How O2-Binding Affects Structural Evolution of Medium Even-Sized Gold Clusters Aun- (n = 20-34).

We report the first joint anion photoelectron spectroscopy and theoretical study on how O2-binding affects the structures of medium even-sized gold clusters, Aun- (n = 20-34), a special size region that entails a variety of distinct structures. Under the temperature conditions in the current photoelectron spectroscopy experiment, O2-bound gold clusters were observed only for n = 22-24 and 34. Nevertheless, O2 binding with the clusters in the size range of n = 20-34 can be still predicted based on the obtained global-minimum structures. Consequently, a series of structural transitions, from the pyramidal to fused-planar to core-shell structures, are either identified or predicted for the AunO2- clusters, where the O2-binding is in either superoxo or peroxo fashion. The identified global-minimum structures of AunO2- (n = 20-34) also allow us to gain improved understanding of why the clusters Aun- (n = 26-32) are less reactive with O2 in comparison to others.

Eigenvector centrality for characterization of protein allosteric pathways.

Determining the principal energy-transfer pathways responsible for allosteric communication in biomolecules remains challenging, partially due to the intrinsic complexity of the systems and the lack of effective characterization methods. In this work, we introduce the eigenvector centrality metric based on mutual information to elucidate allosteric mechanisms that regulate enzymatic activity. Moreover, we propose a strategy to characterize the range of correlations that underlie the allosteric processes. We use the V-type allosteric enzyme imidazole glycerol phosphate synthase (IGPS) to test the proposed methodology. The eigenvector centrality method identifies key amino acid residues of IGPS with high susceptibility to effector binding. The findings are validated by solution NMR measurements yielding important biological insights, including direct experimental evidence for interdomain motion, the central role played by helix h[Formula: see text], and the short-range nature of correlations responsible for the allosteric mechanism. Beyond insights on IGPS allosteric pathways and the nature of residues that could be targeted by therapeutic drugs or site-directed mutagenesis, the reported findings demonstrate the eigenvector centrality analysis as a general cost-effective methodology to gain fundamental understanding of allosteric mechanisms at the molecular level.

Probing the structures of gold-aluminum alloy clusters AuxAly(-): a joint experimental and theoretical study.

Besides the size and structure, compositions can also dramatically affect the properties of alloy nanoclusters. Due to the added degrees of freedom, determination of the global minimum structures for multi-component nanoclusters poses even greater challenges, both experimentally and theoretically. Here we report a systematic and joint experimental/theoretical study of a series of gold-aluminum alloy clusters, AuxAly(-) (x + y = 7,8), with various compositions (x = 1-3; y = 4-7). Well-resolved photoelectron spectra have been obtained for these clusters at different photon energies. Basin-hopping global searches, coupled with density functional theory calculations, are used to identify low-lying structures of the bimetallic clusters. By comparing computed electronic densities of states of the low-lying isomers with the experimental photoelectron spectra, the global minima are determined. It is found that for y ≥ 6 there is a strong tendency to form the magic-number square bi-pyramid motif of Al6(-) in the AuxAly(-) clusters, suggesting that the Al-Al interaction dominates the Au-Au interaction in the mixed clusters. A closely related trend is that for x > 1, the gold atoms tend to be separated by Al atoms unless only the magic-number Al6(-) square bi-pyramid motif is present, suggesting that in the small-sized mixed clusters, Al and Au components do not completely mix with one another. Overall, the Al component appears to play a more dominant role due to the high robustness of the magic-number Al6(-) square bi-pyramid motif, whereas the Au component tends to be either "adsorbed" onto the Al6(-) square bi-pyramid motif if y ≥ 6, or stays away from one another if x < y < 6.

B27(-): Appearance of the smallest planar boron cluster containing a hexagonal vacancy.

Photoelectron spectroscopy and ab initio calculations have been carried out to probe the structures and chemical bonding of the B27 (-) cluster. Comparison between the experimental spectrum and the theoretical results reveals a two-dimensional (2D) global minimum with a triangular lattice containing a tetragonal defect (I) and two low-lying 2D isomers (II and III), each with a hexagonal vacancy. All three 2D isomers have 16 peripheral boron atoms and 11 inner boron atoms. Isomer I is shown to be mainly responsible for the observed photoelectron spectrum with isomers II and III as minor contributors. Chemical bonding analyses of these three isomers show that they all feature 16 localized peripheral B-B σ-bonds. Additionally, isomer I possesses 16 delocalized σ bonds and nine delocalized π bonds, while isomers II and III each contain 17 delocalized σ bonds and eight delocalized π bonds. It is found that the hexagonal vacancy is associated generally with an increase of delocalized σ bonds at the expense of delocalized π bonds in 2D boron clusters. The hexagonal vacancy, characteristic of borophenes, is found to be a general structural feature for mid-sized boron clusters. The current study shows that B27 (-) is the first boron cluster, where a hexagonal vacancy appears among the low-lying isomers accessible experimentally.

Enantioselective desymmetrization via carbonyl-directed catalytic asymmetric hydroboration and Suzuki-Miyaura cross-coupling.

The rhodium-catalyzed enantioselective desymmetrization of symmetric γ,δ-unsaturated amides via carbonyl-directed catalytic asymmetric hydroboration (directed CAHB) affords chiral secondary organoboronates with up to 98% ee. The chiral γ-borylated products undergo palladium-catalyzed Suzuki-Miyaura cross-coupling via the trifluoroborate salt with stereoretention.

Computational insights on crystal structures of the oxygen-evolving complex of photosystem II with either Ca(2+) or Ca(2+) substituted by Sr(2+).

The oxygen-evolving complex of photosystem II can function with either Ca(2+) or Sr(2+) as the heterocation, but the reason for different turnover rates remains unresolved despite reported X-ray crystal structures for both forms. Using quantum mechanics/molecular mechanics (QM/MM) calculations, we optimize structures with each cation in both the resting state (S1) and in a series of reduced states (S0, S-1, and S-2). Through comparison with experimental data, we determine that the X-ray crystal structures with either Ca(2+) or Sr(2+) are most consistent with the S-2 state (i.e., Mn4[III,III,III,II] with O4 and O5 protonated). As expected, the QM/MM models show that Ca(2+)/Sr(2+) substitution results in the elongation of the heterocation bonds and the displacement of terminal waters W3 and W4. The optimized structures also show that hydrogen-bonded W5 is displaced in all S states with Sr(2+) as the heterocation, suggesting that this water may play a critical role during water oxidation.

A photoelectron spectroscopy and ab initio study of the structures and chemical bonding of the B25(-) cluster.

Photoelectron spectroscopy and ab initio calculations are used to investigate the structures and chemical bonding of the B25(-) cluster. Global minimum searches reveal a dense potential energy landscape with 13 quasi-planar structures within 10 kcal/mol at the CCSD(T)/6-311+G(d) level of theory. Three quasi-planar isomers (I, II, and III) are lowest in energy and nearly degenerate at the CCSD(T) level of theory, with II and III being 0.8 and 0.9 kcal/mol higher, respectively, whereas at two density functional levels of theory isomer III is the lowest in energy (8.4 kcal/mol more stable than I at PBE0/6-311+G(2df) level). Comparison with experimental photoelectron spectroscopic data shows isomer II to be the major contributor while isomers I and III cannot be ruled out as minor contributors to the observed spectrum. Theoretical analyses reveal similar chemical bonding in I and II, both involving peripheral 2c-2e B-B σ-bonding and delocalized interior σ- and π-bonding. Isomer III has an interesting elongated ribbon-like structure with a π-bonding pattern analogous to those of dibenzopentalene. The high density of low-lying isomers indicates the complexity of the medium-sized boron clusters; the method dependency of predicting relative energies of the low-lying structures for B25(-) suggests the importance of comparison with experiment in determining the global minima of boron clusters at this size range. The appearance of many low-lying quasi-planar structures containing a hexagonal hole in B25(-) suggests the importance of this structural feature in maintaining planarity of larger boron clusters.

Isomerism and structural fluxionality in the Au26 and Au26(-) nanoclusters.

Using the minima hopping global optimization method at the density functional level, we found low-energy nanostructures for neutral Au26 and its anion. The local-density and a generalized gradient approximation of the exchange­correlation functional predict different nanoscale motifs. We found a vast number of isomers within a small energy range above the respective putative global minima with each method. Photoelectron spectroscopy of Au26(-) under different experimental conditions revealed definitive evidence of the presence of multiple isomers, consistent with the theoretical predictions. Comparison between the experimental and simulated photoelectron spectra suggests that the photoelectron spectra of Au26(-) contain a mixture of three isomers, all of which are low-symmetry core­shell-type nanoclusters with a single internal Au atom. We present a disconnectivity graph for Au26(-) that has been computed completely at the density functional level. The transition states used to build this disconnectivity graph are complete enough to predict Au26(-) to have a possible fluxional shell, which facilitates the understanding of its catalytic activity.

Mechanistic Insights into Carbonyl-Directed Rhodium-Catalyzed Hydroboration: ab Initio Study of a Cyclic γ,δ-Unsaturated Amide.

A two-point binding mechanism for the cationic rhodium(I)-catalyzed carbonyl-directed catalytic asymmetric hydroboration of a cyclic γ,δ-unsaturated amide is investigated using density functional theory. Geometry optimizations and harmonic frequency calculations for the model reaction are carried out using the basis set 6-31+G** for C, O, P, B, N, and H and LANL2DZ for Rh atoms. The Gibbs free energy of each species in THF solvent is obtained based on the single-point energy computed using the PCM model at the ECP28MWB/6-311+G(d,p) level plus the thermal correction to Gibbs free energy by deducting translational entropy contribution. The Rh-catalyzed reaction cycle involves the following sequence of events: (1) chelation of the cyclic γ,δ-unsaturated amide via alkene and carbonyl complexation in a model active catalytic species, [Rh(L2)2S2]+, (2) oxidative addition of pinacol borane (pinBH), (3) migratory insertion of the alkene double bond into Rh-H (preferred pathway) or Rh-B bond, (4) isomerization of the resulting intermediate, and finally, (5) reductive elimination to form the B-C or H-C bond with regeneration of the catalyst. Free energy profiles for potential pathways leading to the major γ-borylated product are computed and discussed in detail. The potential pathways considered include (1) pathways proceeding via migratory insertion into the Rh-H bond (pathways I, I-1, and I-2), (2) a potential pathway proceeding via migratory insertion into the Rh-B bond (pathway II), and two potential competing routes to a ß-borylated byproduct (pathway III). The results find that the Rh-H migratory insertion pathway I-2, followed in sequence by an unanticipated isomerization via amide rotation and reductive elimination, is the most favorable reaction pathway. A secondary consequence of amide rotation is access to a competing ß-hydride elimination pathway. The pathways computed in this study are supported by and help explain related experimental results.

S0-State model of the oxygen-evolving complex of photosystem II.

The S0 → S1 transition of the oxygen-evolving complex (OEC) of photosystem II is one of the least understood steps in the Kok cycle of water splitting. We introduce a quantum mechanics/molecular mechanics (QM/MM) model of the S0 state that is consistent with extended X-ray absorption fine structure spectroscopy and X-ray diffraction data. In conjunction with the QM/MM model of the S1 state, we address the proton-coupled electron-transfer (PCET) process that occurs during the S0 → S1 transition, where oxidation of a Mn center and deprotonation of a µ-oxo bridge lead to a significant rearrangement in the OEC. A hydrogen bonding network, linking the D1-D61 residue to a Mn-bound water molecule, is proposed to facilitate the PCET mechanism.

Spectral tuning in halorhodopsin: the chloride pump photoreceptor.

The spectral tuning of halorhodopsin from Halobacterium salinarum (shR) during anion transport was analyzed at the molecular level using DFT-QM/MM [SORCI+Q//B3LYP/6-31G(d):Amber96] hybrid methods. Insights into the influence of Cl(-) depletion, Cl(-) substitution by N3(-) or NO3(-), and mutation of key amino acid residues along the ion translocation pathway (H95A, H95R, Q105E, R108H, R108I, R108K, R108Q, T111V, R200A, R200H, R200K, R200Q, and T203V) were analyzed for the first time in a fully atomistic model of the shR photoreceptor. We found evidence that structural rearrangements mediated by specific hydrogen bonds of internal water molecules and counterions (D238 and Cl(-)) in the active site induce changes in the bond-length alternation of the all-trans retinyl chromophore and affect the wavelength of maximal absorption in shR.

γ-Selective directed catalytic asymmetric hydroboration of 1,1-disubstituted alkenes.

Directed catalytic asymmetric hydroborations of 1,1-disubstituted alkenes afford γ-dioxaborato amides and esters in high enantiomeric purity (90-95% ee).

Unraveling the mechanisms of O2 activation by size-selected gold clusters: transition from superoxo to peroxo chemisorption.

The activation of dioxygen is a key step in CO oxidation catalyzed by gold nanoparticles. It is known that small gold cluster anions with even-numbered atoms can molecularly chemisorb O(2) via one-electron transfer from Au(n)(-) to O(2), whereas clusters with odd-numbered atoms are inert toward O(2). Here we report spectroscopic evidence of two modes of O(2) activation by the small even-sized Au(n)(-) clusters: superoxo and peroxo chemisorption. Photoelectron spectroscopy of O(2)Au(8)(-) revealed two distinct isomers, which can be converted from one to the other depending on the reaction time. Ab initio calculations show that there are two close-lying molecular O(2)-chemisorbed isomers for O(2)Au(8)(-): the lower energy isomer involves a peroxo-type binding of O(2) onto Au(8)(-), while the superoxo chemisorption is a slightly higher energy isomer. The computed detachment transitions of the superoxo and peroxo species are in good agreement with the experimental observation. The current work shows that there is a superoxo to peroxo chemisorption transition of O(2) on gold clusters at Au(8)(-): O(2)Au(n)(-) (n = 2, 4, 6) involves superoxo binding and n = 10, 12, 14, 18 involves peroxo binding, whereas the superoxo binding re-emerges at n = 20 due to the high symmetry tetrahedral structure of Au(20), which has a very low electron affinity. Hence, the two-dimensional (2D) Au(8)(-) is the smallest anionic gold nanoparticle that prefers peroxo binding with O(2). At Au(12)(-), although both 2D and 3D isomers coexist in the cluster beam, the 3D isomer prefers the peroxo binding with O(2).

Interlocked catenane-like structure predicted in Au24(SR)20: implication to structural evolution of thiolated gold clusters from homoleptic gold(I) thiolates to core-stacked nanoparticles.

Atomic structure of a recently synthesized ligand-covered cluster Au(24)(SR)(20) [J. Phys. Chem. Lett., 2010, 1, 1003] is resolved based on the developed classical force-field based divide-and-protect approach. The computed UV-vis absorption spectrum and powder X-ray diffraction (XRD) curve for the lowest-energy isomer are in good agreement with experimental measurements. Unique catenane-like staple motifs are predicted for the first time in core-stacked thiolate-group (RS-) covered gold nanoparticles (RS-AuNPs), suggesting the onset of structural transformation in RS-AuNPs at relatively low Au/SR ratio. Since the lowest-energy structure of Au(24)(SR)(20) entails interlocked Au(5)(SR)(4) and Au(7)(SR)(6) oligomers, it supports a recently proposed growth model of RS-AuNPs [J. Phys. Chem. Lett., 2011, 2, 990], that is, Au(n)(SR)(n-1) oligomers are formed during the initial growth of RS-AuNPs. By comparing the Au-core structure of Au(24)(SR)(20) with other structurally resolved RS-AuNPs, we conclude that the tetrahedral Au(4) motif is a prevalent structural unit for small-sized RS-AuNPs with relatively low Au/SR ratio. The structural prediction of Au(24)(SR)(20) offers additional insights into the structural evolution of thiolated gold clusters from homoleptic gold(I) thiolate to core-stacked RS-AuNPs. Specifically, with the increase of interfacial bond length of Au(core)-S in RS-AuNPs, increasingly larger "metallic" Au-core is formed, which results in smaller HOMO-LUMO (or optical) gap. Calculations of electronic structures and UV-vis absorption spectra of Au(24)(SR)(20) and larger RS-AuNPs (up to ~2 nm in size) show that the ligand layer can strongly affect optical absorption behavior of RS-AuNPs.

Structure evolution of gold cluster anions between the planar and cage structures by isoelectronic substitution: Au(n)- (n = 13-15) and MAu(n)- (n = 12-14; M = Ag, Cu).

The structural and electronic effects of isoelectronic substitution by Ag and Cu atoms on gold cluster anions in the size range between 13 and 15 atoms are studied using a combination of photoelectron spectroscopy and first-principles density functional calculations. The most stable structures of the doped clusters are compared with those of the undoped Au clusters in the same size range. The joint experimental and theoretical study reveals a new C(3v) symmetric isomer for Au(13)(-), which is present in the experiment, but has hitherto not been recognized. The global minima of Au(14)(-) and Au(15)(-) are resolved on the basis of comparison between experiment and newly computed photoelectron spectra that include spin-orbit effects. The coexistence of two isomers for Au(15)(-) is firmly established with convincing experimental evidence and theoretical calculations. The overall effect of the isoelectronic substitution is minor on the structures relative to those of the undoped clusters, except that the dopant atoms tend to lower the symmetries of the doped clusters.

Observation of earlier two-to-three dimensional structural transition in gold cluster anions by isoelectronic substitution: MAu(n)(-) (n=8-11; M=Ag,Cu).

The effects of isoelectronic substitution on the electronic and structural properties of gold clusters are investigated in the critical size range of the two-dimensional (2D)-three-dimensional (3D) structural transition (MAu(n)(-), n=8-11; M=Ag,Cu) using photoelectron spectroscopy and density functional calculations. Photoelectron spectra of MAu(n)(-) are found to be similar to those of the bare gold clusters Au(n+1)(-), indicating that substitution of a Au atom by a Ag or Cu atom does not significantly alter the geometric and electronic structures of the clusters. The only exception occurs at n=10, where very different spectra are observed for MAu(10)(-) from Au(11)(-), suggesting a major structural change in the doped clusters. Our calculations confirm that MAu(8)(-) possesses the same structure as Au(9)(-) with Ag or Cu simply replacing one Au atom in its C(2v) planar global minimum structure. Two close-lying substitution isomers are observed, one involves the replacement of a center Au atom and another one involves an edge site. For Au(10)(-) we identify three coexisting low-lying planar isomers along with the D(3h) global minimum. The coexistence of so many low-lying isomers for the small-sized gold cluster Au(10)(-) is quite unprecedented. Similar planar structures and isomeric forms are observed for the doped MAu(9)(-) clusters. Although the global minimum of Au(11)(-) is planar, our calculations suggest that only simulated spectra of 3D structures agree with the observed spectra for MAu(10)(-). For MAu(11)(-), only a 3D isomer is observed, in contrast to Au(12)(-) which is the critical size for the 2D-3D structural transition with both the 2D and 3D isomers coexisting. The current work shows that structural perturbations due to even isoelectronic substitution of a single Au atom shift the 2D to 3D structural transition of gold clusters to a smaller size.

Isomer identification and resolution in small gold clusters.

A variety of experimental techniques are used to resolve energetically close isomers of Au(7)(-) and Au(8)(-) by combining photoelectron spectroscopy and ab initio calculations. Two structurally distinct isomers are confirmed to exist in the cluster beam for both clusters. Populations of the different isomers in the cluster beam are tuned using Ar-tagging, O(2)-titration, and isoelectronic atom substitution by Cu and Ag. A new isomer structure is found for Au(7)(-), which consists of a triangular Au(6) unit with a dangling Au atom. Isomer-specific photoelectron spectra of Au(8)(-) are obtained from O(2)-titration experiment. The global minimum and low-lying structures of Au(7)(-), Au(8)(-), and MAu(n)(-) (n=6,7; M=Ag,Cu) are obtained through basin-hopping global minimum searches. The results demonstrate that the combination of well-designed photoelectron spectroscopy experiments (including Ar-tagging, O(2)-titration, and isoelectronic substitution) and ab initio calculation is not only powerful for obtaining the electronic and atomic structures of size-selected clusters, but also valuable in resolving structurally and energetically close isomers of nanoclusters.

CO chemisorption on the surfaces of the golden cages.

We report a joint experimental and theoretical study of CO chemisorption on the golden cages. We find that the Au(17)(-) cage is highly robust and retains its cage structure in Au(17)(CO)(-). On the other hand, the Au(16)(-) cage is transformed to a structure similar to Au(17)(-) upon the adsorption of CO. Au(18)(-) is known to consist of two nearly degenerate structures, i.e., a cage and a pyramidal isomer, which coexist in the cluster beam. However, upon CO chemisorption only the cage isomer is observed while the pyramidal isomer no longer exists due to its less favorable interaction with CO, compared to the cage isomer. We find that inclusion of the spin-orbit effects is critical in yielding simulated spectra in quantitative agreement with the experimental data and providing unequivocal structural information and molecular insights into the chemical interactions between CO and the golden cages.

Structural transition of gold nanoclusters: from the golden cage to the golden pyramid.

How nanoclusters transform from one structural type to another as a function of size is a critical issue in cluster science. Here we report a study of the structural transition from the golden cage Au(16)(-) to the pyramidal Au(20)(-). We obtained distinct experimental evidence that the cage-to-pyramid crossover occurs at Au(18)(-), for which the cage and pyramidal isomers are nearly degenerate and coexist experimentally. The two isomers are observed and identified by their different interactions with O(2) and Ar. The cage isomer is observed to be more reactive with O(2) and can be preferentially "titrated" from the cluster beam, whereas the pyramidal isomer has slightly stronger interactions with Ar and is favored in the Au(18)Ar(x)(-) van der Waals complexes. The current study allows the detailed structural evolution and growth routes from the hollow cage to the compact pyramid to be understood and provides information about the structure-function relationship of the Au(18)(-) cluster.

Structural evolution of doped gold clusters: MAu(x)(-) (M = Si, Ge, Sn; x = 5-8).

We report a joint experimental and theoretical study on the structures of a series of gold clusters doped with a group-14 atom: MAu(x)(-) (M = Si, Ge, Sn; x = 5-8). Well-resolved photoelectron spectra were obtained and compared to calculations at several levels of theory to identify the low-lying structures of MAu(5-8)(-). We found that the structure of SiAu(5)(-) is dominated by the tetrahedrally coordinated Si motif, which can be viewed as built from the tetrahedral SiAu(4)(-) by an extra Au atom bonded to a terminal gold atom. However, SiAu(6)(-) and SiAu(7)(-) have quasi-planar structures, similar to those of GeAu(6)(-)/SnAu(6)(-) and GeAu(7)(-)/SnAu(7)(-), respectively. SiAu(8)(-) again has a tetrahedrally coordinated Si structure, which displays a structural motif of a dangling Au-Si unit sitting on a gold cluster surface, resembling that of the larger Si-doped gold cluster SiAu(16)(-). For M = Ge, Sn, our results show that the major isomers of GeAu(5-8)(-) have structures similar to those of the corresponding SnAu(5-8)(-) clusters, and they can be viewed as grown from the previously suggested square-pyramidal GeAu(4)(-) and SnAu(4)(-), respectively. Population of minor isomers was observed for SnAu(5)(-), GeAu(6)(-), SnAu(6)(-), and GeAu(8)(-). The 3D to quasi-2D to 3D structural evolution for SiAu(5)(-) to SiAu(8)(-) and the structural convergence for MAu(x)(-) (M = Si, Ge, Sn) at x = 6, 7 manifest competitions between the tendency of forming molecule-like structures around the group-14 dopant (optimizing M-Au interactions) and the strong tendency of forming planar structures for small gold anion clusters (optimizing Au-Au interactions).