatization. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Free energy reconstruction from steered dynamics without post-processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Athenes, Manuel, E-mail: Manuel.Athenes@cea.f; Condensed Matter and Materials Division, Physics and Life Sciences Directorate, LLNL, Livermore, CA 94551; Marinica, Mihai-Cosmin

2010-09-20

Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable one to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-{alpha}. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, wemore » accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing.« less

Coupling microscopic and mesoscopic scales to simulate chemical equilibrium between a nanometric carbon cluster and detonation products fluid.

PubMed

Bourasseau, Emeric; Maillet, Jean-Bernard

2011-04-21

This paper presents a new method to obtain chemical equilibrium properties of detonation products mixtures including a solid carbon phase. In this work, the solid phase is modelled through a mesoparticle immersed in the fluid, such that the heterogeneous character of the mixture is explicitly taken into account. Inner properties of the clusters are taken from an equation of state obtained in a previous work, and interaction potential between the nanocluster and the fluid particles is derived from all-atoms simulations using the LCBOPII potential (Long range Carbon Bond Order Potential II). It appears that differences in chemical equilibrium results obtained with this method and the "composite ensemble method" (A. Hervouet et al., J. Phys. Chem. B, 2008, 112.), where fluid and solid phases are considered as non-interacting, are not significant, underlining the fact that considering the inhomogeneity of such system is crucial.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

PubMed

Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

2016-05-05

Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

Hydrogen-bonded ring closing and opening of protonated methanol clusters H(+)(CH3OH)(n) (n = 4-8) with the inert gas tagging.

PubMed

Li, Ying-Cheng; Hamashima, Toru; Yamazaki, Ryoko; Kobayashi, Tomohiro; Suzuki, Yuta; Mizuse, Kenta; Fujii, Asuka; Kuo, Jer-Lai

2015-09-14

The preferential hydrogen bond (H-bond) structures of protonated methanol clusters, H(+)(MeOH)n, in the size range of n = 4-8, were studied by size-selective infrared (IR) spectroscopy in conjunction with density functional theory calculations. The IR spectra of bare clusters were compared with those with the inert gas tagging by Ar, Ne, and N2, and remarkable changes in the isomer distribution with the tagging were found for clusters with n≥ 5. The temperature dependence of the isomer distribution of the clusters was calculated by the quantum harmonic superposition approach. The observed spectral changes with the tagging were well interpreted by the fall of the cluster temperature with the tagging, which causes the transfer of the isomer distribution from the open and flexible H-bond network types to the closed and rigid ones. Anomalous isomer distribution with the tagging, which has been recently found for protonated water clusters, was also found for H(+)(MeOH)5. The origin of the anomaly was examined by the experiments on its carrier gas dependence.

Helium behavior in oxide dispersion strengthened (ODS) steel: Insights from ab initio modeling

NASA Astrophysics Data System (ADS)

Sun, Dan; Li, Ruihuan; Ding, Jianhua; Huang, Shaosong; Zhang, Pengbo; Lu, Zheng; Zhao, Jijun

2018-02-01

Using first-principles calculations, we systemically investigate the energetics and stability behavior of helium (He) atoms and small Hen (n = 2-4) clusters inside oxide dispersion strengthened (ODS) steel, as well as the incorporation of large amount of He atoms inside Y2O3 crystal. From the energetic point of view, He atom inside Y2O3 cluster is most stable, followed by the interstitial sites at the α-Fe/Y2O3 interface, and the tetrahedral interstitial sites inside α-Fe region. We further consider Hen (n = 2-4) clusters at the tetrahedral interstitial site surrounded by four Y atoms, which is the most stable site in the ODS steel model. The incorporation energies of all these Hen clusters are lower than that of single He atom in α-Fe, while the binding energy between two He atoms is relatively small. With insertion of 15 He atoms into 80-atom unit cell of Y2O3 crystal, the incorporation energy of He atoms is still lower than that of He4 cluster in α-Fe crystal. These theoretical results suggest that He atoms tend to aggregate inside Y2O3 clusters or at the α-Fe/Y2O3 interface, which is beneficial to prevent the He embrittlement in ODS steels.

Graphene/MoS2 heterostructures as templates for growing two-dimensional metals: Predictions from ab initio calculations

NASA Astrophysics Data System (ADS)

Šljivančanin, Željko; Belić, Milivoj

2017-09-01

Preparation of single-atom-thick layers of ordinary metals has been a challenging task since their closely packed atoms lack layered structure with highly anisotropic bonding. Using computational modeling based on density functional theory we showed that graphene/MoS2 heterostructures can be used as suitable templates to grow stable two-dimensional (2D) clusters, as well as extended monoatomic layers of metals with nonlayered structure in the bulk. Considering gold and lithium as two metals with markedly different properties, we found that Li intercalants strengthen coupling between graphene (G) and MoS2, mainly due to electrostatic attraction of 2D materials with positively charged Li atoms. However, intercalation with large Au atoms gives rise to a significant increase in the distance between G and MoS2 and thus, weakens their interaction. In addition to strong preference for 2D growth, we demonstrated that Au intercalants weakly interact with both G and MoS2, and hence G /MoS2 vertical heterostructures could be a promising framework to prepare gold 2D structures with electronic properties closely resembling those of the hypothetical free-standing hexagonal gold monolayer.

Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Kumagai, Takashi

2015-08-01

Hydrogen(H)-bond dynamics are involved in many elementary processes in chemistry and biology. Because of its fundamental importance, a variety of experimental and theoretical approaches have been employed to study the dynamics in gas, liquid, solid phases, and their interfaces. This review describes the recent progress of direct observation and control of H-bond dynamics in several model systems on a metal surface by using low-temperature scanning tunneling microscopy (STM). General aspects of H-bond dynamics and the experimental methods are briefly described in chapter 1 and 2. In the subsequent four chapters, I present direct observation of an H-bond exchange reaction within a single water dimer (chapter 3), a symmetric H bond (chapter 4) and H-atom relay reactions (chapter 5) within water-hydroxyl complexes, and an intramolecular H-atom transfer reaction (tautomerization) within a single porphycene molecule (chapter 6). These results provide novel microscopic insights into H-bond dynamics at the single-molecule level, and highlight significant impact on the process from quantum effects, namely tunneling and zero-point vibration, resulting from the small mass of H atom. Additionally, local environmental effect on H-bond dynamics is also examined by using atom/molecule manipulation with the STM.

N′-[(E)-3-Chloro-2-fluoro­benzyl­idene]-6-methyl­nicotinohydrazide monohydrate

PubMed Central

Fun, Hoong-Kun; Quah, Ching Kheng; Shyma, P. C.; Kalluraya, Balakrishna; Vidyashree, J. H. S.

2012-01-01

The title compound, C14H11ClFN3O·H2O, exists in an E conformation with respect to the N=C bond. The pyridine ring forms a dihedral angle of 5.00 (9)° with the benzene ring. In the crystal, the ketone O atom accepts one O—H⋯O and one C—H⋯O hydrogen bond, the water O atom accepts one N—H⋯O and two C—H⋯O hydrogen bonds and the pyridine N atom accepts one O—H⋯N hydrogen bond, forming layers parallel to the ab plane. PMID:22798798

Transition metal atomic multiplets in the ligand K-edge x-ray absorption spectra and multiple oxidation states in the L2,3 emission of strongly correlated compounds

NASA Astrophysics Data System (ADS)

Jiménez-Mier, J.; Olalde-Velasco, P.; Yang, W.-L.; Denlinger, J.

2014-07-01

We present results that show that atomic multiplet ligand field calculations are in very good agreement with experimental x-ray absorption spectra at the L2,3 edge of transition metal (TM) di-fluorides (MF2, MCrCu). For chromium more than one TM oxidation state is needed to achieve such an agreement. We also show that signature of the TM atomic multiplet can be found at the pre-edge of the fluorine K-edge x-ray absorption spectra. TM atomic multiplet ligand field calculations with a structureless core hole show good agreement with the observed pre-edges in the experimental fluorine absorption spectra. Preliminary results for the comparison between calculated and experimental resonant x-ray emission spectra for nominal CrF2 with more than one oxidation state indicate the presence of three chromium oxidation states in the bulk.

On the temperature dependence of H-U{sub iso} in the riding hydrogen model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lübben, Jens; Volkmann, Christian; Grabowsky, Simon

The temperature dependence of hydrogen U{sub iso} and parent U{sub eq} in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-U{sub iso} in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U{sub iso} below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for thismore » study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.« less

Change of Energy of the Cubic Subnanocluster of Iron Under Influence of Interstitial and Substitutional Atoms.

PubMed

Nedolya, Anatoliy V; Bondarenko, Natalya V

2016-12-01

Energy change of an iron face-centred cubic subnanocluster was evaluated using molecular mechanics method depending on the position of a carbon interstitial atom and substitutional atoms of nickel. Calculations of all possible positions of impurity atoms show that the energy change of the system are discrete and at certain positions of the atoms are close to continuous.In terms of energy, when all impurity atoms are on the same edge of an atomic cluster, their positions are more advantageous. The presence of nickel atoms on the edge of a cubic cluster resulted in decrease of potential barrier for a carbon atom and decrease in energy in the whole cluster. A similar drift of a carbon atom from central octahedral interstitial site to the surface in the direction <011> occurred under the influence of surface factors.Such configuration corresponds to decreasing symmetry and increasing the number of possible energy states of a subnanocluster, and it corresponds to the condition of spontaneous crystallization process in an isolated system.Taking into account accidental positions of the nickel atom in the iron cluster, such behaviour of the carbon atom can explain the mechanism of growth of a new phase and formation of new clusters in the presence of other kind of atoms because of surface influence.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

PubMed

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

2017-05-01

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Nature of water and hydrogen reactions on transition metal surfaces studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tatarkhanov, Mouslim Magomedovich

Scanning Tunneling Microscopy (STM) has already been established as a tool for the investigation of simple reaction mechanisms. In this work I present results of two parallel studies using STM: first, hydrogen on Ru(0001) surface and second, water on Ru(0001) and Pd(111). In both studies initial stages of adsorption up to saturation monolayer coverage were investigated by variable temperature scanning tunneling microscopy (VT STM). The first step of the hydrogen adsorption study was the identification and characterization of the various coverage structures on clean Ru(0001). Hydrogen was found to adsorb dissociatively forming ( 3x3 )R30°, 3 domains of (2x1), (2x2)-3H and (1x1) for increasing coverages of theta=0.3 ML, 0.5 ML, 0.75 ML and 0.1 ML respectively. Some of these structures were observed to coexist at intermediate coverage values. In addition effects of impurities such as oxygen and carbon on hydrogen adsorption has been discussed. Next, near saturation coverage the interesting mechanism of how H 2 dissociates and binds to the surface of Ru(0001) has been observed. We found that the H2 dissociation takes place only on Ru sites where the metal atom is not bound to any H atom. Such active sites are formed when at least 3 H-vacancies aggregate by thermal diffusion. Sites formed by single H-vacancies (i.e. unoccupied Ru sites) or pairs of adjoining vacancies were found to be unreactive toward H2. H-vacancies were observed as single entities diffusing on the surface at 50 K and able to form transient triangular shaped aggregations where H2 molecules dissociated. It was found that the diffusion and aggregation of the H-vacancies is essential in creation of active sites where dissociative adsorption of hydrogen occurs. The first step of water studies was the initial stages of growth of water on the hexagonal surfaces of Pd(111) and Ru(0001) in the temperature range between 40 K and 130 K. In addition, DFT calculations and STM image simulations were used to validate the models. Below 130 K water dissociation does not occur at any appreciable rate and only molecular films are formed. At these temperatures the kinetics of water growth leads to structures where the molecules bind to the metal substrate through the O-lone pair while making 3 H-bonds with neighboring molecules and form clusters of hexagonal units with a honeycomb structure. This bonding geometry imposes limitations to the size of the clusters, with unsaturated H-bonds confined to the cluster periphery. It is found that growth proceeds by attachement of water molecules to the edge of the clusters by H-bonds. These molecules bind only weakly to the metal substrate and can hop around the edges. Comparison of DFT and STM image calculations with experiments shows that on Pd the edge-attached molecules form two different structures, a metastable one where the molecule is elevated by 2.7 A with respect to the cluster molecules, and another where they are elevated by only 0.4 A. On Ru only the less elevated (0.4 A higher) edge-attached molecules are observed. In next final step, water structures on Ru(0001) were studied at temperatures above 140K. STM findings were backed by x-ray absorption spectroscopy. Additional DFT calculations and STM simulations provided validation of proposed models. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H 2O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentiallymostly parallel to the surface. STM images show that the mixed H2O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H2O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripes geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

PubMed

Zhang, Jun; Dolg, Michael

2013-07-09

An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

The study of structures and properties of PdnHm(n=1-10, m=1,2) clusters by density functional theory

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Chen, Guo-Xiang; Zhang, Jian-Min; Wu, Hua

2018-04-01

The geometrical evolution, local relative stability, magnetism and charge transfer characteristics of PdnHm(n = 1-10, m = 1,2) have been systematically calculated by using density functional theory. The studied results show that the most stable geometries of PdnH and PdnH2 (n = 1-10) can be got by doping one or two H atoms on the sides of Pdn clusters except Pd6H and Pd6H2. It is found that doping one or two H atoms on Pdn clusters cannot change the basic framework of Pdn. The analysis of stability shows that Pd2H, Pd4H, Pd7H, Pd2H2, Pd4H2 and Pd7H2 clusters have higher local relative stability than neighboring clusters. The analysis of magnetic properties demonstrates that absorption of hydrogen atoms decreases the average atomic magnetic moments compared with pure Pdn clusters. More charges transfer from H atoms to Pd atoms for Pd6H and Pd6H2 clusters, demonstrating the adsorption of hydrogen atoms change from side adsorption to surface adsorption.

The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer.

PubMed

Wei, Yuanxin; Li, Qingzhong; Scheiner, Steve

2018-03-19

The positive region that lies above the plane of F 2 TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H-bond. The T atom of F 2 TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F 2 TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F 2 SiO engages in a much stronger interaction than does F 2 CO, reaching nearly 200 kJ mol -1 . The π-tetrel bond strengthens/weakens the MDA H-bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an accompanying inhibition/promotion of proton transfer within this H-bond; this effect is stronger for F 2 SiO. These same aspects can be tuned by substituents placed on any of the C atoms of MDA, although their effects are not fully correlated with the electron-withdrawing or electron-releasing properties of the substituent. A new type of π-π tetrel bond occurs when the π-hole on the T atom of F 2 TO approaches the middle carbon atom of MDA from above, and a similar configuration is also found between F 2 TO and benzene. Evidence for extensive C⋅⋅⋅C π-π tetrel bonding in crystal materials is presented. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insight from first principles into the stability and magnetism of alkali-metal superoxide nanoclusters

NASA Astrophysics Data System (ADS)

Arcelus, Oier; Suaud, Nicolas; Katcho, Nebil A.; Carrasco, Javier

2017-05-01

Alkali-metal superoxides are gaining increasing interest as 2p magnetic materials for information and energy storage. Despite significant research efforts on bulk materials, gaps in our knowledge of the electronic and magnetic properties at the nanoscale still remain. Here, we focused on the role that structural details play in determining stability, electronic structure, and magnetic couplings of (MO2)n (M = Li, Na, and K, with n = 2-8) clusters. Using first-principles density functional theory based on the Perdew-Burke-Ernzerhof and Heyd-Scuseria-Ernzerhof functionals, we examined the effect of atomic structure on the relative stability of different polymorphs within each investigated cluster size. We found that small clusters prefer to form planar-ring structures, whereas non-planar geometries become more stable when increasing the cluster size. However, the crossover point depends on the nature of the alkali metal. Our analysis revealed that electrostatic interactions govern the highly ionic M-O2 bonding and ultimately control the relative stability between 2-D and 3-D geometries. In addition, we analyzed the weak magnetic couplings between superoxide molecules in (NaO2)4 clusters comparing model Hamiltonian methods based on Wannier function projections onto πg states with wave function-based multi-reference calculations.

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

Charge dynamics of 57Fe probe atoms in La2Li0.5Cu0.5O4

NASA Astrophysics Data System (ADS)

Presniakov, I. A.; Sobolev, A. V.; Rusakov, V. S.; Moskvin, A. S.; Baranov, A. V.

2018-06-01

The objective of this study is to characterize the electronic state and local surrounding of 57Fe Mössbauer probe atoms within iron-doped layered perovskite La2Li0.5Cu0.5O4 containing transition metal in unusual formal oxidation states "+3". An approach based on the qualitative energy diagrams analysis and the calculations within the cluster configuration interaction method have been developed. It was shown that a large amount of charge is transferred via Cu-O bonds from the O: 2p bands to the Cu: 3d orbitals and the ground state is dominated by the d9L configuration ("Cu2+-O-" state). The dominant d9L ground state for the (CuO6) sublattice induces in the environment of the 57Fe probe cations a charge transfer Fe3+ + O-(L) → Fe4+ + O2-, which transforms "Fe3+" into "Fe4+" state. The experimental spectra in the entire temperature range 77-300 K were described with the use of the stochastic two-level model based on the assumption of dynamic equilibrium between two Fe3+↔Fe4+ valence states related to the iron atom in the [Fe(1)O4]4- center. The relaxation frequencies and activation energies of the corresponding charge fluctuations were estimated based on Mössbauer data. The results are discussed assuming a temperature-induced change in the electronic state of the [CuO4]5- clusters in the layered perovskite.

Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins.

PubMed

Yamashita, Satoshi; Mizuno, Misao; Tran, Duy Phuoc; Dokainish, Hisham M; Kitao, Akio; Mizutani, Yasuhisa

2018-05-10

A pathway of vibrational energy flow in myoglobin was studied by time-resolved anti-Stokes ultraviolet resonance Raman spectroscopy combined with site-directed mutagenesis. Our previous study suggested that atomic contacts in proteins provide the dominant pathway for energy transfer while covalent bonds do not. In the present study, we directly examined the contributions of covalent bonds and atomic contacts to the pathway of vibrational energy flow by comparing the anti-Stokes resonance Raman spectra of two myoglobin mutants: one lacked a covalent bond between heme and the polypeptide chain and the other retained the intact bond. The two mutants showed no significant difference in temporal changes in the anti-Stokes Raman intensities of the tryptophan bands, implying that the dominant channel of vibrational energy transfer is not through the covalent bond but rather through van der Waals atomic contacts between heme and the protein moiety. The obtained insights contribute to our general understanding of energy transfer in the condensed phase.

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

PubMed Central

Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

2014-01-01

An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

PubMed

Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

2014-05-28

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

Cluster reactivity experiments: Employing mass spectrometry to investigate the molecular level details of catalytic oxidation reactions

PubMed Central

Johnson, Grant E.; Tyo, Eric C.; Castleman, A. W.

2008-01-01

Mass spectrometry is the most widely used tool in the study of the properties and reactivity of clusters in the gas phase. In this article, we demonstrate its use in investigating the molecular-level details of oxidation reactions occurring on the surfaces of heterogeneous catalysts via cluster reactivity experiments. Guided ion beam mass spectrometry (GIB-MS) employing a quadrupole–octopole–quadrupole (Q–O–Q) configuration enables mass-selected cluster ions to be reacted with various chemicals, providing insight into the effect of size, stoichiometry, and ionic charge state on the reactivity of catalyst materials. For positively charged tungsten oxide clusters, it is shown that species having the same stoichiometry as the bulk, WO3+, W2O6+, and W3O9+, exhibit enhanced activity and selectivity for the transfer of a single oxygen atom to propylene (C3H6), suggesting the formation of propylene oxide (C3H6O), an important monomer used, for example, in the industrial production of plastics. Furthermore, the same stoichiometric clusters are demonstrated to be active for the oxidation of CO to CO2, a reaction of significance to environmental pollution abatement. The findings reported herein suggest that the enhanced oxidation reactivity of these stoichiometric clusters may be due to the presence of radical oxygen centers (W–O●) with elongated metal–oxygen bonds. The unique insights gained into bulk-phase oxidation catalysis through the application of mass spectrometry to cluster reactivity experiments are discussed. PMID:18687883

Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priyanka,; Dharamvir, Keya; Sharma, Hitesh

2011-12-12

The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding siliconmore » doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.« less

Understanding Chemistry: Current and Possible

ERIC Educational Resources Information Center

Sanderson, R. T.

1976-01-01

Describes an instructional approach for teaching the cause-and-effect relationship between the qualities of atoms and the properties of their chemical compositions. Discusses atomic structure, ionization energies, homonuclear and heteronuclear bonding, and bond dissociation. (MLH)

2-Acetyl-1,1,3,3-tetra­methyl­guanidine

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the mol­ecule of the title compound, C7H15N3O, the central C atom is surrounded in a nearly ideal trigonal–planar geometry by three N atoms. The C—N bond lengths in the CN3 unit are 1.3353 (13), 1.3463 (12) and 1.3541 (13) Å, indicating an inter­mediate character between a single and a double bond for each C—N bond. The bonds between the N atoms and the terminal C-methyl groups all have values close to that of a typical single bond [1.4526 (13)–1.4614 (14) Å]. In the crystal, the guanidine mol­ecules are connected by weak C—H⋯O and C—H⋯N hydrogen bonds, generating layers parallel to the ab plane. PMID:23125768

Hydrogen bond asymmetric local potentials in compressed ice.

PubMed

Huang, Yongli; Ma, Zengsheng; Zhang, Xi; Zhou, Guanghui; Zhou, Yichun; Sun, Chang Q

2013-10-31

A combination of the Lagrangian mechanics of oscillators vibration, molecular dynamics decomposition of volume evolution, and Raman spectroscopy of phonon relaxation has enabled us to resolve the asymmetric, local, and short-range potentials pertaining to the hydrogen bond (O:H-O) in compressed ice. Results show that both oxygen atoms in the O:H-O bond shift initially outwardly with respect to the coordination origin (H), lengthening the O-O distance by 0.0136 nm from 0.2597 to 0.2733 nm by Coulomb repulsion between electron pairs on adjacent oxygen atoms. Both oxygen atoms then move toward right along the O:H-O bond by different amounts upon being compressed, approaching identical length of 0.11 nm. The van der Waals potential VL(r) for the O:H noncovalent bond reaches a valley at -0.25 eV, and the lowest exchange VH(r) for the H-O polar-covalent bond is valued at -3.97 eV.

(2E,5E)-2,5-Bis(4-hy-droxy-3-meth-oxy-benzyl-idene)cyclo-penta-none ethanol monosolvate.

PubMed

Da'i, Muhammad; Yanuar, Arry; Meiyanto, Edy; Jenie, Umar Anggara; Supardjan, Amir Margono

2013-04-01

In the title structure, C21H20O5·C2H5OH, the curcumine-type mol-ecule has a double E conformation for the two benzyl-idene double bonds [C=C = 1.342 (4) and 1.349 (4) Å] and is nearly planar with respect to the non-H atoms (r.m.s. deviation from planarity = 0.069 Å). The two phenolic OH groups form bifurcated hydrogen bonds with intra-molecular branches to adjacent meth-oxy O atoms and inter-molecular branches to either a neighbouring mol-ecule or an ethanol solvent mol-ecule. The ethanol O atom donates a hydrogen bond to the keto O atom. These hydrogen bonds link the constituents into layers parallel to (101) in the crystal structure.

Atomic dynamics and the problem of the structural stability of free clusters of solidified inert gases

NASA Astrophysics Data System (ADS)

Verkhovtseva, É. T.; Gospodarev, I. A.; Grishaev, A. V.; Kovalenko, S. I.; Solnyshkin, D. D.; Syrkin, E. S.; Feodos'ev, S. B.

2003-05-01

The dependence of the rms amplitudes of atoms in free clusters of solidified inert gases on the cluster size is investigated theoretically and experimentally. Free clusters are produced by homogeneous nucleation in an adiabatically expanding supersonic stream. Electron diffraction is used to measure the rms amplitudes of the atoms; the Jacobi-matrix method is used for theoretical calculations. A series of distinguishing features of the atomic dynamics of microclusters was found. This was necessary to determine the character of the formation and the stability conditions of the crystal structure. It wass shown that for clusters consisting of less than N˜103 atoms, as the cluster size decreases, the rms amplitudes grow much more rapidly than expected from the increase in the specific contribution of the surface. It is also established that an fcc structure of a free cluster, as a rule, contains twinning defects (nuclei of an hcp phase). One reason for the appearance of such defects is the so-called vertex instability (anomalously large oscillation amplitudes) of the atoms in coordination spheres.

Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon.

PubMed

Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei

2016-07-11

A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pauling bond strength, bond length and electron density distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-01-18

A power law regression equation, = 1.46(/r)-0.19, connecting the average experimental bond lengths, , with the average accumulation of the electron density at the bond critical point, , between bonded metal M and oxygen atoms, determined at ambient conditions for oxide crystals, where r is the row number of the M atom, is similar to the regression equation R(M-O) = 1.39(ρ(rc)/r)-0.21 determined for three perovskite crystals for pressures as high as 80 GPa. The two equations are also comparable with those, = 1.43( /r)-0.21, determined for a large number of oxide crystals at ambient conditions and = 1.39(/r)-0.22, determined formore » geometry optimized hydroxyacid molecules, that connect the bond lengths to the average Pauling electrostatic bond strength, , for the M-O bonded interactions. On the basis of the correspondence between the two sets of equations connecting ρ(rc) and the Pauling bond strength s with bond length, it appears that Pauling’s simple definition of bond strength closely mimics the accumulation of the electron density between bonded pairs of atoms. The similarity of the expressions for the crystals and molecules is compelling evidence that the M-O bonded interactions for the crystals and molecules 2 containing the same bonded interactions are comparable. Similar expressions, connecting bond lengths and bond strength, have also been found to hold for fluoride, nitride and sulfide molecules and crystals. The Brown-Shannon bond valence, σ, power law expression σ = [R1/(R(M-O)]N that has found wide use in crystal chemistry, is shown to be connected to a more universal expression determined for oxides and the perovskites, = r[(1.41)/]4.76, demonstrating that the bond valence for a bonded interaction is likewise closely connected to the accumulation of the electron density between the bonded atoms. Unlike the Brown-Shannon expression, it is universal in that it holds for the M-O bonded interactions for a relatively wide range of M atoms of the periodic table. The power law equation determined for the oxide crystals at ambient conditions is similar to the power law expression = r[1.46/]5.26 determined for the perovskites at pressures as high as 80 GPa, indicating that the intrinsic connection between R(M-O) and ρ(rc) that holds at ambient conditions also holds, to a first approximation, at high pressures.« less

Influences of the cold atmospheric plasma jet treatment on the properties of the demineralized dentin surfaces

NASA Astrophysics Data System (ADS)

Xiaoming, ZHU; Heng, GUO; Jianfeng, ZHOU; Xiaofei, ZHANG; Jian, CHEN; Jing, LI; Heping, LI; Jianguo, TAN

2018-04-01

Improvement of the bonding strength and durability between the dentin surface and the composite resin is a challenging job in dentistry. In this paper, a radio-frequency atmospheric-pressure glow discharge (RF-APGD) plasma jet is employed for the treatment of the acid-etched dentin surfaces used for the composite restoration. The properties of the plasma treated dentin surfaces and the resin-dentin interfaces are analyzed using the x-ray photoemission spectroscopy, contact angle goniometer, scanning electron microscope and microtensile tester. The experimental results show that, due to the abundant chemically reactive species existing in the RF-APGD plasma jet under a stable and low energy input operating mode, the contact angle of the plasma-treated dentin surfaces decreases to a stable level with the increase of the atomic percentage of oxygen in the specimens; the formation of the long resin tags in the scattered clusters and the hybrid layers at the resin-dentin interfaces significantly improve the bonding strength and durability. These results indicate that the RF-APGD plasma jet is an effective tool for modifying the chemical properties of the dentin surfaces, and for improving the immediate bonding strength and the durability of the resin-dentin bonding in dentistry.

Defects in Amorphous Semiconductors: The Case of Amorphous Indium Gallium Zinc Oxide

NASA Astrophysics Data System (ADS)

de Jamblinne de Meux, A.; Pourtois, G.; Genoe, J.; Heremans, P.

2018-05-01

Based on a rational classification of defects in amorphous materials, we propose a simplified model to describe intrinsic defects and hydrogen impurities in amorphous indium gallium zinc oxide (a -IGZO). The proposed approach consists of organizing defects into two categories: point defects, generating structural anomalies such as metal—metal or oxygen—oxygen bonds, and defects emerging from changes in the material stoichiometry, such as vacancies and interstitial atoms. Based on first-principles simulations, it is argued that the defects originating from the second group always act as perfect donors or perfect acceptors. This classification simplifies and rationalizes the nature of defects in amorphous phases. In a -IGZO, the most important point defects are metal—metal bonds (or small metal clusters) and peroxides (O - O single bonds). Electrons are captured by metal—metal bonds and released by the formation of peroxides. The presence of hydrogen can lead to two additional types of defects: metal-hydrogen defects, acting as acceptors, and oxygen-hydrogen defects, acting as donors. The impact of these defects is linked to different instabilities observed in a -IGZO. Specifically, the diffusion of hydrogen and oxygen is connected to positive- and negative-bias stresses, while negative-bias illumination stress originates from the formation of peroxides.

Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Zhou, Yu; Liang, Qin; Chen, Da-Fu; Guo, Rui; Lai, Rong-Cai

2016-10-01

In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)-H2O/CH3CH2OH and apigenin (II)-H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin-H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X-H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4-O5···H, C9-O4···H and C13-O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

Ferromagnetic order in diamond-like carbon films by Co implantation

NASA Astrophysics Data System (ADS)

Gupta, Prasanth; Williams, Grant; Markwitz, Andreas

2016-02-01

We report the observation of ferromagnetic order in diamond-like carbon (DLC) films made by mass selective ion beam deposition and after low energy implantation with Co ions. Different Co fluences were studied with a peak concentration of up to 25% at an average Co implantation depth of 30 nm. The saturation moment per Co atom (0.2-0.3 μ B) was found to be strongly dependent on temperature and it was significantly lower than that reported in bulk cobalt or cobalt nanoparticles (1.67 μ B per Co atom). The observed magnetic moment cannot be attributed to ferromagnetic nanoparticles as no evidence for superparamagnetism was detected. The magnetic order observed may be due to Co bonding in DLC possibly leading to dilute ferromagnetic semiconductor behaviour with an inhomogeneous distribution of cobalt atoms. Raman spectroscopy measurements showed that Co implantation resulted in an increase in the sp2 clustering with increasing Co fluence. Thus, our results show that Co implantation into DLC films increases the graphitic properties of the film and leads to magnetic order at room temperature.

Photoelectron spectroscopy of nitromethane anion clusters

NASA Astrophysics Data System (ADS)

Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

2016-08-01

Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Site-Specific Biomolecule Labeling with Gold Clusters

PubMed Central

Ackerson, Christopher J.; Powell, Richard D.; Hainfeld, James F.

2013-01-01

Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: Linker-mediated bioconjugation, direct gold–biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (His)-tagged proteins. PMID:20887859

Self-assembled monolayer and method of making

DOEpatents

Fryxell, Glen E [Kennewick, WA; Zemanian, Thomas S [Richland, WA; Liu, Jun [West Richland, WA; Shin, Yongsoon [Richland, WA

2003-03-11

According to the present invention, the previously known functional material having a self-assembled monolayer on a substrate has a plurality of assembly molecules each with an assembly atom with a plurality of bonding sites (four sites when silicon is the assembly molecule) wherein a bonding fraction (or fraction) of fully bonded assembly atoms (the plurality of bonding sites bonded to an oxygen atom) has a maximum when made by liquid solution deposition, for example a maximum of 40% when silicon is the assembly molecule, and maximum surface density of assembly molecules was 5 silanes per square nanometer. Note that bonding fraction and surface population are independent parameters. The method of the present invention is an improvement to the known method for making a siloxane layer on a substrate, wherein instead of a liquid phase solution chemistry, the improvement is a supercritical phase chemistry. The present invention has the advantages of greater fraction of oxygen bonds, greater surface density of assembly molecules and reduced time for reaction of about 5 minutes to about 24 hours.

Self-assembled monolayer and method of making

DOEpatents

Fryxell, Glen E.; Zemanian, Thomas S.; Liu, Jun; Shin, Yongsoon

2004-05-11

According to the present invention, the previously known functional material having a self-assembled monolayer on a substrate has a plurality of assembly molecules each with an assembly atom with a plurality of bonding sites (four sites when silicon is the assembly molecule) wherein a bonding fraction (or fraction) of fully bonded assembly atoms (the plurality of bonding sites bonded to an oxygen atom) has a maximum when made by liquid solution deposition, for example a maximum of 40% when silicon is the assembly molecule, and maximum surface density of assembly molecules was 5 silanes per square nanometer. Note that bonding fraction and surface population are independent parameters. The method of the present invention is an improvement to the known method for making a siloxane layer on a substrate, wherein instead of a liquid phase solution chemistry, the improvement is a supercritical phase chemistry. The present invention has the advantages of greater fraction of oxygen bonds, greater surface density of assembly molecules and reduced time for reaction of about 5 minutes to about 24 hours.

Self-Assembled Monolayer And Method Of Making

DOEpatents

Fryxell, Glen E.; Zemanian, Thomas S.; Liu, Jun; Shin, Yongsoon

2004-06-22

According to the present invention, the previously known functional material having a self-assembled monolayer on a substrate has a plurality of assembly molecules each with an assembly atom with a plurality of bonding sites (four sites when silicon is the assembly molecule) wherein a bonding fraction (or fraction) of fully bonded assembly atoms (the plurality of bonding sites bonded to an oxygen atom) has a maximum when made by liquid solution deposition, for example a maximum of 40% when silicon is the assembly molecule, and maximum surface density of assembly molecules was 5 silanes per square nanometer. Note that bonding fraction and surface population are independent parameters. The method of the present invention is an improvement to the known method for making a siloxane layer on a substrate, wherein instead of a liquid phase solution chemistry, the improvement is a supercritical phase chemistry. The present invention has the advantages of greater fraction of oxygen bonds, greater surface density of assembly molecules and reduced time for reaction of about 5 minutes to about 24 hours.

Self-Assembled Monolayer And Method Of Making

DOEpatents

Fryxell, Glen E.; Zemanian, Thomas S.; Liu, Jun; Shin, Yongsoon

2005-01-25

According to the present invention, the previously known functional material having a self-assembled monolayer on a substrate has a plurality of assembly molecules each with an assembly atom with a plurality of bonding sites (four sites when silicon is the assembly molecule) wherein a bonding fraction (or fraction) of fully bonded assembly atoms (the plurality of bonding sites bonded to an oxygen atom) has a maximum when made by liquid solution deposition, for example a maximum of 40% when silicon is the assembly molecule, and maximum surface density of assembly molecules was 5 silanes per square nanometer. Note that bonding fraction and surface population are independent parameters. The method of the present invention is an improvement to the known method for making a siloxane layer on a substrate, wherein instead of a liquid phase solution chemistry, the improvement is a supercritical phase chemistry. The present invention has the advantages of greater fraction of oxygen bonds, greater surface density of assembly molecules and reduced time for reaction of about 5 minutes to about 24 hours.

Density functional theory study of the structural and bonding mechanism of molecular oxygen (O2) with C3Si

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Behera, C.; Sahu, Sridhar

2018-07-01

The investigations of pure and heteroatom doped carbon clusters have created great interest because of their enormous prospective applications in various research zones, for example, optoelectronics, semiconductors, material science, energy storage devices, astro-science and so on. In this article, the interaction of molecular oxygen (O2) with C3Si has explored within a density functional theory (DFT). Different possible types of structure for C3SiO2 have collected. Among five different kinds of structure, the structure-1a, 1A1 is more energetically stable. The nature of the bonding of O2 and C3Si, in C3SiO2 has been studied by using Bader's topological analysis of the electron charge density distribution ρ(r) , Laplacian ∇2 ρ(r) and total energy density H(r) at the bond critical points (BCPs) of the structures within the framework of the atoms in molecules theory (AIM). The bonding mechanism of O2 and C3Si in C3SiO2 prompts to the fundamental understanding of the interaction of C3Si with oxygen molecule. It is interesting to note that, two types of bonding mechanism are established in same C3SiO2 system such as (i) shared-kind interactions (ii) closed-shell interactions. From various kinds of structure, Csbnd C bonds in all structures are shown as shared-kind interactions whereas Csbnd Si, Osbnd O bonds are classified as closed-shell type interactions with a certain degree of covalent character.

Tuning the oxidative power of free iron-sulfur clusters.

PubMed

Lang, Sandra M; Zhou, Shaodong; Schwarz, Helmut

2017-03-15

The gas-phase reactions between a series of di-iron sulfur clusters Fe 2 S x + (x = 1-3) and the small alkenes C 2 H 4 , C 3 H 6 , and C 4 H 8 have been investigated by means of Fourier-transform ion-cyclotron resonance mass spectrometry. For all studied alkenes, the reaction efficiency is found to increase in the order Fe 2 S + < Fe 2 S 2 + < Fe 2 S 3 + . In particular, Fe 2 S + and Fe 2 S 2 + only form simple association products, whereas the sulfur-rich Fe 2 S 3 + is able to dehydrogenate propene and 2-butene via desulfurization of the cluster and formation of H 2 S. This indicates an increased propensity to induce oxidation reactions, i.e. oxidative power, of Fe 2 S 3 + that is attributed to an increased formal oxidation state of the iron atoms. Furthermore, the ability of Fe 2 S 3 + to activate and dissociate the C-H bonds of the alkenes is observed to increase with increasing size of the alkene and thus correlates with the alkene ionization energy.

Exploration of dynamical regimes of irradiated small protonated water clusters

NASA Astrophysics Data System (ADS)

Ndongmouo Taffoti, U. F.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.; Wang, Z. P.

2010-05-01

We explore from a theoretical perspective the dynamical response of small water clusters, (H2O)nH3O+ with n=1,2,3, to a short laser pulse for various frequencies, from infrared (IR) to ultra-violet (UV) and intensities (from 6×10^{13} W/cm^2 to 5×10^{14} W/cm^2). To that end, we use time-dependent local-density approximation for the electrons, coupled to molecular dynamics for the atomic cores (TDLDA-MD). The local-density approximation is augmented by a self-interaction correction (SIC) to allow for a correct description of electron emission. For IR frequencies, we see a direct coupling of the laser field to the very light H+ ions in the clusters. Resonant coupling (in the UV) and/or higher intensities lead to fast ionization with subsequent Coulomb explosion. The stability against Coulomb pressure increases with system size. Excitation to lower ionization stages induced strong ionic vibrations. The latter maintain a rather harmonic pattern in spite of the sizeable amplitudes (often 10% of the bond length).