Structural and electronic properties of adsorbed nucleobases on Si-doped hexagonal boron nitride nanoflake: a computational study

Structural Chemistry - Effect of doping on surface reactivity and molecular adsorption mechanism is a key feature for many applications, including molecular sensing, molecular recognition, and...     

Ab initio study of structural and electronic properties of zigzag graphene nanoribbons on hexagonal boron nitride

Results of the study of structural and electronic properties of the 8-ZGNR/h-BN(001) heterostructure by the pseudopotential method using plane waves within density functional theory are presented. Within one approximation the features of the spin state at the Fermi level are studied along with the role of the edge and substrate effects in the opening of the energy gap in the 8-ZGNR/h-BN(001) heterostructure in both ferromagnetic and antiferromagnetic orderings. The effect of a substrate made of hexagonal boron nitride was found for the first time. It consists in the opening of the energy gap in the π electron spectrum of the 8-ZGNR/h-BN(001) heterostructure for the ferromagnetic spin ordering. It is shown that the gap was 30 meV. Contributions of the edge effects of the graphene nanoribbon and the substrate to the energy gap formation are differentiated for the first time. It is found that in the 8-ZGNR/h-BN(001) heterostructure the dominant role in the opening of the energy gap at the Fermi level is played by the edge effects. However, when the nanoribbon width decreases, e.g., to six dimmers the substrate role in the gap opening increases and amounts to 45%. Local magnetic moments of carbon atoms are estimated. It is shown that small magnetic moments are induced on boron and nitrogen atoms at the interface.     

Hydrostatic-pressure-induced porous gallium nitride from nanotube bundles: an ab initio study

Ab initio calculations show that (5,5) and (6,6) single-walled gallium nitride nanotubes (GaN NTs) in bundles could aggregate spontaneously to form new condensed phases when bundled tubes are close enough under hydrostatic pressure. The new GaN phases have typical porous structures, constructed by alternating tetragons and hexagons around the original tube walls. Owing to the different compatibilities of the chirality of the tube with the symmetry of the array, the new phase formed from (5,5) GaN NT bundles is triclinic and that from (6,6) ones is hexagonal. These porous GaN phases possess tetrahedral bonding corresponding to sp(3) hybridization, different from sp(2) hybridized bonding in individual GaN NTs. The interaction between tubes not only controls the structural transformation but also influences the electronic structure of porous GaN. We expect that the two-dimensional-channeled porous structure of GaN is advantageous for the usage of GaN as the molecular sieve and as the excellent dilute magnetic semiconductor by considerable magnetic doping.     

Adsorption of RDX and TATP on IRMOF-1: an ab initio study

The adsorption of 1,3,5-trinitro-s-triazine (RDX) and triacetone triperoxide (TATP) on representative fragments of metal organic framework (IRMOF-1) was studied at the B3LYP/6-31G(d) level of theory. For examined adsorbates several possible adsorption positions toward the IRMOF-1 fragments were found. The adsorption strength of the adsorbate on IRMOF-1 is largely affected by the geometry of the active site of IRMOF-1 which controls the orientation of the target molecule with respect to the IRMOF-1 fragment. The calculations show that the adsorption on these fragments occurs due to the formation of hydrogen bonds between the molecular C–H groups and the oxygen atoms of IRMOF-1. The RDX and TATP molecules are the most strongly adsorbed on the linker fragment of IRMOF-1. This type of adsorption results in the polarization of RDX and TATP on the IRMOF-1 fragments. The interaction energy of two most stable RDX-, and TATP-IRMOF-1 adsorption systems are ?9.8 and ?12.8 kcal/mol, respectively. It can be concluded that the 1,4-benzenedicarboxylate site of IRMOF-1 shows the stronger molecular adsorption of RDX and TATP than the site containing [Zn₄O(CO₂)₆] and also it is characterized by higher reactivity than the other considered sites. The binding of studied explosive molecules to IRMOF-1 consists of interplay between attractive interactions between the target molecule and MOF as well as the shielding by the IRMOF-1 fragment induced by the molecular adsorption. The relative importance of these effects depends on the chemical nature, the size, and the shape of the molecule and MOF. Small-size molecules require smaller space for the adsorption and also they are less shielded by the sizeable adsorbent. So they interact better when adsorbed on larger IRMOF-1 fragment. On the other side, larger molecules show higher adsorption strength with small fragments of IRMOF-1.     

Neutron damage of hexagonal boron nitride: h-BN

Hexagonal boron nitride (h-BN) was neutron damaged at an integral flux of 2.40 × 10¹² n cm⁻² s⁻¹ for 1, 2, 3 and 4 h. The h-BN samples undergo a transition from sp² to sp³ hybridization as a consequence of the neutron induced damage with the formation of cubic boron nitride (c-BN) spots, as suggested both by FT–IR and Raman spectroscopy. In addition to c-BN, also a certain degree of amorphization is achieved by h-BN already at the lowest neutron fluence of 8.64 × 10¹⁵ n cm⁻² as clearly evidenced by Raman spectroscopy. The Wigner or stored energy to the radiation-damaged h-BN samples was studied by DSC and also in this case there was a clear evidence that the neutron damage was partly irreversible and insensitive to the thermal annealing up to 630 °C. Electron spin resonance (ESR) was employed to further study the structural defects induced by the neutron bombardment of h-BN. Two kinds of paramagnetic defective structures centered on ¹¹B atoms were identified.

     

Attachment of molecular hydrogen to an isolated boron cation: an infrared and ab initio study

Structural properties of the B(+)-H2 electrostatic complex are investigated through its rotationally resolved infrared spectrum in the H-H stretch region (3905-3975 cm(-1)). The spectrum, which was obtained by monitoring B(+) photofragments while the IR wavelength was scanned, is consistent with the complex having a T-shaped structure and a vibrationally averaged intermolecular separation of 2.26 A, which decreases by 0.04 A when the H2 subunit is vibrationally excited. The H-H stretch transition of B(+)-H2 is red-shifted by 220.6 +/- 1.5 cm(-1) from that of the free H2 molecule, much more than for other dihydrogen complexes with comparable binding energies. Properties of B(+)-H2 and the related Li(+)-H2, Na(+)-H2, and Al(+)-H2 complexes are explored through ab initio calculations at the MP2/aug-cc-pVTZ level. The unusually large red-shift for B(+)-H2 is explained as due to electron donation from the H2 sigma(g) bonding orbital to the unoccupied 2p(z) orbital on the B(+) ion.     

Oxidation of a two-dimensional hexagonal boron nitride monolayer: a first-principles study

Two-dimensional (2D) hexagonal boron-nitride oxide (h-BNO) is a structural analogue of graphene oxide. Motivated by recent experimental studies of graphene oxide, we have investigated the chemical oxidation of 2D h-BN sheet and the associated electronic properties of h-BNO. Particular emphasis has been placed on the most favorable site(s) for chemisorption of atomic oxygen, and on the migration barrier for an oxygen atom hopping to the top, bridge, or hollow site on the h-BN surface, as well as the most likely pathway for the dissociation of an oxygen molecule on the h-BN surface. We find that when an oxygen atom migrates on the h-BN surface, it is most likely to be over an N atom, but confined by three neighbor B atoms (forming a triangle ring). In general, chemisorption of an oxygen atom will stretch the B-N bond, and under certain conditions may even break the B-N bond. Depending on the initial location of the first chemisorbed O atom, subsequent oxidation tends to form an O domain or O chain on the h-BN sheet. The latter may lead to a synthetic strategy for the unzipping of the h-BN sheet along a zigzag direction. A better understanding of the oxidation of h-BN sheet has important implications for tailoring the properties of the h-BN sheet for applications.     

Ab initio determination of the ionization potentials of DNA and RNA nucleobases

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.     

Cleaning of pyrolytic hexagonal boron nitride surfaces

Hexagonal boron nitride (h‐BN) has recently garnered significant interest as a substrate and dielectric for two‐dimensional materials and devices based on graphene or transition metal dichalcogenides such as molybdenum disulfide (MoS₂). As substrate surface impurities and defects can negatively impact the structure and properties of two‐dimensional materials, h‐BN surface preparation and cleaning are a critical consideration. In this regard, we have utilized X‐ray photoelectron spectroscopy to investigate the influence of several ex situ wet chemical and in situ thermal desorption cleaning procedures on pyrolytic h‐BN surfaces. Of the various wet chemistries investigated, a 10 : 1 buffered HF solution was found to produce surfaces with the lowest amount of oxygen and carbon contamination. Ultraviolet/ozone oxidation was found to be the most effective ex situ treatment for reducing carbon contamination. Annealing at 1050 °C in vacuum or 10^?5 Torr NH₃ was found to further reduce oxygen and carbon contamination to the XPS detection limits. Copyright © 2015 John Wiley & Sons, Ltd.     

Adsorption of transition-metal atoms on boron nitride nanotube: a density-functional study

Adsorption of transition atoms on a (8,0) zigzag single-walled boron nitride (BN) nanotube has been investigated using density-functional theory methods. Main focuses have been placed on configurations corresponding to the located minima of the adsorbates, the corresponding binding energies, and the modified electronic properties of the BN nanotubes due to the adsorbates. We have systemically studied a series of metal adsorbates including all 3d transition-metal elements (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn) and two group-VIIIA transition-metal elements (Pd and Pt). We found that many transition-metal atoms can be chemically adsorbed on the outer surface of the BN nanotubes and that the adsorption process is typically exothermic. Upon adsorption, the binding energies of the Sc, Ti, Ni, Pd, and Pt atoms are relatively high (>1.0 eV), while those of V, Fe, and Co atoms are modest, ranging from 0.62 to 0.92 eV. Mn atom forms a weak bond with the BN nanotube, while Zn atom cannot be chemically adsorbed on the BN nanotube. In most cases, the adsorption of transition-metal atoms can induce certain impurity states within the band gap of the pristine BN nanotube, thereby reducing the band gap. Most metal-adsorbed BN nanotubes exhibit nonzero magnetic moments, contributed largely by the transition-metal atoms.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

Homopairing possibilities of the DNA base thymine and the RNA base uracil: an ab initio density functional theory study

All planar homopairings of the DNA base thymine and the RNA base uracil are reported for the first time in this study. Using the idea of binding sites discussed in our previous work (Kelly et al. J. Phys. Chem. B 2005, 109, 11933; J. Phys. Chem. B 2005, 109, 22045) and ab initio density functional theory, we predict and relax 10 thymine and 10 uracil homopairs. The stabilization energies of the homopairs vary from just below zero to -0.82 eV. The results on the pair geometry and energetics are compared with those available in the literature. The collected data on all planar thymine and uracil homopairs can be used to construct the thymine and uracil superstructures seen experimentally on various surfaces.     

Size-expanded DNA bases: an ab initio study of their structural and electronic properties

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order M?ller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.     

Thermal decomposition of decalin: an ab initio study

Density functional theory calculations (B3LYP and BH&HLYP functionals) of the potential energy surface have been performed to investigate the mechanisms of decalin breakdown, and the Rice-Ramsperger-Kassel-Marcus and transition state theory methods have been used to compute the high-pressure limit thermal rate constants for the new reaction pathways. The new pathways connect decalin to five primary monoaromatic species: benzene, toluene, styrene, ethylbenzene, and xylene. The reactions used for the new routes are carbon-carbon bond cleavage reaction, dissociation reaction, and hydrogen abstraction and addition reactions. A kinetic analysis was performed for pyrolytic conditions, and benzene, toluene, and xylene were identified as major products.     

Adsorption and vibrational spectroscopy of ammonia at mordenite: ab initio study

The adsorption of ammonia at various active centers at the outer and inner surfaces of mordenite, involving Br?nsted acid (BA) sites, terminal silanol groups, and Lewis sites has been investigated using periodic ab initio density-functional theory. It is shown that ammonia forms an ammonium ion when adsorbed at strong BA sites. The calculated adsorption energies for different BA sites vary in the interval from 111.5 to 174.7 kJ/mol depending on the local environment of the adduct. The lowest adsorption energy is found for a monodentate complex in the main channel, the highest for a tetradentate configuration in the side pocket. At weak BA sites such as terminal silanol groups or a defect with a BA site in a two-membered ring ammonia is H bonded via the N atom. Additional weak H bonds are formed between H atoms of ammonia and O atoms of neighboring terminal silanol groups. The calculated adsorption energies for such adducts range between 61.7 and 70.9 kJ/mol. The interaction of ammonia with different Lewis sites is shown to range between weak (DeltaE(ads)=17.8 kJ/mol) and very strong (DeltaE(ads)=161.7 kJ/mol), the strongest Lewis site being a tricoordinated Al atom at the outer surface. Our results are in very good agreement with the distribution of desorption energies estimated from temperature-programmed desorption (TPD) and microcalorimetry experiments, the multipeaked structure of the TPD spectra is shown to arise from strong and weak Br?nsted and Lewis sites. The vibrational properties of the adsorption complexes are investigated using a force-constant approach. The stretching and bending modes of NH(4) (+) adsorbed to the zeolite are strongly influenced by the local environment. The strongest redshift is calculated for the asymmetric stretching mode involving the NH group hydrogen bonded to the bridging O atom of the BA site, the shift is largest for a monodentate and smallest for a tetradentate adsorption complex. The reduced symmetry of the adsorbate also leads to a substantial splitting of the stretching and bending modes. In agreement with experiment we show that the main vibrational feature which differentiates coordinatively bonded ammonia from a hydrogen-bonded ammonium ion is the absence of bending modes above 1630 cm(-1) and in the region between 1260 and 1600 cm(-1), and a low-frequency bending band in the range from 1130 to 1260 cm(-1). The calculated distribution of vibrational frequencies agrees very well with the measured infrared adsorption spectra. From the comparison of the adsorption data and the vibrational spectra we conclude that due to the complex adsorption geometry the redshift of the asymmetric stretching is a better measure of the acidity of an active sites than the adsorption energy.     

Wheland intermediates: an ab initio valence bond study

The traditional resonance model for electrophilic attacks on substituted aromatic rings is revisited using high level valence bond (VB) calculations. A large π-donation is found in the X = NH(2) case and a weaker one for the X = Cl case, not only for ortho and para isomers but also for the meta case, which can be explained by considering five (not three) fundamental VB structures. No substantial π-effect is found in the X = NO(2) case, generally viewed as π-attractive.     

Pseudorotation motion in tetrahydrofuran: an ab initio study

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.     

Towards SiC surface functionalization: an ab initio study

We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular-dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for biocompatible devices.