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

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.     

Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO₂) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon–carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.     

True nanocable assemblies with insulating BN nanotube sheaths and conducting Cu nanowire cores

Nanocable models comprised of BN nanotubes filled with close-packed Cu nanowires were investigated by gradient-corrected density functional theory (DFT) computations. The optimal distance between the sidewall of BN nanotubes and the atoms in a copper nanowire is about 0.35 nm, with a weak insertion energy (ca. -0.04 eV per Cu atom). Hence, such nanocables are assembled by weaker van der Waals (vdW) forces, rather than by chemical bonding interactions. The electronic band structures of the BN/Cu hybrid systems are superposition of those of the separate components, the BN nanotubes, and the Cu nanowires. Since charge density analyses show that the conduction electrons are distributed only on the copper atoms, charge transport will occur only in these inner nanowires, which are effectively insulated by the outer BN nanotubes. On the basis of these computational results, BN/Cu hybrid structures should be ideal nanocables.     

Modeling chemical reactions for drug design

Chemical reactions are involved at many stages of the drug design process. This starts with the analysis of biochemical pathways that are controlled by enzymes that might be downregulated in certain diseases. In the lead discovery and lead optimization process compounds have to be synthesized in order to test them for their biological activity. And finally, the metabolism of a drug has to be established. A better understanding of chemical reactions could strongly help in making the drug design process more efficient. We have developed methods for quantifying the concepts an organic chemist is using in rationalizing reaction mechanisms. These methods allow a comprehensive modeling of chemical reactivity and thus are applicable to a wide variety of chemical reactions, from gas phase reactions to biochemical pathways. They are empirical in nature and therefore allow the rapid processing of large sets of structures and reactions. We will show here how methods have been developed for the prediction of acidity values and of the regioselectivity in organic reactions, for designing the synthesis of organic molecules and of combinatorial libraries, and for furthering our understanding of enzyme-catalyzed reactions and of the metabolism of drugs.     

Metal-free organocatalysis through explicit hydrogen bonding interactions

The metal (ion)-free catalysis of organic reactions is a contemporary challenge that is just being taken up by chemists. Hence, this field is in its infancy and is briefly reviewed here, along with some rough guidelines and concepts for further catalyst development. Catalysis through explicit hydrogen bonding interactions offers attractive alternatives to metal (ion)-catalyzed reactions by combining supramolecular recognition with chemical transformations in an environmentally benign fashion. Although the catalytic rate accelerations relative to uncatalyzed reactions are often considerably less than for the metal (ion)-catalyzed variants, this need not be a disadvantage. Also, owing to weaker enthalpic binding interactions, product inhibition is rarely a problem and hydrogen bond additives are truly catalytic, even in water.     

Approximate scheme for calculating van der Waals interactions between finite cylindrical volume elements

A successful approach to calculating van der Waals (vdW) forces between irregular bodies is to divide the bodies into small cylindrical volume elements and integrate the vdW interactions between opposing elements. In this context it has been common to use Hamaker's expression for parallel plates to approximate the vdW interactions between the opposing elements. This present study shows that Hamaker's vdW expression for parallel plates does not accurately describe the vdW interactions for co-axial cylinders having a ratio of cylinder radius to separation distance (R/D) of 10 or less. This restricts the systems that can be simulated using this technique and explicitly excludes consideration of topographical or compositional variations at the nanoscale for surfaces that are in contact or within a few nm of contact. To address this limitation, approximate analytical expressions for nonretarded vdW forces between finite cylinders in different orientations are derived and are shown to produce a high level of agreement with forces calculated using full numerical solutions of the corresponding Hamaker's equations. The expressions developed here allow accurate calculation of vdW forces in systems where particles are in contact or within a few nm of contact with surfaces and the particles and/or surfaces have heterogeneous nanoscale morphology or composition. These calculations can be performed at comparatively low computational cost compared to the full numerical solution of Hamaker's equations.     

Solventless Formation of G‐Quartet Complexes Based on Alkali and Alkaline Earth Salts on Au(111)

Template cations have been extensively employed in the formation, stabilization and regulation of structural polymorphism of G‐quadruplex structures in vitro. However, the direct addition of salts onto solid surfaces, especially under ultra‐high‐vacuum (UHV) conditions, to explore the feasibility and universality of the formation of G‐quartet complexes in a solventless environment has not been reported. By combining UHV‐STM imaging and DFT calculations, we have shown that three different G‐quartet‐M (M: Na/K/Ca) complexes can be obtained on Au(111) using alkali and alkaline earth salts as reactants. We have also identified the driving forces (intra‐quartet hydrogen bonding and electrostatic ionic bonding) for the formation of these complexes and quantified the interactions involved. Our results demonstrate a novel route to fabricate G‐quartet‐related complexes on solid surfaces, providing an alternative feasible way to bring metal elements to surfaces for constructing metal–organic systems.     

Partially hydroxylated polycrystalline ionic oxides: a new route toward electron-rich surfaces

Charge traps at the surface of oxide materials play a fundamental role in various chemical processes, such as the activation of supported metal clusters. In this study, combining electron paramagnetic resonance with cluster model DFT calculations, we show that excess electrons at the surface of MgO, CaO, and SrO polycrystalline materials can be generated by preparing weakly hydroxylated surfaces followed by deposition of small amounts of alkali metals. The residual OH groups present on specific sites of the partially dehydroxylated surface act as stable traps for electrons donated by the alkali metal (Na in this case) which forms a Na+ ion distant from the trapped electron. This process results in the formation of thermally stable (H+)(e-) color centers at the surface of the oxide. The procedure could be of interest for the stabilization and activation of supported metal nanoparticles with potential use in catalysis.     

Structure, spectroscopy, and reactivity properties of porphyrin pincers: a conceptual density functional theory and time-dependent density functional theory study

Porphyrin and pincer complexes are both important categories of compounds in biological and catalytic systems. The idea to combine them is computationally investigated in this work. By employment of density functional theory (DFT), conceptual DFT, and time-dependent DFT approaches, structure, spectroscopy, and reactivity properties of porphyrin pincers are systematically studied for a selection of divalent metal ions. We found that the porphyrin pincers are structurally and spectroscopically different from their precursors and are more reactive in electrophilic and nucleophilic reactions. A few quantitative linear/exponential relationships have been discovered between bonding interactions, charge distributions, and DFT chemical reactivity indices. These results are implicative in chemical modification of hemoproteins and understanding chemical reactivity in heme-containing and other biologically important complexes and cofactors.     

Understanding the Effect of the Exchange-Correlation Functionals on Methane and Ethane Formation over Ruthenium Catalysts

Density functional theory (DFT) has been established as a powerful research tool for heterogeneous catalysis research in obtaining key thermodynamic and/or kinetic parameters like adsorption energies, enthalpies of reaction, activation barriers, and rate constants. Understanding of density functional exchange-correlation approximations is essential to reveal the mechanism and performance of a catalyst. In the present work, we reported the influence of six exchange-correlation density functionals, including PBE, RPBE, BEEF+vdW, optB86b+vdW, SCAN, and SCAN+rVV10, on the adsorption energies, reaction energies and activation barriers of carbon hydrogenation and carbon-carbon couplings during the formation of methane and ethane over Ru(0001) and Ru(1011) surfaces. We found the calculated reaction energies are strongly dependent on exchange-correlation density functionals due to the difference in coordination number between reactants and products on surfaces. The deviation of the calculated elementary reaction energies can be accumulated to a large value for chemical reaction involving multiple steps and vary considerably with different exchange-correlation density functionals calculations. The different exchange-correlation density functionals are found to influence considerably the selectivity of Ru(0001) surface for methane, ethylene, and ethane formation determined by the adsorption energies of intermediates involved. However, the influence on the barriers of the elementary surface reactions and the structural sensitivity of Ru(0001) and Ru(1011) are modest. Our work highlights the limitation of exchange-correlation density functionals on computational catalysis and the importance of choosing a proper exchange-correlation density functional in correctly evaluating the activity and selectivity of a catalyst.     

Activation of a Metal‐Halogen Bond by Halogen Bonding

In recent years, the non‐covalent interaction of halogen bonding (XB) has found increasing application in organocatalysis. However, reports of the activation of metal‐ligand bonds by XB have so far been limited to a few reactions with elemental iodine or bromine. Herein, we present the activation of metal‐halogen bonds by two classes of inert halogen bond donors and the use of the resulting activated complexes in homogenous gold catalysis. The only recently explored class of iodolium derivatives were shown to be effective activators in two test reactions and their activity could be modulated by blocking of the Lewis acidic sites. Bis(benzimidazolium)‐based halogen bonding activators provided even more rapid conversion, while the non‐iodinated reference compound showed little activity. The role of halogen bonding in the activation of metal‐halogen bonds was further investigated by NMR experiments and DFT calculations, which support the mode of activation occurring via halogen bonding.     

van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface

We investigate the performance of several van der Waals (vdW) functionals at calculating the interactions between benzene and the copper (111) surface, using the local orbital approach in the SIESTA code. We demonstrate the importance of using surface optimized basis sets to calculate properties of pure surfaces, including surface energies and the work function. We quantify the errors created using (3 × 3) supercells to study adsorbate interactions using much larger supercells, and show non‐negligible errors in the binding energies and separation distances. We examine the eight high‐symmetry orientations of benzene on the Cu (111) surface, reporting the binding energies, separation distance, and change in work function. The optimized vdW‐DF(optB88‐vdW) functional provides superior results to the vdW‐DF(revPBE) and vdW‐DF2(rPW86) functionals, and closely matches the experimental and experimentally deduced values. This work demonstrates that local orbital methods using appropriate basis sets combined with a vdW functional can model adsorption between metal surfaces and organic molecules.     

Duality of Orbital‐Symmetry‐Allowed Transition States for Thermal Sigmatropic Hydrogen Shifts in Transition Metal Compounds

Herein, the Zimmerman Möbius/Hückel concept is extended to pericyclic reactions involving transition metals. While sigmatropic hydrogen shifts in parent hydrocarbons are either uniquely antarafacial or suprafacial, we have shown by theoretical orbital topology considerations and quantum chemical computations at DFT level that both modes of stereoselectivity must become allowed in the same system as a consequence of Craig–Möbius‐type orbital arrays, in which a transition metal d orbital induces a phase dislocation in metallacycles. This may have fundamental implications for the understanding of reactivity and bonding in organometallic chemistry.     

Mechanistic Insight into the Catalytic Oxidation of Cyclohexane over Carbon Nanotubes: Kinetic and In Situ Spectroscopic Evidence

As some of the most interesting metal‐free catalysts, carbon nanotubes (CNTs) and other carbon‐based nanomaterials show great promise for some important chemical reactions, such as the selective oxidation of cyclohexane (C₆H₁₂). Due to the lack of fundamental understanding of carbon catalysis in liquid‐phase reactions, we have sought to unravel the role of CNTs in the catalytic oxidation of C₆H₁₂ through a combination of kinetic analysis, in situ spectroscopy, and density functional theory. The catalytic effect of CNTs originates from a weak interaction between radicals and their graphene skeletons, which confines the radicals around their surfaces. This, in turn, enhances the electron‐transfer catalysis of peroxides to yield the corresponding alcohol and ketone.     

Chemistry at surfaces: from ab initio structures to quantum dynamics

Recent years have witnessed an ever growing interest in theoretically studying chemical processes at surfaces. Apart from the interest in catalysis, electrochemistry, hydrogen economy, green chemistry, atmospheric and interstellar chemistry, theoretical understanding of the molecule–surface chemical bonding and of the microscopic dynamics of adsorption and reaction of adsorbates are of fundamental importance for modeling known processes, understanding new experimental data, predicting new phenomena, controlling reaction pathways. In this work, we review the efforts we have made in the last few years in this exciting field. We first consider the energetics and the structural properties of some adsorbates on metal surfaces, as deduced by converged, first-principles, plane-wave calculations within the slab-supercell approach. These studies comprise water adsorption on Ru(0001), a subject of very intense debate in the past few years, and oxygen adsorption on aluminum, the prototypical example of metal passivation. Next, we address dynamical processes at surfaces with classical and quantum methods. Here the main interest is in hydrogen dynamics on metallic and semi-metallic surfaces, because of its importance for hydrogen storage and interstellar chemistry. Hydrogen sticking is studied with classical and quasi-classical means, with particular emphasis on the relaxation of hot–atoms following dissociative chemisorption. Hot atoms dynamics on metal surfaces is investigated in the reverse, hydrogen recombination process and compared to Eley–Rideal dynamics. Finally, Eley–Rideal, collision-induced desorption, and adsorbate-induced trapping are studied quantum mechanically on a graphite surface, and unexpected quantum effects are observed.     

An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases

We apply the van der Waals density functional (vdW-DF) to study hydrogen bonding and stacking interactions between nucleobases. The excellent agreement of our results with high level quantum chemical calculations highlights the value of the vdW-DF for first-principles investigations of biologically important molecules. Our results suggest that, in the case of hydrogen-bonded nucleobase pairs, dispersion interactions reduce the cost of propeller twists while having a negligible effect on buckling. Furthermore, the efficient scaling of DFT methods allowed for the easy optimization of separation distance between nucleobase stacks, indicating enhancements in the interaction energy of up to 3 kcalmol over previous fixed distance calculations. We anticipate that these results are significant for extending the vdW-DF method to model larger vdW complexes and biological molecules.     

Assessment of density functional theory to calculate the phase transition pressure of ice

To assess the accuracy of density functional theory (DFT) methods in describing hydrogen bonding in condensed phases, we benchmarked their performance in describing phase transitions among different phases of ice. We performed DFT calculations of ice for phases Ih, II, III, VI and VII using BLYP, PW91, PBE, PBE-D, PBEsol, B3LYP, PBE0, and PBE0-D, and compared the calculated phase transition pressures between Ih-II, Ih-III, II-VI, and VI-VII with the 0 K experimental values of Whalley [J. Chem. Phys., 1984, 81, 4087]. From the geometry optimization of many different candidates, we found that the most stable proton orientation as well as the phase transition pressure does not show much functional dependence for the generalized gradient approximation and hybrid functionals. Although all these methods overestimated the phase transition pressure, the addition of van der Waals (vdW) correction using PBE-D and PBE0-D reduced the transition pressure and improved the agreement for Ih-II. On the other hand, energy ordering between VI and VII reversed and gave an unphysical negative transition pressure. Binding energy profiles of a few conformations of water dimers were calculated to understand the improvement for certain transitions and failures for others with the vdW correction. We conclude that vdW dispersion forces must be considered to accurately describe the hydrogen bond in many different phases of ice, but the simple addition of the R(-6) term with a small basis set tends to over stabilize certain geometries giving unphysical ordering in the high density phases.     

Imaging with chemical analysis: adsorbed structures formed during surface chemical reactions

Imaging surfaces and interfaces with structural and chemical specificity has been essential for understanding a variety of phenomena occurring in adsorbed layers during surface chemical reactions. A recent achievement of chemical imaging with spectroscopic analysis is the experimental proof of theoretically predicted spontaneous formation of regular patterns of metal adatoms during surface chemical reactions. An attractive feature of this finding is that the reaction rate and adlayer coverage can be employed to precisely control the morphology of the structures. The mechanisms of these self-organisation phenomena, driven by the interplay between energetic principles and kinetics, opens a conceptually novel route to creating a wide range of surface-supported functional structures at the micro- and nanometre length scales.     

Metal complex-assisted activation of small molecules. From NO to superoxide and peroxides

Transition metal centres are one of the primary targets for nitric oxide (NO), superoxide (O2(-)) and hydrogen peroxide (H2O2), which are small molecules present in a biological milieu, and of industrial and environmental interest. Coordination to a metal centre modulates their redox behaviour in such a way that they become activated for an inner-sphere oxidation or reduction, depending on the electronic and redox properties of a particular transition metal ion. Since the related redox reactions play multiple roles in physiological and pathophysiological processes, as well as in chemical catalysis in terms of synthetic applications and exhaust gas purification, the elucidation of the mechanisms of the elementary reaction steps behind these complex processes is of fundamental importance. This review concentrates on our work in this area, where by applying low temperature and high pressure kinetic and thermodynamic techniques we shed more light on the mechanisms of the particular reaction steps involved in the activation of NO, O2(-) and various peroxides. The studies include work on solvent exchange reactions that control the binding of small molecules to the metal centre and subsequent electron-transfer processes. We paid special attention to different iron and manganese complexes with heme and non-heme ligand systems.     

Revisiting the main group cyclopentadienyl metal complexes in terms of the through-space coupling concept

The structures and properties of metal complexes are traditionally treated in terms of hybridization and electronic ligand effects. What is notoriously neglected, however, is the fact that in such an aggregate the ligands approach so closely to one another — on the order of van der Waals (vdW) distances — that intramolecular packing effects come into play. Actually, non-bonded interactions between any atoms bonded to some central atom are increasingly recognized as an important factor in determining bond distances, bond angles and the like. The class of the main group cyclopentadienyl (Cp) metal complexes appears to be a case study in this respect, because of the large extension of the Cp group and its ring structure on the one hand, and on the other, the minimal d-orbital involvement, dissimilar to the transition-metal analogues. It is shown that the diverse array of structural arrangements, such as linear, ring-slipped, bent, and polymeric chain structures, as well as their reactivities, are brought under the umbrella of one treatment with the aid of the through-space coupling (TSC) concept. This is the molecular orbital representation of vdW repulsive–attractive forces. As a central feature, the individual ligands are at first combined to a united system of TSC orbitals and then allowed to interact with the metal AOs. The energy splitting of the TSC orbitals and the electron density shift from one of them to a vacant metal orbital determine the repulsive and attractive interligand forces and hence fine-tune the geometry of the complex. Along these lines a physical explanation for the interplay between vdW attraction and repulsion becomes available. More specifically we are dealing here with complexes of the type Cp′_nML_m (n=1–3, m=0–3) via united {Cp′_nL_m} molecular orbitals. Bending and slipping of the Cp′ ligands are rooted in vdW attraction and repulsion, respectively, with geometry and hapticity of the Cp′-metal bonding adjusted so as to optimize TSC.