Structure and stability of graphene edges in O2 and H2 environments from ab initio thermodynamics

Edges play a determining role in the electronic and transport properties of graphene, however, their actual morphology and configuration remain unknown. Using ab initio thermodynamics, we have systematically studied the stability and structure of armchair and zigzag edges of graphene in pure O₂ and combined O₂ and H₂ environments. In total, 81 different nanostructures were investigated, however, only a few of them domain the phase diagram. Our calculations show that zigzag edges are less stable than armchair edges. Nonetheless, the former exhibit a much richer diversity in terms of structures. The oxygen-terminated edges occupy the largest regions in the phase stability diagram in comparison with hydrogen-oxygen-terminated edges, which correspond to carboxyl and alcohol functional groups.     

Application of carbon nanostructures toward SO2 and SO3 adsorption: a comparison between pristine graphene and N-doped graphene by DFT calculations

We studied the adsorption of SO_x (x?=?2,3) molecules on the surface of pristine graphene (PG) and N-doped graphene (NDG) by density functional theory (DFT) calculations at the B3LYP/6-31G(d) level. We used Mulliken and NBO charge analysis to calculate the net charge transfer of adsorbed SO_x on pristine and defected graphene systems. Our calculations reveal much higher adsorption energy and higher net charge transfer by using NDG instead of pristine graphene. Furthermore, the density of state (DOS) graphs point to major orbital hybridization between the SO_x and NDG, while there is no evidence of hybridization by using pristine graphene. Based on our results, it is found that SO₂ and SO₃ molecules can be adsorbed on the surface of NDG physically and chemically with adsorption energies (E_ads) of ?27.5 and 65.2?kJ?mol^?1 (19.6 and 51.4?kJ?mol^?1 BSSE), respectively, while low adsorption energies were calculated in the case of using pristine graphene. So we introduced NDG as a sensitive adsorbent/sensor for detection of SO₂ and SO₃.     

Hydrogen bond connectivity in jennite from ab initio simulations

The protonation scheme and the hydrogen bond connectivity in the structure of jennite were investigated by ab initio molecular dynamics simulations. The calculated statistics of hydrogen bonds at ambient conditions is consistent with the protonation scheme proposed by Bonaccorsi et al. (2004) based on the bond valence theory. The protons in the system are associated with the 2Ca–OH linkage and H₂O molecules. The dangling Si–O bond on the bridging tetrahedra is de-protonated. The proton dynamics revealed in the molecular dynamic simulations explains the apparent discrepancies in the NMR and X-ray diffraction studies of jennite.     

Erosion of refractory carbides in high-temperature hydrogen from ab initio computations

Advanced concepts for in-space propulsion require coatings that are resistant to erosion in high temperature and pressure hydrogen. The erosion of refractory carbides of interest for this application (ZrC, NbC, HfC, and TaC) is investigated using combined ab initio thermodynamic computations and equilibrium product analyses. The carbides are shown to erode through a combination of four governing reactions, the relative extent of which depend on environmental conditions. The product profiles from these reactions are complex but exhibit lower hydrogen saturation at higher temperatures and lower pressures. A metric is derived to determine the applicability of equilibrium analyses for erosion rates, based on experimental conditions. Heritage mass loss experiments on ZrC in hydrogen satisfy the equilibrium criteria, and, correspondingly, the computed equilibrium erosion rate agrees quantitatively. The results suggest that previously postulated non-equilibrium effects, namely the prolonged incongruent vaporization originating from high carbon mobility, do not drive erosion over the hours-long timescales of the experiments. For specific in-space propulsion designs, comparisons of carbide performance show TaC and HfC outperform other carbides and meet the criteria needed to close designs.     

Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores

The unique properties of green fluorescent protein (GFP) have been harnessed in a variety of bioimaging techniques, revolutionizing many areas of the life sciences. Molecular-level understanding of the underlying photophysics provides an advantage in the design of new fluorescent proteins (FPs) with improved properties; however, because of its complexity, many aspects of the GFP photocycle remain unknown. In this Account, we discuss computational studies of FPs and their chromophores that provide qualitative insights into mechanistic details of their photocycle and the structural basis for their optical properties. In a reductionist framework, studies of well-defined model systems (such as isolated chromophores) help to understand their intrinsic properties, while calculations including protein matrix and/or solvent demonstrate, on the atomic level, how these properties are modulated by the environment. An interesting feature of several anionic FP chromophores in the gas phase is their low electron detachment energy. For example, the bright excited ππ* state of the model GFP chromophore (2.6 eV) lies above the electron detachment continuum (2.5 eV). Thus, the excited state is metastable with respect to electron detachment. This autoionizing character needs to be taken into account in interpreting gas-phase measurements and is very difficult to describe computationally. Solvation (and even microsolvation by a single water molecule) stabilizes the anionic states enough such that the resonance excited state becomes bound. However, even in stabilizing environments (such as protein or solution), the anionic chromophores have relatively low oxidation potentials and can act as light-induced electron donors. Protein appears to affect excitation energies very little (<0.1 eV), but alters ionization or electron detachment energies by several electron volts. Solvents (especially polar ones) have a pronounced effect on the chromophore's electronic states; for example, the absorption wavelength changes considerably, the ground-state barrier for cis-trans isomerization is reduced, and fluorescence quantum yield drops dramatically. Calculations reveal that these effects can be explained in terms of electrostatic interactions and polarization, as well as specific interactions such as hydrogen bonding. The availability of efficient computer implementations of predictive electronic structure methods is essential. Important challenges include developing faster codes (to enable better equilibrium sampling and excited-state dynamics modeling), creating algorithms for properties calculations (such as nonlinear optical properties), extending standard excited-state methods to autoionizing (resonance) states, and developing accurate QM/MM schemes. The results of sophisticated first-principle calculations can be interpreted in terms of simpler, qualitative molecular orbital models to explain general trends. In particular, an essential feature of the anionic GFP chromophore is an almost perfect resonance (mesomeric) interaction between two Lewis structures, giving rise to charge delocalization, bond-order scrambling, and, most importantly, allylic frontier molecular orbitals spanning the methine bridge. We demonstrate that a three-center Hückel-like model provides a useful framework for understanding properties of FPs. It can explain changes in absorption wavelength upon protonation or other structural modifications of the chromophore, the magnitude of transition dipole moment, barriers to isomerization, and even non-Condon effects in one- and two-photon absorption.     

Lateral homogeneity of the electronic properties in pristine and ion-irradiated graphene probed by scanning capacitance spectroscopy

In this article, a scanning probe method based on nanoscale capacitance measurements was used to investigate the lateral homogeneity of the electron mean free path both in pristine and ion-irradiated graphene. The local variations in the electronic transport properties were explained taking into account the scattering of electrons by charged impurities and point defects (vacancies). Electron mean free path is mainly limited by charged impurities in unirradiated graphene, whereas an important role is played by lattice vacancies after irradiation. The local density of the charged impurities and vacancies were determined for different irradiated ion fluences.     

Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores

We discuss the basic process of photoinduced isomerization as a building block for the design of complex, multifunctional molecular devices. The excited-state dynamics associated with isomerization is detailed through application of the ab initio multiple spawning (AIMS) method, which solves the electronic and nuclear Schr?dinger equations simultaneously. This first-principles molecular dynamics approach avoids the uncertainties and extraordinary effort associated with fitting of potential energy surfaces and allows for bond rearrangement processes with no special input. Furthermore, the AIMS method allows for the breakdown of the Born-Oppenheimer approximation and thus can correctly model chemistry occurring on multiple electronic states. We show that charge-transfer states play an important role in photoinduced isomerization and argue that this provides an essential "design rule" for multifunctional devices based on isomerizing chromophores.     

The role and perspective of ab initio molecular dynamics in the study of biological systems

Ab initio molecular dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing number of applications to biochemical systems. Here we describe the principles on which ab initio MD is based. We focus on the most popular implementation, based on density functional theory and plane wave basis set. By a survey of recent applications, we show that despite the current limitations of size and time scale, ab initio MD (and hybrid ab initio MD/MM approaches) can play an important role for the modeling of biological systems. Finally, we provide a perspective for the advancement of methodological approaches which may further expand the scope of ab initio MD in biomolecular modeling.     

Identifying and characterizing binding sites on the irreversible inhibition of human glutathione S-transferase P1-1 by S-thiocarbamoylation

Human glutathione S-transferase P1-1 (hGST P1-1) is involved in cell detoxification processes through the conjugation of its natural substrate, reduced glutathione (GSH), with xenobiotics. GSTs are known to be overexpressed in tumors, and naturally occurring isothiocyanates, such as benzyl isothiocyanate (BITC), are effective cancer chemopreventive compounds. To identify and characterize the potential inhibitory mechanisms of GST P1-1 induced by isothiocyanate conjugates, we studied the binding of GST P1-1 and some cysteine mutants to the BITC-SG conjugate as well as to the synthetic S-(N-benzylcarbamoylmethyl)glutathione conjugate (BC-SG). We report here the inactivation of GST P1-1 through the covalent modification of two Cys47 residues per dimer and one Cys101. The evidence has been compiled by isothermal titration calorimetry (ITC) and electrospray ionization mass spectrometry (ESI-MS). ITC experiments suggest that the BITC-SG conjugate generates adducts with Cys47 and Cys101 at physiological temperatures through a corresponding kinetic process, in which the BITC moiety is covalently bound to these enzyme cysteines through an S-thiocarbamoylation reaction. ESI-MS analysis of the BITC-SG incubated enzymes indicates that although the Cys47 in each subunit is covalently attached to the BITC ligand moiety, only one of the Cys101 residues in the dimer is so attached. A plausible mechanism is given for the emergence of inactivation through the kinetic processes with both cysteines. Likewise, our molecular docking simulations suggest that steric hindrance is the reason why only one Cys101 per dimer is covalently modified by BITC-SG. No covalent inactivation of GST P1-1 with the BC-SG inhibitor has been observed. The affinities and inhibitory potencies for both conjugates are high and very similar, but slightly lower for BC-SG. Thus, we conclude that the presence of the sulfur atom from the isothiocyanate moiety in BITC-SG is crucial for its irreversible inhibition of GST P1-1.     

Calculated energies of adsorption of non-hydrocarbon species on diamond H/C(1 1 1) surface and the abstraction energies of these species abstracted by hydrogen atoms using ab initio calculation

The energetics of adsorption of non-hydrocarbon radical species on H/C(1 1 1) diamond surface and the abstraction energies of these species abstracted by hydrogen atoms, which are in excess in gas phase in the diamond thin film growth using the chemical vapor deposition (CVD) method, were examined using ab initio calculation method. Based on the calculated results for the examined species, which include H, F, OH, NH₂, Cl, CH_mX_n (X=F or Cl) radicals, the tendency of incorporation of F, O, N, H and Cl atoms in the diamond thin film is discussed. The high adsorption energy and the high abstraction energy abstracted by excess gas-phase H atoms for F radicals suggest that F atom has the highest tendency to stay in the diamond thin film among the examined non-carbon atoms. In contrast, the comparable adsorption energy of Cl atom with other examined radicals except F radical, and its low abstraction energy, indicate that Cl atom possesses the least tendency to be incorporated in the diamond thin film. For O, N and H atoms, their calculated abstraction energy values suggest that the overall order of tendency of incorporation in diamond thin film is F>O>N>H>Cl. In addition, the energetically comparable adsorption energy for the CH₂Cl radical, compared with the other examined CH_mX_n species, and the low abstraction energy of Cl atom support that CH₂Cl is a good growth species in diamond CVD thin film growth.     

Clusters, liquids, and crystals of dialkyimidazolium salts. A combined perspective from ab initio and classical computer simulations

We summarize results obtained by a combination of ab initio and classical computer simulations of dialkylimidazolium ionic liquids in different states of aggregation, from crystals to liquids and clusters. Unusual features arising from the competition between electrostatic, dispersion, and hydrogen-bonding interactions are identified at the origin of observed structural patterns. We also discuss the way Br?nsted acids interact with ionic liquids leading to the formation of hydrogen-bonded anions.     

Epitaxial deposition of silver ultra-fine nano-clusters on defect-free surfaces of HOPG-derived few-layer graphene in a UHV multi-chamber by in situ STM, ex situ XPS, and ab initio calculations

ABSTRACT: The growth of three-dimensional ultra-fine spherical nano-particles of silver on few layers of graphene derived from highly oriented pyrolytic graphite in ultra-high vacuum were characterized using in situ scanning tunneling microscopy (STM) in conjunction with X-ray photoelectron spectroscopy. The energetics of the Ag clusters was determined by DFT simulations. The Ag clusters appeared spherical with size distribution averaging approximately 2 nm in diameter. STM revealed the preferred site for the position of the Ag atom in the C-benzene ring of graphene. Of the three sites, the C-C bridge, the C-hexagon hollow, and the direct top of the C atom, Ag prefers to stay on top of the C atom, contrary to expectation of the hexagon-close packing. Ab initio calculations confirm the lowest potential energy between Ag and the graphene structure to be at the exact site determined from STM imaging.     

The nature of high surface energy sites in graphene and graphite

Variations in the adsorption enthalpies of acetone to few-layer graphene and graphite nanopowders were analyzed as a function of surface coverage. The adsorption enthalpies were measured by inverse gas chromatography at low monolayer coverage levels (0.1–20%). The adsorption enthalpies increased from −13 kcal/mol at the lowest coverage to −7.5 kcal/mol. We fitted the measured adsorption enthalpies as a function of coverage using a two-state model and estimated the number of high-energy sites on both materials. The graphite powder had seven times more high-energy sites than the few-layer graphene, which explains why the adsorption enthalpies for graphite increased more slowly with increasing coverage. We also performed a theoretical study based on density functional theory calculations using a functional that accounts for dispersive interactions to elucidate the nature of the high-energy adsorption sites. The calculated adsorption enthalpies ranged from −16 to −1 kcal/mol while the adsorption enthalpy to a plain graphite surface was −9 kcal/mol. The high-energy adsorption sites were localized on surface steps and edge-cavities. The adsorption enthalpies at very low coverage therefore corresponded to adsorption on steps and edge cavities, while those measured at coverage levels of ∼4% or more reflected adsorption to the flat surface.     

Origin of the distinction in hardness of lower tungsten carbides: An experimental and ab initio theoretical study

The so-called lower tungsten carbides W₂C and Fe₃W₃C often appear in tungsten carbide–reinforced iron matrix (WC–Fe) composites. The effect of their presence on the mechanical properties of the material, such as hardness, is not well understood. In this study, we extensively measured the hardness distribution in the WC–Fe composites and also performed hundreds of microhardness measurements to determine the hardness values for the lower carbides. The hardness values calculated by ab initio were compared, where the theoretical values of Fe₃W₃C had little difference from the experimental values. However, the experimentally obtained hardness data for W₂C were significantly smaller than the reported theoretical data. Moreover, the experimental hardness values for W₂C reported in the literatures are very different. To understand the origin of the discrepancy, the focused-ion-beam–transmission-electron-microscopy technique was used to obtain the high-resolution images of W₂C, which revealed a high density of planar defects. As a further comparison, ab initio molecular dynamics simulations illustrate that the complex interactions between different atomic pairs in Fe₃W₃C make it difficult for this type of crystal defect to occur. The lattice of W₂C can adjust—resulting in shuffle defects and stacking faults—to a certain degree affecting its hardness, which was not revealed in previous studies.     

The prediction and characterization of metal binding sites in proteins

The rational engineering of novel functions into proteins canonly be attempted when the underlying structural scaffold onwhich the new function is displayed and the structure of thetarget protein are both well understood. To introduce functionsmediated by metals it is therefore necessary to identify theprincipal liganding residues for the chosen metal, the requiredarchitecture of the metal-ligand complex and sites within thetarget protein that could accommodate such sites. Here we presenta method that applies structural information from the proteindata bank to the ab initio design and characterization of novelmetal binding sites. The prediction method has been tested on28 metalloprotein structures from the Brookhaven Protein DataBank. It successfully identified >90% of the metal bindingsites. In addition, we have used the method to design and characterizezinc binding sites in two antibody structures. Metal bindingstudies on one of these putative metalloantibodies showed metalbinding, confirming the predictive power of the method.     

Experimental and theoretical studies of methanol oxidation in the presence of Co-Pd @ polyaniline/N-doped reduced graphene oxide electrocatalyst

Journal of Applied Electrochemistry - Nanocomposites of polyaniline (PANI) with nitrogen-doped reduced graphene oxide (NRGO) were synthesized through a chemical polymerization method. The...     

The bonding in thiolate protected gold nanoparticles from Au4f photoemission core level shifts

Density functional theory calculations are used to evaluate Au4f core level shifts of methyl thiolate protected Au(25), Au(102) and Au(144) nanoparticles. The shifts are found to provide sensitive fingerprints of the chemical environment. In particular, Au atoms in protective gold-thiolate complexes have higher binding energies than Au atoms with solely metal neighbors. The core level shifts for the nanoparticles are compared to the corresponding results for methyl thiolates adsorbed on Au(111) and implications for the understanding of the gold-sulfur bond is discussed.     

Identifying efficient natural bioreductants for the preparation of graphene and graphene-metal nanoparticle hybrids with enhanced catalytic activity from graphite oxide

The implementation of green approaches towards the preparation of graphene and graphene-based materials with enhanced functionality from graphite oxide has been relatively little explored. Particularly, the use of bioreductants and the testing of their relative efficacies is an incipient area of research. Here, a pool of 20 environmentally friendly, natural antioxidants have been tested for their ability to reduce graphene oxide. These antioxidants were mostly vitamins, amino acids and organic acids. By establishing a protocol to systematically compare and optimize their performance, several new efficient bioreductants of graphene oxide have been identified, namely, pyridoxine and pyridoxamine (vitamin B₆), riboflavin (vitamin B₂), as well as the amino acids arginine, histidine and tryptophan. These biomolecules were used to prepare reduced graphene oxide–silver nanoparticle hybrids that displayed colloidal stability in water in the absence of additional dispersants. Particularly, hybrids prepared with pyridoxamine exhibited a combination of long-term colloidal stability and exceptionally high catalytic activity among silver nanoparticle-based catalysts in the reduction of p-nitrophenol with NaBH₄. Thus, in addition to expanding substantially the number of green reductants available for graphene oxide reduction, the present results underline the idea that proper selection of bioreductant can be relevant to achieve graphene-based materials with improved performance.