Geometric and electronic structure and magnetic properties of Fe–Au nanoalloys: insights from ab initio calculations

Physical Chemistry Chemical Physics
We have performed density functional theory (DFT) based calculations of Fe–Au nanoalloys containing 113 atoms, FexAu113−x (x = 23, 56, 90), to determine their preferred geometric structure and the ensuing electronic structural and magnetic properties. We find that these nanoalloys prefer the formation of a core–shell structure and the Fe core maintains almost a constant magnetic moment of ∼2.8 μB regardless of the Fe content, which is 27% enhancement from the bulk value and in qualitative agreement with some previous results. The local magnetic moment of Fe atoms is well correlated with the local coordination of the Fe atoms. Furthermore, the enhancement of the magnetic moment may be traced to charge depletion from the Fe atoms in the core to the Au atoms in the shell. The preference for the core–shell structure over one with segregated Fe and Au parts could be...  Read more

Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics

Journal of Computational Chemistry
The electrophilic N-trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the SN2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with N- and S-nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar...  Read more

Electronic and Structural Elements That Regulate the Excited-State Dynamics in Purine Nucleobase Derivatives

Journal of the American Chemical Society
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited 1nπ* state. Following vibrational and conformational relaxation, the 1nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the...  Read more

Penn Algorithm Including Damping for Calculating the Electron Inelastic Mean Free Path

The Journal of Physical Chemistry C
We present an approach for introducing damping into the Penn algorithm by using the Mermin dielectric function instead of the Lindhard dielectric function. We find that for a damping of 1.5 eV, the electron inelastic mean free path calculated by the present algorithm for Al is in excellent agreement with experimental values in the energy range 5–9 eV. Meanwhile, for a damping of 2.0 eV, our result for Au is consistent with the GW+T ab initio calculation at several electronvolts. In particular, at an energy of 1 eV, our result for Au is 297 Å and lies within the range 220–330 Å obtained from measurements by ballistic electron emission microscopy.Read more

Binding of bivalent metal cations by α-L-guluronate: insights from the DFT-MD simulations

New Journal of Chemistry
The negatively charged polyuronates exhibit a high affinity for binding the bivalent metal cations. This feature is used for the removal of heavy metals from aqueous solutions. The aim of the present paper is to: (i) present the computational strategy, helpful in simulating the metal ion–uronate complexes; (ii) illustrate its applicability to the example of the α-L-guluronate anion (the monomeric unit of alginates) interacting with bivalent metal ions: Zn2+, Cu2+, Cd2+, Mn2+ and Co2+. The study was carried out on the basis of the ‘hybrid’ molecular dynamics simulations in which the selected part of the system (uronate anions and metal cations) is treated with the ab initio level of accuracy, whereas the interactions within the rest of the system are approximated by the classical force fields. The results allowed for...  Read more

An ab initio and DFT study of the autoxidation of THF and THP

Organic & Biomolecular Chemistry
Tetrahydropyran (THP) is known to undergo autoxidation much more slowly than tetrahydrofuran (THF). To investigate the difference in reactivity in the autoxidation of these two ethers, ab initio and DFT calculations were carried out. At the BHandHLYP/aug-cc-pVDZ//BHandHLYP/cc-pVDZ level of theory, the energy barrier for hydrogen abstraction from THP is predicted to be 104.1 kJ mol−1, whereas that for THF is calculated as 94.1 kJ mol−1. Including solvation effects in the calculations lowers these barriers to 98.0 (THP) and 84.4 kJ mol−1 (THF); the energy barrier for the process involving THP is smaller by 14 kJ mol−1 than that for THF. While scanning the potential energy surface for the radical coupling process between the THP (or THF) radical with molecular oxygen, an energy barrier of 11.2 kJ mol−1 (BHandHLYP/6-311G**) was found for the...  Read more

Modelling of phase diagrams of nanoalloys with complex metallic phases: application to Ni–Sn

Physical Chemistry Chemical Physics
A method for modelling of size-dependent phase diagrams was developed by combining the semiempirical CALPHAD method and ab initio calculations of surface stresses for intermetallic phases. A novel approach was devised for the calculation of surface energy, free of systematic errors from the selection of different parameters of the software (e.g. number of the k-points) and for handling layered structures and off-stoichiometric slabs. Our approach allows the determination of complex size-dependent phase diagrams of systems with intermetallic phases, which was not possible up to now. The method was verified for the modelling of the phase diagram of the Ni–Sn system and basic comparison with rare experimental results was shown. There is reasonable agreement between the calculated and experimental results. The modelling of size-dependent phase diagrams of real systems allows the prediction of phase equilibria existing in nanosystems and possible...  Read more

Structural, Magnetic, and Redox Diversity of First-Row Transition Metal Complexes of a Pyridine-Based Macrocycle: Well-Marked Trends Supported by Theoretical DFT Calculations

Inorganic Chemistry
A series of first-row transition metal complexes with 15-membered pyridine-based macrocycle (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene = L) was prepared ([MII(L)Cl2], where M = Mn, Co, Ni, Zn (1, 3, 4, 6); [FeIII(L)Cl2]Cl (2), [CuII(L)Cl]Cl (5)) and thoroughly characterized. Depending on the complexated metal atom, the coordination number varies from 7 (Mn, Fe, Co), through 5 + 2 for Ni and 4 + 1 for Cu, to 5 for Zn accompanied by changes in the coordination geometry from the pentagonal bipyramid (14) to the square pyramid (5 and 6). Along the series, the metal–oxygen distances were prolonged in such manner that their bonding character was investigated, apart from X-ray structural analysis, also by ab initio calculations (Mayer’s bond order, electron localization function), which confirmed that, in...  Read more

Investigating the Role of CH2 Radicals in the HACA Mechanism

The Journal of Physical Chemistry A
Detailed mechanisms of PAH growth involving methylene (CH2) were studied using accurate ab initio density functional theory B3LYP/6-311+G(d,p) calculations, as well as approximate QCISD(T,full)/6-311++G(3df,2pd) calculations. The PAH growth can be divided into five essential reaction steps, namely, addition C2H2 → intramolecular hydrogen migration → addition CH2 → cyclization → H-elimination. The aliphatic species of indene and 1H-phenalene are found in the pathways of PAH growth, which is in accord with the experimental results that reveal the formation of aliphatic species in flames. It was found that the simultaneous removal of two H atoms in one reaction step is feasible in PAH evolution, and this can reasonably interpret the absence of a H atom in the post-flame region. The corresponding rate coefficients at 1 atm were evaluated by using TST and RRKM theory by solving the master equations in the temperature range of 500–2500...  Read more

Molecular Determinants of Polyubiquitin Recognition by Continuous Ubiquitin-Binding Domains of Rad18

Biochemistry
Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins through its bipartite ubiquitin-binding domains UBZ and LRM with extra residues between them. Rad18 binds K63-linked polyubiquitin chains as well as K48-linked ones and monoubiquitin. However, the detailed molecular basis of polyubiquitin recognition by UBZ and LRM remains unclear. Here, we examined the interaction of Rad18(201–240), including UBZ and LRM, with linear polyubiquitin chains that are structurally similar to the K63-linked ones. Rad18(201–240) binds linear polyubiquitin chains (Ub2–Ub4) with affinity similar to that of a K63-linked one for diubiquitin. Ab initio modeling suggests that LRM and the extra residues at the C-terminus of UBZ (residues 227–237) likely form a continuous helix, termed the “extended LR motif” (ELRM). We obtained a molecular envelope for Rad18 UBZ-ELRM:linear...  Read more

Accurate Adsorption Thermodynamics of Small Alkanes in Zeolites. Ab initio Theory and Experiment for H-Chabazite

The Journal of Physical Chemistry C
Heats of adsorption of methane, ethane, and propane in H-chabazite (Si/Al = 14.4) have been measured and entropies have been derived from adsorption isotherms. For these systems quantum chemical ab initio calculations of Gibbs free energies have been performed. The deviations from the experimental values for methane, ethane, and propane are below 3 kJ/mol for the enthalpy, and the Gibbs free energy. A hybrid high-level (MP2/CBS): low-level (DFT+dispersion) method is used to determine adsorption structures and energies. Vibrational entropies and thermal enthalpy contributions are obtained from vibrational partition functions for the DFT+dispersion potential energy surface. Anharmonic corrections have been evaluated for each normal mode separately. One-dimensional Schrödinger equations are solved for potentials obtained by (curvilinear) distortions of the normal modes using a representation in internal coordinates.Read more

Ab initio modeling of single wall nanotubes folded from α- and γ-V2O5 monolayers: structural, electronic and vibrational properties

CrystEngComm
We have performed first-principles calculations to study the atomic and electronic structures of single wall nanotubes (NTs) of two possible chirality types rolled up from monolayers of α- and γ-V2O5 phases. We have used a hybrid exchange–correlation PBE0 functional within density functional theory and a basis set of localized atomic orbitals. A dispersion correction has been taken into account. All the lattice parameters and atomic positions have been totally optimized. The strain energies calculated for the nanotubes folded from the layers of both phases along the [100] direction are close to zero. This reflects the unique flexibility of the layers for folding in the [100] direction. The electronic structure of the nanotubes of both phases appeared to be similar to that of the parent layer. It was found that for both considered phases, the nanotubes of the same chirality are energetically equivalent but the shape of γ-NTs is...  Read more

Theoretical understanding of two-photon-induced fluorescence of isomorphic nucleoside analogs

Physical Chemistry Chemical Physics
We use ab initio Density Functional Theory (DFT) and Time-dependent DFT (TDDFT) calculations for a detailed understanding of one-photon absorption (1PA) and two-photon absorption (2PA) cross sections of eight different nucleoside analogs. The results are compared and contrasted with the available experimental data. Our calculated results show that the low energy peaks in the absorption spectra mainly arise because of the π–π* electronic transition of the nucleoside analogs. The emission spectra of the nucleoside analogs are also calculated using TDDFT methods. The calculated absorption and emission spectra in the presence of a solvent follow the same trend as those found experimentally. Our results demonstrate that the nucleoside analogs show significantly different electronic and optical properties, although their bonding aspects towards Watson–Crick base pairing remain the same. We also derive the microscopic details of the origin of nonlinear optical properties of...  Read more

Insights into the C–HF–C hydrogen bond by Cambridge Structural Database analyses and computational studies

RSC Advances
Fluorine bound to a carbon atom (C–F group) behaves differently than its heavier analogues. Weak interactions involving C–F groups in crystal structures have been found to be of immense interest in recent literature. Herein, a series of dimers of ethylene and fluoroethylene have been studied by an ab initio method to calculate the stabilization energy offered by weak C–HF interactions with benchmark accuracy by using a complete basis set (CBS) extrapolation technique. The model complexes have been studied in a systematic fashion to explore the structural and electronic parameters. The total interaction energies of all the complexes have been decomposed to obtain information about the nature of such interactions. Dispersion energy has been found to be the major component in the stabilization energy and C–HF...  Read more

Kinetic and mechanistic investigations of the thermal decomposition of methyl-substituted cycloalkyl radicals

RSC Advances
A systematic theoretical study on the thermal decomposition of 2-Me-cyclobutyl, 2-Me-cyclopentyl and 2-Me-cyclohexyl radicals is performed using the high-level ab initio CBS-QB3 and CCSD(T) quantum chemical calculations. The calculation reveals that the detailed reaction mechanism of the thermal decomposition of these cyclic alkyl radicals incorporates ring opening, vinyl rearrangements (exocyclization), beta-site C–C bond cleavage and H-elimination processes. The standard reaction enthalpies (ΔrH0298) and Gibbs free energies (ΔrG0298) for each elementary reaction involved in the 2-Me-cyclohexyl radical reactive system are also determined with the composite CBS-QB3 method. All the investigated vinyl rearrangements reactions are exothermic and spontaneous, while the ring opening, C–C bond scission...  Read more

Organic–Clay Interfacial Chemical Bonds Probed by ab Initio Calculations

The Journal of Physical Chemistry C
Evaluating the nature of binding of the organic phase (called kerogen) with clays and other minerals in gas and oil shale is of critical importance for developing optimal processes for hydrocarbon extraction and recovery. Here we report the results of an ab initio reactive study of a gaseous oil/clay interface, which consists of grafting fragments of sp3 methane and sp2 benzene onto the basal surface of illite. Methane and benzene fragments were selected as they correspond to the simplest monomers of the immature (aliphatic sp3 carbon atoms) and mature (aromatic sp2 carbon atoms) stages of the kerogen macromolecule while illite is encountered in many shale formations. We find that the methyl or phenyl radicals always bond upright to one of the outmost Si atoms of the clay phase, while the H atom attaches to the inner Al–OH group forming a water molecule. The covalent attachment of the radicals to the oxygen atoms of the clay surface...  Read more

Optical Resonances of Colloidal Gold Nanorods: From Seeds to Chemically Thiolated Long Nanorods

The Journal of Physical Chemistry C
Following an adapted three-step seed-mediated method, we synthesize colloidal Au thin and long (L > 100 nm) nanorods (NRs) and characterize the metallic nanostructures evolving from the initial Au nanoparticle (NPs) seeds to thiolate-functionalized NRs, using HRTEM and ultraviolet, visible, and near-infrared absorption spectroscopy (UV–vis–NIR). For the long NRs we analyze the role of several solvents and rod concentration on the spectral features of the assembled products, which are further studied with simulated spectra. Superimposed to a broad resonance in the range 700–900 nm, which corresponds to short (L < 100 nm) interacting nanorods, the growth of long nanorods is clearly identified with the emergence of a robust resonance at 960 nm, linked to the three half-wavelength antenna plasmon mode. This mode is enhanced when the nanorod concentration decreases and splits into two peaks when the thiolate coverage chemically modifies the rod surface by a thin...  Read more

Adsorption and Dissociation of H2O on Monolayered MoS2 Edges: Energetics and Mechanism from ab Initio Simulations

The Journal of Physical Chemistry C
The dissociation of water on 2D monolayer molybdenum disulfide (MoS2) edges was studied with density functional theory. The catalytically active sites for H2O, H, and OH adsorption on MoS2 edges with 0% (Mo-edge), 50% (S50-edge), and 100% (S100-edge) sulfur coverage were determined, and the Mo-edge was found to be the most favorable for adsorption of all species. The water dissociation reaction was then simulated on all edges using the climbing image nudged elastic band (CI-NEB) technique. The reaction was found to be endothermic on the S100-edge and exothermic for the S50- and Mo-edges, with the Mo-edge having the lowest activation energy barrier. Water dissociation was then explored on the Mo-edge using metadynamics biased ab initio molecular dynamics (AIMD) methods to explore the reaction mechanism at finite temperature. These simulations revealed that water dissociation can proceed by two mechanisms: the first by splitting into adsorbed OH...  Read more

Hydrated Electrons in Water Clusters: Inside or Outside, Cavity or Noncavity?

Journal of Chemical Theory and Computation
In this work, we compare the applicability of three electron–water molecule pseudopotentials in modeling the physical properties of hydrated electrons. Quantum model calculations illustrate that the recently suggested Larsen–Glover–Schwartz (LGS) model and its modified m-LGS version have a too-attractive potential in the vicinity of the oxygen. As a result, LGS models predict a noncavity hydrated electron structure in clusters at room temperature, as seen from mixed one-electron quantum–classical molecular dynamics simulations of water cluster anions, with the electron localizing exclusively in the interior of the clusters. Comparative calculations using the cavity-preferring Turi–Borgis (TB) model predict interior-state and surface-state cluster isomers. The computed associated physical properties are also analyzed and compared to available experimental data. We find that the LGS and m-LGS potentials provide results that appear to be inconsistent with the size dependence of...  Read more

Ab initio study of doping effects on LiMnO2 and Li2MnO3 cathode materials for Li-ion batteries

Journal of Materials Chemistry A
For the over-lithiated-oxides (OLOs), a composite of layered Li2MnO3 and LiMO2 (M = Mn, Co, Ni), the Li2MnO3 part is not stable after the 1st charge–discharge cycle and partly transforms into layered LiMnO2, which in practice indicates that the phase used is actually a mixture of both Li2MnO3 and LiMnO2. In the present work, the influence of 10 cationic (Mg, Ti, V, Nb, Fe, Ru, Co, Ni, Cu, and Al) and 2 anionic (N and F) dopants on the phase stability, redox potential, ionic and electronic conductivity of both Li2MnO3 and LiMnO2 is investigated in detail using density functional theory. The calculations show that all the cationic dopants and F can be thermodynamically stable in...  Read more