Theoretical study of hydrogen-bonded complexes of chlorophenols with water or ammonia: Correlations and predictions of pKa values

Chlorine Substitution Effect on the S1 Relaxation Dynamics of Chlorobenzene and Chlorophenols

The S1 state relaxation dynamics of chlorobenzene (CB), 3-chlorophenol (3-CP), 3-CP·H2O, and 2-chlorophenol·H2O (2-CP·H2O) have been investigated by means of picosecond time-resolved pump-probe spectroscopy in a state-specific manner. For CB, the S1 state relaxes via the S1-S0 internal conversion in the low internal energy region (<2000 cm-1), whereas the direct C-Cl bond dissociation channel mediated by the upper-lying repulsive πσCCl* state is opened to give the rather sharp increase of the S1 relaxation rate in the high internal energy region (>2000 cm-1). A similar dynamic feature has been observed for 3-CP in terms of the lifetime behavior with an increase in the S1 internal energy, suggesting that the H atom tunneling dissociation reaction from OH might contribute less compared to the internal conversion, although it is not clear at the present time whether or not the sharp increase of the S1 relaxation rate in the high internal energy region of 3-CP (>1500 cm-1) is entirely due to that of the internal conversion. The fact that the internal conversion is facilitated by the Cl substitution implies that the energetic location of the S1/S0 conical intersection should have been strongly influenced by chlorine substitution on the aromatic ring. The approximate energetic location of the saddle point of the S1(ππ*)/πσCCl* conical intersection along the seam coordinate for CB or 3-CP could be inferred from the energy-dependent S1 lifetime measurements. It is discussed in comparison with the dynamic role of the S1(ππ*)/πσCCl* conical intersection, which is strongly influenced by the O-H···Cl intramolecular hydrogen bond in the rather complicated yet ultrafast S1 relaxation dynamics of the cis-2-CP. The S1 lifetimes of 3-CP·H2O and 2-CP·H2O reveal the importance of the conformational structures, especially in terms of the intramolecular hydrogen bonding.

Far-UVC (UV222) based photolysis, photooxidation, and photoreduction of chlorophenols using a KrCl-excimer lamp: Degradation, dechlorination, and detoxification

The KrCl-excimer lamp, emitting far-UVC light at 222 nm (UV222), offers a promising alternative to conventional UVC light at 254 nm (UV254) for the photolysis of organic pollutants and the activation of radical sensitizers. This study was aimed to investigate the efficiencies of UV222 in the treatment of halogenated aromatics, focusing on its performance in degradation, dechlorination and detoxification. Chlorophenols, representative recalcitrant and toxic halogenated aromatics, were used as target pollutants. The pathways of direct photolysis, photooxidation and photoreduction under UV222 illumination were compared. UV222 outperformed UV254 in photolyzing chlorophenols (1.4-34.1 times faster), especially protonated chlorophenols, due to substantially higher UV absorption (17.1-108.0 times) and quantum yields (2.1-3.4 times). The quantum yields of chlorophenols were influenced by the inducive electron-withdrawing effect of Cl-substitutes. Moreover, UV222 improved the dechlorination of chlorophenols to 95 % compared to 60 % by UV254. The introduction of radical sensitizer (e.g., H2O2, nitrate, and sulfite) reduced 4-chlorophenol photolysis by competing for UV222 absorption, though the sensitizers partially increased radical oxidation via generating •OH or eaq-. UV222 photolysis of 4-chlorophenol increased the toxicity by 88.6 times through forming toxic intermediates (e.g., hydroquinone and resorcinol). Notably, •OH and eaq- (i.e., UV222/H2O2 and UV222/sulfite) increased the dechlorination and •OH (i.e., UV222/H2O2) detoxified the mixture solution. Moreover, UV222 photolysis remained effective for 4-chlorophenol removal in real paper-mill wastewater, indicating the potential application of KrCl* lamp UV222.

pKa prediction of per- and polyfluoroalkyl acids in water using in silico gas phase stretching vibrational frequencies and infrared intensities

To successfully understand and model the environmental fate of per- and polyfluoroalkyl substances (PFAS), it is necessary to know key physicochemical properties (PChPs) such as pKa; however, measured PChPs of PFAS are scarce and of uncertain reliability. In this study, quantitative structure-activity relationships (QSARs) were developed by correlating calculated (M062-X/aug-cc-pVDZ) vibrational frequencies (VF) and corresponding infrared intensities (IRInt) to the pKa of carboxylic acids, sulfonic acids, phosphonic acids, sulfonamides, betaines, and alcohols. Antisymmetric stretching VF of the anionic species were used for all subclasses except for alcohols where the OH stretching VF performed better. The individual QSARs predicted the pKa for each subclass mostly within 0.5 pKa units from the experimental values. The inclusion of IRInt as a pKa predictor for carboxylic acids improved the results by decreasing the root-mean-square error from 0.35 to 0.25 (n > 100). Application of the developed QSARs to estimate the pKa of PFAS within each subclass revealed that the length of the perfluoroalkyl chain has minimal effect on the pKa, consistent with other models but in stark contrast with the limited experimental data available.

Correlation between C═O Stretching Vibrational Frequency and pKa Shift of Carboxylic Acids

Identifying the pK_a values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we investigated the correlation between the C=O stretching vibrational frequency (ν_C=O) of protonated carboxylic acids and the pK_a values using density functional theory calculations. In unsaturated carboxylic acids (e.g., benzoic acid analogues), ν_C=O decreases as the pK_a increases (the negative correlation), whereas in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and Glu), ν_C=O increases as the pK_a increases (the positive correlation) as long as the structure of the H-bond network around the acid is identical. The negative/positive correlation between ν_C=O and pK_a can be rationalized by the presence or absence of the C=C double bond. The pK_a shift was estimated from the ν_C=O shift of Asp and Glu in proteins on the basis of the negative correlation derived from benzoic acids. The previous estimations should be revisited by using the positive correlation derived in this study, as demonstrated by quantum mechanical/molecular mechanical calculations of ν_C=O and electrostatic calculations of pK_a on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.

NMR quantification of H-bond donating ability for bioactive functional groups and isosteres

The H-bond donating ability for 127 compounds including drug fragments and isosteres have been quantified using a simple and rapid method with ³¹P NMR spectroscopy. Functional groups important to medicinal chemistry were evaluated including carboxylic acids, alcohols, phenols, thioic acids and nitrogen group H-bond donors. ³¹P NMR shifts for binding to a phosphine oxide probe have a higher correlation with equilibrium constants for H-bonding (log K^H_A) than acidity (pK_a), indicating that these binding experiments are representative of H-bonding ability and not proton transfer. Additionally, ³¹P NMR binding data for carboxylic acid isosteres correlates with physicochemical properties such as lipophilicity, membrane permeability and plasma protein binding. This method has been used to evaluate the H-bond donating ability of small molecule drug compounds such as NSAIDs and antimicrobials.

Intramolecular hydrogen bonding protects the hydroxyl group from attack by fluctuating solvent forces

Ultrafast spectroscopy of molecular systems involving hydrogen- (H-) bonding has been at the forefront of fundamental chemical and physical research for several decades. Among the spectroscopic observables of the ultrafast dynamics is the pure dephasing of vibrationally excited molecules. Using third-order nonlinear vibrational spectroscopy, including polarization-selective transient grating measurements of vibrational lifetime and orientational diffusion as well as two-dimensional infrared spectroscopy, we determined different individual line shape components of hydroxyl stretching (νOH) excitations in a homologous series of chlorophenols and obtained the corresponding pure dephasing rates. The pure dephasing rates are correlated with vibrational anharmonicity of the νOH mode, which is tuned remotely from the hydroxyl site by changing the position of the chlorine substituents on the phenol ring. We found that in molecules where the hydroxyl group is in its free form, the pure dephasing rates scale linearly with the mode's anharmonicity such that assuming it is dominated by the third-order diagonal term, the ultrafast dynamics follow the prediction of the Kubo-Oxtoby theory. However, in the intramolecularly H-bonded ortho-chlorophenols, this trend is reversed, and the pure dephasing slows down by ∼50% for an increase in anharmonicity of only a few wavenumbers. Because the νOH mode's anharmonicity is known to reflect the H-bonding strength, our results suggest that intramolecular H-bonding can serve as a mechanism of protection from fluctuating forces exerted by the solvent. Such an effect can be relevant for ultrafast dynamics in biomolecules, where H-bonding plays a central role.

Oxidative dehalogenation and denitration by a flavin-dependent monooxygenase is controlled by substrate deprotonation

Enzymes that are capable of detoxifying halogenated phenols (HPs) and nitrophenols (NPs) are valuable for bioremediation and waste biorefining. HadA monooxygenase was found to perform dual functions of oxidative dehalogenation (hydroxylation plus halide elimination) and denitration (hydroxylation plus nitro elimination). Rate constants associated with individual steps of HadA reactions with phenol, halogenated phenols and nitrophenols were measured using combined transient kinetic approaches of stopped-flow absorbance/fluorescence and rapid-quench flow techniques. Density functional theory was used to calculate the thermodynamic and electronic parameters associated with hydroxylation and group elimination steps. These parameters were correlated with the rate constants of hydroxylation, group elimination, and overall product formation to identify factors controlling individual steps. The results indicated that the hydroxylation rate constant is higher when the pK a of the phenolic group is lower, i.e. it is more easily deprotonated, but not higher when the energy gap between the E LUMO of the C4a-hydroperoxy-FAD intermediate and the E HOMO of the phenolate substrate is lower. These data suggest that the substrate deprotonation has a higher energy barrier than the -OH transfer, and thus controls the hydroxylation step. For the group elimination, the process is controlled by the ability of the C-X bond to break. For the overall product formation (hydroxylation and group elimination combined), this analysis showed that the rate constant of product formation is dependent on the pK a value of the substrate, indicating that the overall reaction is controlled by substrate deprotonation. This step also likely has the highest energy barrier and thus controls the overall process of oxidative dehalogenation and denitration by HadA. This report is the first to identify a key mechanistic factor controlling the enzymatic processes of oxidative dehalogenation and denitration.

New insight into adsorption mechanism of ionizable compounds on carbon nanotubes

We studied the pH-dependent adsorption of benzoic acid (BA), phthalic acid (PA), and 2,6-dichloro-4-nitrophenol (DCNP) by hydroxylated, carboxylated, and graphitized carbon nanotubes (CNTs). Adsorption is contributed by formation of a negative charge-assisted H-bond (-)CAHB between a carboxyl group on the solute and a phenolate or carboxylate group on the surface having a comparable pKa. This exceptionally strong H-bond is depicted as (RCO2···H···O-CNTs)(-). Over a limited pH range the free anion undergoes proton exchange with water concurrent with adsorption, releasing hydroxide ion in a stoichiometry of up to 1.0 for BA, 1.7 for PA, and 0.5 for DCNP. Little hydroxide is released upon adsorption by the O-sparse graphitized CNTs. Anion exchange and ligand exchange reactions as a source of hydroxide release were ruled out. The higher stoichiometry for PA indicates involvement of both carboxyl groups with adjacent surface oxyl groups. The lower stoichiometry for DCNP is consistent with steric inhibition of H-bonding by the ortho chlorines. Formation of (-)CAHB helps overcome the unfavorable free energy of proton exchange with water, and results in an upward shift in the pKa in the adsorbed state compared to the dissolved state from 0.9 to 3.1 units. The proposed mechanism is further supported by additional structure-activity considerations. The findings provide new understanding of the interactions between ionizable organic compounds and carbonaceous surfaces, which has implications for noncovalent derivatization of CNTs, fate of ionizable pollutants, and associations of natural organic matter with CNTs and other carbonaceous materials in the environment.

Synthesis of novel inorganic-organic hybrid materials for simultaneous adsorption of metal ions and organic molecules in aqueous solution

In this paper, atom transfer radical polymerization (ATRP) and radical grafting polymerization were combined to synthesize a novel amphiphilic hybrid material, meanwhile, the amphiphilic hybrid material was employed in the absorption of heavy metal and organic pollutants. After the formation of attapulgite (ATP) ATRP initiator, ATRP block copolymers of styrene (St) and divinylbenzene (DVB) were grafted from it as ATP-P(S-b-DVB). Then radical polymerization of acrylonitrile (AN) was carried out with pendent double bonds in the DVD units successfully, finally we got the inorganic-organic hybrid materials ATP-P(S-b-DVB-g-AN). A novel amphiphilic hybrid material ATP-P(S-b-DVB-g-AO) (ASDO) was obtained after transforming acrylonitrile (AN) units into acrylamide oxime (AO) as hydrophilic segment. The adsorption capacity of ASDO for Pb(II) could achieve 131.6 mg/g, and the maximum removal capacity of ASDO towards phenol was found to be 18.18 mg/g in the case of monolayer adsorption at 30°C. The optimum pH was 5 for both lead and phenol adsorption. The adsorption kinetic suited pseudo-second-order equation and the equilibrium fitted the Freundlich model very well under optimal conditions. At the same time FT-IR, TEM and TGA were also used to study its structure and property.

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.

Compound-class specific estimation of solid organic compound vapour pressure and aqueous solubility from simple molecular structure descriptors and the temperature of melting

For many solid organic compounds, experimental data for their aqueous solubility and vapour pressure are lacking. Therefore, estimation procedures for these compound properties are needed. On theoretical grounds, this study derives a general compound-class specific estimation procedure for solid organic compound aqueous solubility and vapour pressure. The estimation procedure uses a linear combination of simple molecular descriptors for the molecular structure variation within the compound class and a polynomial for the temperature of melting. This procedure is applied to the vapour pressure of polycyclic aromatic hydrocarbons (PAHs), alkylated PAHs, polychlorinated dibenzo-p-dioxins and biphenyls and to the aqueous solubility of PAHs, methylated PAHs, chlorinated benzenes, polychlorinated and polybrominated biphenyls, chlorinated phenols, cresols, and chlorinated 2-methoxyphenols. The standard error of the solid vapour pressure or aqueous solubility estimates from the various compound-class specific regression equations was about 0.2 log units. For PAHs, chlorobenzenes, and PCBs used in the present study, aqueous solubility estimated from the regression equations taking the temperature of melting equal to 298 K, i.e. assuming that the compounds are in a hypothetical liquid state, was equal, within 0.1-0.3 log units to the subcooled liquid solubility estimated from literature regression equations.

Quantum-chemical predictions of redox potentials of organic anions in dimethyl sulfoxide and reevaluation of bond dissociation enthalpies measured by the electrochemical methods

A first-principle theoretical protocol was developed that could predict the absolute pK(a) values of over 250 structurally unrelated compounds in DMSO with a precision of 1.4 pK(a) units. On this basis we developed the first theoretical protocol that could predict the standard redox potentials of over 250 structurally unrelated organic anions in DMSO with a precision of 0.11 V. Using the two new protocols we systematically reevaluated the bond dissociation enthalpies (BDEs) measured previously by the electrochemical methods. It was confirmed that for most compounds the empirical equation (BDE = 1.37 pK(HA) + 23.1E(o) + constant) was valid. The constant in this equation was determined to be 74.0 kcal/mol, compared to 73.3 kcal/mol previously reported. Nevertheless, for a few compounds the empirical equation could not be used because the solvation energy changed dramatically during the bond cleavage, which resulted from the extraordinary change of dipole moment during the reaction. In addition, we found 40 compounds (mostly oximes and amides) for which the experimental values were questionable by over 5 kcal/mol. Further analyses revealed that all these questionable BDEs could be explained by one of the three following reasons: (1) the experimental pK(a) value is questionable; (2) the experimental redox potential is questionable; (3) the solvent effect cannot be neglected. Thus, by developing practical theoretical methods and utilizing them to solve realistic problems, we hope to demonstrate that ab initio theoretical methods can now be developed to make not only reliable, but also useful, predictions for solution-phase organic chemistry.

The effect of analyte acidity on signal suppression and the implications to peak purity determinations using atmospheric pressure ionization mass spectrometry

The effect of a co-eluting halogenated phenol, spiked at 1% of the main analyte level, has been examined for a series of halogenated phenols using LC-MS techniques. Similarly, the effect of co-eluting anilines has been investigated. The purpose of the work presented here was to evaluate the degree of signal suppression for structurally similar halogenated phenols and for similar anilines utilizing atmospheric pressure chemical ionization (APCI) in the negative mode and electrospray (ESI) in positive mode, respectively. A correlation between the effects of analyte ionization efficiency resulting from co-eluting compounds (signal suppression) and pK(a) has been made for these compounds. It was found that minimal signal suppression occurs when the spiked impurity has a similar (Delta pK(a)<1.5) acidity when compared to the main peak it is co-eluting with. The degree of signal suppression sharply increases when the difference in pK(a)'s between the main peak and the spiked impurity was greater than 1.5 units. Thus, when the main peak is much less acidic (more than 1.5 pK(a) difference) than the co-eluting impurity, signal suppression of the latter would not occur in negative mode APCI. Similarly, when the main peak is much less basic than the co-eluting peak, signal suppression of the impurity will also not be found for aniline compounds in positive mode ESI. Furthermore, the degree of signal suppression decreases as a function of sample load such that injections of 3 microg or less show no discernible impact on the spiked impurity peak. Ultimately, these results indicate that the use of mass spectrometry (MS) in peak purity determinations requires numerous considerations prior to assessing main peak purity. The optimization of sample load during an impurities assay will maximize co-eluting impurity signal as purity determinations by mass spectrometry made at sample loads above the 3 microg (sample load) threshold increase the risk for false negative assessment of impurities.

Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide

The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of -263.5, -260.2, and -273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the solvents mentioned above.

Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants

Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

Correlations and Predictions of pKa Values of Fluorophenols and Bromophenols Using Hydrogen-Bonded Complexes with Ammonia

Density functional theory calculations have been preformed on a series of the hydrogen-bonded fluorophenol-ammonia and bromophenol-ammonia complexes. Intermolecular and intramolecular properties, particularly those related to hydrogen bonding, have been carefully analyzed. Several properties, such as the bond length and stretching frequency of the hydroxyl group, the hydrogen bond length and binding energy, are shown to be highly correlated with each other and are linearly correlated with known experimental pKa values of the halogenated phenols. The linear correlations have been used to predict the pKa values of all fluorophenols and bromophenols in the series. The predicted pKa values are shown to be consistent from different molecular properties and are in good agreement with available experimental values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow the effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations.