Anastassia N. Alexandrova

Structure of the NaxClx+1− (x=1–4) clusters via ab initio genetic algorithm and photoelectron spectroscopy

The application of the ab initio genetic algorithm with an embedded gradient has been carried out for the elucidation of global minimum structures of a series of anionic sodium chloride clusters, Na(x)Cl(x+1) (-) (x=1-4), produced in the gas phase using electrospray ionization and studied by photoelectron spectroscopy. These are all superhalogen species with extremely high electron binding energies. The vertical electron detachment energies for Na(x)Cl(x+1) (-) were measured to be 5.6, 6.46, 6.3, and 7.0 eV, for x=1-4, respectively. Our ab initio gradient embedded genetic algorithm program detected the linear global minima for NaCl(2) (-) and Na(2)Cl(3) (-) and three-dimensional structures for the larger species. Na(3)Cl(4) (-) was found to have C(3v) symmetry, which can be viewed as a Na(4)Cl(4) cube missing a corner Na(+) cation, whereas Na(4)Cl(5) (-) was found to have C(4v) symmetry, close to a 3x3 planar structure. Excellent agreement between the theoretically calculated and the experimental spectra was observed, confirming the obtained structures and demonstrating the power of the developed genetic algorithm technique.

Electronic structure and chemical bonding of B5− and B5 by photoelectron spectroscopy and ab initio calculations

The electronic structure and chemical bonding of B5− and B5 were investigated using anion photoelectron spectroscopy and ab initio calculations. Vibrationally resolved photoelectron spectra were obtained for B5− and were compared to theoretical calculations performed at various levels of theory. Extensive searches were carried out for the global minimum of B5−, which was found to have a planar C2v structure with a closed-shell ground state (1A1). Excellent agreement was observed between ab initio detachment energies and the experimental spectra, firmly establishing the ground-state structures for both B5− and B5. The chemical bonding in B5− was investigated and compared to that in Al5−. While both B5− and Al5− have a similar C2v planar structure, their π-bonding orbitals are different. In Al5−, a π-bonding orbital was previously observed to delocalize over only the three central atoms in the C2v ground-state structure, whereas a similar π orbital (1b1) was found to completely delocalize over all five atom...

Photoelectron spectroscopy and ab initio study of the doubly antiaromatic B62− dianion in the LiB6− cluster

A metal-boron mixed cluster LiB(6) (-) was produced and characterized by photoelectron spectroscopy and ab initio calculations. A number of electronic transitions were observed and used to compare with theoretical calculations. An extensive search for the global minimum of LiB(6) (-) was carried out via an ab initio genetic algorithm technique. The pyramidal C(2v) ((1)A(1)) molecule was found to be the most stable at all levels of theory. The nearest low-lying isomer was found to be a triplet C(2) ((3)B) structure, 9.2 kcal/mol higher in energy. Comparison of calculated detachment transitions from LiB(6) (-) and the experimental photoelectron spectra confirmed the C(2v) pyramidal global minimum structure. Natural population calculation revealed that LiB(6) (-) is a charge-transfer complex, Li(+)B(6) (2-), in which Li(+) and B(6) (2-) interact in a primarily ionic manner. Analyses of the molecular orbitals and chemical bonding of B(6) (2-) showed that the planar cluster is twofold (pi- and sigma-) antiaromatic, which can be viewed as the fusion of two aromatic B(3) (-) units.

Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination

A series of enzymes for Kemp elimination of 5-nitrobenzisoxazole has been recently designed and tested. In conjunction with the design process, extensive computational analyses were carried out to evaluate the potential performance of four of the designs, as presented here. The enzyme-catalyzed reactions were modeled using mixed quantum and molecular mechanics (QM/MM) calculations in the context of Monte Carlo (MC) statistical mechanics simulations. Free-energy perturbation (FEP) calculations were used to characterize the free-energy surfaces for the catalyzed reactions as well as for reference processes in water. The simulations yielded detailed information about the catalytic mechanisms, activation barriers, and structural evolution of the active sites over the course of the reactions. The catalytic mechanism for the designed enzymes KE07, KE10(V131N), and KE15 was found to be concerted with proton transfer, generally more advanced in the transition state than breaking of the isoxazolyl N-O bond. On the basis of the free-energy results, all three enzymes were anticipated to be active. Ideas for further improvement of the enzyme designs also emerged. On the technical side, the synergy of parallel QM/MM and experimental efforts in the design of artificial enzymes is well illustrated.

B13+: A Photodriven Molecular Wankel Engine†

Revved-up rotary: A molecular Wankel motor, the dual-ring structure B(13)(+), is driven by circularly-polarized infrared electromagnetic radiation. Calculations show that this illumination leads to a guided unidirectional rotation of the outer ring, which is achieved with rotational frequency of the order of 300 GHz.

H·(H2O)n clusters: microsolvation of the hydrogen atom via molecular ab initio gradient embedded genetic algorithm (GEGA).

A new version of the ab initio gradient embedded genetic algorithm (GEGA) program for finding the global minima on the potential energy surface (PES) of mixed clusters formed by molecules and atoms is reported. The performance of the algorithm is demonstrated on the neutral H·(H(2)O)(n) (n = 1-4) clusters, that is, a radical H atom solvated in 1-4 water molecules. These clusters are of a fundamental interest. The solvated hydrogen atom forms during photochemical events in water, or during scavenging of solvated electrons by acids, and transiently exists in biological systems and possibly in inclusion complexes in the deep ocean and in the ice shield of earth. The processes associated with its existence are intriguingly complex, however, and have been the subject of decades-long debates. Using GEGA, we explicate the apparently extreme structural diversity in the H·(H(2)O)(n) (n = 1-4) clusters. All considered clusters have four basic structural types: type I, where the H radical is weakly coordinated to the oxygen atom of one of the water molecules; type II, where H is weakly coordinated to a H atom of one of the water molecules; type III, consisting of H(2), the OH radical, and n - 1 H(2)O molecules; and type IV, consisting of H(3)O and n - 1 H(2)O. There are myriads of isomers of all four types. The lowest energy species of types I and II are the isoenergetic global minima. H·(H(2)O)(n) clusters appear to be a challenging case for GEGA because they have many shallow minima close in energy some of which are significantly less stable than the global minimum. Additionally, the global minima themselves have high structural degeneracy, they are only weakly bound, and they are prone to dissociation. GEGA performed exceptionally well in finding both the global and the low-energy local minima that were subsequently confirmed at higher levels of theory.

Visible-Light-Induced Olefin Activation Using 3D Aromatic Boron-Rich Cluster Photooxidants

We report a discovery that perfunctionalized icosahedral dodecaborate clusters of the type B12(OCH2Ar)12 (Ar = Ph or C6F5) can undergo photo-excitation with visible light, leading to a new class of metal-free photooxidants. Excitation in these species occurs as a result of the charge transfer between low-lying orbitals located on the benzyl substituents and an unoccupied orbital delocalized throughout the boron cluster core. Here we show how these species, photo-excited with a benchtop blue LED source, can exhibit excited-state reduction potentials as high as 3 V and can participate in electron-transfer processes with a broad range of styrene monomers, initiating their polymerization. Initiation is observed in cases of both electron-rich and electron-deficient styrene monomers at cluster loadings as low as 0.005 mol%. Furthermore, photo-excitation of B12(OCH2C6F5)12 in the presence of a less activated olefin such as isobutylene results in the production of highly branched poly(isobutylene). This work introduces a new class of air-stable, metal-free photo-redox reagents capable of mediating chemical transformations.

Mysteries of Metals in Metalloenzymes

Natural metalloenzymes are often the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions. However, metalloenzymes are occasionally surprising in their selection of catalytic metals, and in their responses to metal substitution. Indeed, from the isolated standpoint of producing the best catalyst, a chemist designing from first-principles would likely choose a different metal. For example, some enzymes employ a redox active metal where a simple Lewis acid is needed. Such are several hydrolases. In other cases, substitution of a non-native metal leads to radical improvements in reactivity. For example, histone deacetylase 8 naturally operates with Zn(2+) in the active site but becomes much more active with Fe(2+). For β-lactamases, the replacement of the native Zn(2+) with Ni(2+) was suggested to lead to higher activity as predicted computationally. There are also intriguing cases, such as Fe(2+)- and Mn(2+)-dependent ribonucleotide reductases and W(4+)- and Mo(4+)-dependent DMSO reductases, where organisms manage to circumvent the scarcity of one metal (e.g., Fe(2+)) by creating protein structures that utilize another metal (e.g., Mn(2+)) for the catalysis of the same reaction. Naturally, even though both metal forms are active, one of the metals is preferred in every-day life, and the other metal variant remains dormant until an emergency strikes in the cell. These examples lead to certain questions. When are catalytic metals selected purely for electronic or structural reasons, implying that enzymatic catalysis is optimized to its maximum? When are metal selections a manifestation of competing evolutionary pressures, where choices are dictated not just by catalytic efficiency but also by other factors in the cell? In other words, how can enzymes be improved as catalysts merely through the use of common biological building blocks available to cells? Addressing these questions is highly relevant to the enzyme design community, where the goal is to prepare maximally efficient quasi-natural enzymes for the catalysis of reactions that interest humankind. Due to competing evolutionary pressures, many natural enzymes may not have evolved to be ideal catalysts and can be improved for the isolated purpose of catalysis in vitro when the competing factors are removed. The goal of this Account is not to cover all the possible stories but rather to highlight how variable enzymatic catalysis can be. We want to bring up possible factors affecting the evolution of enzyme structure, and the large- and intermediate-scale structural and electronic effects that metals can induce in the protein, and most importantly, the opportunities for optimization of these enzymes for catalysis in vitro.

Origin of extraordinary stability of square-planar carbon atoms in surface carbides of cobalt and nickel

Surface carbides of cobalt and nickel are exceptionally stable, having stabilities competitive with those of graphitic C on these surfaces. The unusual structure of these carbides has attracted much attention: C assumes a tetracoordinate square-planar arrangement, in-plane with the metal surface, and its binding favors a spontaneous p4g clock surface reconstruction. A chemical bonding model for these systems is presented and explains the unusual structure, special stability, and the reconstruction. C promotes local two-dimensional aromaticity on the surface and the aromatic arrangement is so powerful that the required number of electrons is taken from the void M4 squares, thus leading to Peierls instability. Moreover, this model predicts a series of new transition-metal and main-group-element surface alloys: carbides, borides, and nitrides, which feature high stability, square-planar coordination, aromaticity, and a predictable degree of surface reconstruction.

Lithium cluster anions: Photoelectron spectroscopy and ab initio calculations

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.