A DFT study on the central-ring doped HBC nanographenes

Nanographenes (NGs) are a segment of graphene whose dangling bonds are saturated with hydrogen atoms, introducing different properties and promising applications. Here we investigate the electronic, thermodynamic, optical, and structural properties of four C₃₆X₃Y₃H₁₈ NGs (X = B, and Al; and Y = N, and P) based on the density functional theory calculations. It was mainly found that 1) BN-NG is planar molecule and the others are buckybowl-shaped ones, 2) The bowl-to-bowl inversion Gibbs free energies (ΔG^#) of buckybowl shaped NGs are very huge and the rate constant is very small, hindering the inversion, 3) The relative energetic stability order based on the standard enthalpy of formation (ΔH_f^°) is as BN > AlN > BP > AlP, which the BN, and AlN doped NGs are stable at room temperature but the BP and AlP doped ones are instable, 4) The electrical conductivity order of magnitude is inverse of that of stability, 5) An exciton binding energy is predicted in the range of 0.57–0.75 eV for the NGs which corresponds to Frenkel exciton type, 6) the NGs are not soluble in organic solvent in agreement with the experimental results and is partially soluble in water solvent with Gibbs free energy of solvation (ΔG_solv) in the range of −6.1 to −10.1 kcal/mol.     

Computational assessment of several hydrogen-free high energy compounds

Tetrazino-tetrazine-tetraoxide (TTTO) is an attractive high energy compound, but unfortunately, it is not yet experimentally synthesized so far. Isomerization of TTTO leads to its five isomers, bond-separation energies were empolyed to compare the global stability of six compounds, it is found that isomer 1 has the highest bond-separation energy (1204.6 kJ/mol), compared with TTTO (1151.2 kJ/mol); thermodynamic properties of six compounds were theoretically calculated, including standard formation enthalpies (solid and gaseous), standard fusion enthalpies, standard vaporation enthalpies, standard sublimation enthalpies, lattice energies and normal melting points, normal boiling points; their detonation performances were also computed, including detonation heat (Q, cal/g), detonation velocity (D, km/s), detonation pressure (P, GPa) and impact sensitivity (h₅₀, cm), compared with TTTO (Q = 1311.01 J/g, D = 9.228 km/s, P = 40.556 GPa, h₅₀ = 12.7 cm), isomer 5 exhibites better detonation performances (Q = 1523.74 J/g, D = 9.389 km/s, P = 41.329 GPa, h₅₀ =  28.4 cm).     

Systematic profiling of substrate binding response to multidrug-resistant mutations in HIV-1 protease: Implication for combating drug resistance

Human immunodeficiency virus 1 (HIV-1) protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. However, a number of multidrug-resistant mutations in the enzyme have been observed over the past decades, largely limiting the application of PR inhibitors in antiviral therapy. A systematic investigation of the intermolecular interaction between the multidrug-resistant mutants of HIV-1 PR and its substrates would help to establish a complete profile of substrate response to PR mutations and to design new antiviral agents combating drug resistance. Here, we describe an integrative method to profile 6 clinical multidrug-resistant PR mutants against a panel of 16 substrate octapeptides that flank 12 distinct PR cleavage sites in viral precursor polyproteins. It is found that most multidrug-resistant mutations have only a modest or moderate effect on substrate peptide binding, although these mutations would cause a large free energy loss in PR inhibitor binding. Structural analysis reveals that the substrate peptides are loosely bound within PR active pocket to form a wide contact interface between them, and thus mutation of just single or few residues seems not to influence PR–substrate binding considerably. In addition, peptides derived from variable cleavage sites are generally more sensitive to the mutations as compared to those derived from conserved sites, supporting the co-evaluation mechanism of HIV-1 PR and its substrates under drug suppression. We also identify 12 functionally conserved key residues around the enzyme’s active site, which play crucial role in substrate recognition. In vitro fluorescence anisotropy assays confirm that wild-type PR can bind substrate peptides ARVL/AEAM and NLAF/PQGE with a moderately high affinity (K_D = 2 and 16 μM, respectively). In contrast, the key residue mutations N25D/D29N can completely eliminate (K_D = n.d.) or largely reduce (K_D = 32 and 120 μM, respectively) the binding capability of the two peptides, suggesting that these PR residues could be the potential target sites for developing resistance-free anti-HIV agents.     

Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics

The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein–ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5 ± 0.9 kcal/mol, compared to 3.1 ± 0.8 kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.     

A new metric based on extended spatial frequency and its application to DWT based fusion algorithms

A new quantitative metric is proposed to objectively evaluate the quality of fused imagery. The measured value of the proposed metric is used as feedback to a fusion algorithm such that the image quality of the fused image can potentially be improved. This new metric, called the ratio of spatial frequency error (rSFe), is derived from the definition of a previous measure termed “spatial frequency” (SF) that reflects local intensity variation. In this work, (1) the concept of SF is first extended by adding two diagonal SFs, then, (2) a reference SF (SF_R) is computed from the input images, and finally, (3) the error SF (SF_E) (subtracting the fusion SF from the reference SF), or the ratio of SF error (rSFe = SF_E/SF_R), is used as a fusion quality metric. The rSFe (which can be positive or negative) indicates the direction of fusion error—over-fused (if rSFe > 0) or under-fused (if rSFe < 0). Thus, the rSFe value can be back propagated to the fusion algorithm (BP fusion), thereby directing further parameter adjustments in order to achieve a better-fused image. The accuracy of the rSFe is verified with other quantitative measurements such as the root mean square error (RMSE) and the image quality index (IQI), as well as with a qualitative perceptual evaluation based on a standard psychophysical paradigm. An advanced wavelet transform (aDWT) method that incorporates principal component analysis (PCA) and morphological processing into a regular DWT fusion algorithm is implemented with two adjustable parameters—the number of levels of DWT decompositions and the length of the selected wavelet. Results with aDWT were compared to those with a regular DWT and with a Laplacian pyramid. After analyzing several inhomogeneous image groups, experimental results showed that the proposed metric, rSFe, is consistent with RMSE and IQI, and is especially powerful and efficient for realizing the iterative BP fusion in order to achieve a better image quality. Human perceptual assessment was measured and found to strongly support the assertion that the aDWT offers a significant improvement over the DWT and pyramid methods.     

Simulation of solid thermal explosion and liquid thermal explosion of dicumyl peroxide using calorimetric technique

Dicumyl peroxide (DCPO), is produced by cumene hydroperoxide (CHP) process, is utilized as an initiator for polymerization, a prevailing source of free radicals, a hardener, and a linking agent. DCPO has caused several thermal explosion and runaway reaction accidents in reaction and storage zone in Taiwan because of its unstable reactive property. Differential scanning calorimetry (DSC) was used to determine thermokinetic parameters including 700 J g^–1 of heat of decomposition (ΔH_d), 110 °C of exothermic onset temperature (T₀), 130 kJ mol^–1 of activation energy (E_a), etc., and to analyze the runaway behavior of DCPO in a reaction and storage zone. To evaluate thermal explosion of DCPO with storage equipment, solid thermal explosion (STE) and liquid thermal explosion (LTE) of thermal safety software (TSS) were applied to simulate storage tank under various environmental temperatures (T_e). T_e exceeding the T₀ of DCPO can be discovered as a liquid thermal explosion situation. DCPO was stored under room temperature without sunshine and was prohibited exceeding 67 °C of self-accelerating decomposition temperature (SADT) for a tank (radius = 1 m and height = 2 m). SADT of DCPO in a box (width, length and height = 1 m, respectively) was determined to be 60 °C. The TSS was employed to simulate the fundamental thermal explosion behavior in a large tank or a drum. Results from curve fitting demonstrated that, even at the earlier stage of the reaction in the experiments, ambient temperature could elicit exothermic reactions of DCPO. To curtail the extent of the risk, relevant hazard information is quite significant and must be provided in the manufacturing process.     

Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking,molecular dynamics and MM/PBSA studies

Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔG_bind, −16.83 and −10.99 kcal mol⁻¹) are comparable to that of current commercial drug oseltamivir (−23.62 kcal mol⁻¹). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.     

On identifying codes that are robust against edge changes

Assume that G = (V, E) is an undirected graph, and C ⊆ V. For every v ∈ V, denote I_r(G; v) = {u ∈ C: d(u,v) ≤ r}, where d(u,v) denotes the number of edges on any shortest path from u to v in G. If all the sets I_r(G; v) for v ∈ V are pairwise different, and none of them is the empty set, the code C is called r-identifying. The motivation for identifying codes comes, for instance, from finding faulty processors in multiprocessor systems or from location detection in emergency sensor networks. The underlying architecture is modelled by a graph. We study various types of identifying codes that are robust against six natural changes in the graph; known or unknown edge deletions, additions or both. Our focus is on the radius r = 1. We show that in the infinite square grid the optimal density of a 1-identifying code that is robust against one unknown edge deletion is 1/2 and the optimal density of a 1-identifying code that is robust against one unknown edge addition equals 3/4 in the infinite hexagonal mesh. Moreover, although it is shown that all six problems are in general different, we prove that in the binary hypercube there are cases where five of the six problems coincide.     

Tetrel bonds between PySiX3 and some nitrogenated bases: Hybridization,substitution, and cooperativity

Ab initio calculations have been performed to study the influence of hybridization, substitution, and cooperativity on the tetrel bond in the complexes of PySiX₃ (Py = pyridine and X = halogen). The tetrel bond becomes stronger in the order of p-PySiF₃⋯NCH(sp) < p-PySiF₃⋯NHCH₂(sp²) < p-PySiF₃⋯NH₃(sp³). The electron-donating group in the electron donor strengthens the tetrel bond, and this effect is mainly achieved through electrostatic and polarization interactions. Tetrel bonding displays cooperative effects with triel bonding and chalcogen bonding, characterized by shorter binding distances and greater electron densities. The cooperative effects between triel/chalcogen bond and tetrel bond have been analyzed by molecular electrostatic potentials and charge transfer. Energy decomposition indicates that many-body effects are mainly caused by polarization energy. The geometries of Si⋯N interaction and its applications in crystal materials have been characterized and evidenced by a CSD research.     

The possibility of using C20 fullerene and graphene as semiconductor segments for detection,and destruction of cyanogen-chloride chemical agent

Detection of hazardous chemical species by changing the electrical conductivity of a semiconductor matter is a proposed and applied way for decreasing their subsequent unpleasant effects. Recently, many examples of using inorganic or organic materials, polymeric, and also nano-sized species as sensors were reported in which, in some cases, those matters were strongly affective and suitable.In this project, we have made an assessment on whether the graphene segment or C₂₀ fullerene, able to sense the existence of cyanogen chloride NCCl? In order to gain trustable results, the possible reaction pathways along with the adsorption kinetics were investigated. Moreover, the electronic density of states DOS showed that C₂₀ fullerene senses the existence of cyanogen chloride agent with a clearer signal (ΔE_g = 0.0110 eV) compared to the graphene segment (ΔE_g = 0.0001 eV). Also the adsorption energy calculations showed that cyanogen chloride could be adsorbed by the fullerene in a multi-step process (E_ads1 = −0.852 kcal mol⁻¹; E_ads2 = −0.446 kcal mol⁻¹; E_ads3 = −2.330 kcal mol⁻¹).     

A DFT study on the physical adsorption of cyclophosphamide derivatives on the surface of fullerene C60 nanocage

The physical sorption of a series of cyclophosphamide drug derivatives with formula

where x = 2, X = F (2), Cl (3), Br (4); x = 3, X = F (5), Cl (6), Br (7) and x = 4, X = F (8), Cl (9), Br (10) on the surface of fullerene C₆₀ was studied using density functional theory (DFT) at B3LYP and B3PW91 levels. The most negative binding energies obtained using the B3LYP approach and corrected for geometrical BSSE and dispersion energies (gCP-D3-ΔE_binding) were measured for compounds 8 (among isolated drugs) and 13 (among complexes). The dipole moments of isolated drugs were obtained close to those of their complexes with C₆₀ (∼4.0–5.5 Debye) indicating their hydrophililic nature that is an appropriate property appealing for drug delivery in biological media. The adsorption of all drugs on the surface of fullerene was endergonic with all of the ΔG_adsorption > 0. The ΔH_adsorption values at B3PW91 level were only negative for complexes 14–16 indicating their exothermic adsorption nature. The HOMO–LUMO band gaps of complexes 11–19 were about 2.7 eV and are comparable with the gap in C₆₀ but are much smaller than the gaps in isolated drugs 2–10 (6.5–8.0 eV) reflecting the increase in electrical conductivities upon complexation. The QTAIM data supported the covalent character of the C–O, C–N and N–H bonds, the intermediate character of PO, P–O and P–N bonds while the electrostatic nature of PO…C(fullerene) interactions. According to the gCP-D3-ΔE_binding binding energies and ΔH_adsorption values at B3LYP level, it seems that the complexes 12 and 13 can be the most promising prodrug + carrier delivery systems.

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Doping effect of Ir(ppy)3 on white-light electrophosphorescent devices based on platinum(II) [1,3-difluoro-4,6-di(2-pyridinyl)benzene] chloride

Phosphorescent white organic light-emitting diodes (WOLEDs) based on single doped platinum(II) [1,3-difluoro-4,6-di(2-pyridinyl)benzene] chloride (Pt-4) emission layers were investigated in this paper. The devices exhibited electroluminescence spectra composed of bluish (λ_max = 480 nm) and reddish (λ_max = 660 nm) emission bands, which corresponding to monomer and excimer emission originated from Pt-4 dopants. With optimized device structures, a maximum current efficiency of 11.5 cd/A was obtained and remained above 10 cd/A even the brightness was over 6000 cd/m². Furthermore, by integrating the fac-tris(2-phenylpyridine) iridium(III) as a complementary emitter and an additional 2,2′,2″-(1,3,5-phenylene)-tris(1-phenyl-1H-benzimidazole) space layer, the device efficiency was further improved, which exhibited a maximum current efficiency of 20.4 cd/A at the luminance of 100 cd/m², and maintained the mild efficiency roll-off that similar to its single Pt-4 doped counterpart.     

Computing Modular Invariants of p-groups

Let V be a finite dimensional representation of a p -group, G, over a field,k , of characteristic p. We show that there exists a choice of basis and monomial order for which the ring of invariants, k [ V ]^G, has a finite SAGBI basis. We describe two algorithms for constructing a generating set for k [ V ] G. We use these methods to analyse k [2V₃ ]^U₃where U₃is the p -Sylow subgroup ofGL₃ (F_p) and 2 V₃is the sum of two copies of the canonical representation. We give a generating set for k [2 V₃]^U₃forp =  3 and prove that the invariants fail to be Cohen–Macaulay forp >  2. We also give a minimal generating set for k [mV₂ ]^Z / pwere V₂is the two-dimensional indecomposable representation of the cyclic group Z / p.     

Stereoelectronic interaction effects on the conformational properties of hydrogen peroxide and its analogues containing S and Se atoms: An ab initio,hybrid-DFT study and NBO analysis

Ab initio molecular orbital (MP2/6-311+G**//MP2/6-31G+G**) and hybrid-density functional theory (B3LYP/6-311+G**//MP2/6-311+G**) methods and NBO analysis were used to study the stereoelectronic interaction effects on the conformational properties of hydrogen peroxide (1), hydrogen disulfide (2) and hydrogen diselenide (3). The results showed that the Gibbs free energy difference (G_T − G_S) values at 298.15 K and 1 atm between the skew (S) and trans (T) conformations (ΔG_T–S) increase from compound 1 to compound 2 but decrease from compound 2 to compound 3. The C conformations of compounds 1–3 are less stable than their S and T conformations. Based on these results, the racemization processes of the axial symmetrical (C₂ symmetry) conformations of compounds 1–3 take place via their T conformations. Based on the optimized ground state geometries using the MP2/6-311+G** level of theory, the NBO analysis of donor–acceptor (bond–antibond) interactions revealed that the stabilization (resonance) energy associated with LP₂M2 → σ*_M3-H4 electronic delocalization for the S conformations of compounds 1–3 are 1.35, 5.94 and 4.68 kcal mol⁻¹, respectively. There is excellent agreement between the variations of the calculated ΔG_T–S and stabilization (resonance) energies associated with LP₂M2→σ*_M3-H4 electronic delocalization for the S conformations of compounds 1–3. The correlations between resonance energies, orbital integrals, dipole moments, bond orders, structural parameters and conformational behaviors of compounds 1–3 have been investigated. Test were made of complete basis set methods (CBS-QB3, CBS-4 and CBS-Q), the first two gave results essentially indistinguishable from those we used, but the CBS-Q results were in disagreement with experimental and other theoretical results.     

An Algorithm for the Quillen–Suslin Theorem for Quotients of Polynomial Rings by Monomial Ideals

This paper presents an algorithm for the Quillen–Suslin Theorem for quotients of polynomial rings by monomial ideals, that is, quotients of the form A = k [ x₀, . . . ,x_n ] / I, with I a monomial ideal and k a field. Vorst proved that finitely generated projective modules over such algebras are free. Given a finitely generated module P, described by generators and relations, the algorithm tests whether P is projective, in which case it computes a free basis forP .     

Design and synthesis of a novel class of carbonic anhydrase-IX inhibitor 1-(3-(phenyl/4-fluorophenyl)-7-imino-3H-[1,2,3]triazolo[4,5d]pyrimidin 6(7H)yl)urea

Carbonic anhydrase IX (CAIX) is a promising target in cancer therapy especially in the case of hypoxia-induced tumors. The selective inhibition of CA isozymes is a challenging task in drug design and discovery process. Here, we performed fluorescence-binding studies and inhibition assay combined with molecular docking and molecular dynamics (MD) simulation analyses to determine the binding affinity of two synthesized triazolo-pyrimidine urea derived (TPUI and TPUII) compounds with CAIX and CAII. Fluorescence binding results are showing that molecule TPUI has an excellent binding-affinity for CAIX (k_D = 0.048 μM). The TPUII also exhibits an appreciable binding affinity (k_D = 7.52 μM) for CAIX. TPUI selectively inhibits CAIX as compared to TPUII in the 4-NPA assay. Docking studies show that TPUI is spatially well-fitted in the active site cavity of CAIX, and is involve in H-bond interactions with His94, His96, His119, Thr199 and Thr200. MD simulation studies revealed that TPUI efficiently binds to CAIX and essential active site residual interaction is consistent during the entire simulation of 40 ns. These studies suggest that TPUI appeared as novel class of CAIX inhibitor, and may be used as a lead molecule for the development of potent and selective CAIX inhibitor for the hypoxia-induced cancer therapy.     

Internet use and verbal aggression: The moderating role of parents and peers

This research investigated the influence of parent–adolescent communication quality, as perceived by the adolescents, on the relationship between adolescents’ Internet use and verbal aggression. Adolescents (N = 363, age range 10–16, M_T1 = 12.84, SD = 1.93) were examined twice with a six-month delay. Controlling for social support in general terms, moderated regression analyses showed that Internet-related communication quality with parents determined whether Internet use is associated with an increase or a decrease in adolescents’ verbal aggression scores over time. A three way interaction indicated that high Internet-related communication quality with peers can have disadvantageous effects if the communication quality with parents is low. Implications on resources and risk factors related to the effects of Internet use are discussed.