The interaction of oxygen with TiC(001): photoemission and first-principles studies

High-resolution photoemission and first-principles density-functional slab calculations were used to study the interaction of oxygen with a TiC(001) surface. Atomic oxygen is present on the TiC(001) substrate after small doses of O(2) at room temperature. A big positive shift (1.5-1.8 eV) was detected for the C 1s core level. These photoemission studies suggest the existence of strong O<-->C interactions. A phenomenon corroborated by the results of first-principles calculations, which show a CTiTi hollow as the most stable site for the adsorption of O. Ti and C atoms are involved in the adsorption and dissociation of the O(2) molecule. In general, the bond between O and the TiC(001) surface contains a large degree of ionic character. The carbide-->O charge transfer is substantial even at high coverages (>0.5 ML) of oxygen. At 500 K and large doses of O(2), oxidation of the carbide surface occurs with the removal of C and formation of titanium oxides. There is an activation barrier for the exchange of Ti-C and Ti-O bonds which is overcome only by the formation of C-C or C-O bonds on the surface. The mechanism for the removal of a C atom as CO gas involves a minimum of two O adatoms, and three O adatoms are required for the formation of CO(2) gas. Due to the high stability of TiC, an O adatom alone cannot induce the generation of a C vacancy in a flat TiC(001) surface.     

Exploring the hydration of Pb2+: ab initio studies and first-principles molecular dynamics

Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.     

Adsorption and diffusion on a phosphorene monolayer: a DFT study

A computational study of the adsorption and diffusion behavior of alkali and alkaline earth metal atoms on a phosphorene monolayer is reported. Our calculations were performed within the framework of density functional theory using the Perdew–Burke–Ernzerhof functional and projector augmented wave potentials, as derived from the generalized gradient approximation. Our binding energy calculations for various potential adsorption sites showed that the site located above the center of a triangle formed by three surface phosphorus atoms is the most attractive to all adatoms. In addition, simulation of the diffusion of adatoms across the surface of the phosphorene monolayer showed that the diffusion is anisotropic, with K having the lowest diffusion barrier (0.02 eV along the zigzag pathway). To the best of our knowledge, this is the lowest diffusion barrier of any metal adatom on a single layer of phosphorene. While phosphorene exhibited significantly better adatom adsorption and diffusion than graphene, it also showed a reduced storage capacity compared to graphene, most probably due to the structural distortion induced by the oversaturated phosphorene surface. This finding strongly suggests that a phosphorene–graphene hybrid system could be employed as a promising high-capacity ion anode.     

Temperature-dependent infrared spectroscopy of water from a first-principles approach

The structure and dynamics of the hydrogen-bond network in water is investigated as a function of the temperature through the application of a first-principles approach that combines an ab-initio-based water potential with an explicit quantum treatment of the molecular motion. A molecular-level picture of the rearrangement of the hydrogen-bond network is derived from the direct analysis of linear and nonlinear vibrational spectra. The results indicate that good agreement with the available experimental data is obtained when the temperature scale is defined relative to the corresponding melting points. In particular, the theoretically predicted energy barriers and time scales associated with the hydrogen-bond dynamics are closely comparable to the experimental values obtained from two-dimensional and pump-probe infrared spectra. The present analysis will also serve as a guide for future developments of an improved ab-initio-based model capable to reproduce the properties of water in different environments and under different conditions.     

Generation of molecular graphs for QSAR studies: an approach based on supergraphs

A new algorithm for generation of substituted derivatives of a given structure and its software implementation are described. The program has deterministic and stochastic generation modes and efficiently supports various types of structural constraints. The problem of exhaustive and irredundant generation is discussed, and a new algorithm of the complete rejection of isomorphic molecular graphs is proposed. The main application of the generator is QSAR studies; however, applications in combinatorial chemistry are also possible.     

Attractive interaction between transition-metal atom impurities and vacancies in graphene: a first-principles study

We present a density functional theory study of transition metal adatoms on a graphene sheet with vacancy-type defects. We calculate the strain fields near the defects and demonstrate that the strain fields around these defects reach far into the unperturbed hexagonal network and that metal atoms have a high affinity to the non-perfect and strained regions of graphene. Metal atoms are therefore attracted by the reconstructed defects. The increased reactivity of the strained graphene makes it possible to attach metal atoms much more firmly than to pristine graphene and supplies a tool for tailoring the electronic structure of graphene. Finally, we analyze the electronic band structure of graphene with defects and show that some defects open a semiconductor gap in graphene, which may be important for carbon-based nanoelectronics.     

A density-functional approach to polarizable models: a Kim-Gordon response density interaction potential for molecular simulations

A combined linear-response-frozen electron-density model has been implemented in a molecular-dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory [J. Chem. Phys. 56, 3122 (1972); J. Chem. Phys. 60, 1842 (1974)] and a response contribution determined by the instantaneous ionic configuration of the system. The method is free from empirical pair potentials and the parametrization protocol involves only calculations on properly chosen subsystems. We apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density-functional calculations.     

Channeling on carbon nanotubes: a molecular dynamics approach

We have performed classical molecular dynamics on different kinds of carbon nanotubes in order to examine their response to self-irradiation nearly parallel to the tube axis. We have found that the critical angle for channeling decays as a power law. Following the energy loss along the projectile path, we have determined the maximum range as a function of energy at the critical angle. Narrower tubes seem to be more adequate for transporting particles to longer distances.     

Multitargeting by curcumin as revealed by molecular interaction studies

Curcumin (diferuloylmethane), the active ingredient in turmeric (Curcuma longa), is a highly pleiotropic molecule with anti-inflammatory, anti-oxidant, chemopreventive, chemosensitization, and radiosensitization activities. The pleiotropic activities attributed to curcumin come from its complex molecular structure and chemistry, as well as its ability to influence multiple signaling molecules. Curcumin has been shown to bind by multiple forces directly to numerous signaling molecules, such as inflammatory molecules, cell survival proteins, protein kinases, protein reductases, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca(2+) ATPase, DNA methyltransferases 1, FtsZ protofilaments, carrier proteins, and metal ions. Curcumin can also bind directly to DNA and RNA. Owing to its β-diketone moiety, curcumin undergoes keto-enol tautomerism that has been reported as a favorable state for direct binding. The functional groups on curcumin found suitable for interaction with other macromolecules include the α, β-unsaturated β-diketone moiety, carbonyl and enolic groups of the β-diketone moiety, methoxy and phenolic hydroxyl groups, and the phenyl rings. Various biophysical tools have been used to monitor direct interaction of curcumin with other proteins, including absorption, fluorescence, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy, surface plasmon resonance, competitive ligand binding, Forster type fluorescence resonance energy transfer (FRET), radiolabeling, site-directed mutagenesis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoprecipitation, phage display biopanning, electron microscopy, 1-anilino-8-naphthalene-sulfonate (ANS) displacement, and co-localization. Molecular docking, the most commonly employed computational tool for calculating binding affinities and predicting binding sites, has also been used to further characterize curcumin's binding sites. Furthermore, the ability of curcumin to bind directly to carrier proteins improves its solubility and bioavailability. In this review, we focus on how curcumin directly targets signaling molecules, as well as the different forces that bind the curcumin-protein complex and how this interaction affects the biological properties of proteins. We will also discuss various analogues of curcumin designed to bind selective targets with increased affinity.     

Influence of Se and Zn substitution on the electronic transport on a CdTe nanotube-based molecular device: a first-principles study

The electronic transport property of pure cadmium telluride (CdTe) nanotube, selenium-substituted and zinc-substituted CdTe nanotube-based molecular device are investigated with density functional theory. The electronic transport property of CdTe nanotube is studied in terms of device density of states (DOS), electron density, transmission spectrum, and transmission pathways. The substitution of selenium and zinc atoms along the left electrode and bias voltage has the impact in the DOS. The electron density is found to be more at cadmium site in the left electrode. The transmission spectrum provides the insight into the transmission of electrons from valence band to conduction band across CdTe nanotube. The transmission pathway provides the visualization of electron transmission along CdTe nanotube. The results of present work provide a clear vision to tailor CdTe nanostructures with enhanced electronic property with substitution impurity for optoelectronic devices and photovoltaic cells.     

Configuration interaction studies using biorthogonal approach to VB basis

In the present article, we have attempted a systematic procedure for use of biorthogonal techniques to the configuration interaction studies in molecules using nonorthogonal valence bond (VB ) orbitals. The procedure developed is integral-driven and a program based on this has been developed. Test runs of the program have been carried out in case of full and truncated configuration spaces. © 1995 John Wiley & Sons, Inc.     

Dielectrophoresis of an inhomogeneous colloidal particle under an inhomogeneous field: a first-principles approach

In reality, colloidal particles often possess an arbitrary inhomogeneity profile. We present a first-principles approach to dielectrophoresis of such an inhomogeneous colloidal particle under an inhomogeneous field of an oscillating electric dipole moment. For numerical simulations, we treat the inhomogeneous particle as a specific graded one with a physically motivated dielectric model and conductivity profile. We find that both multipolar interactions and spatial fluctuations inside the particle can affect the dielectrophoretic spectrum of the particle significantly.     

A first-principles study on the interaction between alkyl radicals and graphene

The interaction between alkyl radicals and graphene was studied by means of dispersion-corrected density functional theory. The results indicate that isolated alkyl radicals are not likely to be attached onto perfect graphene. It was found that the covalent binding energies are low, and because of the large entropic contribution, ΔG(298)° is positive for methyl, ethyl, isopropyl, and tert-butyl radicals. Although the alkylation may proceed by moderate heating, the desorption barriers are low. For the removal of the methyl and tert-butyl radicals covalently bonded to graphene, 15.3 and 2.4?kcal mol(-1) are needed, respectively. When alkyl radicals are agglomerated, the binding energies are increased. For the addition in the ortho position and on opposite sides of the sheet, the graphene-CH(3) binding energy is increased by 20?kcal mol(-1), whereas for the para addition on the same side of the sheet, the increment is 9.4?kcal mol(-1). In both cases, the agglomeration turns the ΔG(298)°<0. For the ethyl radical, the ortho addition on opposite sides of the sheet has a negative ΔG(298)°, whereas for isopropyl and tert-butyl radicals the reactions are endergonic. The attachment of the four alkyl radicals under consideration onto the zigzag edges is exergonic. The noncovalent adsorption energies computed for ethyl, isopropyl, and tert-butyl radicals are significantly larger than the graphene-alkyl-radical covalent binding energies. Thus, physisorption is favored over chemisorption. As for the ΔG(298)° for the adsorption of isolated alkyl radicals, only the tert-butyl radical is likely to be exergonic. For the phenalenyl radical we were not able to locate a local minimum for the chemisorbed structure since it moves to the physisorbed structure. An important conclusion of this work is that the consideration of entropic effects is essential to investigate the interaction between graphene and free radicals.     

The resonance Raman spectra of spheroidene revisited with a first-principles approach

The resonance Raman (RR) spectra of different configurations of spheroidene are calculated by means of quantum chemical methods to investigate the nature of the cis configuration of this carotenoid molecule in the photosynthetic reaction center (RC) of the purple bacterium Rhodobacter sphaeroides. For validation of our methodology, we also calculate the spectrum of the all-trans structure present in the light-harvesting complexes of this bacterium. While former theoretical resonance Raman studies only considered truncated models of spheroidene, we report on calculations employing the full pigment here. The calculated frequencies for the all-trans configuration are in good agreement with former experimental and simulated data. Among the possible cis structures, the 15,15'-cis configuration shows a RR spectrum that is in best agreement with the experimental spectrum of spheroidene in the RC. In order to assess model truncation effects, we compare calculations for the full spheroidene molecule to those for the truncated model. While the main features can already be found in the latter, the full model leads to considerably different intensities in the region around 1150 cm(-1), which improve the agreement with experiment. A slight mismatch for the vibrational frequencies in the C=C stretch region is investigated by considering a model for spheroidene in the binding pocket comprising more than 500 atoms in total. The results do not lead to improved agreement with experiment, in contrast to the simpler strategy of introducing constraints in the structural optimization of a truncated spheroidene model. The calculated RR spectrum of the 13,14-cis configuration shows additional features which can also be identified in the experimental RR spectrum. This shows that the most likely cis structure is the 15,15'-cis configuration. Besides this, the 13,14-cis configuration remains a candidate for an additional spheroidene structure in the RC of Rhodobacter sphaeroides mutant R26.     

The interaction of iron pyrite with oxygen, nitrogen and nitrogen oxides: a first-principles study

Sulphide materials, in particular MoS(2), have recently received great attention from the surface science community due to their extraordinary catalytic properties. Interestingly, the chemical activity of iron pyrite (FeS(2)) (the most common sulphide mineral on Earth), and in particular its potential for catalytic applications, has not been investigated so thoroughly. In this study, we use density functional theory (DFT) to investigate the surface interactions of fundamental atmospheric components such as oxygen and nitrogen, and we have explored the adsorption and dissociation of nitrogen monoxide (NO) and nitrogen dioxide (NO(2)) on the FeS(2)(100) surface. Our results show that both those environmentally important NO(x) species chemisorb on the surface Fe sites, while the S sites are basically unreactive for all the molecular species considered in this study and even prevent NO(2) adsorption onto one of the non-equivalent Fe-Fe bridge sites of the (1 × 1)-FeS(2)(100) surface. From the calculated high barrier for NO and NO(2) direct dissociation on this surface, we can deduce that both nitrogen oxides species are adsorbed molecularly on pyrite surfaces.     

Further studies on configuration interaction in the molecular orbital theory of π-systems

The effect of triply-excited configurations on the calculated energies for sixteen electronic transitions in eleven unsaturated hydrocarbons has been investigated. The spectra were calculated using a Pariser-Parr-Pople approach modified by a variable electronegativity self-consistent field treatment. The agreement with experiment is improved, but not as dramatically as expected. The implications of these results for other types of semi-empirical calculations are discussed.

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Zusammenfassung Die Auswirkung des Einschlusses dreifach angeregter Konfigurationen auf 16 übergangsenergien von 11 ungesÄttigten Verbindungen ist untersucht worden, wobei nach einem SCF-PPP-Formalismus mit variabler ElektronegativitÄt vorgegangen wurde. Die übereinstimmung mit dem Experiment ist nur wenig besser, so da\ meist keine Notwendigkeit besteht, Anregungen des obigen Typs in die Rechnung einzuschlie\en.

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Résumé Etude de l'effet des configurations triexcitées sur les énergies calculées pour seize transitions électroniques dans onze hydrocarbures non saturés. Les spectres ont été calculés en utilisant une méthode de type Pariser-Parr-Pople modifiée par un traitement self-consistant à électronégativité variable. L'accord avec l'expérience est amélioré, mais d'une manière moins dramatique que prévu. On discute les conséquences de ces résultats pour d'autres types de calculs semi-empiriques.

     

RRS-PBC: a molecular approach for periodic systems

Technically, when dealing with a perfect crystal, methods in k-(reciprocal) space that impose periodic boundary conditions(PBC) in conjunction with plane-wave basis sets are widely used. Chemists, however, tend to think of a solid as a giant molecule, which offers a molecular way to describe a solid by using a finite cluster model(FCM). However, FCM may fail to simulate a perfect crystal due to its inevitable boundary effects. We propose an RRS-PBC method that extracts the k-space information of a perfect crystalline solid out of a reduced real space(RRS) of an FCM. We show that the inevitable boundary effects in an FCM are eliminated naturally to achieve converged high-quality band structures.     

Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

Electrolysis of water in the diffusion layer: first-principles molecular dynamics simulation

With Car-Parrinello molecular dynamics simulations the elementary reaction steps of the electrolysis of bulk water are investigated. To simulate the reactions occurring near the anode and near the cathode, electrons are removed or added, respectively. The study focuses on the reactions in pure water. Effects depending on a particular electrode surface or a particular electrolyte are ignored. Under anodic conditions, the reaction continues till molecular oxygen is formed, under cathodic conditions the formation of molecular hydrogen is observed. In addition the formation of hydrogen peroxide is observed as an intermediate of the anodic reaction. The simulations demonstrate that the electrochemistry of oxygen formation without direct electrode contact can be explained by radical reactions in a solvent. These reactions may involve the intermediate formation of ions. The hydrogen formation is governed by rapid proton transfers between water molecules.     

Coordination mode of nitrate in uranyl(VI) complexes: a first-principles molecular dynamics study

According to Car-Parrinello molecular dynamics simulations for [UO(2)(NO(3))(3)](-), [UO(2)(NO(3))(4)](2-), and [UO(2)(OH(2))(4-)(NO(3))](+) complexes in the gas phase and in aqueous solution, the nitrate coordination mode to uranyl depends on the interplay between ligand-metal attractions, interligand repulsions, and solvation. In the trinitrate, the eta(2)-coordination is clearly favored in water and in the gas phase, leading to a coordination number (CN) of 6. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, a change in free energy of +6 kcal/mol is predicted for eta(2)- to eta(1)-transition of one of the three nitrate ligands in the gas phase. In the gas phase, the mononitrate-hydrate complex also prefers a eta(2)-binding mode but with a CN of 5, one H(2)O molecule being in the second shell. This contrasts with the aqueous solution where the nitrate binds in a eta(1)-fashion and uranyl coordinates to four H2O ligands. A driving force of ca. -3 kcal/mol is predicted for the eta(2)- to eta(1)- transition in water. This structural preference is interpreted in terms of steric arguments and differential solvation of terminal vs uranyl-coordinated O atoms of the nitrate ligands. The [UO(2)(NO(3))(4)](2-) complex with two eta(2)- and two eta(1)- coordinated nitrates, observed in the solid state, is stable for 1-2 ps in the gas phase and in solution. In the studied series, the modulation of uranyl-ligand distances upon immersion of the complex in water is found to depend on the nature of the ligand and the composition of the complex.