Small Cluster Models Research Articles

Effect of a Single Platinum Atom within a Small Metal Oxide Cluster: Reaction of DMMP with Size-Selected Pt1Zr2O7 Supported on HOPG.

Chemical warfare agents (CWAs) are a persistent threat facing civilians and military personnel across the modern geopolitical landscape. The development of the next generation of protective and sensing materials stands to benefit from an improved fundamental understanding of the interaction of CWA molecules with the active components of such candidate materials. The use of model systems in well-controlled environments offers a route to glean such information and has been applied here to investigate the fundamental interaction of a nerve agent simulant molecule, dimethyl methylphosphonate (DMMP), with a small cluster model of a single atom catalyst (SAC) active site. The cluster models, Pt1Zr2O7, were prepared by depositing mass-selected cluster anions synthesized in the gas phase onto a 100 K highly oriented pyrolytic graphite (HOPG) substrate surface prepared in ultra-high vacuum (UHV) at sub-monolayer coverage. Upon deposition, the cluster anions lost their charge to the electrically conductive surface to yield free-standing neutral clusters. The HOPG-supported clusters were characterized by X-ray photoelectron spectroscopy (XPS) to determine the oxidation states and chemical environment of the metal atoms present within the clusters. The reactivity of the clusters with DMMP was investigated via temperature-programmed desorption/reaction (TPD/R) and XPS experiments in which the clusters were exposed to DMMP and incrementally heated to higher temperatures. In contrast to two other HOPG-supported clusters, (ZrO2)3 and Pt1Ti2O7, recently investigated in our laboratory, Pt1Zr2O7 decomposed DMMP to primarily evolve a methane species, which was completely absent for the other clusters.

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica

AbstractAl(OC(CF3)3)(PhF) reacts with silanols present on partially dehydroxylated silica to form well‐defined ≡SiOAl(OC(CF3)3)2(O(Si≡)2) (1). 27Al NMR and DFT calculations with a small cluster model to approximate the silica surface show that the aluminum in 1 adopts a distorted trigonal bipyramidal coordination geometry by coordinating to a nearby siloxane bridge and a fluorine from the alkoxide. Fluoride ion affinity (FIA) calculations follow experimental trends and show that 1 is a stronger Lewis acid than B(C6F5)3 and Al(OC(CF3)3)(PhF) but is weaker than Al(OC(CF3)3) and iPr3Si+. Cp2Zr(CH3)2 reacts with 1 to form [Cp2ZrCH3][≡SiOAl(OC(CF3)3)2(CH3)] (3) by methide abstraction. This reactivity pattern is similar to reactions of organometallics with the proposed strong Lewis acid sites present on Al2O3.

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica.

Al(OC(CF3 )3 )(PhF) reacts with silanols present on partially dehydroxylated silica to form well-defined ≡SiOAl(OC(CF3 )3 )2 (O(Si≡)2 ) (1). 27 Al NMR and DFT calculations with a small cluster model to approximate the silica surface show that the aluminum in 1 adopts a distorted trigonal bipyramidal coordination geometry by coordinating to a nearby siloxane bridge and a fluorine from the alkoxide. Fluoride ion affinity (FIA) calculations follow experimental trends and show that 1 is a stronger Lewis acid than B(C6 F5 )3 and Al(OC(CF3 )3 )(PhF) but is weaker than Al(OC(CF3 )3 ) and i Pr3 Si+ . Cp2 Zr(CH3 )2 reacts with 1 to form [Cp2 ZrCH3 ][≡SiOAl(OC(CF3 )3 )2 (CH3 )] (3) by methide abstraction. This reactivity pattern is similar to reactions of organometallics with the proposed strong Lewis acid sites present on Al2 O3 .

Highly efficient CO2 conversion on a robust metal-organic framework Cu(I)-MFU-4l: Prediction and mechanistic understanding from DFT calculations

As a bioinspired metal-organic framework (MOF) with a unique trigonal pyramidal Cu(I) site in a bowl-shaped pocket, Cu(I)-MFU-4l has emerged as an advanced single-site heterogeneous catalyst for several important reactions. Herein, we computationally investigate Cu(I)-MFU-4l combining with tetrabutylammonium bromide (TBAB) as a high-performance catalyst for CO2 conversion with propylene oxide (PO) into propylene carbonate (PC), a reaction of great significance in achieving carbon neutrality and sustainable development. Four paths are proposed depending on the initial activation of either PO or CO2 by Cu(I), as well as the ring-opening of PO at Cα-O bond or Cβ-O bond. Density functional theory calculations over a large cluster model reveal that Cu(I) is prone to interact with PO first and the most favorable path (Path 3) involves the sequential ring-opening of PO at Cβ-O bond, CO2 insertion and ring closure with Gibbs energy barriers of 8.0, 2.8 and 10.3 kcal/mol, respectively. In view of such low energy barriers, Cu(I)-MFU-4l/TBAB is predicted to be highly active for CO2 cycloaddition with PO at ambient conditions. Significant confinement effect is demonstrated in Cu(I)-MFU-4l by comparing Path 3 over both large and small cluster models. The observed confinement not only stabilizes the intermediates and transition states thermodynamically, but also promotes the ring-opening of PO kinetically, which is mainly attributed to the van der Waals (vdW) interactions between reactive fragments and surrounding frameworks through non-covalent interaction (NCI) analysis. A mechanism of electronic effect competing with steric effect is proposed to rationalize the regioselectivity of ring-opening of PO under different scenarios via natural bond orbital (NBO) charge and NCI analysis. Our results also suggest that Cu(I)-MFU-4l/TBAB outperforms Cu(II) paddle-wheel MOFs/TBAB reported previously for CO2 cycloaddition with PO. The structural robustness, the soft electron-rich Cu(I) site and the inherent confinement promote Cu(I)-MFU-4l to be an appealing candidate catalyst for a wide range of reactions.

DFT study of hydrogen bonding between metal hydroxides and organic molecules containing N, O, S, and P heteroatoms: clusters vs. surfaces

Hydrogen bonds between either a water molecule or metal hydroxides and small organic molecules with functional groups that contain N, O, S, or P heteroatoms were analyzed using DFT calculations to shed some light on the question of whether hydroxylated nanoparticles and surfaces can be stabilized with organic molecules via hydrogen bonding interactions. Two different models of metal hydroxides were used, that is, small discrete clusters and periodic slab models of surfaces, where Al(OH)3 and Cu(OH)2 served as model systems. For small discrete cluster models, formula units of Al(OH)3 and Cu(OH)2 were taken, whereas for extended surface models, boehmite-AlOOH(010) and Cu(OH)2(001) surfaces were used. According to our results, the Cu(OH)2 cluster is usually a better H-bond acceptor and donor than the water molecule, whereas the Al(OH)3 cluster prefers to either act as an H-bond donor or to form two H-bonds, one as an H-bond donor and the other as an H-bond acceptor. Among the considered organic molecules with functional groups containing N, O, S, or P heteroatoms, imidazole and (CH3)2POOH form the strongest H-bonds; the two molecules are very good H-bond acceptors as well as H-bond donors. These two molecules were also used to analyze hydrogen bonding with the boehmite-AlOOH(010) and Cu(OH)2(001) surfaces. The comparison between the surface and small-cluster calculations reveals that although cluster calculations can give reasonable estimates of adsorption energy provided that all formed H-bonds are properly accounted for (which is not always trivial), there are nevertheless structural intricacies—such as additional H-bonds with second-neighbor OH groups that may form on surfaces—that cannot be captured with small clusters. The more realistic aqueous conditions were also analyzed using the continuum solvation model. They not only influence the properties of H-bonds that are usually shorter than in vacuum but also induce deprotonation of adsorbed molecules, as observed for (CH3)2POOH on a Cu(OH)2 surface.

Leaching of palladium atoms from small cluster models during Heck reactions – An experimental and theoretical study

Relevant parameters for the leaching of palladium atoms from small Pd clusters during Heck reactions of bromobenzene and styrene have been explored computationally and experimentally. With density functional theory calculations, we modeled reaction free energies for removing a Pd atom from a Pd6 model cluster and for forming Pd-ligand complexes. Oxidative addition of bromobenzene decreases the dissolution energy. Additional parameters and mechanisms, especially bromide ions render the leaching process notably exergonic. Model results exhibit the same trends as the targeted experiments where Pd leaching from supported catalysts (Pd/C, Pd/SiO2) was monitored as function of reaction temperature, time and components.

Small practical cluster models for perovskites based on the similarity criterion of central location environment and their applications.

Developing universal theoretical models for perovskites (often denoted as ABX3) can contribute to the rational design of novel perovskite photovoltaic materials. However, few models can be successfully applied to study the intrinsic electronic structure due to the poor accuracy and unaffordable computational cost. Herein, we report the innovative construction of small practical cluster models through the similarity criterion of the central location environment, which retains only the central A-site as the original cation while the others are substituted by Cs to keep the clusters electrically neutral. The central cation has a chemical environment similar to that of the bulk perovskite. The binding energy between A and the BX framework, geometric structures (B-X distances and B-X-B angles), and the electronic structures (the gap and the spatial distribution of HOMO and LUMO, electron distribution) of these clusters have been investigated and compared with the corresponding properties of bulk materials. The results suggest that the cluster model with twelve B-atoms suitably describes these properties. The geometric structures and gaps are closer to the bulk situations than the quasi-one-dimensional and quasi-two-dimensional cluster models with all-primitive cations, respectively. Other organic cations, such as NH3(CH2)nCH3 (n = 1, 2, and 3 for EA, PA, and BA, respectively), and (NH2)2CH (FA) can, therefore, mimic perovskite materials. Clusters with different sizes of A indicate that PA and BA will distort the quasi-cubic structures, which is consistent with the judgment of the tolerance factor of bulk materials. The reliable cluster model provides the research foundation for some basic issues of perovskites, such as vibrational spectroscopy and hydrogen bonding strength, to gain detailed insight into the interactions between A and the BX framework.

SN1 reaction mechanisms of tert-butyl chloride in aqueous solution: What can be learned from reaction path search calculations and trajectory calculations for small hydrated clusters?

The SN1 reaction mechanisms of tert-butyl chloride (t-BuCl) in aqueous solution were studied using a small hydrated cluster model, t-BuCl·(H2O)n (n = 1–3), and density functional theory calculations. Our explicit solvation model is combined with a polarizable continuum model. Reaction path search calculations yielded various transition state structures associated with configurations to form retained and inverted t-BuOH (t-BuOH2+) products, respectively. Intrinsic reaction coordinate (IRC) analyses revealed that the retention process occurs via a three-step mechanism comprising initial CCl elongation, subsequent translational motion of the Cl−·(H2O)n moiety, and finally CO bond formation, while the inversion process essentially occurs via a concerted mechanism. To further elucidate the differences in the reaction mechanism between retention and inversion, on-the-fly trajectories were integrated starting from the identified transition state structures. The calculated trajectories exhibited non-IRC dynamic behavior.

Reveal the nature of particle size effect for CO2 reduction over Pd and Au

Small cluster and periodic surface models with low coverages of intermediates are frequently employed to investigate reaction mechanisms and identify active sites on nanoparticles (NPs) in density functional theory (DFT) studies. However, diverse active sites on NPs cannot be sufficiently represented by these simple models, hampering the in-depth insights into the catalytic behavior of NPs. This paper describes the crucial roles of both model and coverage effect on understanding the nature of active sites for CO2 reduction over Au and Pd NPs using DFT calculations. Terrace sites exhibit higher selectivity for CO than edge sites on Au NPs, which is opposite to the results on Au periodic surfaces. This contradiction reveals the computational model effect on clarifying active site properties. For Pd catalysts, the coverage effect is more significant. On bare Pd NPs and periodic surfaces, the selectivity for CO at edge sites is nearly identical to that at terrace sites, whereas edge sites display higher selectivity for CO than terrace sites in the case of high CO coverages. Through considering the more realistic models and the coverage effect, we successfully describe the size effect of Au and Pd NPs on CO selectivity. More importantly, this work reminds us of the necessity of reasonable models in DFT calculations.

Binding Energies of Interstellar Molecules on Crystalline and Amorphous Models of Water Ice by Ab Initio Calculations

Abstract In the denser and colder (≤20 K) regions of the interstellar medium (ISM), near-infrared observations have revealed the presence of submicron-sized dust grains covered by several layers of H2O-dominated ices and “dirtied” by the presence of other volatile species. Whether a molecule is in the gas or solid-phase depends on its binding energy (BE) on ice surfaces. Thus, BEs are crucial parameters for the astrochemical models that aim to reproduce the observed evolution of the ISM chemistry. In general, BEs can be inferred either from experimental techniques or by theoretical computations. In this work, we present a reliable computational methodology to evaluate the BEs of a large set (21) of astrochemical relevant species. We considered different periodic surface models of both crystalline and amorphous nature to mimic the interstellar water ice mantles. Both models ensure that hydrogen bond cooperativity is fully taken into account at variance with the small ice cluster models. Density functional theory adopting both B3LYP-D3 and M06-2X functionals was used to predict the species/ice structure and their BEs. As expected from the complexity of the ice surfaces, we found that each molecule can experience multiple BE values, which depend on its structure and position at the ice surface. A comparison of our computed data with literature data shows agreement in some cases and (large) differences in others. We discuss some astrophysical implications that show the importance of calculating BEs using more realistic interstellar ice surfaces to have reliable values for inclusion in the astrochemical models.

Absorption spectra of benzoic acid in water at different pH and in the presence of salts: insights from the integration of experimental data and theoretical cluster models

The absorption spectra of molecular organic chromophores in aqueous media are of considerable importance in environmental chemistry. In this work, the UV-vis spectra of benzoic acid (BA), the simplest aromatic carboxylic acid, in aqueous solutions at varying pH and in the presence of salts are measured experimentally. The solutions of different pH provide insights into the contributions from both the non-dissociated acid molecule and the deprotonated anionic species. The microscopic interpretation of these spectra is then provided by quantum chemical calculations for small cluster models of benzoic species (benzoic acid and benzoate anion) with water molecules. Calculations of the UV-vis absorbance spectra are then carried out for different clusters such as C6H5COOH·(H2O)n and C6H5COO-·(H2O)n, where n = 0-8. The following main conclusions from these calculations and the comparison to experimental results can be made: (i) the small water cluster yields good quantitative agreement with observed solution experiments; (ii) the main peak position is found to be very similar at different levels of theory and is in excellent agreement with the experimental value, however, a weaker feature about 1 eV to lower energy (red shift) of the main peak is correctly reproduced only by using high level of theory, such as Algebraic Diagrammatic Construction (ADC); (iii) dissociation of the BA into ions is found to occur with a minimum of water molecules of n = 8; (iv) the deprotonation of BA has an influence on the computed spectrum and the energetics of the lowest energy electronic transitions; (v) the effect of the water on the spectra is much larger for the deprotonated species than for the non-dissociated acid. It was found that to reproduce experimental spectrum at pH 8.0, additional continuum representation for the extended solvent environment must be included in combination with explicit solvent molecules (n ≥ 3); (vi) salts (NaCl and CaCl2) have minimal effect on the absorption spectrum and; (vii) experimental results showed that B-band of neutral BA is not sensitive to the solvent effects whereas the effect of the water on the C-band is significant. The water effects blue-shift this band up to ∼0.2 eV. Overall, the results demonstrate the ability to further our understanding of the microscopic interpretation of the electronic structure and absorption spectra of BA in aqueous media through calculations restricted to small cluster models.

How external perturbations affect the chemoselectivity of substrate activation by cytochrome P450 OleTJE.

Cytochrome P450 enzymes are versatile biocatalysts found in most forms of life. Generally, the cytochrome P450s react with dioxygen and hence are haem-based mono-oxygenases; however, in specific isozymes, H2O2 rather than O2 is used and these P450s act as peroxygenases. The P450 OleTJE is a peroxygenase that binds long to medium chain fatty acids and converts them to a range of products originating from Cα-hydroxylation, Cβ-hydroxylation, Cα-Cβ desaturation and decarboxylation of the substrate. There is still controversy regarding the details of the reaction mechanism of P450 OleTJE; how the products are formed and whether the product distributions can be influenced by external perturbations. To gain further insights into the structure and reactivity of P450 OleTJE, we set up a range of large active site model complexes as well as full enzymatic structures and did a combination of density functional theory studies and quantum mechanics/molecular mechanics calculations. In particular, the work focused on the mechanisms leading to these products under various reaction conditions. Thus, for a small cluster model, we find a highly selective Cα-hydroxylation pathway that is preferred over Cβ-H hydrogen atom abstraction by at least 10 kcal mol-1. Introduction of polar residues to the model, such as an active site protonated histidine residue or through external electric field effects, lowers the Cβ-H hydrogen atom abstraction barriers are lowered, while a full QM/MM model brings the Cα-H and Cβ-H hydrogen atom abstraction barriers within 1 kcal mol-1. Our studies; therefore, implicate that environmental effects in the second-coordination sphere can direct and guide selectivities in enzymatic reaction mechanisms.

Experimental and theoretical study of thermoelectric properties of rhombohedral GeSb5Te10 thin films

Rhombohedral GeSb5Te10 thin films are synthesized onto Al2O3 substrate by a pulsed-DC magnetron sputtering method using a target prepared by hot-pressing method. Thermoelectric properties of these films are studied as a function of temperature from room temperature to 773 K and correlated to the microstructural and surface properties. It is found that the phase transformation from amorphous to rhombohedral phase of GeSb5Te10, observed in temperature range 473–773 K, involved lattice-swelling and atomic diffusion within the crystalline structure. The completion of phase transformation at annealing temperature 673 K minimized the average crystallite size of thin film and enhanced the Seebeck coefficients (~140 μVK−1) and thermoelectric power factor (~4.5 mWm−1 K−2). Molecular orbital simulations of small cluster model, performed using linearly decreasing scattering variable along with the temperature dependent Fermi energy for onto determining the electrical and thermoelectric properties, were found in agreement to the experimental results.

Mechanistic Insight into Propylene Epoxidation with H2O2 over Titanium Silicalite-1: Effects of Zeolite Confinement and Solvent.

Density functional theory (DFT) calculations were performed to investigate the effects of zeolite confinement and solvent on propylene epoxidation with H2O2 over the titanium silicalite-1 (TS-1) catalyst. The 144T and 143T cluster models containing typical 10MR channels of TS-1 were constructed to represent the tripodal(2I) and Ti/defect sites. It was found that the confinement of the zeolite pore channel not only impacts the adsorption stability of guest molecules but also alters reaction barriers, as compared to the results obtained based on small cluster models. When dispersion corrections were considered, an enhancement of the adsorption stability of guest molecules was observed because of the important contribution from van der Waals interactions, especially for propylene adsorption. An explicit protic methanol molecule was introduced into the catalytic system to probe the influence of the solvent on propylene epoxidation, based on which a significant enhancement of CH3OH-H2O2 co-adsorption was obtained owing to H-bond formation. More importantly, the energy barrier for H2O2 dissociation was largely reduced by ∼13 kcal/mol because of the participation of the methanol in the H-transfer process and the formation of H-bond network, resulting in an alteration of the rate-limiting step. By comparison, adding an aprotic acetonitrile solvent did not have substantial effect on reaction path and kinetics. The calculation results clearly demonstrate the important role of the protic methanol solvent, which not only strengthens the adsorption of guest molecules but also promotes the kinetics for propylene epoxidation with H2O2 over TS-1 catalyst.

Tuning the laser-induced ultrafast demagnetization of transition metals

The ultrafast demagnetization (UFD) dynamics of itinerant ferromagnets is theoretically investigated as a function of the characteristics of the initial laser excitation. A many-body pd-band Hamiltonian is considered which takes into account hybridizations, Coulomb interactions, spin-orbit interactions and the coupling to the laser field on the same electronic level. In this way, a fruitful connection is established between the non-adiabatic quantum dynamics and the well-known equilibrium statistical mechanics of itinerant-electron ferromagnets. The time evolution during and after the pulse absorption is determined exactly by performing numerical Lanczos propagations on a small cluster model with parameters appropriate for Ni. The most relevant laser parameters, namely, the fluence, wave length, polarization and pulse duration are varied systematically. The results show how they allow one to control the total absorbed energy, the spectral distribution of the initial excitation, and the subsequent magnetization dynamics. The calculations show that reasonable changes in these parameters do not affect the UFD dynamics qualitatively and have only a minor influence on the time scale which characterizes the initial demagnetization. In contrast, our model predicts that the degree of demagnetization correlates well with the average number of electrons excited by the laser or average number of absorbed photons. The theoretical results are discussed by comparing them with available experiments. From a fundamental perspective, the robustness of the ultrafast demagnetization effect is theoretically demonstrated, as a phenomenon reflecting the intrinsic dynamics of the metallic 3d valence electrons. A wide variety of well-focused possibilities of tailoring the efficacy of the ultrafast demagnetization process is thereby opened.

EDRIXS: An open source toolkit for simulating spectra of resonant inelastic x-ray scattering

Resonant inelastic x-ray scattering (RIXS) has become a very powerful experimental technique to probe a broad range of intrinsic elementary excitations, for example, from low energy phonons and (bi-)magnons to high energy d-d, charge-transfer and plasmon excitations in strongly correlated electronic systems. Due to the complexity of the RIXS cross-section and strong core-hole effects, theoretical simulation of the experimental RIXS spectra is still a difficult task which hampers the understanding of RIXS spectra and the development of the RIXS technique. In this paper, we present an open source toolkit (dubbed EDRIXS) to facilitate the simulations of RIXS spectra of strongly correlated materials based on exact diagonalization (ED) of certain model Hamiltonians. The model Hamiltonian can be from a single atom, small cluster or Anderson impurity model, with model parameters from density functional theory plus Wannier90 or dynamical mean-field theory calculations. The spectra of x-ray absorption spectroscopy (XAS) and RIXS are then calculated using Krylov subspace techniques. This toolkit contains highly efficient ED, XAS and RIXS solvers written in modern Fortran 90 language and a convenient Python library used to prepare inputs and set up calculations. We first give a short introduction to RIXS spectroscopy, and then we discuss the implementation details of this toolkit. Finally, we show three examples to demonstrate its usage. Program summaryProgram title: EDRIXSProgram Files doi:http://dx.doi.org/10.17632/wvd5x3mtg4.1Licensing provisions: GNU General Public Licence 3.0Programming language: Fortran 90 and Python3External routines/libraries used: BLAS, LAPACK, Parallel ARPACK, numpy, scipy, sympy, matplotlib, sphinx, numpydocNature of problem: Simulating the spectra of resonant inelastic x-ray scattering for strongly correlated electronic systems.Solution method: Exact diagonalization of model Hamiltonians and Krylov subspace methods.

Water Oxidation and Surface Protonation of Small IrOx Clusters

Electrochemical water oxidation on the anode is a common bottleneck of electrocatalytic processes. For their efficiency and relative stability, IrOx-type anodes are among the best ones in acidic environment. In spite of all the efforts, however, it is still a complicated system from theoretical point of view. The small band gap and complicated band structure around Fermi level, strong electron correlation makes Ir(IV) oxides challenging itself, and the amorphous structure or nanoparticle structure of the electrodes just adds to the complications. We focused on these later aspects and studied the behavior of small cluster models of IrOx (Ir3 and up), instead of regular slab models. Crystalline IrO2 has a rutile lattice where Ir atoms are forming Ir-O-Ir chains along the x/y and Ir-O2-Ir chains z direction. In amorphous oxides and nanoclusters those chains are terminated by –OH or –OH2 groups, to compensate the missing positive charges. In our cluster models we mostly kept the local environment around most Ir similar to bulk, but studied the effect of terminating –OH and –OH2 groups, i.e. the H isomerism on the cluster surface. For the calculation we used DFT (DMol3) with the PBE (GGG) functional and DNP (4.4) basis set. The convergence criteria of for geometry optimization was 1.0-5 Ha and 1.0-6 for the SCF. Due to the large number of states around the HOMO-LUMO gap, we applied thermal smearing. The accuracy of the calculations was assessed compared to calculations with B3LYP hybrid functional, however the geometry and charges remained essentially the same. We found that surface protonation can significantly stabilize the lower valence states of Ir, therefore mobile H on the surface can reduce the energy required for each step of the water oxidation cycle.

Integrated Computational Study of the Cu-Catalyzed Hydration of Alkenes in Water Solvent and into the Context of an Artificial Metallohydratase

Despite the increasing efforts in the last few years, the identification of efficient catalysts able to perform the enantioselective addition of water to double bonds has not been achieved yet. Natural hydratases represent an interesting pool of biocatalysts to generate chiral alcohols, but modifying their substrate scope remains an issue. The use of artificial metalloenzymes (ArMs) appears as a promising solution in this field. In the last few years, Roelfes and co-workers have been designing a variety of DNA- and protein-based ArMs able to carry out the copper-mediated addition of water to conjugated alkenes with promising enantioselective levels. Still, from a mechanistic point of view, the copper-mediated hydration reaction remains unclear and a matter of debate. This lack of information greatly hampers further designs and optimizations of the LmrR-based copper hydratases in terms of substrates and/or enantioselective profiles. In this study, we aim to provide a better understanding of the copper-catalyzed hydration of alkenes occurring both in water solvent and into the context of the LmrR protein as designed by Roelfes and co-workers. For that purpose, we make use of an integrated computational protocol that combines quantum mechanics (QM) (including small and large cluster models as well as ab initio molecular dynamics (AIMD)) and force-field approaches (including protein–ligand docking and classical molecular dynamics (MD) simulation). This integrative study sheds light on the general doubts around the copper-catalyzed hydration mechanism and also paves the way toward more conscious designs of ArMs able to efficiently catalyze the enantioselective addition of water to double bonds.

Partnership model for small industry in cluster perspective in encouraging regional development (case study on some small industries in Jambi City)

This study aims to analyze: 1)the profile of the small industry clusters in Jambi City, those are batik industry cluster, tofu/tempeh industry cluster and furniture industry cluster; 2)the collaboration/partnership between various business actors and other parties in small industry cluster in Jambi Cityworks;3) aneffective partnership models for small industry clusters. This research is a collective case study (survey and case study). The analysis was carried out on the profile of the small industry cluster and the partnership between various industrial groups in the small industry cluster.The results of the study showedthat Jambi Cityhas potential for the development of small industries. Itcan be seen from the development of business and employment in small industries. Based on the partnership between industry groups, in Batik industry cluster and tofu/tempe industry cluster, it showed the existence of upstream partnership to the source of raw materials, downstream partnership to the consumers, and partnership with supporting industries. In terms of pattern, the partnerships are directed towards traditional partnerships which are based on trust. Meanwhile in the furniture industry cluster, there is no partnership at all, both upstream and downstream, as well as partnership with the supporting industries. However, the partnerships have not been effective. For this reason, it is necessary to build a partnership in small industry cluster that pays attention to the principle of mutual benefit, equality, legality, empowerment, and social capital.Keywords: Small industry cluster, effective partnership,regional developmentJEL Classification: L22, L26, L52INTRODUCTIONMSMEs in general and small industries in particular are one of the drivers for regional economic growthuntil now. It can be seenfromthe role of MSMEs in their contribution to GRDP and employment opportunities for a region. However, in its development, small industries are stillfaced with various problems so that they have not been able to provide optimal contributions to the economy of a region. Various problems faced by small industries today are related to capital, market access and limited facilities and infrastructure for the development of small industries (Lestari, 2010).Given the roleof MSMEsand problems faced by MSMEs, especially of small industries, the government has made various efforts in order to encourage the development of these small industries, one of them through cluster approach. In general,Nugroho et al. (2008) definedindustrial clusters as a network of interrelated industrial

Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase?

In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.