A DFT study on non-enzymatic degradations of anti-tuberculosis drug isoniazid.

CONTEXT: Isoniazid (INH) is one of the medications most used for tuberculosis (TB) treatment. However, long-term continuous therapy can cause hepatotoxicity and peripheral neuritis. The degradation of INH is an important aspect of the research in the field of drug stability as well as drug formulation for controlling release. It is thought that tautomerization, hydrolysis as well as nucleophilic substitutions can cause decrease in INH as non-enzymatic degradation. Therefore, it is crucial to understand the mechanisms and energies of the major reactions in order to provide reference for future drug formulation and application. This study is an effort to understand the kinetic and thermodynamic properties of the non-enzymatic degradation reactions. The chemical reaction phenomena are investigated using the density functional theory (DFT) method. This study shows that major degradation of INH can be done via tautomerization followed by hydrolysis. The general trends in nucleophilic degradation presented here are consistent with experimental pKa of nucleophiles. METHODS: All DFT calculations were performed using the Gaussian Software Packages (Gaussian 09 revision B.01 and GaussView 5.0.8). MOLEKEL 4.3 software was utilized to visualize the molecular graphics of all relevant species. The optimized molecular geometries were calculated using B3LYP/6-311 + G(d,p) level in the gas phase. The IEF-PCM/B3LYP/6-311 + G(d,p) level was selected for single-point and frequency calculations in aqueous media.

Supramolecular self-assembled polymeric nanospheres based on hydrazino naphthalimide functionalised pillar[5]arene for long chain aldehyde detection.

A novel fluorescent sensor HNP5A is constructed consisting of bis-hydrazine naphthalimide decorated pillar[5]arene. Interestingly, this sensor possessed the potential for sensitive and selective detection of long-chain aldehydes, particularly nonanal (C9), and subsequently formed supramolecular pseudorotaxane polymeric nanoparticles inducing a strong fluorescence enhancement. In addition, this as-produced HNP5A⊂C9 exhibited an unexpected reduction of Ag+ to produce AgNPs in an aqueous system and the resulting AgNPs-HNP5A⊂C9 demonstrated a significant fluorescence enhancement under metal-enhanced fluorescence (MEF) behaviour.

Characterization of a bioscaffold containing polysaccharide acemannan and native collagen for pulp tissue regeneration.

Dental pulp regeneration exploits tissue engineering concepts using stem cells/scaffolds/growth-factors. Extracted collagen is commonly used as a biomaterial-scaffold due to its biocompatibility/biodegradability and mimics the natural extracellular matrix. Adding biomolecules into a collagen-scaffold enhanced pulp regeneration. Acemannan, ß-(1-4)-acetylated-polymannose, is a polysaccharide extracted from aloe vera. Acemannan is a regenerative biomaterial. Therefore, acemannan could be a biomolecule in a collagen-scaffold. Here, acemannan and native collagen were obtained and characterized. The AceCol-scaffold's physical properties were investigated using FTIR, SEM, contact angle, swelling, pore size, porosity, compressive modulus, and degradation assays. The AceCol-scaffold's biocompatibility, growth factor secretion, osteogenic protein expression, and calcification were evaluated in vitro. The AceCol-scaffolds demonstrated higher hydrophilicity, swelling, porosity, and larger pore size than the collagen scaffolds (p < 0.05). Better cell-cell and cell-scaffold adhesion, and dentin extracellular matrix protein (BSP/OPN/DSPP) expression were observed in the AceCol-scaffold, however, DSPP expression was not detected in the collagen group. Significantly increased cellular proliferation, VEGF and BMP2 expression, and mineralization were detected in the AceCol-scaffold compared with the collagen-scaffold (p < 0.05). Computer simulation revealed that acemannan's 3D structure changes to bind with collagen. In conclusion, the AceCol-scaffold synergistically provides better physical and biological properties than collagen. The AceCol-scaffold is a promising material for tissue regeneration.

A DFT study on N2O oxidation and methanol synthesis over Bi4O6: single-site catalytic model of α-Bi2Mo3O12.

Catalytic conversion of methane to methanol is one of the most promising processes for effective natural gas resource utilization. In this work, Bi4O6-catalyzed oxidation of methane to methanol with N2O as an oxidizing reactant has been investigated by DFT calculation. For the overall reaction mechanism of three N2O molecules on Bi4O6 catalyst, two catalytic cycles were proposed. Cycle 1 involved the consecutive decomposition of the first two N2O molecules. Cycle 2 corresponded to the decomposition of the third N2O molecule. The activation barriers of the first and second N2O decomposition were computed to be 27.6 and 35.0 kcal/mol, respectively. The third N2O decomposition in cycle 2 required 36.1 kcal/mol activation barriers. Thus, cycle 1 was the main catalytic cycle for N2O as the cycle required lower in barriers than those of the other. Oxidation of methane to methanol on Bi4O7 and Bi4O8 catalysts was supposed to be a two-step mechanism consisting of H3C-H bond breaking and CH3-OH formation. The activation energies of the two steps were 32.7, 41.1, and 21.6, 17.2 kcal/mol for Bi4O7 and Bi4O8, respectively. Thus, methane oxidation over Bi4O8 was found to be more energetically favorable than those of Bi4O7, in which C-H bond breaking is the RDS. The present catalyst could be a promising material for the oxidation of methane to methanol. In summary, the single-site catalytic model study would be beneficial for guiding and searching for potential catalysts in heterogeneously catalyzed N2O decomposition and methanol synthesis as green as possible. However, theoretical investigation of this kind of catalyst's extended model system must be taken into account.

Improvement of Fusel Alcohol Production by Engineering of the Yeast Branched-Chain Amino Acid Aminotransaminase.

Branched-chain higher alcohols (BCHAs), or fusel alcohols, including isobutanol, isoamyl alcohol, and active amyl alcohol, are useful compounds in several industries. The yeast Saccharomyces cerevisiae can synthesize these compounds via the metabolic pathways of branched-chain amino acids (BCAAs). Branched-chain amino acid aminotransaminases (BCATs) are the key enzymes for BCHA production via the Ehrlich pathway of BCAAs. BCATs catalyze a bidirectional transamination reaction between branched-chain α-keto acids (BCKAs) and BCAAs. In S. cerevisiae, there are two BCAT isoforms, Bat1 and Bat2, which are encoded by the genes BAT1 and BAT2. Although many studies have shown the effects of deletion or overexpression of BAT1 and BAT2 on BCHA production, there have been no reports on the enhancement of BCHA production by functional variants of BCATs. Here, to improve BCHA productivity, we designed variants of Bat1 and Bat2 with altered enzyme activity by using in silico computational analysis: the Gly333Ser and Gly333Trp Bat1 and corresponding Gly316Ser and Gly316Trp Bat2 variants, respectively. When expressed in S. cerevisiae cells, most of these variants caused a growth defect in minimal medium. Interestingly, the Gly333Trp Bat1 and Gly316Ser Bat2 variants achieved 18.7-fold and 17.4-fold increases in isobutanol above that for the wild-type enzyme, respectively. The enzyme assay revealed that the catalytic activities of all four BCAT variants were lower than that of the wild-type enzyme. Our results indicate that the decreased BCAT activity enhanced BCHA production by reducing BCAA biosynthesis, which occurs via a pathway that directly competes with BCHA production. IMPORTANCE Recently, several studies have attempted to increase the production of branched-chain higher alcohols (BCHAs) in the yeast Saccharomyces cerevisiae. The key enzymes for BCHA biosynthesis in S. cerevisiae are the branched-chain amino acid aminotransaminases (BCATs) Bat1 and Bat2. Deletion or overexpression of the genes encoding BCATs has an impact on the production of BCHAs; however, amino acid substitution variants of Bat1 and Bat2 that could affect enzymatic properties-and ultimately BCHA productivity-have not been fully studied. By using in silico analysis, we designed variants of Bat1 and Bat2 and expressed them in yeast cells. We found that the engineered BCATs decreased catalytic activities and increased BCHA production. Our approach provides new insight into the functions of BCATs and will be useful in the future construction of enzymes optimized for high-level production of BCHAs.

A DFT calculation on nonenzymatic degradation of isoaspartic residue.

ßAsp is an isomer of Asp that can be formed by either deamidation of Asn or isomerization of Asp and known as biological clock. The presence of ßAsp affects the proteolytic stability of the protein. Formation of the isomerized Asp plays a diverse and crucial role in aging, cancer, autoimmune, neurodegenerative, and other diseases. A number of methods have been developed to detect ßAsp, and they are usually used in conjunction. Because of identical mass, differentiation of ßAsp and Asp residues is challenged. Degradation of ßAsp is still unclear and needed to be explored. The energetics and mechanism of five possible pathways for cleavages at ßAsp in peptide model have been investigated by DFT/B3LYP/6-311 + + G(d,p) level of the theory. The calculations show that peptide bond cleavage at α-chain (amino side) due to αOC → αCN ring closure is the most favorable reaction. The result is in agreement with experiment utilizing PSD/CRF method. The second most favorable pathway is due to αOC → ßC ring closure results in ß-chain cleavage. The cleavage products ßAsp and Asp fragments can be used to signify an abundance of ßAsp residue in nonenzymatic condition. Other three cyclizations initiated by either α- or ß-amino nitrogen result in various cleavages, isomerization to Asp, and reconversion to original ßAsp. These three cyclization pathways are obstructed because they require mostly high activation barriers and their intermediates are quite less thermodynamically stable. Thus, computational results also confirm that ßAsp → Asp is prohibited in case of nonenzymatic condition which means that protein L-isoaspartyl O-methyl transferase (PIMT) is needed for this modification.

Masking Phosphate with Rare-Earth Elements Enables Selective Detection of Arsenate by Dipycolylamine-ZnII Chemosensor.

Functional reassessment of the phosphate-specific chemosensors revealed their potential as arsenate detectors. A series of dipicolylamine (Dpa)-ZnII chemosensors were screened, among which acridine Dpa-ZnII chemosensor showed the highest capability in sensing arsenate. The presence of excess ZnII improved sensitivity and strengthened the binding between acridine Dpa-ZnII complex to arsenate as well as phosphate. However, due to their response to phosphate, these sensors are not suited for arsenate detection when phosphate is also present. This study demonstrated for the first time that rare-earth elements could effectively mask phosphate, allowing the specific fluorescence detection of arsenate in phosphate-arsenate coexisting systems. In addition, detection of arsenate contamination in the real river water samples and soil samples was performed to prove its practical use. This sensor was further employed for the visualization of arsenate and phosphate uptake in vegetables and flowering plants for the first time, as well as in the evaluation of a potent inhibitor of arsenate/phosphate uptake.

Stabilisation of copper(i) polypyridyl complexes toward aerobic oxidation by zinc(ii) in combination with acetate anions: a facile approach and its application in ascorbic acid sensing in aqueous solution.

A new and facile approach to stabilise copper(i) complexes in aqueous solution by the addition of zinc(ii) ions in combination with acetate ions (OAc-) was demonstrated. This stability enhancement toward the aerobic oxidation of copper(i) species was investigated by various techniques including UV-vis spectroscopy, 1H-NMR, FT-IR, and ESI-MS. Our experimental results together with DFT calculations led to a proposed structure of [(adpa)Cu-OAc-Zn(OAc)(H2O)2]+/2+. It was also postulated that zinc(ii) with its Lewis acidity may attract electrons from the Cu centre through the bridging ligands (OAc-), resulting in the lower reactivity of Cu(i) with O2. In addition, this strategy was shown to be applicable to ascorbic acid detection by monitoring a change in the redox states of copper complexes using fluorescence spectroscopy. Moreover, it was demonstrated that the method was sensitive and accurate for the quantitative analysis of ascorbic acid in vitamin C tablets.

Tuning the reactivity of copper complexes supported by tridentate ligands leading to two-electron reduction of dioxygen.

A series of copper complexes bearing polypyridyl tridentate ligands have been prepared to fine tune their reactivity toward the oxygen reduction reaction (ORR). During the process of preparation of our copper complexes, we successfully obtained two new crystal structures which are [Cu2(µ-Cl)2(adpa)2](ClO4)2 (2b) and [Cu2(addpa)(CH3CN)2(ClO4)2](ClO4)2 (3a) and a new structure [Cu2(addpa)(CH3CN)2(H2O)2](ClO4)4 (3b) captured after the catalytic ORR. Electrochemical studies and stoichiometric chemical reduction of copper(ii) complexes by ascorbic acid indicated that the presence of an anthracene unit helps to facilitate the reduction of Cu(ii) as well as the stabilisation of Cu(i) species. Regarding oxygen activation, the dinuclear Cu(i) complex 3a showed significantly higher ORR activity than its analogous mononuclear complex 2a. Complex 3a was also found to be relatively robust and competent in catalytic O2 reduction. The observed H2O2 product after this catalysis, together with the data obtained from DFT calculations supported that 3a exhibited a 2H+, 2e- catalytic activity towards the ORR as opposed to the expected 4H+, 4e- process usually found in copper complexes with tridentate ligands. The proton (H+) source for this process was expected from ascorbic acid which also serves as a reducing agent in this reaction. This work highlighted an approach for tuning the ORR activity of the copper complexes by the introduction of a conjugated-π moiety to the supporting ligand.

Self-assembly of Gd3+/SDS/HEPES complex and curcumin entrapment for enhanced stability, fluorescence image in cellular system.

At present, strategies to disperse hydrophobic molecules in water without altering their chemical structures include conventional surfactant-based micellar and vesicular systems, encapsulation into water dispersible polymeric nanoparticles, and loading onto the surface of various metal nanoparticles. Here, we report a simple and low cost platform to incorporate hydrophobic molecules into a stable water dispersible nanostructure that can significantly increase the stability of the encapsulated materials. The platform is based on the incorporation of hydrophobic molecules into the self-assembled complex of gadolinium ion (Gd3+), sodium dodecyl sulfate (SDS), and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) called GdSH. After being incorporated, the two model hydrophobic dyes, curcumin and curcumin borondifluoride show approximately 50% and 30% improved stability, respectively. Investigation of the self-assembled 10-14 multilayered 60nm spheres with inter-layer distances of 4.25nm indicates coordination of SDS and HEPES with Gd3+. Incorporation of the hydrophobic molecules into the multilayered spheres results in reduction of the interlayer distance of the multilayer spheres to 4.17nm, suggesting enhanced packing of the hydrophobic chain of SDS and HEPES around the Gd3+. The incorporation of the two curcuminoids into the self-assembled complex also causes an increase in fluorescence quantum yield of the two dyes, thus suggesting spatial confinement of the packed dye molecules. The better cellular uptake of the nanoparticles is responsible for the expected enhancement in fluorescence image of the encapsulated materials.

Acemannan increases NF-κB/DNA binding and IL-6/-8 expression by selectively binding Toll-like receptor-5 in human gingival fibroblasts.

Acemannan, an acetylated polymannose from Aloe vera, has immunomodulatory effects. We investigated whether acemannan induces IL-6 and -8 expression and NF-κB/DNA binding in human gingival fibroblasts. IL-6 and -8 expression levels were assessed via RT-PCR and ELISA. The NF-κB p50/p65-DNA binding was determined. The structures of acemannan mono-pentamers and Toll-like receptor 5 (TLR5) were simulated. The binding energies between acemannan and TLR5 were identified. We found that acemannan significantly stimulated IL-6/-8 expression at both the mRNA and protein level and significantly increased p50/DNA binding. Preincubation with an anti-TLR5 neutralizing antibody abolished acemannan-induced IL-6/-8 expression and p50/DNA binding, and co-incubation of acemannan with Bay11-7082, a specific NF- κB inhibitor, abolished IL-6/-8 expression. The computer modeling indicated that monomeric/dimeric single stranded acemannan molecules interacted with the TLR5 flagellin recognition sites with a high binding affinity. We conclude that acemannan induces IL-6/-8 expression, and p50/DNA binding in gingival fibroblasts, at least partly, via a TLR5/NF-κB-dependent signaling pathway. Furthermore, acemannan selectively binds with TLR5 ectodomain flagellin recognition sites.

Tautomeric transformation of temozolomide, their proton affinities and chemical reactivities: A theoretical approach.

The gas-phase geometry optimizations of bare, mono- and dihydrated complexes of temozolomide isomers were carried out using density functional calculation at the M06-2X/6-31+G(d,p) level of the theory. The structures and protonation energies of protonated species of temozolomide are reported. Chemical indices of all isomers and protonated species are also reported. Energies, thermodynamic quantities, rate constants and equilibrium constants of tautomeric and rotameric transformations of all isomers I1↔TZM↔HIa↔HIb↔I2↔I3 in bare and hydrated systems were obtained.

Arsenite and arsenate removal from wastewater using cationic polymer-modified waste tyre rubber.

Waste tyre rubber (WTR) granulate was modified with a cationic polymer, poly(3-acrylamidopropyl)trimethylammonium chloride (p(APTMACl)). The resulting WTR/p(APTMACl) was utilized for the adsorption of arsenite, As(III) and arsenate, As(V) from aqueous medium in both batch and column methods. The level of adsorption increased gradually with increasing monomer concentration and contact time. The adsorption behavior obeyed the Freundlich model, and the rate of adsorption could be predicted by employing the pseudo-second order model. In the column method, As(V) could be adsorbed onto the sorbent more effectively than As(III). Remarkable desorption of As(III) and As(V) (99 and 92%, respectively) from the adsorbent was achieved using 0.10 M HCl as eluent. An approach of evaluation of adsorption capacity uncertainty is proposed.

Deacetylation affects the physical properties and bioactivity of acemannan, an extracted polysaccharide from Aloe vera.

Acemannan, an acetylated polymannose from Aloe vera, induces tissue repair. We investigated the role of acemannan's acetyl-groups on its physical and biological properties. Deacetylated acemannan (DeAcAM) was prepared and characterized. The physical properties and microscopic structure of DeAcAM were evaluated using water solubility, contact angle, X-ray diffraction, and scanning-electron microscopy. The activity of DeAcAM on cell proliferation and gene expression were assessed. Acemannan and DeAcAM structures were simulated and the acemannan tetramer diad and its completely deacetylated structure were also determined. Increased acemannan deacetylation reduced its water solubility and hydrophilicity. Complete deacetylation altered acemannan's conformation to a partial crystal structure. The bioactivity of acemannan was reduced corresponding to its deacetylation. Acemannan induced cell proliferation, and VEGF and Collagen I expression; however, 100% DeAcAM did not. The simulated structures of the acemannan diad and the completely deacetylated diad were different. We conclude acetyl-groups affect acemannan's structure and physical/biological properties.

Discriminate sensing of pyrophosphate using a new tripodal tetramine-based dinuclear Zn(II) complex under an indicator displacement assay approach.

In this research, the dinuclear Zn(ii) complex of anthracene based tripodal tetramine Zn2L was synthesized, and its sensing abilities towards anions was investigated using the indicator displacement assay (IDA) approach with four complexometric indicators: pyrocatechol violet (PV), bromopyrogallol red (BPG), methylthymol blue (MTB) and xylenol orange (XO). UV-vis spectrophotometry results indicated that the Zn2L-MTB ensemble sensor could discriminate the pyrophosphate anion (PPi) from other phosphate containing anions. (1)H and (31)P NMR spectroscopy as well as DFT calculations confirmed that PPi bound to Zn2L in a 2 : 2 manner. Both NMR spectroscopy and UV-vis spectrophotometry suggested that the two bulky tripodal tetramine units in Zn2L played an important role to provide the ensemble cleft for MTB, giving rise to an ensemble that could be displaced exclusively by PPi. The detection limit of PPi for the reported IDA system was 0.3 µM in 20% (v/v) water-acetonitrile buffered at pH 7.4 with HEPES.

Exploring molecular structures, orbital interactions, intramolecular proton-transfer reaction kinetics, electronic transitions and complexation of 3-hydroxycoumarin species using DFT methods.

Optimal structures and electronic properties of various species of 3-hydroxycoumarin (3-HCou) have been explored using density functional theory (DFT) methods under polarizable continuum model (PCM) of solvation. Electron transfer from pyrone to benzene moieties is enhanced upon deprotonation. Anionic and radical species have similar orbital-interaction characteristics but the charges in the former are distributed more uniformly. The rate of intramolecular proton transfer for the neutral species increases many folds upon excitation. The HOMO-LUMO transition with π→π* character mainly accounts for the UV absorption of most 3-HCou species in solution. The wavelengths of maximal absorption predicted using TD-DFT method are in agreement with the previous experiment. For the charged species, calculations with the range-corrected functional yield better agreement with the previous experiment. Anionic 3-HCou species shows high degrees of complexation with chromium(III) and copper(II) compared with oxovanadium(IV) and zinc(II). Either oxovanadium(IV) or zinc(II) prefers forming two isomeric complexes with comparable degrees of formation.

A density functional theory study on peptide bond cleavage at aspartic residues: direct vs cyclic intermediate hydrolysis.

In this work, peptide bond cleavages at carboxy- and amino-sides of the aspartic residue in a peptide model via direct (concerted and step-wise) and cyclic intermediate hydrolysis reaction pathways were explored computationally. The energetics, thermodynamic properties, rate constants, and equilibrium constants of all hydrolysis reactions, as well as their energy profiles were computed at the B3LYP/6-311++G(d,p) level of theory. The result indicated that peptide bond cleavage of the Asp residue occurred most preferentially via the cyclic intermediate hydrolysis pathway. In all reaction pathways, cleavage of the peptide bond at the amino-side occurred less preferentially than at the carboxy-side. The overall reaction rate constants of peptide bond cleavage of the Asp residue at the carboxy-side for the assisted system were, in increasing order: concerted < step-wise < cyclic intermediate.

Theoretical study on isomerization and peptide bond cleavage at aspartic residue.

Isomerization and peptide bond cleavage at aspartic residue (Asp) in peptide models have been reported. In this study, the mechanisms and energies concerning the isomerization and peptide bond cleavage at Asp residue were investigated by the density functional theory (DFT) at B3LYP/6-311++G(d,p). The integral equation formalism-polarizable continuum model (IEF-PCM) was utilized to calculate solvation effect by single-point calculation of the gas-phase B3LYP/6-311++G(d,p)-optimized structure. Mechanisms and energies of the dehydration in isomerization reaction of Asp residue were comparatively analyzed with the deamidation reaction of Asn residue. The results show that the succinimide intermediate was formed preferentially through the step-wise reaction via the tetrahedral intermediate. The cleavage at C-terminus is more preferential than those at N-terminus. In comparison to isomerization, peptide bond cleavage is ≈ 20 kcal mol(-1) and lower in activation barrier than the isomerization. So, in this case, the isomerization of Asp is inhibited by the peptide bond cleavage.

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes.

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Density functional investigation of hydrogen gas adsorption on Fe-doped pristine and Stone-Wales defected single-walled carbon nanotubes.

The adsorptions of hydrogen molecule of the Fe - doped pristine and Stone - Wales defected armchair (5,5) single - walled carbon nanotubes (SWCNTs) compared with the pristine SWCNT were investigated by using the density functional theory at the B3LYP/LanL2DZ level. The doping of Fe atom into SWCNTs occurring via an exothermic process was found. The adsorptions of hydrogen molecule on the Fe - doped structures of either perfect or SW defected SWCNTs are stronger than on their corresponding undoped structures. The structural and electronic properties of the pristine and SW defected SWCNTs, their Fe - doped structures and their hydrogen molecule adsorptions are reported.