Anhydrous crystals of DNA bases are wide gap semiconductors

We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.     

Electronic properties of metal-modified DNA base pairs

The electronic properties of several metal-modified Watson-Crick guanine-cytosine base pairs are investigated by means of first-principle density functional theory calculations. Focus is placed on a new structure recently proposed as a plausible model for building an antiparallel duplex with Zn-guanine-cytosine pairs, but we also inspect several other conformations and the incorporation of Ag and Cu ions. We analyze the effects induced by the incorporation of one metal cation per base pair by comparing the structures and the electronic properties of the metalated pairs to those of the natural guanine-cytosine pair, particularly for what concerns the modifications of energy levels and charge density distributions of the frontier orbitals. Our results reveal the establishment of covalent bonding between the metal cation and the nucleobases, identified in the presence of hybrid metal-guanine and metal-cytosine orbitals. Attachment of the cation can occur either at the N1 or the N7 site of guanine and is compatible with altering or not altering the H-bond pattern of the natural pair. Cu(II) strongly contributes to the hybridization of the orbitals around the band gap, whereas Ag(I) and Zn(II) give hybrid states farther from the band gap. Most metalated pairs have smaller band gaps than the natural guanine-cytosine pair. The band gap shrinking along with the metal-base coupling suggests interesting consequences for electron transfer through DNA double helices.     

DFT+U study of defects in bulk rutile TiO(2)

We present a systematic study of electronic gap states in defected titania using our implementation of the Hubbard-U approximation in the grid-based projector-augmented wave density functional theory code, GPAW. The defects considered are Ti interstitials, O vacancies, and H dopants in the rutile phase of bulk titanium dioxide. We find that by applying a sufficiently large value for the Hubbard-U parameter of the Ti 3d states, the excess electrons localize spatially at the Ti sites and appear as states in the band gap. At U=2.5?eV, the position in energy of these gap states are in fair agreement with the experimental observations. In calculations with several excess electrons and U=2.5?eV, all of these end up in gap states that are spatially localized around specific Ti atoms, thus effectively creating one Ti(3+) ion per excess electron. An important result of this investigation is that regardless of which structural defect is the origin of the gap states, at U=2.5?eV, these states are found to have their mean energies within a few hundredths of an eV from 0.94 eV below the conduction band minimum.     

Surface/interface electronic structure in C(60) anchored aminothiolate self-assembled monolayer: an approach to molecular electronics

Electronic structure in self-assembled monolayers (SAMs) of C(60) anchored 11-amino-1-undecane thiol (C(60)-11-AUT) on Au(111) was studied by means of ultraviolet photoelectron spectroscopy and hybrid density functional theory calculations. Valence band features of the molecular conformation revealed the interface electronic structure to be dominated by sigma(S-Au), localized at the thiolate anchor to Au. Formation of a localized covalent bond as a result of hybridization between N P(z) orbital of -NH(2) group of the thiolate SAM and the pi level of C(60) resulted in a symmetry change from I(h) in C(60) to C1 in C(60)-11-AUT SAM. Appearance of low, but finite amplitude surface electronic states of bonded C(60), much beyond the Fermi level, ruled out Au-C(60) end group contact. The band gap E(g) of the SAM, determined to be 2.7 eV, was drastically reduced from the insulating alkanethiol SAMs ( approximately 8.0 eV) and fell intermediate between the C(60) ground state (N electrons, 1.6 eV) and C(60) solid (N+/-1 electrons, 3.7 eV).     

Efficient and accurate calculations on the electronic structure of B-type poly(dG).poly(dC) DNA by elongation method: first step toward the understanding of the biological properties of aperiodic DNA

Elongation method was applied to determine the electronic structures of B-type poly(dG).poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10(-8) hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.     

First Principles Investigations of the Crystal Structure,Electron Spectra,and Chemical Bonding in the Low-Temperature Phase of Lithium Imide

The density functional method in the full-electron approximation is used to calculate optimized structural parameters, band spectrum, density of states, electron density maps and to study chemical bonding in the low-temperature phase of lithium imide with a crystal structure of the space group Ima2. The valence band width is 15.14 eV, and it consists of three subzones (slightly dispersed bottom subzone, medium subzone, and top subzone with a width of ~2.4 eV) due to dispersion cased by hybridization of hydrogen s states and nitrogen p states. The top of the valence band and the bottom of the conduction band are in the center of the Brillouin zone, the width of the band gap is 4.48 eV, the absorption edge is direct. The electron density maps demonstrate chains of N–H complexes bound by pairs of Li atoms. The Li–N bond is predominantly ionic, while the N–H bond is polar covalent.     

Li2B12Si2: the first ternary compound in the system Li/B/Si: synthesis, crystal structure, hardness, spectroscopic investigations, and electronic structure

We present the synthesis, crystal structure, hardness, IR/Raman and UV/Vis spectra, and FP-LAPW calculations of the electronic structure of Li(2)B(12)Si(2), the first ternary compound in the system Li/B/Si. Yellow, transparent single crystals were synthesized from the elements in tin as solvent at 1500 degrees C in h-BN crucibles in arc-welded Ta ampoules. Li(2)B(12)Si(2) crystallizes orthorhombic in the space group Cmce (no. 64) with a=6.1060(6), b=10.9794(14), c=8.4050(8) A, and Z=4. The crystal structure is characterized by a covalent network of B(12) icosahedra connected by Si atoms and Li atoms located in interstitial spaces. The structure is closely related to that of MgB(12)Si(2) and fulfils the electron-counting rules of Wade and Longuet-Higgins. Measurements of Vickers (H(V)=20.3 GPa) and Knoop microhardness (H(K)=20.4 GPa) revealed that Li(2)B(12)Si(2) is a hard material. The band gap was determined experimentally and calculated by theoretical means. UV/Vis spectra revealed a band gap of 2.27 eV, with which the calculated value of 2.1 eV agrees well. The IR and Raman spectra show the expected oscillations of icosahedral networks. Theoretical investigations of bonding in this structure were carried out with the FP-LAPW method. The results confirm the applicability of simple electron-counting rules and enable some structural specialties to be explained in more detail.     

Electronic structures and conductivity in peptide nanotubes

Self-assembling cyclic D,L-peptide nanotubes are electronically insulating and possess wide band gaps (E(g) > 4 eV). Our ab initio electronic structure calculations indicate that the presence of aromatic rings in the side chain of peptide nanotubes significantly reduces the band gap. We investigate the conductivity of the modified peptide nanotubes through calculations of the electron tunneling probability. The electron tunneling probability through a molecule depends on the length of the molecule, L, as e-beta(E)L, where the tunneling beta(E)-factor is strongly energy-dependent. We have calculated beta(E) in three types of peptide nanotubes that have different sequences of amino acid residue, (L-Gln, D-Ala)(4), (L-Gln, D-Leu)(4) and (L-Gln, D-Phe)(4), using the complex band structure approach. We find large beta values near midgap, making these peptide nanotubes a poor tunneling conductor.     

Halogen modified two-dimensional covalent triazine frameworks as visible-light driven photocatalysts for overall water splitting

The covalent triazine framework CTF-1 as a member of the two-dimensional covalent organic frameworks(COFs) is a category of novel metal-free photocatalysts for water splitting. The large band gap severely restricts its energy conversion efficiency. By means of the first-principles calculations, we proposed the decoration of CTF-1 by anchoring halogen atoms onto benzene moieties for improving the solar-to-hydrogen(STH) efficiency. The electronic structures reveal that the halogen substitution successfully decreases the band gap of CTF-1. Meanwhile, the calculated free energy changes along the reaction pathway indicate that all these COFs can spontaneously drive overall water splitting under light irradiation in a specific acid-base environment. The time-dependent ab initio non-adiabatic molecular dynamics simulations suggest that the electron-hole recombination periods of these COFs fall in a few to tens of nanoseconds. Excitingly, CTF-1 modified by linking six iodine atoms onto the benzene ring in the para-position(CTF-1-6I) shows a quite low band gap of 2.81 eV, indicating that it is a visible-light driven COF for overall photocatalytic water splitting. Correspondingly, CTF-1-6I also exhibits an extraordinarily promising STH efficiency of 3.70%, which is an order magnitude higher than that of the pristine CTF-1.     

Interaction of diatomic germanium with lithium atoms: electronic structure and stability

Quantum chemical calculations were applied to investigate the electronic structure of mono-, di-, and trilithiated digermanium (Ge2Lin) and their cations (n=0-3). Computations using a multiconfigurational quasidegenerate perturbation approach based on complete active space self-consistent-field wave functions, and density functional theory reveal that Ge2Li has a 2B1 ground state with a doublet-quartet energy gap of 33 kcal/mol. Ge2Li2 has a singlet ground state with a 3Au-1A1 gap of 29 kcal/mol, and Ge2Li3 a doublet ground state with a 4B2-2A2 separation of 22 kcal/mol. The cation Ge2Li+ has a 3B1 ground state, being 13 kcal/mol below the open-shell 1B1 state. The computed electron affinities for diatomic germanium are EA(1)=1.9 eV, EA(2)=-2.5 eV, and EA(3)=-6.0 eV, for Ge2-, Ge2 (2-), and Ge2 (3-), respectively, indicating that only the monoanion is stable with respect to electron detachment, in such a way that Ge2Li is composed by Ge2-Li+ ions. An "atoms-in-molecules" analysis shows the absence of a ring critical point in Ge(2)Li. An electron localization function analysis on Ge2Li supports the view that the Ge-Li bond is predominantly ionic; however, a small covalent character could be anticipated from the analysis of the Laplacian at the Ge-Li bond critical point. The ionic picture of the Ge-Li bond is further supported by a natural-bond-order analysis and the Laplacian of the electron density. The calculated Li affinity value for Ge2 is 2.08 eV, while the Li+ cation affinity value for Ge2- is 5.7 eV. The larger Li+ cation affinity value of Ge2- suggests a Ge2-Li+ interaction and thus supports the ionic nature of Ge-Li bond. In GeLi4 and Ge2Li, the presence of trisynaptic basins indicates a three-center bond connecting the germanium and lithium atoms.     

Tuning the Properties of Tetracene-Based Nanoribbons by Fluorination and N-Doping

The structural stabilities and electronic properties are studied for the recently synthesized one-dimensional (1-D) tetracene-based nanoribbons with four-membered rings by using first-principles calculation. All three configurations (named as straight, zigzag, and armchair) are stable and exhibit an indirect band gap of 1.46, 0.73, and 0.32 eV, respectively. The band gaps can be effectively tuned by substituting hydrogen with fluorine atoms and by doping with nitrogen atoms. Substituting hydrogen with fluorine atoms leads to gradual decrease of the electronic band gaps of all configurations. Nitrogen doping changes the band gap from indirect to direct, displaying flexibility of tuning the band structure.     

The Kohn-Sham density of states and band gap of water: from small clusters to liquid water

Electronic properties of water clusters (H2O)(n), with n=2, 4, 8, 10, 15, 20, and 30 molecules were investigated by sequential Monte Carlo/density-functional theory (DFT) calculations. DFT calculations were carried out over uncorrelated configurations generated by Monte Carlo simulations of liquid water with a reparametrized exchange-correlation functional that reproduces the experimental information on the electronic properties (first ionization energy and highest occupied molecular orbital-lowest unoccupied molecular orbital gap) of the water dimer. The dependence of electronic properties on the cluster size (n) shows that the density of states (DOS) of small water clusters (n>10) exhibits the same basic features that are typical of larger aggregates, such as the mixing of the 3a1 and 1b1 valence bands. When long-ranged polarization effects are taken into account by the introduction of embedding charges, the DOS associated with 3a1 orbitals is significantly enhanced. In agreement with valence-band photoelectron spectra of liquid water, the 1b1, 3a1, and 1b2 electron binding energies in water aggregates are redshifted by approximately 1 eV relative to the isolated molecule. By extrapolating the results for larger clusters the threshold energy for photoelectron emission is 9.6+/-0.15 eV (free clusters) and 10.58+/-0.10 eV (embedded clusters). Our results for the electron affinity (V0=-0.17+/-0.05 eV) and adiabatic band gap (E(G,Ad)=6.83+/-0.05 eV) of liquid water are in excellent agreement with recent information from theoretical and experimental works.     

Electron affinities of Al(n) clusters and multiple-fold aromaticity of the square Al4(2-) structure

The concept of aromaticity was first invented to account for the unusual stability of planar organic molecules with 4n + 2 delocalized pi electrons. Recent photoelectron spectroscopy experiments on all-metal MAl(4)(-) systems with an approximate square planar Al(4)(2-) unit and an alkali metal led to the suggestion that Al(4)(2-) is aromatic. The square Al(4)(2-) structure was recognized as the prototype of a new family of aromatic molecules. High-level ab initio calculations based on extrapolating CCSD(T)/aug-cc-pVxZ (x = D, T, and Q) to the complete basis set limit were used to calculate the first electron affinities of Al(n)(), n = 0-4. The calculated electron affinities, 0.41 eV (n = 0), 1.51 eV (n = 1), 1.89 eV (n = 3), and 2.18 eV (n = 4), are all in excellent agreement with available experimental data. On the basis of the high-level ab initio quantum chemical calculations, we can estimate the resonance energy and show that it is quite large, large enough to stabilize Al(4)(2-) with respect to Al(4). Analysis of the calculated results shows that the aromaticity of Al(4)(2-) is unusual and different from that of C(6)H(6). Particularly, compared to the usual (1-fold) pi aromaticity in C(6)H(6), which may be represented by two Kekulé structures sharing a common sigma bond framework, the square Al(4)(2-) structure has an unusual "multiple-fold" aromaticity determined by three independent delocalized (pi and sigma) bonding systems, each of which satisfies the 4n + 2 electron counting rule, leading to a total of 4 x 4 x 4 = 64 potential resonating Kekulé-like structures without a common sigma frame. We also discuss the 2-fold aromaticity (pi plus sigma) of the Al(3)(-) anion, which can be represented by 3 x 3 = 9 potential resonating Kekulé-like structures, each with two localized chemical bonds. These results lead us to suggest a general approach (applicable to both organic and inorganic molecules) for examining delocalized chemical bonding. The possible electronic contribution to the aromaticity of a molecule should not be limited to only one particular delocalized bonding system satisfying a certain electron counting rule of aromaticity. More than one independent delocalized bonding system can simultaneously satisfy the electron counting rule of aromaticity, and therefore, a molecular structure could have multiple-fold aromaticity.     

Manipulating the electronic structures of silicon carbide nanotubes by selected hydrogenation

We show that the electronic and atomic structures of silicon carbide nanotubes (SiCNTs) undergo dramatic changes with hydrogenation from first-principles calculations based on density-functional theory. The exo-hydrogenation of a single C atom results in acceptor states close to the highest occupied valence band of pristine SiCNT, whereas donor states close to the lowest unoccupied conduction band appear as a Si atom being hydrogenated. Upon fully hydrogenating Si atoms, (8,0) and (6,6) SiCNTs become metallic with very high density of states at the Fermi level. The full hydrogenation of C atoms, on the other hand, increases the band gap to 2.6 eV for (8,0) SiCNT and decreases the band gap to 1.47 eV for (6,6) SiCNT, respectively. The band gap of SiCNTs can also be greatly increased through the hydrogenation of all the atoms.     

Density functional study of the interaction between small Au clusters, Au(n) (n=1-7) and the rutile TiO(2) surface. I. Adsorption on the stoichiometric surface

This is the first paper in a series of four dealing with the adsorption site, electronic structure, and chemistry of small Au clusters, Au(n) (n=1-7), supported on stoichiometric, partially reduced, or partially hydroxylated rutile TiO(2)(110) surfaces. Analysis of the electronic structure reveals that the main contribution to the binding energy is the overlap between the highest occupied molecular orbitals of Au clusters and the Kohn-Sham orbitals localized on the bridging and the in-plane oxygen of the rutile TiO(2)(110) surface. The structure of adsorbed Au(n) differs from that in the gas phase mostly because the cluster wants to maximize this orbital overlap and to increase the number of Au-O bonds. For example, the equilibrium structures of Au(5) and Au(7) are planar in the gas phase, while the adsorbed Au(5) has a distorted two-dimensional structure and the adsorbed Au(7) is three-dimensional. The dissociation of an adsorbed cluster into two adsorbed fragments is endothermic, for all clusters, by at least 0.8 eV. This does not mean that the gas-phase clusters hitting the surface with kinetic energy greater than 0.8 eV will fragment. To place enough energy in the reaction coordinate for fragmentation, the impact kinetic energy needs to be substantially higher than 0.8 eV. We have also calculated the interaction energy between all pairs of Au clusters. These interactions are small except when a Au monomer is coadsorbed with a Au(n) with odd n. In this case the interaction energy is of the order of 0.7 eV and the two clusters interact through the support even when they are fairly far apart. This happens because the adsorption of a Au(n) cluster places electrons in the states of the bottom of the conduction band and these electrons help the Au monomer to bind to the five-coordinated Ti atoms on the surface.     

Microscopic Kinetics in Poly(Methyl Methacrylate) Exposed to a Single Ultra-Short XUV/X-ray Laser Pulse

We study the behavior of poly(methyl methacrylate) (PMMA) exposed to femtosecond pulses of extreme ultraviolet and X-ray laser radiation in the single-shot damage regime. The employed microscopic simulation traces induced electron cascades, the thermal energy exchange of electrons with atoms, nonthermal modification of the interatomic potential, and a triggered atomic response. We identify that the nonthermal hydrogen decoupling triggers ultrafast fragmentation of PMMA strains at the absorbed threshold dose of ~0.07 eV/atom. At higher doses, more hydrogen atoms detach from their parental molecules, which, at the dose of ~0.5 eV/atom, leads to a complete separation of hydrogens from carbon and oxygen atoms and fragmentation of MMA molecules. At the dose of ~0.7 eV/atom, the band gap completely collapses indicating that a metallic liquid is formed with complete atomic disorder. An estimated single-shot ablation threshold and a crater depth as functions of fluence agree well with the experimental data collected.     

Mechanism of the electronic stabilization of the 3MR and divalent carbon of bis(diisopropylamino)cyclopropenylidene

Analysis of the topology of the electron density of bis(dimethylamino)cyclopropenylidene as a model of the recently synthesized, stable bis(diisopropylamino)cyclopropenylidene with the quantum theory of atoms in molecules is used to investigate the stabilizing electronic effects at the reactive carbene site by amino substitution. This work demonstrates that the plane perpendicular lone pairs of nitrogen utilize in-plane sigma-aromaticity as a conduit to delocalize charge to the carbene carbon C2, where it is transferred preferentially back into the pi-plane at the site through sigma-pi polarization. C2 is thus stabilized relative to the parent cyclopropenylidene, c-C(3)H(2), by a very different mechanism than that suggested in the orbital view of n(pi)(N) and pi(C=C) conjugation and n(pi)(N) --> p(pi)*(C2) hyperconjugation. Validation of this premise is also found in properties of asymmetric atomic quadrupole tensors, bond path ellipticities, and diamagnetic/paramagnetic components of NMR shielding tensors.     

Chemische Bindung anschaulich: die Elektronen-Lokalisierungs-Funktion

The Electron Localization Function (ELF) describes chemical bonding through localized pairs of electrons and gives a quantum mechanical basis to the representation of the chemical bond as a line. Computer graphics produce illustrative and intuitive pictures of the shell structure of atoms, ionic, covalent, and coordinative bonds, or multiple bonds and lone pairs of electrons. Resonance formulas, delocalized bonds, and the space occupied by electron pairs can be visualized in the same manner.     

Connecting terminal carboxylate groups in nine-coordinate lanthanide podates: consequences on the thermodynamic,structural, electronic,and photophysical properties

The hydrolysis of terminal (t)butyl-ester groups provides the novel nonadentate podand tris[2-[N-methylcarbamoyl-(6-carboxypyridine-2)-ethyl]amine] (L13) which exists as a mixture of slowly interconverting conformers in solution. At pH = 8.0 in water, its deprotonated form [L13 - 3H](3-) reacts with Ln(ClO(4))(3) to give the poorly soluble and stable podates [Ln(L13 - 3H)] (log(beta(110)) = 6.7-7.0, Ln = La-Lu). The isolated complexes [Ln(L13 - 3H)](H(2)O)(7) (Ln = Eu, 8; Tb, 9; Lu, 10) are isostructural, and their crystal structures show Ln(III) to be nine-coordinate in a pseudotricapped trigonal prismatic site defined by the donor atoms of the three helically wrapped tridentate binding units of L13. The Ln-O(carboxamide) bonds are only marginally longer than the Ln-O(carboxylate) bonds in [Ln(L13 - 3H)], thus producing a regular triple helix around Ln(III) which reverses its screw direction within the covalent Me-TREN tripod. High-resolution emission spectroscopy demonstrates that (i) the replacement of terminal carboxamides with carboxylates induces only minor electronic changes for the metallic site, (ii) the solid-state structure is maintained in water, and (iii) the metal in the podate is efficiently protected from interactions with solvent molecules. The absolute quantum yields obtained for [Eu(L13 - 3H)] (Phi(Eu)(tot)= 1.8 x 10(-3)) and [Tb(L13 - 3H)] (Phi(Eu)(tot)= 8.9 x 10(-3)) in water remain modest and strongly contrast with that obtained for the lanthanide luminescence step (Phi(Eu) = 0.28). Detailed photophysical studies assign this discrepancy to the small energy gap between the ligand-centered singlet ((1)pi pi*) and triplet ((3)pi pi*) states which limits the efficiency of the intersystem crossing process. Theoretical TDDFT calculations suggest that the connection of a carboxylate group to the central pyridine ring prevents the sizable stabilization of the triplet state required for an efficient sensitization process. The thermodynamic and electronic origins of the advantages (stability, lanthanide quantum yield) and drawbacks (solubility, sensitization) brought by the "carboxylate effect" in lanthanide complexes are evaluated for programming predetermined properties in functional devices.