Kinetics of the Crystalline Nuclei Growth in Glassy Systems

Physical Chemistry Chemical Physics
In this work, we study the crystalline nuclei growth in glassy systems focusing primarily on the early stages of the process, at which the size of a growing nucleus is still comparable with the critical size. On the basis of molecular dynamics simulation results for two crystallizing glassy systems, we evaluate the growth laws of the crystalline nuclei and the parameters of the growth kinetics at the temperatures corresponding to deep supercoolings; herein, the statistical treatment of the simulation results is done within the mean-first-passage-time method. It is found for the considered systems at different temperatures that the crystal growth laws rescaled onto the waiting times of the critically-sized nucleus follow the unified dependence, that can simplify significantly theoretical description of the post-nucleation growth of crystalline nuclei. The evaluated size-dependent growth rates are characterized by transition to the steady-state growth regime, which depends on the...  Read more

Protic Ammonium Carboxylate Ionic Liquids: Insight into Structure, Dynamics and Thermophysical Properties by Alkyl Group Functionalization

Physical Chemistry Chemical Physics
This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site–site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of both the charged entities, cations and anions, on the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic...  Read more

Production of doubly-charged highly reactive species from the long-chain amino acid GABA initiated by Ar9+ ionization

Physical Chemistry Chemical Physics
We present a combined experimental and theoretical study of the fragmentation of multiply- charged γ-aminobutyric acid molecules (GABAz+, z = 2,3) in the gas phase. The combination of ab initio molecular dynamics simulations with multiple-coincidence mass spectrometry techniques allows us to observe and identify doubly-charged fragments in coincidence with another charged moiety. The present results indicate that double and triple electron capture lead to the formation of doubly-charged reactive nitrogen and oxygen species (RNS and ROS) with different probability due to the different charge localisation and fragmentation behaviour of GABA2+ and GABA3+. The MD simulations unravel the fast (femtosecond) formation of large doubly charged species, observed in the experimental microsecond timescale. The excess of positive charge is stabilised by the presence of cyclic X −member (X = 3 − 5) ring structures....  Read more

Aromatic ionene topology and counterion-tuned gelation of acidic aqueous solutions

Soft Matter
Unusual gelation of acidic solutions was achieved using polycations bearing quaternary ammonium moieties. These ionene polymers are based on a disubstituted phenylene dibenzamide core, which allows the construction of different topomers (i.e. ortho-1, meta-2 and para-3). The topology of the polymers was found to play a key role on their aggregation behaviour both in pure water and in a variety of aqueous acidic solutions leading to the formation of stable acidic gels. Specifically, ortho-1 showed superior gelation ability than the analogues meta-2 and para-3 in numerous solutions of different pH and ionic strengths. Lower critical gelation concentrations, higher gel-to-sol transition temperatures and faster gelation were usually observed for ortho-1 regardless the solvent system. Detailed computational molecular dynamic simulations revealed a major role of the counterion (Cl¯) and specific polymer···polymer interactions. In particular, hydrogen bonds, N–H···π interactions...  Read more

Bifunctionality of the pyrone functional group in oxidized carbon nanotubes towards Oxygen Reduction Reaction

Catalysis Science & Technology
Oxidised carbon nanotubes were submitted to a controlled thermal treatment at different temperatures, under N2-atmosphere. X-ray photoelectron spectroscopy confirmed the presence of acid and basic groups on the starting sample. For samples submitted to higher temperatures, only the basic oxygen functional groups remained on the surface, namely quinone and pyrone groups. The oxygen reduction reaction (ORR) performance of all electrocatalysts was evaluated under alkaline medium in O2-saturated solutions. Increasing the basic character leads to a better ORR activity in terms of potential onset values (from -0.230 to -0.194 V). Two well-defined cathodic peaks associated to the reduction of oxygen are observed on the cyclic voltammograms when the acid oxygen groups are removed from the electrocatalyst surface. The computational simulations of a carbon surface functionalized with quinone and pyrone groups were a relevant tool to explain...  Read more

Delineation of Disease Phenotypes Associated with Esophageal Adenocarcinoma by MALDI-IMS-MS Analysis of Serum N-linked Glycans

N-linked glycans, extracted from patient sera and healthy control individuals, are analyzed by Matrix-assisted laser desorption ionization (MALDI) in combination with ion mobility spectrometry (IMS), mass spectrometry (MS) and pattern recognition methods. MALDI-IMS-MS data were collected in duplicate for 58 serum samples obtained from individuals diagnosed with Barrett’s esophagus (BE, 14 patients), high-grade dysplasia (HGD, 7 patients), esophageal adenocarcinoma (EAC, 20 patients) and disease-free control (NC, 17 individuals). A combined mobility distribution of 9 N-linked glycans is established for 90 MALDI-IMS-MS spectra (training set) and analyzed using a genetic algorithm for feature selection and classification. Two models for phenotype delineation are subsequently developed and as a result, the four phenotypes (BE, HGD, EAC and NC) are unequivocally differentiated. Next, the two models are tested against 26 blind measurements. Interestingly, these models allowed for the...  Read more

Spacer length dependent architectural diversity in bis-dipyrrin copper(II) complexes

Dalton Transactions
A series of copper(II) complexes (1-9 and 3') derived from bis-dipyrrin ligands (L1-L9 and L3′) with diverse spacer lengths [-(CH2)n-] have been described. Structural diversity in these complexes have been explicitly established by spectral and structural studies on these and a closely related nickel(II) complex (3ʺ). All the ligands and complexes have been thoroughly characterized by spectroscopic studies (ESI-MS, IR, 1H, 13C NMR, UV/vis) and structures of 2, 3', 3ʺ, 6, 8 and 9 determined by X-ray single crystal analyses. It has been unambiguously established that ligands with n < 6 gave heteroleptic binuclear (1-5), while those with n > 7 yielded homoleptic mononuclear (69) bis-dipyrrinato complexes. Spectral and structural studies revealed distorted square planer (1-5) and distorted tetrahedral geometry (69) about the copper(II) centre in these complexes which has further been evidenced by EPR and electrochemical studies. Structural differences based on odd and even...  Read more

FDHALO17: The 15N NMR chemical shift in the characterization of weak halogen bonding in solution

Faraday Discussions
We have studied the applicability of 15N NMR spectroscopy in the characterisation of the very weak halogen bonds of nonfluorinated halogen bond donors with a nitrogeneous Lewis base in solution. The ability of the technique to detect the relative strength of iodine-, bromine- and chlorine-centered halogen bonds, as well as solvent and substituent effects was evaluated. Whereas computations on the DFT level indicate that 15N NMR chemical shifts reflect the diamagnetic deshielding associated with the formation of a weak halogen bond, the experimentally observed chemical shift differences were on the edge of detectability due to the low molar fraction of halogen-bonded complexes in solution. The formation of the analogous yet stronger hydrogen bond of phenols have induced approximately ten times larger chemical shift changes, and could be detected and correlated to the electronic properties of substituents of the hydrogen bond donors....  Read more

Thermochemical CO2 splitting using double perovskite-type Ba2Ca0.66Nb1.34−xFexO6−δ

Journal of Materials Chemistry A
A carbon-neutral fuel is desired when it comes to solving the issues associated with climate change. A smart approach would be to develop new materials to produce such fuels, which could be integrated with renewables to improve the efficiency (e.g., solid oxide fuel cells (SOFCs) in smart grid and concentrated solar fuel technologies). In this study, we report the utilization of nonstoichiometric perovskite oxides, Ba2Ca0.66Nb1.34−xFexO6−δ (BCNF) (0 ≤ x ≤ 1), to split CO2 into carbon, carbon monoxide, and oxygen at elevated temperatures. Powder X-ray diffraction shows the chemical stability of double perovskite-type BCNF after being exposed to 2000 ppm CO2 in Ar at 700 °C. Furthermore, all x ≤ 0.66 BCNF members exhibit high chemical...  Read more

Predicting protein lysine phosphoglycerylation sites by hybridizing many sequence based features

Molecular BioSystems
Post-translational modification (PTM) is essential for many biological processes. Covalent and generally enzymatic modification of proteins can impact the activity of proteins. Modified proteins would have more complex structures and functions. Knowing whether a specific residue is modified or not is significant to ravel out the function and structure of this protein. As experimental approaches to discover protein PTM sites are always costly and time consuming, computational prediction methods are desired as alternative methods. Lysine phosphoglycerylation is a type of newly-discovered PTM that is related to glycolytic process and glucose metabolism. Since the lysine phosphoglycerylation process requires no catalytic enzyme, its site selectivity mechanism is still not fully understood. In this study, we designed a novel computational method, namely PhoglyPred, to identify lysine phosphoglycerylation sites. By utilizing several different protein sequence descriptors, PhoglyPred...  Read more

A Systematic Reconstruction and Constraint-based Analysis of Leishmania donovani Metabolic Network: Identification of Potential Antileishmanial Drug Targets

Molecular BioSystems
Visceral leishmaniasis, a lethal parasitic disease, is caused by protozoan parasite Leishmania donovani. Absence of effective vaccine, drug toxicity and parasite resistance necessitates the identification of novel drug targets. Reconstruction of genome-scale metabolic models and its simulation has been established as an important tool for systems-level understanding of microorganism’s metabolism. In this work, amalgamating the tools and techniques of computational systems biology with rigorous manual curation, a constraint-based metabolic model for Leishmania donovani BPK282A1 has been developed. New functional annotations for 18 formerly hypothetical or erroneously annotated genes (encountered during iterative refinement of the model) have been proposed. Further, to formulate an accurate biomass objective function, experimental determination of previously uncharacterized biomass constituents was performed. The developed model is a highly compartmentalized metabolic model,...  Read more

Interface Engineering for a Rational Design of Poison-free Bimetallic CO Oxidation Catalysts

We use density functional theory calculations of Pt@Cu core@shell nanoparticles (NPs) to design of a bifunctional poison-free CO oxidation catalysts. By calculating the adsorption chemistry under CO oxidation conditions, we find that the Pt@Cu NPs will be active for CO oxidation with resistance to CO-poisoning. The CO oxidation pathway at the Pt-Cu interface is determined on the Pt NP covered with a full- and partial-shell of Cu. The exposed portion of the Pt core preferentially binds CO and the Cu shell binds O2, supplying oxygen for the reaction. The Pt-Cu interface provides CO-oxidation sites that are not poisoned by either CO or O2. Additional computational screening shows that this separation of reactant binding sites is possible for several other core@shell NPs. Our results indicate that the metal-metal interface within a single NP can be optimized for design of bifunctional catalytic...  Read more

A New Heterostructured SERS Substrate: Free-standing Silicon Nanowires Decorated with Graphene-encapsulated Gold Nanoparticles

Heterostructures of one-dimensional nanowires supported graphene/plasmonic nanoparticles are promising for future SERS-based chemical sensors. In this paper, we report a novel heterostructured SERS substrate composed of free-standing Si nanowires and surface-decorating Au/graphene nanoparticles. We successfully developed a unique CVD approach for the cost-effective and large-scale growth of free-standing Si nanowires. Au nanoparticles were decorated on the Si nanowires using a galvanic deposition – annealing approach. This was followed by the selective growth of multilayer graphene shell on the Au nanoparticles via a xylene-based CVD approach. Discrete Dipole Approximation simulation was used to understand the plasmonic properties of These Si nanowire-based heterostructures. The results indicate the incorporation of Au nanoparticles and graphene on Si nanowires has a significant influence on their light absorption and scattering properties. Meanwhile, strong surface plasmon coupling...  Read more

Interior-filled Self-assemblies of Tyrosyl Bolaamphiphiles Regulated by Hydrogen Bonds

Physical Chemistry Chemical Physics
Bolaamphiphilic molecules with tyrosyl end groups formed interior-filled spherical self-assemblies, which are distinct from the vesicular or tubular structures of other similar peptidic bolaamphiphile assemblies reported in the literature. In this study, the self-assembly mechanism of these tyrosyl bolaamphiphiles was investigated taking into consideration the solvent effects on the molecular interaction forces using molecular modeling. The dissipative particle dynamics simulation of an aqueous tyrosyl bolaamphiphile solution suggested that the interior-filled assemblies were produced by a solvent-regulated assembly of small aggregates of bolaamphiphiles. These small aggregates were generated by hydrophobic interactions at an early stage, and then further assembled to form large spherical assemblies through intermolecular forces, including hydrogen bonds between the intermediate aggregates. Additional experiments and density functional theory calculations based on solvent variations...  Read more

Effects of orientation at the phthalocyanine–CdSe interface on the electron transfer characteristics

Physical Chemistry Chemical Physics
Phthalocyanine molecule adsorbed on the (101 @#x0305;0) surface of wurtzite CdSe is theoretically modeled by DFT method. We have found that linker does not affect substantially redox properties of phthalocyanine, while saturation of the macrocycle with peripheral substituent groups causes downward shift in the energy position of its frontier orbitals that can hinder electron injection to the CdSe surface. Tilting of the phthalocyanine molecule to the surface also leads to the lowering of its molecular electronic levels relative to the bands of CdSe. At tilting angle of 30°, the LUMO level of the dye appears to be lower than the conduction band minimum of cadmium selenide, which makes unfavorable the electron transfer to its hybridized surface. By contrast, the HOMO level of the phenylbutyric acid linker provides a suitable intermediate channel for the hole transfer from the valence band of CdSe to the phthalocyanine that points to the possible acceptor behavior of the phthalocyanine...  Read more

Structural and Dynamical instability of DNA by high occurrence of d5SICS and dNaM unnatural nucleotides

Physical Chemistry Chemical Physics
In vivo inclusion of unnatural base pairs (UBPs) into functional DNA was recently reported for compounds 2,6-dimethyl-2H-isoquiniline-1-thione (d5SICS, X) and 2-methoxy-3-methylnaphthalene (dNaM, Y) in a modified E. coli strand, for which high fidelity replication was observed. Yet, little is known about possible genetic consequences they have in largely substituted DNA. Using a converged microsecond long molecular dynamics (MD) simulation of the sequences 5’-GCGCAAXTTGCGC-3’ and 5’-GCGCXAXTXGCGC-3’, where X represents the UBP, we show that in the system with only a single XY UBP pair present, the global RMS deviation from canonical B-DNA in our control simulations is ~3 Å and a fully converged ensemble is achieved within 2 µs. With three UBPs, deviation increases to ~5 Å and convergence is not achieved within 10 µs of sampling time. With five UBPs no convergence is observed and the double helix collapses into a globular structure. A fully optimized structure of the trimer...  Read more

Impact of graphyne on structural and dynamical properties of calmodulin

Physical Chemistry Chemical Physics
Carbon-based nanomaterials such as graphyne, graphene, and carbon nanotubes have attracted considerable attention for their applications, but questions remain regarding their biosafety through potential adverse interactions with important biomolecules. Here, we investigate the binding of a graphyne nanosheet and a graphyne quantum dot to calmodulin (CaM), a dynamic Ca2+binding protein. Simulation results show that both the graphyne nanosheet and graphyne quantum dot are able to bind both Ca2+-bound and Ca2+-free CaM with similar binding affinities. From our simulations, graphyne quantum dots appear particularly worrisome for potential toxicity as they bind to and occlude the hydrophobic binding pocket of both Ca2+-bound and Ca2+-free CaM. In both the nanosheet and quantum dot systems, the binding interactions between graphyne and CaM are markedly hydrophobic and heavily suppress the Ca2+-free CaM dynamics. Our results reiterate that graphitic nanomaterials including graphyne may have...  Read more

Evaporation Induced Nanoparticle – Binder Interaction in Electrode Film Formation

Physical Chemistry Chemical Physics
Processing induced nanoparticle agglomeration and binder distribution affect the electrode microstructure formation and corresponding electrochemical performance in lithium-ion batteries. In the present study, stochastic dynamics computations based on a morphologically detailed mesoscale model are performed to illustrate the microstructural variability of electrode films affected by the evaporation condition (drying temperature) and the binder length (molecular weight). Micropores are observed at the surface of the electrode film when dried at a lower temperature. The pore formation depth tends to increase as the binder length increases. The solvent chemical potential also affects the surface topography of the electrode film. The solvent with higher volatility (more negative chemical potential) tends to produce more micropores. A lower drying temperature is beneficial for improving the electronic conductivity of the porous electrode film due to the better distribution of the...  Read more

Delineating the role of ripples on thermal expansion of 2D honeycomb materials: graphene, 2D h-BN and monolayer (ML)-MoS2

Physical Chemistry Chemical Physics
We delineated the role of thermally excited ripples on thermal expansion properties of 2D honeycomb materials (free-standing graphene, 2D h-BN, and ML-MoS2), by explicitly carrying out three-dimensional (3D) and two-dimensional (2D) molecular dynamics simulations. In 3D simulations, the in-plane lattice parameter (a-lattice) of graphene and 2D h-BN shows thermal contraction over a wide range of temperatures and exhibits a strong system size dependence. The 2D simulations of the very same system show a reverse trend, where the a-lattice is expanding in the whole computed temperature range. Contrary to graphene and 2D h-BN, the a-lattice of ML-MoS2 shows thermal expansion in both 2D and 3D simulations and their system size dependence is marginal. By analyzing the phonon dispersion at 300 K, we found that the discrepancy between 2D and 3D simulations of graphene and 2D h-BN is due to the absence of out-of-plane bending mode (ZA) in 2D simulations, which is responsible for thermal...  Read more

Electron-triggered chemistry in HNO3/H2O complexes

Physical Chemistry Chemical Physics
Polar stratospheric clouds, which consist mainly of nitric acid containing ice particles, play a pivotal role in stratospheric chemistry. We investigate mixed nitric acid-water clusters (HNO3)m(H2O)n, m ≈ 1-6, n ≈ 1-15, in a laboratory molecular beam experiment using electron attachment and mass spectrometry and interpret our experiments with DFT calculations. The reactions are triggered by the attachment of free electrons (0-14 eV) which leads to subsequent intracluster ion-molecule reactions. In these reactions, the nitrate anion NO3 turns out to play the central role. This contradicts the electron attachment to the gas-phase HNO3 molecule, which leads almost exclusively to NO2. The nitrate containing...  Read more