Density functional theory studies of the adsorption of hydrogen sulfide on aluminum doped silicane

First principles total energy calculations have been performed to study the hydrogen sulfide (H₂S) adsorption on silicane, an unusual one monolayer of Si(111) surface hydrogenated on both sides. The H₂S adsorption may take place in dissociative or non-dissociative forms. Silicane has been considered as: (A) non-doped with a hydrogen vacancy, and doped in two main configurations; (B) with an aluminum replacing a hydrogen atom and (C-n; n?=?1, 2, 3) with an aluminum replacing a silicon atom at a lattice site. In addition, three supercells; 4x4, 3x3 and 2x2 have been explored for both non-doped and doped silicane. The non-dissociative adsorption takes place in geometries (A), (C-1), (C-2) and (C-3) while the dissociative in (B). Adsorption energies of the dissociative case are larger than those corresponding to the non-dissociated cases. In the dissociative adsorption, the molecule is fragmented in a HS structure and a H atom which are bonded to the aluminum to form a H-S-Al-H structure. The presence of the doping produces some electronic changes as the periodicity varies. Calculations of the total density of states (DOS) indicate that in most cases the energy gap decreases as the periodicity changes from 4x4 to 2x2. The features of the total DOS are explained in terms of the partial DOS. The reported charge density plots explain quite well the chemisorptions and physisorptions of the molecule on silicane in agreement with adsorption energies.     

First principle study of cysteine molecule on intrinsic and Au-doped graphene surface as a chemosensor device

To search for a high sensitivity sensor for cysteine, we investigated the adsorption of cysteine on intrinsic and Au-doped graphene sheets using density functional theory calculations. Binding energy is primarily determined by the type of atom which is closer to the adsorbed sheet. Compared with intrinsic graphene, Au-doped graphene system has higher binding energy value and shorter connecting distance, in which strong Au-S, Au-N and Au-O chemical bond interaction play the key role for stability. Furthermore, the density of states results show orbital hybridization between cysteine and Au-doped graphene sheet, but slight hybridization between the cysteine molecule and intrinsic graphene sheet. Large charge transfers exist in Au-doped graphene-cysteine system. The results of DOS and charge transfer calculations suppose that the electronic properties of graphene can be tuned by the adsorption site of cysteine. Therefore, graphene and Au-doped graphene system both possess sensing ability, except that Au-doped graphene is a better sensor for cysteine than intrinsic graphene.     

Two-dimensional boron nitride structures functionalization: first principles studies

Density functional theory calculations have been performed to investigate two-dimensional hexagonal boron nitride (2D hBN) structures functionalization with organic molecules. 2x2, 4x4 and 6x6 periodic 2D hBN layers have been considered to interact with acetylene. To deal with the exchange-correlation energy the generalized gradient approximation (GGA) is invoked. The electron-ion interaction is treated with the pseudopotential method. The GGA with the Perdew-Burke-Ernzerhoff (PBE) functionals together with van der Waals interactions are considered to deal with the composed systems. To investigate the functionalization two main configurations have been explored; in one case the molecule interacts with the boron atom and in the other with the nitrogen atom. Results of the adsorption energies indicate chemisorption in both cases. The total density of states (DOS) displays an energy gap in both cases. The projected DOS indicate that the B-p and N-p orbitals are those that make the most important contribution in the valence band and the H-s and C-p orbitals provide an important contribution in the conduction band to the DOS. Provided that the interactions of the acetylene with the 2D layer modify the structural and electronic properties of the hBN the possibility of structural functionalization using organic molecules may be concluded.     

Interaction between an icosahedron Li13 cluster and a graphene layer doped with a hydrogen atom

It is known that graphene reacts with atomic hydrogen to form a hydrogenated sheet of graphene. In order to understand the nature of the interaction between hydrogen and lithium in hydrogenated samples, we have carried out first principle calculations. Density functional theory and molecular dynamics were used to study the interaction between an icosahedron Li₁₃ cluster, and a graphene layer doped with a hydrogen atom. It was found that a hydrogen atom is levitated from the graphene layer and absorbed into the cluster of Li at 300?K and atmospheric pressure, with a binding energy far exceeding that of the adsorption energy of a hydrogen atom on the graphene layer.     

Adsorption and dimerisation of thiol molecules on Au(111) using a Z-matrix approach in density functional theory

The adsorption energetics of methanethiolate and benzenethiolate on Au(111) have been calculated using periodic density functional theory (DFT), based on the SIESTA methodology, with an internal coordinates implementation for geometry input and structure optimisation. Both molecules are covalently bound with interaction energies of 1.85 and 1.43 eV for methanethiolate and benzenethiolate, respectively. The preferred binding site is slightly offset from the bridge site in both cases towards the fcc-hollow. The potential energy surfaces (PES) have depths of 0.36 and 0.22 eV, the hollow sites are local maxima in both cases, and there is no barrier to diffusion of the molecule at the bridge site. The corresponding dimers are weakly bound for methanethiolate and benzenethiolate, with binding energies of 0.38 and 0.16 eV, respectively, and the preferred binding geometry is with the two sulphur atoms close to adjacent atop sites. The barrier to dissociation of the dimer dimethyl disulphide is estimated to lie between 0.3 and 0.35 eV.     

Electrochemical CO2 Reduction with Atomic Iron‐Dispersed on Nitrogen‐Doped Graphene

Electrochemical reduction of CO₂ provides an opportunity to reach a carbon‐neutral energy recycling regime, in which CO₂ emissions from fuel use are collected and converted back to fuels. The reduction of CO₂ to CO is the first step toward the synthesis of more complex carbon‐based fuels and chemicals. Therefore, understanding this step is crucial for the development of high‐performance electrocatalyst for CO₂ conversion to higher order products such as hydrocarbons. Here, atomic iron dispersed on nitrogen‐doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO₂ reduction to CO. Fe/NG has a low reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen‐confined atomic Fe moieties on the nitrogen‐doped graphene layer is confirmed by aberration‐corrected high‐angle annular dark‐field scanning transmission electron microscopy and X‐ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. The CO₂ reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N₄) embedded in nitrogen‐doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.     

A large gap opening of graphene induced by the adsorption of CO on the Al-doped site

We investigated CO adsorption on the pristine, Stone-Wales (SW) defected, Al- and Si- doped graphenes by using density functional calculations in terms of geometric, energetic and electronic properties. It was found that CO molecule is weakly adsorbed on the pristine and SW defected graphenes and their electronic properties were slightly changed. The Al- and Si- doped graphenes show high reactivity toward CO, so calculated adoption energies are about ?11.40 and ?13.75 kcal mol^?1 in the most favorable states. It was found that, among all the structures, the electronic properties of Al-doped graphene are strongly sensitive to the presence of CO molecule. We demonstrate the existence of a large E_g opening of 0.87 eV in graphene which is induced by Al-doping and CO adsorption.     

DFT studies of the phenol adsorption on boron nitride sheets

We perform first principles total energy calculations to investigate the atomic structures of the adsorption of phenol (C₆H₅OH) on hexagonal boron nitride (BN) sheets. Calculations are done within the density functional theory as implemented in the DMOL code. Electron-ion interactions are modeled according to the local-spin-density-approximation (LSDA) method with the Perdew-Wang parametrization. Our studies take into account the hexagonal h-BN sheets and the modified by defects d-BN sheets. The d-BN sheets are composed of one hexagon, three pentagons and three heptagons. Five different atomic structures are investigated: parallel to the sheet, perpendicular to the sheet at the B site, perpendicular to the sheet at the N site, perpendicular to the central hexagon and perpendicular to the B-N bond (bridge site). To determine the structural stability we apply the criteria of minimum energy and vibration frequency. After the structural relaxation phenol molecules adsorb on both h-BN and d-BN sheets. Results of the binding energies indicate that phenol is chemisorbed. The polarity of the system increases as a consequence of the defects presence which induces transformation from an ionic to covalent bonding. The elastic properties on the BN structure present similar behavior to those reported in the literature for graphene.     

Effect of the Si,Al and B doping on the sensing behaviour of carbon nanotubes toward ethylene oxide: a computational study

ABSTRACT

Exo– and endo–adsorption of ethylene oxide (EO) on pristine (9,0) (zigzag) carbon nanotube (CNT) and its doped forms with silicon (Si–CNT), aluminum (Al–CNT) and boron (B–CNT) were investigated using density functional theory (DFT) at M06–2X/6–311++G** level. The natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analyses were also performed by using the same level of theory. The effect of the doping on sensing behaviour of the CNT toward EO molecule was investigated through intermolecular interactions studies by calculation of total and partial density of states (DOS, PDOS). The enhanced sensitivity of doped–CNTs towards EO molecule associated with adsorption energies (E_ads) and the changes in geometric and electronic structures was examined and the global chemical reactivity parameters were calculated and comprehensively analysed. The thermodynamic property changes were calculated and compared. The results indicated that the EO adsorption on the pristine and doped CNTs was an exothermic spontaneous process. Moreover, based on the calculated E_g change (ΔE_g) and E_ads values, Al–CNT with superior sensitivity for sensing of EO molecule, indicates promising perspectives for its use in fabrication of new EO gas–sensing devices.     

A quantum chemical investigation of the electronic structure of thionine

We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of π→π* (S(1), S(2), T(1), T(2)) and n→π* (S(3), T(3)) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S(1) and T(1) states (~0.02 eV). The relaxation effects on the energies of S(2) and T(2) are moderate (0.14-0.20 eV). The very small emission energy results in a very low fluorescence rate. While we were not able to locate the energetic minimum of the S(3) state, we found a non-planar minimum for the T(3) state with an energy which is very close to the energy of the S(1) minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→π* states S(3) and T(3) are strongly blueshifted (0.33 and 0.46 eV), while the π→π* states are only slightly affected (<0.06 eV).     

First-principles investigation of the interaction of gold and palladium with armchair carbon nanotube

In this paper, we investigate the adsorption mechanisms at the interface between carbon nanotubes and metal electrodes that can influence the Schottky barrier (SB). We developed a theoretical model based on the first-principles density functional theory for the interaction of an armchair single-wall carbon nanotube (SWNT) with either Au(111) or Pd(111) surface. We considered the side-wall contact by modelling the full SWNT as well as the end-contact geometry using the graphene ribbon model to mimic the contact with very large diameter nanotubes. Strong interaction has been found for the Pd–SWNT interface where the partial density of states (DOS) shows that d-orbitals of palladium are dominant at the Fermi energy so that the hybrid Pd-orbitals have the correct symmetry to overlap with π-electrons and form covalent bonds. The SWNT can only be physisorbed on the gold surface for which the contribution to the DOS of the d-orbitals is very low. Moreover, the filling of antibonding states makes the Au–SWNT bond unstable. The average and ‘atom to atom’ energy barriers at the interface have been evaluated. The matching of open-edge carbon dimers with metal lattice in the end-contact geometry is more likely for large diameter SWNTs and this makes lower the SB at the interface.     

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.     

How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

Journal of Molecular Modeling - We studied the doping effects on the electronic and structural properties of graphene upon interaction with phenol. Calculations were performed within the periodic...     

Molecular structure,spectroscopic (FT-IR,FT-Raman,UV–vis), NBO,thermochemistry analysis of bis(thiourea)zinc(II) chloride crystals

The experimental and theoretical studies on the molecular structure and vibrational spectra of bis(thiourea)zinc(II) chloride (BTZC) crystals were investigated. The Fourier transform infrared, Fourier transform Raman and UV–vis spectra of BTZC were recorded. The molecular geometry and vibrational frequencies of BTZC in the ground state were calculated by using B3LYP with LANL2DZ as basis set. Comparison of the observed structural parameters of BTZC with single-crystal X-ray studies yields a good agreement. Vibrational analysis of the simultaneous IR and Raman activation of the Zn–Cl stretching mode in the molecule provides the evidence for the charge transfer interaction taking place within the molecule. The energy and oscillator strength are calculated by time-dependent density functional theory. The simulated spectra satisfactorily coincide with the experimental spectra.     

A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules

We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in expressing the peptides binding activity as a profile of amino acid contributions, amino acid similarity being accounted for by their characteristic physicochemical properties and their position within the sequence. The higher level of the strategy is based on a meticulous analysis of the contact interface of the peptides with the cleft constituting the receptor region of a particular class I MHC molecule. Interaction interfaces are inferred by docking the peptide onto the receptor groove of the MHC molecule; evaluation of the affinity of the peptide to the receptor is then performed by analysis of the electrostatic and hydrophobic energies on points of the interaction interface.The result is a robust system for analysis of peptide affinity to class I MHC molecules since while the first analysis dictates the composition of active sequences at the amino acid level, the second translates this information to the atomic level, where the molecular interaction can be analyzed in terms of the intrinsic interatomic forces and energies. Evaluation results for the methodology are encouraging since high affinity peptides are reflected by high scores at both levels of information, and are proportionally lower for peptides of medium and lower affinity for which interaction surfaces show relatively lower electrostatic complementarity and hydrophobic correlation than for the former.     

Structure of the alpha-actinin-vinculin head domain complex determined by cryo-electron microscopy

The vinculin binding site on alpha-actinin was determined by cryo-electron microscopy of 2D arrays formed on phospholipid monolayers doped with a nickel chelating lipid. Chicken smooth muscle alpha-actinin was cocrystallized with the beta1-integrin cytoplasmic domain and a vinculin fragment containing residues 1-258 (vinculin(D1)). Vinculin(D1) was located at a single site on alpha-actinin with 60-70% occupancy. In these arrays, alpha-actinin lacks molecular 2-fold symmetry and the two ends of the molecule, which contain the calmodulin-like and actin binding domains, are held in distinctly different environments. The vinculin(D1) difference density has a shape very suggestive of the atomic structure. The atomic model of the complex juxtaposes the alpha-actinin binding site on vinculin(D1) with the N-terminal lobe of the calmodulin-like domain on alpha-actinin. The results show that the interaction between two species with weak affinity can be visualized in a membrane-like environment.     

Si-doped graphene: an ideal sensor for NO- or NO<Subscript>2</Subscript>-detection and metal-free catalyst for N<Subscript>2</Subscript>O-reduction

Exploring and evaluating the potential applications of two-dimensional graphene is an increasingly hot topic in graphene research. In this paper, by studying the adsorption of NO, N₂O, and NO₂ on pristine and silicon (Si)-doped graphene with density functional theory methods, we evaluated the possibility of using Si-doped graphene as a candidate to detect or reduce harmful nitrogen oxides. The results indicate that, while adsorption of the three molecules on pristine graphene is very weak, Si-doping enhances the interaction of these molecules with graphene sheet in various ways: (1) two NO molecules can be adsorbed on Si-doped graphene in a paired arrangement, while up to four NO₂ molecules attach to the doped graphene with an average adsorption energy of −0.329 eV; (2) the N₂O molecule can be reduced easily to the N₂ molecule, leaving an O-atom on the Si-doped graphene. Moreover, we find that adsorption of NO and NO₂ leads to large changes in the electronic properties of Si-doped graphene. On the basis of these results, Si-doped graphene can be expected to be a good sensor for NO and NO₂ detection, as well as a metal-free catalyst for N₂O reduction.     

Cation-pi interaction in a folded polypeptide.

Cationic and aromatic side chains from protein residues interact to stabilize tertiary structure. The stabilization energy originates in part from electrostatic attraction between the cation, and regions of high electron density in pi-orbitals of the aromatic group, leading to the name cation-pi interaction. The lysine and tyrosine containing peptide, N-acetyl-Pro-Pro-Lys-Tyr-Asp-Lys-NH(2), has near uv CD characteristic of tyrosine in a structured environment. Nuclear Overhauser effect (NOE), coupling constant, and ring current chemical shift constraints obtained with (1)H NMR confirm that the peptide (t6p) folds. Simulated annealing consistent with all NMR constraints produces a 40-structure ensemble for t6p with potential energies within one standard deviation of the lowest value observed. Calculated binding energies indicate that cation-pi and cation-phenolic OH interactions exists between the Lys3 and Tyr4 side chains in most of the structures. The t6p peptide in solution is a model for these interactions in a protein. A perturbing electric field from the cationic ground state charge intermingles the excited states of the aromatic group. This intermingling effect may provide a cation-pi signature effect in the tyrosine spectroscopy. The absorption and CD for the lowest energy electronic transitions of the tyrosine phenol were computed for the ensemble. Red-shifted peak energy and hypochromicity in the absorbance band, and decreasing rotational strength, correlates with increasing binding energy of the complex indicating the cation-pi spectroscopic signature. The ensemble average spectroscopic signature effects in t6p are small and in agreement with observation.     

Rapid and Nondestructive Determination of Graphene Thickness with an all Dielectric Metasurface

We report a simple, rapid, and nondestructive approach for precise determination of the number of graphene layers by placing the graphene on top of an all dielectric metasurface. The all dielectric metasurface is constituted with a periodic lattice of a rectangular silicon bar and a silicon ring. Due to the destructive interference between the radiation losses from bar and ring resonators, Fano resonance with high quality (Q) factor has been achieved from the metasurface, and thus the strong light-graphene interaction on top of the structure is allowed. By placing single layer, bi-layer, and few layers graphene above the metasurface, we find that both the amplitude and wavelength of Fano resonance can be dramatically changed. And such changes are large enough to be detected by a Fourier transform infrared spectrometer (FTIR). As a result, the thickness of graphene can be simply determined by monitoring the Fano resonance and the corresponding figure-of-merit(FOM) is as large as 6.5.