Density functional theory studies of the adsorption of hydrogen sulfide on aluminum doped silicane

First principles total energy calculations have been performed to study the hydrogen sulfide (H₂S) adsorption on silicane, an unusual one monolayer of Si(111) surface hydrogenated on both sides. The H₂S adsorption may take place in dissociative or non-dissociative forms. Silicane has been considered as: (A) non-doped with a hydrogen vacancy, and doped in two main configurations; (B) with an aluminum replacing a hydrogen atom and (C-n; n?=?1, 2, 3) with an aluminum replacing a silicon atom at a lattice site. In addition, three supercells; 4x4, 3x3 and 2x2 have been explored for both non-doped and doped silicane. The non-dissociative adsorption takes place in geometries (A), (C-1), (C-2) and (C-3) while the dissociative in (B). Adsorption energies of the dissociative case are larger than those corresponding to the non-dissociated cases. In the dissociative adsorption, the molecule is fragmented in a HS structure and a H atom which are bonded to the aluminum to form a H-S-Al-H structure. The presence of the doping produces some electronic changes as the periodicity varies. Calculations of the total density of states (DOS) indicate that in most cases the energy gap decreases as the periodicity changes from 4x4 to 2x2. The features of the total DOS are explained in terms of the partial DOS. The reported charge density plots explain quite well the chemisorptions and physisorptions of the molecule on silicane in agreement with adsorption energies.     

First principles studies of the graphene-phenol interactions

Studies of the interaction between phenol and intrinsic graphene, as well as phenol and aluminum doped graphene layer are performed using first principles total energy calculations within the periodic density functional theory. A 4x4 periodic structure is used to explore the adsorption of a phenol molecule on the intrinsic graphene and on aluminum doped graphene layer. The electron-ion interactions are modeled using ultra-soft pseudo-potentials, and the exchange-correlation energies are treated according to the generalized gradient approximation (GGA) with the PBE parameterization. We consider different molecule orientations: parallel and perpendicular to the graphene layer to relax the atomic structure. To explain the optimized atomic geometry we determine binding energies for all cases and the density of states (DOS) and partial DOS for the most relevant configurations. Results indicate that the direct interaction of oxygen with aluminum yields the ground state geometry with the phenol molecule adsorbed on the graphene layer. Binding energies and DOS structures also demonstrate that the ground state configuration is that where the O and Al atoms interact with a separation distance of 1.97 ?.     

Interaction of photosynthetic pigments with various organic solvents 2. Application of magnetic circular dichroism to bacteriochlorophyll a and light-harvesting complex 1

Magnetic circular dichroism (MCD) and absorption spectra of metal bacteriochlorin complexes have been measured on bacteriochlorophyll (BChl) a in various solvents and different forms of light-harvesting complexes 1 (LH1 complexes). In hydrophilic organic solvents, the MCD intensity of the Q(y)(0-0) transition of BChl a was sensitive to the wavelength of absorption maximum of Q(x)(0-0), and the ratio of MCD Q(y)(0-0) intensity to the dipole strength (B/D) was inversely proportional to the difference in energy between the Q(x)(0-0) and Q(y)(0-0). The similar correlation has been observed in metal chlorin derivatives as previously reported. The correlation depends on the coordination number of the Mg atom in BChl a and the molecules ligating to it. In a hydrophobic solvent such as carbon tetrachloride (CCl(4)), however, the correlation did not hold because of the existence of aggregates. Hence, the correlation between the values of B/D and the energy difference can be used to estimate the type and number of the molecules ligated to the Mg atom and to disclose the existence of aggregated pigments. We further apply the correlation to the LH 1 complex treated with n-octyl beta-D-glucopyranoside.     

2D Crystals Significantly Enhance the Performance of a Working Fuel Cell

2D atomic crystals such as single layer graphene (SLG) and hexagonal boron nitride (hBN) have been shown to be “unexpectedly permeable” to hydrogen ions under ambient conditions with the proton conductivity rising exponentially with temperature. Here, the first successful addition of SLG made by a chemical vapor deposition (CVD) method is shown to an operational direct methanol fuel cell significantly enhancing the performance of the cell once the temperature is raised above 60 °C, the temperature at which the proton conductivity of SLG is higher than the Nafion membrane on which it is mounted. Above this temperature, the resistance to proton transport of the system is not affected by the graphene but the barrier properties of graphene inhibit methanol crossover. The performance of the fuel cell is shown to increase linearly with coverage of SLG above this temperature. Results show that the maximum power density is increased at 70 °C by 45% in comparison to the standard membrane electrode assembly without graphene. In addition, a membrane with CVD hBN shows enhanced performance across the entire temperature range due to better proton conductivity at lower temperatures.     

Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus

The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.     

QSAR of aromatic substances: EGFR inhibitory activity of quinazoline analogues

The flip regression procedure that we used earlier for handling the xanthones system has been applied to phenylaminoquinazoline analogues. It is known that the substituents at the 6- and 7- positions of the polycyclic system have been identified as the most important structural features. The steric as well as the electrostatic interactions proved to be the most important for the inhibitory effect. In this contribution it is shown that the orientation of nodes in their occupied pi orbitals, and also the energies of these orbitals explains a further large portion of the variance in their inhibitory activity.     

QSAR of aromatic substances: EGFR inhibitory activity of quinazoline analogues

The flip regression procedure that we used earlier for handling the xanthones system has been applied to phenylaminoquinazoline analogues. It is known that the substituents at the 6- and 7- positions of the polycyclic system have been identified as the most important structural features. The steric as well as the electrostatic interactions proved to be the most important for the inhibitory effect. In this contribution it is shown that the orientation of nodes in their occupied π orbitals, and also the energies of these orbitals explains a further large portion of the variance in their inhibitory activity.     

Molecular dynamics simulations on the aggregation behavior of indole type organic dye molecules in dye-sensitized solar cells

In Ti0₂ nanostructured dye-sensitized solar cells indole based organic dyes D149, D205 exhibits greater power conversion efficiency. Such organic dye molecules are easily undergone for aggregation. Aggregation in dye molecules leads to reduce electron transfer process in dye-sensitized solar cells. Therefore, anti-aggregating agents such as chenodeoxycholic acid are commonly added to organic dye solution in DSSCs. Studying aggregation of such dye molecules in the absence of semiconductors gives a detailed influence of anti-aggregating agents on dye molecules. Atomistic level of molecular dynamics (MD) simulations were performed on aggregation of indole type dye molecules D149, D205 and D205-F with anti-aggregating agent chenodeoxy cholic acid using AMBER program. The trajectories of the MD simulations were analyzed with order parameters such as radial atom pair distribution functions g(r), diffusion coefficients and root mean square deviations values. MD results suggest that addition of chenodeoxy cholic acid to dyes significantly reduces structural arrangement and increases conformational flexibility and mobility of dye molecules. The influence of semi-perfluorinated alkyl chains in indole dye molecules was analyzed. The parameters such as open-circuit voltage (V_oc) and power conversion efficiency (η) of dye-sensitized solar cells are corroborated with flexibility and diffusion values of dye molecules.     

Diversity-oriented synthesis: exploring the intersections between chemistry and biology

Diversity-oriented synthesis (DOS) is an emerging field involving the synthesis of combinatorial libraries of diverse small molecules for biological screening. Rather than being directed toward a single biological target, DOS libraries can be used to identify new ligands for a variety of targets. Several different strategies for library design have been developed to target the biologically relevant regions of chemical structure space. DOS has provided powerful probes to investigate biological mechanisms and also served as a new driving force for advancing synthetic organic chemistry.     

Small structural alterations greatly influence the membrane affinity of lipophilic ligands: Membrane interactions of bafilomycin A1 and its desmethyl derivative bearing 19F-labeling

Molecular behavior under bilayer membrane environments is one of the important research topics concerning how organic molecules exert their biological activities when interacting with cellular membranes. However, chemistry-based approaches to this property have not been successful when compared with the structural biological strategy on ligand-receptor interactions. Here, we investigated the molecular behavior of the lipophilic ATPase inhibitor bafilomycin A₁ and its derivatives under a lipid environment from a chemical point of view. Our results revealed significant differences in membrane affinity and dynamics among ligands having different inhibitory potencies, suggesting the specific contribution of ligand-membrane interactions to their biological activity.     

Identification of acidic dileucine signals in LRP9 that interact with both GGAs and AP-1/AP-2

The Golgi-localized, gamma-ear-containing, ADP ribosylation factor-binding family of monomeric clathrin adaptors (GGAs) is known to bind cargo molecules through short C-terminal peptide motifs conforming to the sequence DXXLL (X = any amino acid), while the heterotetrameric adaptors AP-1 and AP-2 utilize a similar but discrete sorting motif of the sequence [D,E]XXXL[L,I]. While it has been established that a single cargo molecule may contain either or both types of these acidic cluster-dileucine (AC-LL) sorting signals, there are no examples of cargo with overlapping GGA and AP-1/AP-2-binding motifs. In this study, we report that the cytosolic tail of low-density lipoprotein receptor-related protein (LRP)9 contains a bifunctional GGA and AP-1/AP-2-binding motif at its carboxy-terminus (EDEPLL). We further demonstrate that the internal EDEVLL sequence of LRP9 also binds to GGAs in addition to AP-2. Either AC-LL motif of LRP9 is functional in endocytosis. These findings represent the first study characterizing the trafficking of LRP9 and also have implications for the identification of additional GGA cargo molecules.     

Deep generative models for 3D molecular structure

Deep generative models have gained recent popularity for chemical design. Many of these models have historically operated in 2D space; however, more recently explicit 3D molecular generative models have become of interest, which are the topic of this article. Dozens of published models have been developed in the last few years to generate molecules directly in 3D, outputting both the atom types and coordinates, either in one-shot or adding atoms or fragments step-by-step. These 3D generative models can also be guided by structural information such as a binding pocket representation to successfully generate molecules with docking score ranges similar to known actives, but still showing lower computational efficiency and generation throughput than 1D/2D generative models and sometimes producing unrealistic conformations. We advocate for a unified benchmark of metrics to evaluate generation and propose perspectives to be addressed in next implementations.     

Detection of QTL for immune response to sheep red blood cells in laying hens

The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergently selected lines for either high (H line) or low (L line) primary antibody response to SRBC. The F2 population consisted of six half-sib families, three families per each of reciprocal crosses. Total antibody titres to SRBC were determined by agglutination in serum from all birds. F2, F1 and F0 generations were genotyped for 170 microsatellite markers, using a whole-genome scan approach. The half-sib and the line-cross analyses were performed to determine QTL regions associated with regulation of the immune response. In the half-sib analysis, four QTL for SRBC primary response have been identified: on GGA3, GGA5, GGA16 and GGA23. No QTL was identified for SRBC secondary response under the half-sib model. In the line-cross analysis, three QTL were identified on GGA10, GGA16 and GGA27 for SRBC primary response and five QTL were identified on GGA6, GGA9, GGA15, GGA16 and GGA27 for SRBC secondary response. Subsequently, the family contribution of individual families to the QTL was analysed. The family with the largest contribution was genotyped with additional microsatellite markers in the QTL region on GGA5. The extended half-sib analysis with additional genotype information results in narrowing down the QTL region on GGA5.     

Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements

The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.     

First-principles investigation of the interaction of gold and palladium with armchair carbon nanotube

In this paper, we investigate the adsorption mechanisms at the interface between carbon nanotubes and metal electrodes that can influence the Schottky barrier (SB). We developed a theoretical model based on the first-principles density functional theory for the interaction of an armchair single-wall carbon nanotube (SWNT) with either Au(111) or Pd(111) surface. We considered the side-wall contact by modelling the full SWNT as well as the end-contact geometry using the graphene ribbon model to mimic the contact with very large diameter nanotubes. Strong interaction has been found for the Pd–SWNT interface where the partial density of states (DOS) shows that d-orbitals of palladium are dominant at the Fermi energy so that the hybrid Pd-orbitals have the correct symmetry to overlap with π-electrons and form covalent bonds. The SWNT can only be physisorbed on the gold surface for which the contribution to the DOS of the d-orbitals is very low. Moreover, the filling of antibonding states makes the Au–SWNT bond unstable. The average and ‘atom to atom’ energy barriers at the interface have been evaluated. The matching of open-edge carbon dimers with metal lattice in the end-contact geometry is more likely for large diameter SWNTs and this makes lower the SB at the interface.     

Ultraviolet photoelectron studies of 5-halouracils

Ultravoilet photoelectron spectroscopy has been employed to exmamin the valence electronic structure of 5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil. Photoelectron bands associted with the three highest π orbitals and the two oxygen atom lone-pair orbitals were assigned by a comparison to similar bands observed in the photoelectron spectrum of uraciul. Bands arising from the halogen atom lone-pair orbitals were assigned by comparing the present results with photoelectron spectra measured for halobenzenes, and by considering the linear dependence of halogen atom lone-pair ionization potentials upon halogen atom electronegativities. The present spectroscopic results have been compared with results from studies of association constants of 5-halouracil–adenine complexes. This examination in dicates that the complex association constants incresase as the ionization potentials of the highest occupied π orbital and the halogen atom lone-pair orbitals of th halouracils decrease.     

Effect of protein backbone folding on the stability of protein-ligand complexes

The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding of the protein S correlates in a significant way with the free energy and enthalpy of the protein-peptide interactions. A much better correlation is found with the local contribution to the degree of folding of one amino acid residue: Thr36. This residue is shown to have a destabilizing interaction with Lys41, which interacts directly with peptide S. Another system, consisting of the interactions of small organic molecules with HIV-1 protease was also studied. In this case, the global change in the degree of folding of the protease backbone does not explain the binding energetics of protein-ligand interactions. However, a significant correlation is observed between the free energy of binding and the contribution of two amino acid residues in the HVI-1 protease: Gly49 and Ile66. In general, it was observed that the changes in the degree of folding are not restricted to the binding site of the protein chain but are distributed along the whole protein backbone. This study provides a basis for further consideration of the degree of folding as a parameter for empirical structural parametrizations of the binding energetics of protein folding and binding.     

Function, regulation and pathological roles of the Gab/DOS docking proteins

Since their discovery a little more than a decade ago, the docking proteins of the Gab/DOS family have emerged as important signalling elements in metazoans. Gab/DOS proteins integrate and amplify signals from a wide variety of sources including growth factor, cytokine and antigen receptors as well as cell adhesion molecules. They also contribute to signal diversification by channelling the information from activated receptors into signalling pathways with distinct biological functions. Recent approaches in protein biochemistry and systems biology have revealed that Gab proteins are subject to complex regulation by feed-forward and feedback phosphorylation events as well as protein-protein interactions. Thus, Gab/DOS docking proteins are at the centre of entire signalling subsystems and fulfil an important if not essential role in many physiological processes. Furthermore, aberrant signalling by Gab proteins has been increasingly linked to human diseases from various forms of neoplasia to Alzheimer's disease. In this review, we provide a detailed overview of the structure, effector functions, regulation and evolution of the Gab/DOS family. We also summarize recent findings implicating Gab proteins, in particular the Gab2 isoform, in leukaemia, solid tumours and other human diseases.