Structure and stability of CaH2 surfaces: on the possibility of electron-rich surfaces in metal hydrides for catalysis

Journal of Materials Chemistry A
Structure, thermodynamic stability, and electronic properties of CaH2 surfaces in (001), (110), and (111) crystallographic orientations are investigated using ab initio modeling. We show that stoichiometric surfaces terminated with a hydrogen atomic plane are the most energetically favorable and discuss properties of hydrogen vacancies (VH) at these surfaces. The average calculated work function of the most stable pristine surfaces (∼5.2 eV) is in agreement with experimental data for powder samples. Neutral hydrogen vacancies host localized electrons and induce defect states in the band gap, thereby shifting the effective work function to much lower values of ∼2.7 eV. Surface VH are predicted to aggregate into dimers and form electron-rich centers (e)Ca2+(e) stable to over 800 K. These results suggest that...  Read more

Imaging rotations and vibrations in polyatomic molecules with X-ray scattering

Physical Chemistry Chemical Physics
An approach for calculating elastic X-ray scattering from polyatomic molecules in specific electronic, vibrational, and rotational states is presented, and is used to consider the characterization of specific states in polyatomic molecules using elastic X-ray scattering. Instead of the standard independent atom model (IAM) method, the X-ray scattering is calculated directly from ab initio wavefunctions. The role of molecular symmetry and Friedel's law is examined, with the molecules BF3, C5H5, NF3, and 1,3-cyclohexadiene used as specific examples. The contributions to the elastic X-ray scattering from the electronic, vibrational, and rotational portions of the molecular wavefunction are examined in CS2. In particular, it is observed that the rotational states give rise to distinct signatures in the scattering signal.Read more

Models for biomedical interfaces: a computational study of quinone-functionalized amorphous silica surface features

Physical Chemistry Chemical Physics
A density functional theory (PBE functional) investigation is carried out, in which a model of an amorphous silica surface is functionalized by ortho-benzoquinone. Surface functionalization with catechol and quinone-based compounds is relevant in biomedical fields, from prosthetic implants to dentistry, to develop multifunctional coatings with antimicrobial properties. The present study provides atomistic information on the specific interactions between the functionalizing agent and the silanol groups at the silica surface. The distinct configurations of the functional groups, the hydrogen bond pattern, the role of dispersion forces and the simulated IR spectra provide detailed insight into the features of this model surface coating. Ab initio molecular dynamics gives further insights into the mobility of the functionalizing groups. As a final step, we studied the condensation reaction with allylamine, via Schiff base formation, to ground subsequent...  Read more

Graphene flakes obtained by local electro-exfoliation of graphite with a STM tip

Physical Chemistry Chemical Physics
Graphite surfaces can be manipulated by several methods to create graphene structures of different shapes and sizes. Scanning tunneling microscopy (STM) can be used to create these structures either through mechanical contact between the tip and the surface or through electro-exfoliation. In the latter, the mechanisms involved in the process of exfoliation at an applied voltage are not fully understood. Here, we show how a graphite surface can be locally exfoliated in a systematic manner by applying an electrostatic force with a STM tip at the edge of a terrace, forming triangular flakes several nanometers in length. We demonstrate, through experiments and simulations, how these flakes are created by a two-step process: first a voltage ramp must be applied at the edge of the terrace, and then the tip must be scanned perpendicular to the edge. Ab initio electrostatic calculations reveal that the presence of charges on the graphite surface weakens the interaction between layers...  Read more

A velocity map imaging study of the photodissociation of the methyl iodide cation

Physical Chemistry Chemical Physics
The photodissociation dynamics of the methyl iodide cation has been studied using the velocity map imaging technique. A first laser pulse is used to ionize methyl iodide via a (2 + 1) REMPI scheme through the 5pπ → 6p Rydberg state two-photon transition. The produced CH3I+([X with combining tilde]2E3/2) ions are subsequently excited at several wavelengths between 242 and 260 nm. The reported translational energy distributions for the methyl and iodine ions present a Boltzmann-type unstructured distribution at low excitation energies as well as a recoiled narrow structure at higher excitation energies highlighting two different dissociation processes. High level ab initio calculations have been performed in order to obtain a deeper understanding of the photodissociation dynamics...  Read more

Prediction of thermodynamically stable Li–B compounds at ambient pressure

Physical Chemistry Chemical Physics
To clarify controversial structures and phase stability in the Li–B system, we predicted energetically favorable compounds and crystal structures of the Li–B binary system at ambient pressure, mainly including Li6B5, LiB2, and LiB3, from ab initio evolutionary structure simulations and further investigated physical properties of stable Li–B compounds using first-principles methods. Metallic Li6B5, predicted in our simulations, has trigonal symmetry with space group R32 and contains linear B chains, but its superconducting Tc is low according to the electron–phonon coupling calculations. Orthorhombic LiB2 (Pnma) and tetragonal LiB3 (P4/mbm) are zero-gap semiconductors;...  Read more

An insight into methanol oxidation mechanisms on RuO2(100) under an aqueous environment by DFT calculations

Physical Chemistry Chemical Physics
In this work, we have studied methanol oxidation mechanisms on RuO2(100) by using density functional theory (DFT) calculations and ab initio molecular dynamics (MD) simulations with some explicit interfacial water molecules. The overall mechanisms are identified as: CH3OH* → CH3O* → HCHO* → HCH(OH)2* → HCHOOH* → HCOOH* → mono-HCOO* → CO2*, without CO formation. This study provides a theoretical insight into C1 molecule oxidation mechanisms at atomic levels on metal oxide surfaces under an aqueous environment.Read more

The staging mechanism of AlCl4 intercalation in a graphite electrode for an aluminium-ion battery

Physical Chemistry Chemical Physics
Identifying a suitable electrode material with desirable electrochemical properties remains a primary challenge for rechargeable Al-ion batteries. Recently an ultrafast rechargeable Al-ion battery was reported with high charge/discharge rate, (relatively) high discharge voltage and high capacity that uses a graphite-based cathode. Using calculations from first-principles, we have investigated the staging mechanism of AlCl4 intercalation into bulk graphite and evaluated the stability, specific capacity and voltage profile of AlCl4 intercalated compounds. Ab initio molecular dynamics is performed to investigate the thermal stability of AlCl4 intercalated graphite structures. Our voltage profiles show that the first AlCl4 intercalation step could be a more sluggish step than the successive intercalation steps. However, the diffusion of AlCl4 is very...  Read more

Computational study of phononic resonators and waveguides in monolayer transition metal dichalcogenides

Physical Chemistry Chemical Physics
Using molecular dynamics and semi-empirical potentials, large scale transition metal dichalcogenides monolayers (TMDM) were examined. The focus of the study was the modification of the phonon spectrum of TMDMs by engineering substitutional defects to produce phononic resonators and waveguides on the atomic scale. The resonant frequencies of the aforementioned structures can be tuned by applying tensile or compressive stresses. The TMDMs exhibited wide phononic band gaps (PBG) in their phonon spectrum because they consist of atoms with quite different atomic masses. The PBG from the present semi-empirical calculations were found to be in reasonable agreement with previous ab initio calculations. The problem is very broad since many varieties of TMDMs (with or without defects) can be made. The present study focused on MX2 composites with M being Mo or W and X being S or Se. The most interesting behavior was found in WS2 with...  Read more

Ab initio study of aspirin adsorption on single-walled carbon and carbon nitride nanotubes

Physical Chemistry Chemical Physics
Using density functional theory, we investigate the adsorption properties of acetylsalicylic acid (aspirin) on the outer surfaces of a (10,0) carbon nanotube (CNT) and a (8,0) triazine-based graphitic carbon nitride nanotube (CNNT). The adsorption energies for the CNNT and CNT are 0.67 and 0.51 eV, respectively, and hence, the aspirin molecule binds more strongly to the CNNT. The stronger adsorption energy for the binding to the CNNT is ascribed to the high reactivity of its nitrogen atoms with high electron affinity. The CNNT exhibits local electric dipole moments that cause strong charge redistribution in the adsorbed aspirin molecule. The influence of an external electric field on the adsorption of aspirin on the nanotubes is explored by examining modifications in their electronic band structures, partial densities of states, and charge distributions. An electric field applied along a particular direction is found to induce molecular states of aspirin that lie within the in-gap...  Read more

Theoretical study of HCN–water interaction: five dimensional potential energy surfaces

Physical Chemistry Chemical Physics
A new five-dimensional potential energy surface is calculated at the coupled-cluster CCSD(T) level of theory for the HCN–water system, treating both monomers as rigid rotors. The associated methodology, which combines extensive ab initio calculations of moderate accuracy (CCSD(T)/AVDZ) and a fitting procedure involving a much lower angular coverage with more accurate ab initio calculations (CCSD(T)/CBS), is described in detail. This methodology provides a time-saving approach to compute quantitatively accurate potential energy surfaces with reasonable computational effort. Our potential reproduces the main features reported in the literature, and will allow us to perform the first quantum and semi-classical simulations of the collisional dynamic on this system.Read more

Synthesis, structural studies and stability of model cysteine containing DNA–protein cross-links

New Journal of Chemistry
DNA–protein cross-links (DPCs) are bulky, helix-distorting lesions that are formed upon irreversible bonding of proteins to chromosomal DNA in the presence of cross-linking agents. Among a broad range of such agents are α,β-unsaturated carbonyl compounds, which act essentially as bifunctional alkylating agents and form adducts with DNA bases. These adducts can further undergo interactions with other cellular macromolecules leading to the formation of cross-linked products. We synthesized and structurally characterized N-acetylcysteine cross-links formed in the reactions with aldehydic adducts of adenine nucleosides, which possess enol functionality and represent model α,β-unsaturated carbonyl systems. Studies performed by the use of NMR spectroscopy, DFT and ab initio methods established that two of these cross-links exist as rotamers stable at room temperature. Application of Atoms in Molecules Theory enabled hydrogen bonding and other stabilizing interactions...  Read more

Rovibrational Spectroscopic Constants of the Interaction between Ammonia and Metallo-Phthalocyanines: A Theoretical Protocol for Ammonia Sensor Design

Physical Chemistry Chemical Physics
In the present contribution, we develop an adapted theoretical approach based on DFT calculations (B3LYP functional) and solution of the nuclear Schrödinger equation by using the Discrete Variable Representation method to model the interaction of ammonia with metallo-phthalocyanines (MPcs, where M = Fe2+, Co2+, Ni2+, Cu2+ or Zn2+). This approach is intended to be a general protocol for the rational design of chemical sensors. The as-obtained binding energy curves, obtained from ab initio points, permitted us to calculate rovibrational energies and spectroscopic constants, as well as to establish the relative population of rovibrational states in different types of MPc-NH3 thermodynamic systems. Simulated binding energy curves show that the binding energy in MPc-NH3 systems is dependent on the type-M central ion in this decreasing order: FePc>ZnPc>CoPc>CuPc>NiPc, with values spanning from -170 to -16 kJ·mol-1. Also, MPc-NH3 systems have at least 16 rovibrational levels,...  Read more

Atomically-resolved edge states on surface-nanotemplated graphene explored at room temperature

Nanoscale
Graphene edges present localized electronic states strongly depending on their shape, size and border configuration. Chiral- or zigzag-ended graphene nanostructures develop spatially and spectrally localized edge states around the Fermi level; however, atomic scale investigations of such graphene terminations and their related electronic states are very challenging and many of their properties remain unexplored. Here we present a combined experimental and theoretical study on graphene stripes showing strong metallic edge states at room temperature. By means of scanning tunneling microscopy, we demonstrate the use of vicinal Pt(111) as a template for the growth of graphene stripes and characterize their electronic structure. We find the formation of a sublattice localized electronic state confined on the free-standing edges of the graphene ribbons at energies close to the Fermi level. These experimental results are reproduced and understood with tight-binding and ab initio...  Read more

Adsorption dynamics of molecular nitrogen at an Fe(111) surface

Physical Chemistry Chemical Physics
We present an extensive theoretical study of N2 adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N2 adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states. Our QCT calculations confirm that there are activated and nonactivated paths for the adsorption of N2 on the Fe(111) surface, which is in agreement with previous experimental investigations. Molecular dynamics at a surface temperature Ts = 300 K...  Read more

Dihydrogen intermolecular contacts in group 13 compounds: H⋯H or E⋯H (E = B, Al, Ga) interactions?

Dalton Transactions
A systematic theoretical analysis of homopolar dihydrogen interactions in group 13 compounds is presented here. Ab initio calculations and structural analysis allow us to demonstrate that interactions involving B–H⋯H–B contacts are comparable in strength to the previously studied C–H⋯H–C ones, yet attractive and important for the stabilization of dimers of large molecules. We have also shown that a polyhedral skeleton enhances the B–H⋯H–B interaction strength with respect to non-polyhedral compounds, and it has also been proven that Al–H⋯H–Al and Ga–H⋯H–Ga interactions can be attractive in some cases. If H⋯E (B, Al and Ga) short contacts are present, the interaction is significantly strengthened, especially for Al and Ga. In general, H⋯H interactions combined with associated H⋯E (B, Al and Ga) short contacts are responsible for the stability of a large number of dimers of group 13 compounds and may play an important role in the packing of...  Read more

A combined high-temperature experimental and theoretical kinetic study of the reaction of dimethyl carbonate with OH radicals

Physical Chemistry Chemical Physics
The reaction kinetics of dimethyl carbonate (DMC) and OH radicals were investigated behind reflected shock waves over the temperature range of 872–1295 K and at pressures near 1.5 atm. Reaction progress was monitored by detecting OH radicals at 306.69 nm using a UV laser absorption technique. The rate coefficients for the reaction of DMC with OH radicals were extracted using a detailed kinetic model developed by Glaude et al. (Proc. Combust. Inst. 2005, 30(1), 1111–1118). The experimental rate coefficients can be expressed in Arrhenius form as: kexpt'l = 5.15 × 1013 exp(−2710.2/T) cm3 mol−1 s−1. To explore the detailed chemistry of the DMC + OH reaction system, theoretical kinetic analyses were performed using high-level ab initio and master equation/Rice–Ramsperger–Kassel–Marcus...  Read more

The molecular mechanism of the ligand exchange reaction of an antibody against a glutathione-coated gold cluster

Nanoscale
The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double SN2-like reaction mechanism, involving a proton transfer, with low activation barriers only if one of the two distinct peptide/peptidic ligands (the one that occupies the side position) is substituted. Positively charged residues in the vicinity of the incoming thiol result in strong interactions between the antibody and the AuMPC, favoring the ligand exchange reaction for suitable protein mutants. These results pave the way for future investigations aimed at engineering biomolecules to increase their reactivity towards a desired gold atom cluster.Read more

2D MoS2/polyaniline heterostructures with enlarged interlayer spacing for superior lithium and sodium storage

Journal of Materials Chemistry A
The exploitation of high-capacity and long-life MoS2-based materials is highly important for developing lithium ion batteries (LIBs) and sodium ion batteries (SIBs). Herein, we demonstrate the confined synthesis of 2D MoS2/polyaniline (MoS2/PANI) nanosheet heterostructures with well-defined interfaces, in which the interlayer distance of MoS2 is greatly enlarged from 0.62 nm to 1.08 nm. The introduction of such a big interlayer distance for efficient Li+/Na+ storage has never been demonstrated before. The unique MoS2/PANI nanosheets can address well the key challenges of traditional MoS2 anode materials related to low conductivity particularly in the vertical direction, easy restacking/aggregation, large volumetric change and sluggish...  Read more

Structural Insights into a Hemoglobin–Albumin Cluster in Aqueous Medium

The Journal of Physical Chemistry Letters
A hemoglobin (Hb) wrapped covalently by three human serum albumins (HSAs) is a triangular protein cluster designed as an artificial O2-carrier and red blood cell substitute. We report the structural insights into this Hb-HSA3 cluster in aqueous medium revealed by 3D reconstruction based on cryogenic transmission electron microscopy (cryo-TEM) data and small-angle X-ray scattering (SAXS) measurements. Cryo-TEM observations showed individual particles with approximately 15 nm diameter in the vitrified ice layer. Subsequent image processing and 3D reconstruction proved the expected spatial arrangements of an Hb in the center and three HSAs at the periphery. SAXS measurements demonstrated the monodispersity of the Hb-HSA3 cluster having a molecular mass of 270 kDa. The pair-distance distribution function suggested the existence of oblate-like particles with a maximum dimeter of ∼17 nm. The supramolecular 3D structure reconstructed from the SAXS intensity...  Read more