Predictive QSPR modeling of the acidic dissociation constant (pKa) of phenols in different solvents

Reaction rate constant: a theoretical description from local temperature

Application of various descriptors based on electron density and its associated quantities to quantify chemical reactivity within the conceptual density functional theory has recently come into spotlight. Among others and particularly relevant to our study, local temperature based on electron density as well as kinetic energy density, as a measure of the kinetic energy of an electron moving in the Kohn-Sham potential of systems, should be mentioned. In this work, we propose to use the local temperature for describing the reaction rate constant, where our main idea originates from the point that the smaller the local temperature at the reaction center, the easier the electron removal, leading to a larger rate constant. On the basis of theoretical considerations, it is proved that the rate constant variations caused by the substituent effects can well be proportional to the local temperature at the reaction center. In order to numerically validate our proposed approach, we have taken the phenol derivatives with the available experimental rate constants of their O-methylation reaction as working models. The reason for this choice is that one of the most versatile approaches for labeling biologically active compounds with the 11C nuclide for positron emission tomography (PET) is methylation by methyl iodide including 11C nuclide, [11C]MeI, where methylation of phenolic oxygen with [11C]MeI is utilized to label some important tracers for PET studies. Our results unveil that the local temperature changes at the reaction center of the aforementioned reaction are reasonably correlated with the rate constant variations. Hopefully, incorporating the proposed correlations between the local temperature and the kinetics data into a computer control algorithm not only provides a simple tool for predicting the rate constant of the O-methylation reaction for other substituted phenols, but also, as a part of the chemical artificial intelligence, the optimum [11C]MeI labeling conditions for a wide variety of phenol derivatives can be controlled.

Bio-based phenolic branched-chain fatty acid in wash water reduced populations of Listeria innocua on apple fruit

Phenolic branched-chain fatty acid (PBC-FA) emulsion was produced by dissolving it in ethanol and mixing with water (pH 7). The resulting monodispersed emulsion droplets were approximately 200 nm in diameter. The stability of the emulsion was evaluated by storing it at 4 and 20 °C for 30 days. The antimicrobial activity of the PBC-FA emulsion was tested against Escherichia coli and Listeria innocua (8 log CFU/mL) by determining the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) using a microdilution method. The PBC-FA was effective against L. innocua with MIC and MBC of 14.1 μg/mL and caused membrane permeation as determined with SEM and Live/Dead cell assay, but was not effective against E. coli O157:H7 at the tested concentrations (5-250 μg/mL). We also evaluated PBC-FA emulsion's potential to be used as a wash against L. innocua inoculated on apples. The results showed that the 500 μg/mL PBC-FA emulsion with 5 % ethanol had equivalent antimicrobial activity (2-3 logs reductions) against L. innocua as the 20 μg/mL chlorine solution, a commonly used sanitizer. 500 μg/mL PBC-FA emulsion had better antimicrobial efficacy when organic matter (chemical oxygen demand: 9.0 g/L) was present compared to 20 μg/mL of chlorine. The effect of PBC-FA on the quality of the apples, was determined by measuring changes in color, firmness, and soluble solids content over a 14-day storage period at 20 °C. The quality of the apples was not affected by PBC-FA over the 14-day storage period, suggesting that PBC-FA emulsion can be used as a wash for apples without affecting their quality.

Bioactive Phenolate Salts: Thymol Salts

Phenolate salts of bioactive agents have been reported only scarcely. This is the first report on the formation and characterization of thymol phenolate salts as representatives of phenol-containing bioactive molecules. Thymol has been used in medicine and agriculture for decades owing to its excellent therapeutic properties. However, in light of its poor aqueous solubility, thermal instability, and especially its high chemical volatility, the utility of thymol is hampered. The present work focuses on tuning the physicochemical properties of thymol by modifying its chemical structure through salt formation. In this context, a series of metal (Na, K, Li, Cu, and Zn) and ammonium (tetrabutylammonium and choline) salts of thymol were synthesized and characterized using IR, NMR, CHN elemental analysis, and DSC analyses. The molecular formulae of thymol salts were determined based on CHN analysis and thymol quantification studies from UV-Vis spectrometric analysis. In most cases, the thymol phenolate was prepared as a 1 : 1 molar ratio with metal/ammonium ion. Only the Cu salt of thymol was isolated at a ratio of two phenolate units per copper ion. Most of the synthesized thymol salts were found to have increased thermal stability relative to thymol. The physicochemical properties such as solubility, thermal stability, and evaporation rate of thymol salts were thoroughly studied in comparison with thymol. The in vitro release studies of Cu from the copper salt of thymol is pH-dependent: rapid release of copper was observed in the lower pH release medium (100 % release at pH 1 for 12 days) and the rates of release were slower at higher pH values (5 % release at pH 2, and <1 % release at pH 4, 6, 8, and 10) over a period of about three weeks.

Impacts of properties of dissolved organic matters on indirect photodegradation of genistein

Excited triplet states of dissolved organic matters (³DOM*) are one of the most important photochemically-produced reactive intermediates leading to transformation of organic contaminants. However, relationships of photodegradation kinetics of different dissociation states of phenolic organic contaminants with chemical components or properties of ³DOM* are largely unknown. In this study, roles of ³DOM* in photodegradation of polyhydroxy phenolic genistein (Gs) at pH 5, 8 and 12 were investigated taking five kinds of DOM from different sources as examples. Relationships between photodegradation kinetics constants and DOM properties were built. Results showed that the contributions of direct ³DOM*-induced reactions to the total indirect photodegradation of Gs and second-order reaction rate constants (k_DOM,Gs) of Gs with ³DOM* increased with pH increases. This was mainly attributed to decreases in vertical ionization energy of Gs at higher pH, endowing Gs with stronger electron donating capacities. k_DOM,Gs was found to positively correlate with the specific ultraviolet absorbance at 254 nm, reflecting aromaticity of DOM, and negatively correlate with the absorbance ratio at 254 and 365 nm and contents of dissociated acidic functional groups of DOM, representing molecular weights of DOM, antioxidants and the repulsive forces between ³DOM* and Gs. This study provided a new insight into relationship between DOM properties and indirect photodegradation kinetics of phenolic contaminants in aquatic environments.

Two-Electron-Induced Reorganization of Cobalt Coordination and Metal-Ligand Cooperative Redox Shifting Co(I) Reactivity toward CO2 Reduction

Electrochemical reorganization of complex structures is directly related to catalytic reactivity; thus, the geometric changes of catalysts induced by electron transfer should be considered to scrutinize the reaction mechanism. Herein, we studied electron-induced reorganization patterns of six-coordinate Co complexes with neutral N-donor ligands. Upon two-electron transfer into a Co center enclosed within a bulky π-acceptor ligand, the catalytic site exhibited different reorganization patterns depending on the ligand characteristics. While a bipyridyl ligand released Co-bound solvent (CH₃CN) to open a reaction site, a phenanthroline ligand caused Co-N_arm (side "arm" of NNN-ligand) bond dissociation. The first electron transfer occurred in the Co(II/I) reduction step and the second electron entered the bulky π-acceptor, of which redox steps were assigned from cyclic voltammograms, magnetic moment measurements, and DFT calculations. In comparison, the Co complex of [NNN^NCH₃-Co(CH₃CN)₃](PF₆)₂ ([1-(CH₃CN)₃](PF₆)₂) showed a high H₂ evolution reactivity (HER), whereas a series of Co complexes with bulky π-acceptors such as [NNN^NCH₃-Co(L)(CH₃CN)](PF₆)₂ (L = phen ([2-CH₃CN](PF₆)₂), bpy ([3-CH₃CN](PF₆)₂), [NNN^NCH₃-Co(tpy)](PF₆)₂ ([4](PF₆)₂), and [NNN^CH₂-Co(phen)(CH₃CN)](PF₆)₂ ([5-CH₃CN](PF₆)₂)) suppressed the HER but rather enhanced the CO₂ reduction reaction. The metal-ligand cooperative redox steps enabled the shift of Co(I) reactivity toward CO₂ reduction. Additionally, the amine pendant attached to the NNN^NCH₃-ligand could stabilize the CO₂ reduction intermediate through the hydrogen-bonding interaction with the Co-CO₂H adduct.

Cs2CO3-Promoted reaction of tertiary bromopropargylic alcohols and phenols in DMF: a novel approach to α-phenoxyketones

The reaction of bromopropargylic alcohols with phenols in the presence of Cs₂CO₃/DMF affords α-phenoxy-α’-hydroxyketones (1:1 adducts) and α,α-diphenoxyketones (1:2 adducts) in up to 92% and 24% yields, respectively. Both products are formed via ring opening of the same intermediates, 1,3-dioxolan-2-ones, generated in situ from bromopropargylic alcohols and Cs₂CO₃.

Methylation with Dimethyl Carbonate/Dimethyl Sulfide Mixtures: An Integrated Process without Addition of Acid/Base and Formation of Residual Salts

Dimethyl sulfide, a major byproduct of the Kraft pulping process, was used as an inexpensive and sustainable catalyst/co-reagent (methyl donor) for various methylations with dimethyl carbonate (as both reagent and solvent), which afforded excellent yields of O-methylated phenols and benzoic acids, and mono-C-methylated arylacetonitriles. Furthermore, these products could be isolated using a remarkably straightforward workup and purification procedure, realized by dimethyl sulfide's neutral and distillable nature and the absence of residual salts. The likely mechanisms of these methylations were elucidated using experimental and theoretical methods, which revealed that the key step involves the generation of a highly reactive trimethylsulfonium methylcarbonate intermediate. The phenol methylation process represents a rare example of a Williamson-type reaction that occurs without the addition of a Brønsted base.

Predicting pKa Values of Quinols and Related Aromatic Compounds with Multiple OH Groups

Quinonoid compounds play central roles as redox-active agents in photosynthesis and respiration and are also promising replacements for inorganic materials currently used in batteries. To design new quinonoid compounds and predict their state of protonation and redox behavior under various conditions, their pK_a values must be known. Methods that can predict the pK_a values of simple phenols cannot reliably handle complex analogues in which multiple OH groups are present and may form intramolecular hydrogen bonds. We have therefore developed a straightforward method based on a linear relationship between experimental pK_a values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pK_a values when intramolecular hydrogen bonds are present. Our approach has been validated by showing that predicted and experimental values for over 100 quinols and related compounds differ by an average of only 0.3 units. This accuracy makes it possible to select proper pK_a values when experimental data vary, predict the acidity of quinols and related compounds before they are made, and determine the sites and orders of deprotonation in complex structures with multiple OH groups.

Prediction of Reaction Yield for Buchwald-Hartwig Cross-coupling Reactions Using Deep Learning

Chemical reaction yield is one of the most important factors for determining reaction conditions. Recently, several machine learning-based prediction models using high-throughput experiment (HTE) data sets were reported for the prediction of reaction yield. However, none of them were at a practical level in terms of predictive ability. In this study, we propose a message passing neural network (MPNN) model for chemical yield prediction, focusing on the Buchwald-Hartwig cross-coupling HTE data set. As an initial atom embedding in MPNN model, we propose to use the Mol2Vec feature vectors pre-trained using a large compound database. Predictive ability of the proposed model was higher than that of previously reported five models for the three out of five data sets. Moreover, visualization of important atoms based on self-attention mechanism was in favor of Mol2Vec as an atom embedding rather than other embeddings including previously employed simple representations.

Phosphate-Based Self-Immolative Linkers for Tuneable Double Cargo Release

Phosphorus-based self-immolative (SI) linkers offer a wide range of applications, such as smart materials and drug-delivery systems. Phosphorus SI linkers are ideal candidates for double-cargo delivery platforms because they have a higher valency than carbon. A series of substituted phosphate linkers was designed for releasing two phenolic cargos through SI followed by chemical hydrolysis. Suitable modifications of the lactate spacer increased the cargo release rate significantly, from 1 day to 2 hours or 5 minutes, as shown for linkers containing p-fluoro phenol. In turn, double cargo linkers bearing p-methyl phenol released their cargo more slowly (4 days, 4 hours, and 15 minutes) than their p-fluoro analogues. The α-hydroxyisobutyrate linker released both cargos in 25 minutes. Our study expands the current portfolio of SI constructs by providing a double cargo delivery option, which is crucial to develop universal SI platforms.

Enhancement of the Antioxidant and Antimicrobial Activities of Porphyran through Chemical Modification with Tyrosine Derivatives

The chemical modification of porphyran hydrocolloid is attempted, with the objective of enhancing its antioxidant and antimicrobial activities. Sulfated galactan porphyran is obtained from commercial samples of the red algae Porphyra dioica using Soxhlet extraction with water at 100 °C and precipitation with isopropyl alcohol. The extracted porphyran is then treated with modified L-tyrosines in aqueous medium in the presence of NaOH, at ca. 70 °C. The modified tyrosines L1 and L2 are prepared through a Mannich reaction with either thymol or 2,4-di-tert-butylphenol, respectively. While the reaction with 2,4-di-tert-butylphenol yields the expected tyrosine derivative, a mixture of products is obtained with thymol. The resulting polysaccharides are structurally characterized and the respective antioxidant and antimicrobial activities are determined. Porphyran treated with the N-(2-hydroxy-3,5-di-tert-butyl-benzyl)-L-tyrosine derivative, POR-L2, presents a noticeable superior radical scavenging and antioxidant activity compared to native porphyran, POR. Furthermore, it exhibited some antimicrobial activity against S. aureus. The surface morphology of films prepared by casting with native and modified porphyrans is studied by SEM/EDS. Both POR and POR-L2 present potential applicability in the production of films and washable coatings for food packaging with improved protecting characteristics.

Phosphate linkers with traceable cyclic intermediates for self-immolation detection and monitoring

A robust method based on NMR traceable cyclic intermediates clearly distinguished self-immolation from other cargo-release processes.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

Electrochemical β-Selective Hydrocarboxylation of Styrene Using CO2 and Water

The carboxylation of hydrocarbons using CO2 as a one-carbon building block is an attractive route for the synthesis of carboxylic acids and their derivatives. Until now, chemical carboxylation catalyzed by organometallic nucleophiles and reductants has been generally adopted particularly for the precise selectivity control of carboxylation sites. As another approach, electrochemical carboxylation has been attempted but these carboxylation reactions are limited to only a few pathways. In the case of styrene, dicarboxylation at the α- and β-positions is mostly observed with electrochemical carboxylation while site-selective hydrocarboxylations are hardly achieved. In this study, electrochemical β-selective hydrocarboxylation of styrene using CO2 and water is developed, in which the site selectivity can be precisely controlled between β-hydrocarboxylation and dicarboxylation without the aid of homogeneous catalysts. In this platform, water is used as proton source in the β-hydrocarboxylation of styrene where its addition results in significant enhancement of the selectivity toward β-hydrocarboxylation. This work provides insights into new strategies for site-selectivity-controllable carboxylation with CO2 using an electrochemical platform.

Chemical dual-site capture of NH3 by unprecedentedly low-viscosity deep eutectic solvents

It is found that ethylamine hydrochloride (EaCl) and phenol (PhOH) can form a new type of deep eutectic solvent (DES) with quite low viscosity, and two active sites for chemical absorption of NH₃.

Derivatization-free method for compound-specific isotope analysis of nonexchangeable hydrogen of 4-bromophenol

RATIONALE

Compound-specific isotope analysis (CSIA) is a valuable tool in environmental chemistry and in other fields of science. Currently, hydrogen CSIA of polar compounds containing exchangeable hydrogen is uncommon. To extend the scope of CSIA applications, we present an alternative method of analysis, bypassing the typical step of derivatization. The method is demonstrated for two environmental contaminants, 4-bromophenol (4BP) and 2,4,6-tribromophenol (TBP).

METHODS

Net isotope ratios obtained by CSIA combine the isotope composition of nonexchangeable, carbon-bound hydrogen and the exchangeable hydroxyl hydrogen. To constrain the isotope composition of the latter, an ethyl acetate solution of 4BP or TBP injected into the IRMS instrument was amended with excess water of known isotope composition. The results were calibrated using bracketing control samples analyzed in sequence with the unknown samples and the known isotope ratios of water present in ethyl acetate solution.

RESULTS

The analytical precision was comparable to the precision for halogenated compounds without exchangeable hydrogen, analyzed using similar instrumentation. The isotope ratios of the bromophenols correlated with the isotope composition of the water in the sample matrix, suggesting that the hydroxyl group of the target compound remained close to the equilibrium with the sample water during the passage through the instrument. Based on this relationship, the signatures of the nonexchangeable hydrogen were obtained using the isotope composition of sample water as the proxy for the isotope composition of the target compound hydroxyl group.

CONCLUSIONS

The developed method could be adopted to analysis of other low molecular weight compounds amenable to gas chromatography without the absolute need for derivatization. Currently, the method can be used for samples from laboratory experiments, with high concentrations of the target compound to provide mechanistic insight into the degradation mechanisms. Further work would be required to optimize the method to low concentration environmental samples.

Dioxygen Reduction to Hydrogen Peroxide by a Molecular Mn Complex: Mechanistic Divergence between Homogeneous and Heterogeneous Reductants

The selective electrocatalytic reduction of dioxygen (O₂) to hydrogen peroxide (H₂O₂) could be an alternative to the anthraquinone process used industrially, as well as enable the on-demand production of a useful chemical oxidant, obviating the need for long-term storage. There are challenges associated with this, since the two-proton/two-electron reduction of H₂O₂ to two equivalents of water (H₂O) or disproportionation to O₂ and H₂O can be competing reactions. Recently, we reported a Mn(III) Schiff base-type complex, Mn(^tbudhbpy)Cl, where 6,6'-di(3,5-di- tert-butyl-2-phenolate)-2,2'-bipyridine = [^tbudhbpy]^2-, which is active for the electrocatalytic reduction of O₂ to H₂O₂ (ca. 80% selectivity). The less-than-quantitative selectivity could be attributed in part to a thermal disproportionation reaction of H₂O₂ to O₂ and H₂O. To understand the mechanism in greater detail, spectrochemical stopped-flow and electrochemical techniques were employed to examine the catalytic rate law and kinetic reaction parameters. Under electrochemical conditions, the catalyst produces H₂O₂ by an ECCEC mechanism with appreciable rates down to overpotentials of 20 mV and exhibits a catalytic response with a strong dependence on proton donor p K_a. Mechanistic studies suggest that under spectrochemical conditions, where the homogeneous reductant decamethylferrocene (Cp*₂Fe) is used, H₂O₂ is instead produced via a disproportionation pathway, which does not show a strong acid dependence. These results demonstrate that differences in mechanistic pathways can occur for homogeneous catalysts in redox processes, dependent on whether an electrode or homogeneous reductant is used.

QSAR modelling using combined simple competitive learning networks and RBF neural networks

The aim of this study was to propose a QSAR modelling approach based on the combination of simple competitive learning (SCL) networks with radial basis function (RBF) neural networks for predicting the biological activity of chemical compounds. The proposed QSAR method consisted of two phases. In the first phase, an SCL network was applied to determine the centres of an RBF neural network. In the second phase, the RBF neural network was used to predict the biological activity of various phenols and Rho kinase (ROCK) inhibitors. The predictive ability of the proposed QSAR models was evaluated and compared with other QSAR models using external validation. The results of this study showed that the proposed QSAR modelling approach leads to better performances than other models in predicting the biological activity of chemical compounds. This indicated the efficiency of simple competitive learning networks in determining the centres of RBF neural networks.

Exploring the effect of hydroxylic and non-hydroxylic solvents on the reaction of [VIVO(β-diketonate)2] with 2-aminobenzoylhydrazide in aerobic and anaerobic conditions

Refluxing [V^IVO(β-diketonate)₂], namely [V^IVO(acetylacetonate)₂] and [V^IVO(benzoylacetonate)₂], separately with an equivalent or excess amount of 2-aminobenzoylhydrazide (ah) in laboratory grade (LG) CH₃OH in aerobic conditions afforded non-oxidovanadium(iv) and oxidovanadium(v) complexes of the type [V^IV(L¹)₂] (1), [V^VO(L¹)(OCH₃)]₂ (3) and [V^IV(L²)₂] (2), and [V^VO(L²)(OCH₃)] (4), respectively. (L¹)^2- and (L²)^2- represent the dianionic forms of 2-aminobenzoylhydrazone of acetylacetone (H₂L¹) and benzoylacetone (H₂L²), respectively, (general abbreviation, H₂L), which was formed by the in situ condensation of ah with the respective coordinated [β-diketonate] in medium-to-good yield. The yield of different resulting products was dependent upon the ratio of ah to [V^IVO(β-diketonate)₂]. For example, the yield of 1 and 2 complexes increased significantly associated with a decrease in the amount of 3 and 4 with an increase in the molar ratio of ah. Upon replacing CH₃OH by a non-hydroxylic solvent, LG CHCl₃, the above reaction yielded only oxidovanadium(v) complexes of the type [V^VO(L¹)(OH)]₂ (5), [V^VO(L²)(OH)] (6) and [VO₃(L)₂] (7, 8) whereas, upon replacing CHCl₃ by another non-hydroxylic solvent, namely LG CH₃CN, only the respective [VO₃(L)₂] (7, 8) complex was isolated in 72-78% yield. However, upon performing the above reactions in the absence of air using dry CH₃OH or dry CHCl₃, only the respective [V^IV(L)₂] complex was obtained, suggesting that aerial oxygen was the oxidising agent and the type of pentavalent product formed was dependent upon the nature of solvent used. Complexes 3 and 4 were converted, respectively, to 7 and 8 on refluxing in LG CHCl₃via the respective unstable complex 5 and 6. The DFT calculated change in internal energy (ΔE) for the reactions 2[V^VO(L²)(OCH₃)] + 2H₂O → 2[V^VO(L²)(OH)] + 2CH₃OH and 2[V^VO(L²)(OH)] → [VO₃(L²)₂] + H₂O was, respectively, +3.61 and -7.42 kcal mol^-1, suggesting that the [V^VO(L²)(OH)] species was unstable and readily transformed to the stable [VO₃(L²)₂] complex. Upon one-electron reduction at an appropriate potential, each of 7 and 8 generated mixed-valence [(L)V^VO-(μ-O)-OV^IV(L)]^- species, which showed valence-delocalisation at room temperature and localisation at 77 K. Some of the complexes showed a wide range of toxicity in a dose-dependent manner against lung cancer cells comparable with that observed with cis-platin.

Enhanced debromination of 4-bromophenol by the UV/sulfite process: Efficiency and mechanism

Halogenated aromatic compounds have attracted increasing concerns due to their toxicity and persistency in the environment, and dehalogenation is one of the promising treatment and detoxification methods. Herein, we systematically studied the debromination efficiency and mechanism of para-bromophenol (4-BP) by a recently developed UV/sulfite process. 4-BP underwent rapid degradation with the kinetics accelerated with the increasing sulfite concentration, pH (6.1-10) and temperature, whereas inhibited by dissolved oxygen and organic solvents. The apparent activation energy was estimated to be 27.8kJ/mol. The degradation mechanism and pathways of 4-BP were explored by employing N₂O and nitrate as the electron scavengers and liquid chromatography/mass spectrometry to identify the intermediates. 4-BP degradation proceeded via at least two pathways including direct photolysis and hydrated electron-induced debromination. The contributions of both pathways were distinguished by quantifying the quantum yields of 4-BP via direct photolysis and hydrated electron production in the system. 4-BP could be readily completely debrominated with all the substituted Br released as Br^-, and the degradation pathways were also proposed. This study would shed new light on the efficient dehalogenation of brominated aromatics by using the UV/sulfite process.

The Influence of para Substituents in Bis(N-Heterocyclic Carbene) Palladium Pincer Complexes for Electrocatalytic CO2 Reduction

The effect of modifying the pyridyl para position of lutidine-linked bis(N-heterocyclic carbene) Pd pincer complexes is studied both experimentally (R = OMe, H, Br, and COOR) and computationally, showing a strong effect on the first reduction potential of the complex and allowing the reduction potential to be tuned over a wide range in relation to the Hammett σ_p constant of the para substituent. The effect of the pyridyl para substituent on electron density of the metal center, frontier orbital energies, and dissociation energy of the trans ligand are also investigated in the context of reactivity with CO₂ through electrochemical characterization of the complexes under N₂ and CO₂ and controlled potential electrolysis experiments where CO₂ is reduced to CO.

Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors

The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues. In order to determine the free energy contribution of Zn(2+) binding by known metalloenzyme inhibitors without the other interactions, valid active site zinc structural mimetics must be formed and binding studies need to be performed in biologically relevant conditions. The potential of each of five ligands to form a structural mimetic with Zn(2+) was investigated in buffer using Isothermal Titration Calorimetry (ITC). All five ligands formed strong 1 : 1 (ligand : Zn(2+)) binary complexes. The complexes were used in further ITC experiments to study their interaction with 8-hydroxyquinoline (8-HQ) and/or acetohydroxamic acid (AHA), two bidentate anionic zinc-chelating enzyme inhibitors. It was found that tetradentate ligands were not suitable for creating zinc structural mimetics for inhibitor binding in solution due to insufficient coordination sites remaining on Zn(2+). A stable binary complex, [Zn(BPA)](2+), which was formed by a tridentate ligand, bis(2-pyridylmethyl)amine (BPA), was found to bind one AHA in buffer or a methanol : buffer mixture (60 : 40 by volume) at pH 7.25 or one 8-HQ in the methanol : buffer mixture at pH 6.80, making it an effective structural mimetic for the active site of zinc metalloenzymes. These results are consistent with the observation that metalloenzyme active site zinc ions have three residues coordinated to them, leaving one or two sites open for inhibitors to bind. Our findings indicate that Zn(BPA)X2 can be used as an active site structural mimetic for zinc metalloenzymes for estimating the free energy contribution of zinc binding to the overall inhibitor active site interactions. Such use will help aid in the rational design of inhibitors to a variety of zinc metalloenzymes.

Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study

Coelenteramide-containing fluorescent proteins are products of bioluminescent reactions of marine coelenterates. They are called 'discharged photoproteins'. Their light-induced fluorescence spectra are variable, depending considerably on external conditions. Current work studies a dependence of light-induced fluorescence spectra of discharged photoproteins obelin, aequorin, and clytin on excitation energy. It was demonstrated that photoexcitation to the upper electron-excited states (260-300nm) of the discharged photoproteins initiates a fluorescence peak in the near UV region, in addition to the blue-green emission. To characterize the UV fluorescence, the light-induced fluorescence spectra of coelenteramide (CLM), fluorophore of the discharged photoproteins, were studied in methanol solution. Similar to photoproteins, the CLM spectra depended on photoexcitation energy; the additional peak (330nm) in the near UV region was observed in CLM fluorescence at higher excitation energy (260-300nm). Quantum chemical calculations by time depending method with B3LYP/cc-pVDZ showed that the conjugated pyrazine-phenolic fragment and benzene moiety of CLM molecule are responsible for the additional UV fluorescence peak. Quantum yields of CLM fluorescence in methanol were 0.028±0.005 at 270-340nm photoexcitation. A conclusion was made that the UV emission of CLM might contribute to the UV fluorescence of the discharged photoproteins. The study develops knowledge on internal energy transfer in biological structures - complexes of proteins with low-weight aromatic molecules.

The rm2 metrics and regression through origin approach: reliable and useful validation tools for predictive QSAR models (Commentary on 'Is regression through origin useful in external validation of QSAR models?')

Quantitative structure-activity relationship (QSAR) is an in silico technique which can be used in drug discovery, environmental fate modeling, property and toxicity prediction of chemical entities and regulatory toxicology. The predictive potential of a QSAR model is judged from various validation metrics in order to evaluate how well it is capable to predict endpoint values of new untested compounds. The rm2 group of metrics is one of the stringent validation metrics currently used by the QSAR fraternity in different reports. We scrutinized a recently published paper which raised an issue that the constructed criteria based on regression through origin (RTO) are not optimal and there is a significant difference in the rm2 metrics values computed from different statistical software packages. According to our point of view, the conclusion drawn in this paper appears to be misleading. Any inconsistency in the software algorithms has nothing to do with the calculation of rm2 metrics, as such computation is not limited by the use of any specific software, rather it depends only on fundamental mathematical formulae that are well established. However, it is a concern to the QSAR users that Excel and SPSS can return different results for the metrics using the RTO method. Thus, a proper validation of the software tool is required before its use for computation of any validation metric.

QSTR with extended topochemical atom (ETA) indices. 15. Development of predictive models for toxicity of organic chemicals against fathead minnow using second-generation ETA indices

Modern industrialisation has led to the production of millions of toxic chemicals having hazardous effects on the ecosystem. It is impracticable to determine the toxic potential of a large number of chemicals in animal models, making the use of quantitative structure-toxicity relationship (QSTR) models an alternative strategy for toxicity prediction. Recently we introduced a set of second-generation extended topochemical atom (ETA) indices for predictive modelling. Here we have developed predictive toxicity models on a large dataset of 459 diverse chemicals against fathead minnow (Pimephales promelas) using the second-generation ETA indices. These descriptors can be easily calculated from two-dimensional molecular representation without the need of time-consuming conformational analysis and alignment, making the developed models easily reproducible. Considering the importance of hydrophobicity for toxicity prediction, AlogP98 was used as an additional predictor in all the models, which were validated rigorously using multiple strategies. The ETA models were comparable in predictability to those involving various non-ETA topological parameters and those previously reported using various descriptors including computationally demanding quantum-chemical ones.

pKa prediction from an ab initio bond length: part 2--phenols

The prediction of pK(a) continues to attract much attention with ongoing investigations into new ways to predict pK(a) accurately, where predicted pK(a) values deviate less than 0.50 log units from experiment. We show that a single descriptor, i.e. an ab initio bond length, can predict pK(a). The emphasis was placed on model simplicity and a demonstration that more accurate predictions emerge from single-bond-length models. A data set of 171 phenols was studied. The carbon-oxygen bond length, connecting the OH to the phenyl ring, consistently provided accurate predictions. The pK(a) of meta- and para-substituted phenols is predicted here by a single-bond-length model within 0.50 log units. However, accurate prediction of the pK(a) of ortho-substituted phenols necessitated their splitting into groups called high-correlation subsets in which the pK(a) of the compounds strongly correlated with a single bond-length. The highly compound-specific single-bond-length models produced better predictions than models constructed with more compounds and more bond lengths. Outliers were easily identified using single-bond-length models and in most cases we were able to determine the reason for the outlier discrepancy. Furthermore, the single-bond-length models showed better cross-validation statistics than the PLS models constructed using more than one bond length. For all of the single-bond-length models, RMSEE was less than 0.50. For the majority of the models, RMSEP was less than 0.50. The results support the use of multiple high-correlation subsets and a single bond-length to predict pK(a). Six one-term linear equations are listed as a starting point for the construction of a more comprehensive list covering a larger variety of compound classes.

QSTR with extended topochemical atom (ETA) indices. 14. QSAR modeling of toxicity of aromatic aldehydes to Tetrahymena pyriformis

Aldehydes are a toxic class of chemicals causing severe health hazards. In this background, quantitative structure-toxicity relationship (QSTR) models have been developed in the present study using Extended Topochemical Atom (ETA) indices for a large group of 77 aromatic aldehydes for their acute toxicity against the protozoan ciliate Tetrahymena pyriformis. The ETA models have been compared with those developed using various non-ETA topological indices. Attempt was also made to include the n-octanol/water partition coefficient (logK(o/w)) as an additional descriptor considering the importance of hydrophobicity in toxicity prediction. Thirty different models were developed using different chemometric tools. All the models have been validated using internal validation and external validation techniques. The statistical quality of the ETA models was found to be comparable to that of the non-ETA models. The ETA models have shown the important effects of steric bulk, lipophilicity, presence of electronegative atom containing substituents and functionality of the aldehydic oxygen to the toxicity of the aldehydes. The best ETA model (without using logK(o/w)) shows encouraging statistical quality (Q(int)(2)=0.709,Q(ext)(2)=0.744). It is interesting to note that some of the topological models reported here are better in statistical quality than previously reported models using quantum chemical descriptors.

Multi-wavelength spectrophotometric determination of acidity constant of some newly synthesized Schiff bases and their QSPR study

The acidity constants of some newly synthesized Schiff base derivatives were determined by hard-model based multivariate data analysis of the spectrophotometric data in the course of pH-metric titration in 50% (v/v) methanol-water binary solvent. The employed data analysis method was also able to extract the pure spectra and pH-dependent concentration profiles of the acid-base species. The molecules that possess different substituents (both electron donating and withdrawing) on the ortho-, meta- and para-positions of one of the phenyl ring showed variable acidity constants ranging from 8.77 to 11.07 whereas the parent molecule had an acidity constant of 10.25. To investigate the quantitative effects of changing of substitution pattern on the acidity constant, a quantitative structure-property relation analysis was conducted using substituent constants and molecular descriptor. Some models with high statistical quality (measured by cross-validation Q(2)) were obtained. It was found that the acidity constant of the studied molecules in the methanol-water mixed solvent not only is affected by electronic features of the solutes but also by the lipophilic interaction between methanol part of solvent and the deprotonated solutes.