Biomedical subjects

Dmitry Yu Zubarev

Publications and source records attributed to Dmitry Yu Zubarev.

8 recordsLinked to original sources

PubMed2007

Comprehensive analysis of chemical bonding in boron clusters.

We present a comprehensive analysis of chemical bonding in pure boron clusters. It is now established in joint experimental and theoretical studies that pure boron clusters are planar or quasi-planar at least up to twenty atoms. Their planarity or quasi-planarity was usually discussed in terms of pi-delocalization or pi-aromaticity. In the current article, we demonstrated that one cannot ignore sigma-electrons and that the presence of two-center two-electron (2c--2e) peripheral B--B bonds together with the globally delocalized sigma-electrons must be taken into consideration when the shape of pure boron cluster is discussed. The global aromaticity (or global antiaromaticity) can be assigned on the basis of the 4n+2 (or 4n) electron counting rule for either pi- or sigma-electrons in the planar structures. We showed that pure boron clusters could have double (sigma- and pi-) aromaticity (B3-, B4, B5+, B6(2+), B7+, B7-, B8, B(8)2-, B9-, B10, B11+, B12, and B13+), double (sigma- and pi-) antiaromaticity (B6(2-), B15), or conflicting aromaticity (B5-,sigma-antiaromatic and pi-aromatic and B14, sigma-aromatic and pi-antiaromatic). Appropriate geometric fit is also an essential factor, which determines the shape of the most stable structures. In all the boron clusters considered here, the peripheral atoms form planar cycles. Peripheral 2c--2e B--B bonds are built up from s to p hybrid atomic orbitals and this enforces the planarity of the cycle. If the given number of central atoms (1, 2, 3, or 4) can perfectly fit the central cavity then the overall structure is planar. Otherwise, central atoms come out of the plane of the cycle and the overall structure is quasi-planar.

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PubMed2006

Theoretical probing of deltahedral closo-auroboranes B(x)Au(x)2- (x = 5-12).

Using density functional theory calculations, here we show that a series of B(x)Au(x)2- (x = 5-12) dianions possesses structure and bonding similar to the famous deltahedral closo-borane cages, B(x)H(x)2-. Effective atomic charges on Au in B(x)Au(x)2- are very similar to those on H in B(x)H(x)2-, indicating that Au in the closo-auroboranes is indeed analogous to H in the closo-boranes. The present theoretical predictions of B(x)Au(x)2- suggest that the closo-auroborane species are viable new chemical building blocks that may be synthesized in bulk. The Au atoms in the closo-auroboranes represent highly atomically dispersed Au and may potentially exhibit novel catalytic and chemical properties.

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PubMed2006

Sn12(2-): stannaspherene.

Stannaspherene. The Sn122- cluster is discovered to be a highly stable and highly symmetric icosahedral cage bonded by four delocalized radial pi bonds and nine delocalized on-sphere sigma bonds from the 5p orbitals of the Sn atoms. It has a diameter of 6.1 A, with a large empty interior volume, and can host most transition metal atoms inside, giving rise to a large class of endohedral chemical building blocks for cluster-assembled nanomaterials.

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PubMed2006

Observation of triatomic species with conflicting aromaticity: AlSi2- and AlGe2-.

We created mixed triatomic clusters, AlCGe(-), AlSi(2)(-), and AlGe(2)(-), and studied their electronic structure and chemical bonding using photoelectron spectroscopy and ab initio calculations. Excellent agreement between theoretical and experimental photoelectron spectra confirmed the predicted global minimum structures for these species. Chemical bonding analysis revealed that the AlSi(2)(-) and AlGe(2)(-) anions can be described as species with conflicting (sigma-antiaromatic and pi-aromatic) aromaticity. The AlCGe(-) anion represents an interesting example of chemical species which is between classical and aromatic.

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PubMed2006

On the structure and chemical bonding of Si6(2-) and Si6(2-) in NaSi6(-) upon Na+ coordination.

Photoelectron spectroscopy was combined with ab initio calculations to elucidate the structure and bonding in Si6 2- and NaSi6 -. Well-resolved electronic transitions were observed in the photoelectron spectra of Si6 - and NaSi6 - at three photon energies (355, 266, and 193 nm). The spectra of NaSi6 - were observed to be similar to those of Si6 - except that the electron binding energies of the former are lower, suggesting that the Si6 motif in NaSi6 - is structurally and electronically similar to that in Si6 -. The electron affinities of Si6 and NaSi6 were measured fairly accurately to be 2.23+/-0.03 eV and 1.80+/-0.05 eV, respectively. Global minimum structure searches for Si6 2- and NaSi6 - were performed using gradient embedded genetic algorithm followed by B3LYP, MP2, and CCSDT calculations. Vertical electron detachment energies were calculated for the lowest Si6 - and NaSi6 - structures at the CCSD(T)/6-311+G(2df), ROVGF/6-311+G(2df), UOVGF/6-311+G(2d), and time-dependent B3LYP/6-311+G(2df) levels of theory. Experimental vertical detachment energies were used to verify the global minimum structure for NaSi6 -. Though the octahedral Si6 2-, analogous to the closo form of borane B6H6 2-, is the most stable form for the bare hexasilicon dianion, it is not the kernel for the NaSi6 - global minimum. The most stable isomer of NaSi6 - is based on a Si6 2- motif, which is distorted into C2v symmetry similar to the ground state structure of Si6 -. The octahedral Si6 2- coordinated by a Na+ is a low-lying isomer and was also observed experimentally. The chemical bonding in Si6 2- and NaSi6 - was understood using natural bond orbital, molecular orbital, and electron localization function analyses.

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PubMed2006

Gold apes hydrogen. The structure and bonding in the planar B7Au2- and B7Au2 clusters.

We produced the B7Au2- mixed cluster and studied its electronic structure and chemical bonding using photoelectron spectroscopy and ab initio calculations. The photoelectron spectra of B7Au2- were observed to be relatively simple with vibrational resolution, in contrast to the complicated spectra observed for pure B7-, which had contributions from three isomers (Alexandrova et al. J. Phys. Chem. A 2004, 108, 3509). Theoretical calculations show that B7Au2- possesses an extremely stable planar structure, identical to that of B7H2-, demonstrating that Au mimics H in its bonding to boron, analogous to the Au-Si bonding. The ground-state structure of B7Au2- (B7H2-) can be viewed as adding two Au (H) atoms to the terminal B atoms of a higher-lying planar isomer of B7-. The bonding and stability in the planar B7Au2- (B7H2-) clusters are elucidated on the basis of the strong covalent B-Au (H) bonding and the concepts of aromaticity/antiaromaticity in these systems.

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PubMed2005

Chemical bonding in Si5(2-) and NaSi5(-) via photoelectron spectroscopy and ab initio calculations.

Photoelectron spectroscopy and ab initio calculations are used to investigate the electronic structure and chemical bonding of Si5(-) and Si5(2-) in NaSi5(-). Photoelectron spectra of Si5(-) and NaSi5(-) are obtained at several photon energies and are compared with theoretical calculations at four different levels of theory, TD-B3LYP, R(U)OVGF, UCCSD(T), and EOM-CCSD(T), all with 6-311+G(2df) basis sets. Excellent agreement is observed between experiment and theory, confirming the obtained ground-state structures for Si5(-) and Si5(2-), which are both found to be trigonal bipyramid with D3h symmetry at several levels of theory. Chemical bonding in Si5, Si5(-), and Si5(2-) is analyzed using NPA, molecular orbitals, ELF, and NICS indices. The bonding in Si5(2-) is compared with that in the isoelectronic and isostructural B5H5(2-) species, but they are found to differ due to the involvement of electron densities, which are supposed to be lone pairs in the skeletal bonding in Si5(2-).

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PubMed2005

Appraisal of the performance of nonhybrid density functional methods in characterization of the Al4C molecule.

In three recent publications it was predicted that an Al(4)C molecule is planar on the basis of nonhybrid density functional calculations. These conclusions contradict our earlier predictions that Al(4)C is tetrahedral. In order to resolve the controversy we probed in this paper a potential energy surface of Al(4)C using a large variety of theoretical methods including multiconfigurational methods and a variety of one-electron basis sets. We confirmed that the nonhybrid Becke's exchange with Perdew-Wang 1991 correlation functional density functional method predicts that Al(4)C has a planar structure in agreement with the reports of the other three groups. However, in this paper we have shown that high level ab initio calculations at the coupled cluster with singles, doubles, and noniterative triples and at the complete active space self-consistent field followed by multireference configurational interaction levels of theory confirm our earlier prediction that Al(4)C is indeed tetrahedral. The failure of nonhybrid density functional methods to correctly characterize the global minimum structure of Al(4)C demonstrates that it is dangerous to rely solely on these density functional methods in characterization of new molecules and clusters, where experimental structure is not known.

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