Energy Barriers for Alkaline Hydrolysis of Carboxylic Acid Esters in Aqueous Solution by Reaction Field Calculations

Shoreline Drying of Microseira (Lyngbya) wollei Biomass Can Lead to the Release and Formation of Toxic Saxitoxin Analogues to the Water Column

The harmful, filamentous cyanobacteria Microseira (Lyngbya) wollei produces several toxic analogues of saxitoxin (Lyngbya wollei toxins 1-6, or LWTs 1-6), grows in shallow water, and can deposit significant biomass on nearby shorelines. Here, we show that the LWTs are stable in the biomass during subsequent drying but that the process facilitates the later release of LWTs upon return to the water column. Under basic conditions, LWTs hydrolyzed to generate products that were significantly more neurotoxic than the initial toxins. Aqueous LWTs were subjected to conditions of covarying temperature and pH, and their degradation rates and products were determined at each condition. LWTs 1, 5, and 6 degraded faster at pH ≥ 8 at all temperatures. Their degradation products, which included decarbamoyl saxitoxin and LWT 4, were consistent with a base-catalyzed hydrolysis mechanism and represented a net increase in total biomass toxicity normalized against the equivalent toxicity of saxitoxin. The corresponding pre-exponential terms and activation energies for hydrolysis were obtained for pH 6-10 over the temperature range 10-40 °C. A locally weighted scatterplot smoothing (LOWESS) regression was developed to predict the loss of parent toxins and subsequent products in the water column under conditions corresponding to those commonly encountered in cyanobacterial blooms.

Insights into a new alternative method with graphene oxide/polyacrylamide/Fe3O4 nanocomposite for the extraction of six odor-active esters from Strong-aroma types of Baijiu

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A novel approach of MSPE-GC/MS based on GO/PAM/Fe₃O₄ was developed for odor-active esters determination in Baijiu samples.

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GO/PAM/Fe₃O₄ earned highly selective recognition properties and larger adsorption capacities for six odor-active esters.

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The method provided lower LODs, better precision and faster separation.

Liquid-liquid extraction (LLE) is the most commonly utilized technique for the extraction of odor-active esters (OAEs) in strong-aroma types of Baijiu (SAB). However, since the contents of different OAEs in SAB vary widely, it is still a puzzle to ensure that all OAEs to be thoroughly extracted by LLE without the problem of saturated adsorption. Herein, a novel approach of magnetic solid phase extraction (MSPE), based on the magnetic graphene oxide nanocomposite modified with polyacrylamide (GO/PAM/Fe₃O₄), was employed for the efficient extraction of six OAEs from SAB. Compared with LLE, GO/PAM/Fe₃O₄ exhibited highly selective recognition properties and larger adsorption capacities for OAEs (ranging from 13.68 to 39.06 mg/g), resulting in better extraction performances for OAEs. Coupled with GC–MS, six OAEs in real SAB were successfully determined, with recoveries ranged from 70.1 ∼ 90.0% and LODs at 0.08 ∼ 1.35 µg/L. Overall, the MSPE-GC/MS is a promising alternative for accurate determination of OAEs in SAB.

Accelerated Degradation of Poly(lactide acid)/Poly(hydroxybutyrate) (PLA/PHB) Yarns/Fabrics by UV and O2 Exposure in South China Seawater

Marine plastic pollution is emerging as a potential hazard to global ecosystems and human health. Micro-fibers derived from synthetic textiles contribute a considerable proportion of plastic debris. Bio-polymers/bio-plastics have been proposed for the application of apparel products, yet their degradability, fate, durability and related environmental parameters are still elusive and need further exploration. Herein, we report the degradation behavior of poly(lactide acid)/poly(hydroxybutyrate) (PLA/PHB) fabrics, made from PLA/PHB multi-filament yarns, in subtropics marine seawater. The degradation experiments were performed under various parallel conditions including static seawater, aerobic seawater in dark box, aerobic seawater under sunlight, static seawater under ultra-violet light and aerobic seawater under ultra-violet light. Continuous mass loss of PLA/PHB fabrics as the immersion time in the seawater increased was confirmed. The hydrolysis rate of PLA/PHB fabrics accelerated in the presence of UV light and dissolved oxygen in the seawater. Moreover, the tensile strength of the PLA/PHB yarns dropped rapidly by 38.54–68.70% in spite of the mass loss percentage being from 9.57% to 14.48% after 2 weeks’ immersion. All the PLA/PHB fabrics after two weeks’ immersion exhibited similar ATR-IR spectra. Therefore, the degradability of PLA/PHB fabrics, in the marine surface water under the synergistic destructive effect of seawater, UV and dissolved oxygen, provides a pathway for more sustainable textile fibers and apparel products.

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

Interfacial reactions are notoriously difficult to characterize, and robust prediction of the chemical evolution and associated functionality of the resulting surface film is one of the grand challenges of materials chemistry. The solid-electrolyte interphase (SEI), critical to Li-ion batteries (LIBs), exemplifies such a surface film, and despite decades of work, considerable controversy remains regarding the major components of the SEI as well as their formation mechanisms. Here we use a reaction network to investigate whether lithium ethylene monocarbonate (LEMC) or lithium ethylene dicarbonate (LEDC) is the major organic component of the LIB SEI. Our data-driven, automated methodology is based on a systematic generation of relevant species using a general fragmentation/recombination procedure which provides the basis for a vast thermodynamic reaction landscape, calculated with density functional theory. The shortest pathfinding algorithms are employed to explore the reaction landscape and obtain previously proposed formation mechanisms of LEMC as well as several new reaction pathways and intermediates. For example, we identify two novel LEMC formation mechanisms: one which involves LiH generation and another that involves breaking the (CH₂)O-C(═O)OLi bond in LEDC. Most importantly, we find that all identified paths, which are also kinetically favorable under the explored conditions, require water as a reactant. This condition severely limits the amount of LEMC that can form, as compared with LEDC, a conclusion that has direct impact on the SEI formation in Li-ion energy storage systems. Finally, the data-driven framework presented here is generally applicable to any electrochemical system and expected to improve our understanding of surface passivation.

Mechanisms of a Cyclobutane-Fused Lactone Hydrolysis in Alkaline and Acidic Conditions

Searching for functional polyesters with stability and degradability is important due to their potential applications in biomedical supplies, biomass fuel, and environmental protection. Recently, a cyclobutane-fused lactone (CBL) polymer was experimentally found to have superior stability and controllable degradability through hydrolysis reactions after activation by mechanical force. In order to provide a theoretical basis for developing new functional degradable polyesters, in this work, we performed a detailed quantum chemical study of the alkaline and acidic hydrolysis of CBL using dispersion-corrected density functional theory (DFT-D3) and mixed implicit/explicit solvent models. Various possible hydrolysis mechanisms were found: B_AC2 and B_AL2 in the alkaline condition and A_AC2, A_AL2, and A_AL1 in the acidic condition. Our calculations indicated that CBL favors the B_AC2 and A_AC2 mechanisms in alkaline and acidic conditions, respectively. In addition, we found that incorporating explicit water solvent molecules is highly necessary because of their strong hydrogen-bonding with reactant/intermediate/product molecules.

Simulations of the Biodegradation of Citrate-Based Polymers for Artificial Scaffolds Using Accelerated Reactive Molecular Dynamics

In this study, we investigate the reactivity and mechanical properties of poly(1,6-hexanediol-co-citric acid) via ReaxFF molecular dynamics simulations. We implement an accelerated scheme within the ReaxFF framework to study the hydrolysis reaction of the polymer which is provided with a sufficient amount of energy known as the restrain energy after a suitable pretransition-state configuration is obtained to overcome the activation energy barrier and the desired product is obtained. The validity of the ReaxFF force field is established by comparing the ReaxFF energy barriers of ester and ether hydrolysis with benchmark DFT values in the literature. We perform chemical and mechanical degradation of polymer chain bundles at 300 K. We find that ester hydrolyzes faster than ether because of the lower activation energy barrier of the reaction. The selectivity of the bond-boost scheme has been demonstrated by lowering the boost parameters of the accelerated simulation, which almost stops the ether hydrolysis. Mechanical degradation of prehydrolyzed and intermittent hydrolyzed polymer bundles is performed along the longitudinal direction at two different strain rates. We find that the tensile modulus of the polymers increases with increase in strain rates, which shows that polymers show a strain-dependent behavior. The tensile modulus of the polyester-ether is higher than polyester but reaches yield stress faster than polyester. This makes polyester more ductile than polyester-ether.

The transition state conformational effect on the activation energy of ethyl acetate neutral hydrolysis

We report a first-principles study on ethyl acetate neutral hydrolysis in which we focus on the activation energy variation resulting from the conformational effect in the transition state. We use the conformers of ethyl formate, ethyl acetate, ethyl fluoroacetate, and ethyl chloroacetate as the ester models and one water molecule with a one-step reaction mechanism. We also consider the long-range interaction and the surrounding water in the form of PCM. Our results show that the various conformers yield a significant range of activation energy. Moreover, the gauche conformer has lower activation energy than the trans conformer. The activation energy in its own right is lowered by the halogen atoms. Finally, we remark that the long-range correction and PCM stabilize the transition state geometry but raise the activation energy.

Development of Prediction Models on Base-Catalyzed Hydrolysis Kinetics of Phthalate Esters with Density Functional Theory Calculation

Many phthalate esters (PAEs) are chemicals of high production volume and of toxicological concern. The second-order rate constant for base-catalyzed hydrolysis ( k_B) is a key parameter for assessing environmental persistence of PAEs. However, the k_B values for most PAEs are lacking, and the experimental determination of k_B encounters various difficulties. Herein, density functional theory (DFT) methods were selected by comparing empirical k_B values of five PAEs and five carboxylic acid esters with the DFT-calculated ones. Results indicate that PAEs with cyclic side chains are more vulnerable to base-catalyzed hydrolysis than PAEs with linear alkyl side chains, followed by PAEs with branched alkyl side chains. By combining experimental and DFT-calculated second-order rate constants for base-catalyzed hydrolysis of one side chain in PAEs ( k_{B_side chain}), quantitative structure-activity relationship models were developed. The models can differentiate PAEs with the departure of the leaving group (or the nucleophilic attack of OH^-) as the rate-determining step in the hydrolysis and estimate k_B values, which provides a promising way to predict hydrolysis kinetics of PAEs. The half-lives of the investigated PAEs were calculated and vary from 0.001 h to 558 years (pH = 7∼9), further illustrating the necessity of prediction models for hydrolysis kinetics in assessing the environmental persistence of chemicals.

Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution

To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.

Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects

It has been difficult to directly measure the spontaneous hydrolysis rate of urea and, thus, 1,1,3,3-tetramethylurea (Me4U) was used as a model to determine the "experimental" rate constant for urea hydrolysis. The use of Me4U was based on an assumption that the rate of urea hydrolysis should be 2.8 times that of Me4U hydrolysis because the rate of acetamide hydrolysis is 2.8 times that of N,N-dimethyl-acetamide hydrolysis. The present first-principles electronic-structure calculations on the competing non-enzymatic hydrolysis pathways have demonstrated that the dominant pathway is the neutral hydrolysis via the CN addition for both urea (when pH < ~11.6) and Me4U (regardless of pH), unlike the non-enzymatic hydrolysis of amides where alkaline hydrolysis is dominant. Based on the computational data, the substituent shift of the free energy barrier calculated for the neutral hydrolysis is remarkably different from that for the alkaline hydrolysis, and the rate constant for the urea hydrolysis should be ~1.3 × 10(9)-fold lower than that (4.2 × 10(-12) s(-1)) measured for the Me4U hydrolysis. As a result, the rate enhancement and catalytic proficiency of urease should be 1.2 × 10(25) and 3 × 10(27) M(-1), respectively, suggesting that urease surpasses proteases and all other enzymes in its power to enhance the rate of reaction. All of the computational results are consistent with available experimental data for Me4U, suggesting that the computational prediction for urea is reliable.

Density functional theory study of selective deacylation of aromatic acetate in the presence of aliphatic acetate under ammonium acetate mediated conditions

Aromatic acetates can be selectively deprotected in the presence of aliphatic acetates under ammonium acetate mediated condition. B3LYP/6-31++G** level of theory was demonstrated to be successfully used to model the relative reaction rates for deacylation reactions for aliphatic and aromatic ester systems. On the basis of the mechanistic studies, acetate anion is most likely to be the active catalyst for the ester deacylation reactions under ammonium acetate mediated condition.

Mechanisms of lactone hydrolysis in neutral and alkaline conditions

The neutral and base-catalyzed hydrolysis of nine carboxylic acid esters was studied using a hybrid supermolecule-PCM approach including six explicit water molecules. The molecules studied included two linear esters, four β-lactones, two γ-lactones, and one δ-lactone: ethyl acetate and methyl formate, β-propiolactone, β-butyrolactone, β-isovalerolactone, diketene (4-methyleneoxetan-2-one), γ-butyrolactone, 2(5H)-furanone, and δ-valerolactone. DFT and ab initio methods were used to analyze the features of the various possible hydrolysis mechanisms. For all compounds, reasonable to very good qualitative and quantitative agreement with experimental work was found, and evidence is provided to support long-standing hypotheses regarding the role of solvent molecule as a base catalyst. In addition, novel evidence is presented for the existence of an elimination-addition mechanism in the basic hydrolysis of diketene. A parallel work addresses the acid-catalyzed hydrolysis of lactones.

Acylglucuronide in alkaline conditions: migration vs. hydrolysis

This work rationalizes the glucuronidation process (one of the reactions of the phase II metabolism) for drugs having a carboxylic acid moiety. At this stage, acylglucuronides (AG) metabolites are produced, that have largely been reported in the literature for various drugs (e.g., mycophenolic acid (MPA), diclofenac, ibuprofen, phenylacetic acids). The competition between migration and hydrolysis is rationalized by adequate quantum calculations, combing MP2 and density functional theory (DFT) methods. At the molecular scale, the former process is a real rotation of the drug around the glucuconic acid. This chemical-engine provides four different metabolites with various toxicities. Migration definitely appears feasible under alkaline conditions, making proton release from the OH groups. The latter reaction (hydrolysis) releases the free drug, so the competition is of crucial importance to tackle drug action and elimination. From the theoretical data, both migration and hydrolysis appear kinetically and thermodynamically favored, respectively.

Thermodynamics of chemical reactions with COSMO-RS: the extreme case of charge separation or recombination

Many technically relevant chemical processes in the condensed phase involve as elementary reactive steps the formation of ions from neutral species or, as the opposite, recombination of ions. Such reactions that generate or annihilate charge defy the standard gas phase quantum chemical treatment, and also continuum solvation models are only partially able to account for the right amount of stabilization in solution. In this work, for such types of reaction, a solvation treatment involving the COSMO-RS method is assessed, which leads to improved results, i.e., errors of only around 10 kJ/mol for both protic and aprotic solvents. The examples discussed here comprise protolysis reactions and organo halide heterolysis, for both of which a comparison with reliable experimental data is possible. It is observed that for protolysis, the quality of results does not strongly depend on the quantum chemical method used for energy calculation. In contrast, in the case of heterolytic carbon-chlorine bond cleavage, clearly better results are obtained for higher correlated (coupled cluster) methods or the density functional M06-2X, which is well known for its accuracy if applied to organic chemistry. This hints at least that the right answer is obtained for the right reason and not due to a compensation of errors from gas phase thermodynamics with those from the solvation treatment. Problems encountered with certain critical solvents or upon decomposing Gibbs free energies into heats or entropies of reaction are found to relate mostly to the parameterization of the H-bonding term within COSMO-RS.

Investigation of solvolysis kinetics of new synthesized fluocinolone acetonide C-21 esters--an in vitro model for prodrug activation

In this study the solvolysis of newly synthesized fluocinolone acetonide C-21 esters was analysed in comparison with fluocinonide during a 24-hour period of time. The solvolysis was performed in an ethanol-water (90:10 v/v) mixture using the excess of NaHCO₃. The solvolytic mixtures of each investigated ester have been assayed by a RP-HPLC method using isocratic elution with methanol-water (75:25 v/v); flow rate 1 mL/min; detection at 238 nm; temperature 25 °C. Solvolytic rate constants were calculated from the obtained data. Geometry optimizations and charges calculations were carried out by Gaussian W03 software. A good correlation (R = 0.9924) was obtained between solvolytic rate constants and the polarity of the C-O2 bond of those esters. The established relation between solvolytic rate constant (K) and lipophilicity (cLogP) with experimental anti-inflammatory activity could be indicative for topical corticosteroid prodrug activation.

Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell

Building on the SVPE (surface and volume polarization for electrostatics) model for electrostatic contributions to the free energy of solvation with explicit consideration of both surface and volume polarization effects, on the SMx approach to including first-solvation-shell contributions, and on the linear relationship between the electric field and short-range electrostatic contributions found by Chipman, we have developed a new method for computing absolute aqueous solvation free energies by combining the SVPE method with semiempirical terms that account for effects beyond bulk electrostatics. The new method is called SMVLE, and the elements it contains are denoted by SVPE-CDSL where SVPE denotes accounting for bulk electrostatic interactions between solute and solvent with both surface and volume contributions, CDS denotes the inclusion of solvent cavitation, changes in dispersion energy, and possible changes in local solvent structure by a semiempirical term utilizing geometry-dependent atomic surface tensions as implemented in SMx models, and L represents the local electrostatic effect derived from the outward-directed normal electric field on the cavity surface. The semiempirical CDS and L terms together represent the deviation of short-range contributions to the free energy of solvation from those accounted for by the SVPE term based on the bulk solvent dielectric constant. A solute training set containing a broad range of molecules used previously in the development of SM6 is used here for SMVLE model calibration. The aqueous solvation free energies predicted by the parameterized SMVLE model correlate exceedingly well with experimental values. The square of the correlation coefficient is 0.9949 and the slope is 1.0079. Comparison of the final SMVLE model against the earlier SMx solvation model shows that the parameterized SMVLE model not only yields good accuracy for neutrals but also significantly increases the accuracy for ions, making it the best implicit solvation model to date for aqueous solvation free energies of ions. The semiempirical terms associated with the outward-directed electric field account in a physical way for the improvement in the predictive accuracy for ions. The SMVLE method greatly decreases the need to include explicit water molecules for accurate modeling of solvation free energies of ions.

First-Principles Determination of Molecular Conformations of Indolizidine (-)-235B' in Solution

Indolizidine (-)-235B' is a particularly interesting natural product, as it is the currently known, most potent and subtype-selective open-channel blocker of the alpha4beta2 nicotinic acetylcholine receptor (nAChR). In the current study, extensive first-principles electronic structure calculations have been carried out in order to determine the stable molecular conformations and their relative free energies of the protonated and deprotonated states of (-)-235B' in the gas phase, in chloroform, and in aqueous solution. The (1)H and (13)C NMR chemical shifts calculated using the computationally determined dominant molecular conformation of the deprotonated state are all consistent with available experimental NMR spectra of (-)-235B' in chloroform, which suggests that the computationally determined molecular conformations are reasonable. Our computational results reveal for the first time that two geminal H atoms on carbon-3 (C3) of (-)-235B' have remarkably different chemical shifts (i.e. 3.24 and 2.03 ppm). The computational results help one to better understand and analyze the experimental (1)H NMR spectra of (-)-235B'. The finding of remarkably different chemical shifts of two C3 geminal H atoms in a certain molecular conformation of (-)-235B' may also be valuable in analysis of NMR spectra of other related ring-containing compounds. In addition, the pK(a) of (-)-235B' in aqueous solution is predicted to be ~9.7. All of the computational results provide a solid basis for future studies of the microscopic and phenomenological binding of various receptor proteins with the protonated and deprotonated structures of this unique open-channel blocker of alpha4beta2 nAChRs. This computational study also demonstrates how one can appropriately use computational modeling and spectroscopic analysis to address the structural and spectroscopic problems that cannot be addressed by experiments alone.

First-principles determination of molecular conformations of cyclic adenosine 3',5'-monophosphate in gas phase and aqueous solution

Extensive first-principles electronic structure calculations were performed in this study to explore the possible molecular structures and their concentration distribution of an intracellular second messenger, that is, cyclic adenosine 3',5'-monophosphate (cAMP), and its protonated form (cAMPH) in the gas phase and aqueous solution. The calculations resulted in prediction of four different stable conformers of cAMP and eight different stable conformers of cAMPH and their relative Gibbs free energies in the gas phase and aqueous solution. All of the computational results consistently demonstrate that the predominant conformers of cAMP and cAMPH are always the cAMP-chair-anti and cAMPH-chair2-syn conformers, respectively, in both the gas phase and aqueous solution. It has been demonstrated that the free energy barriers calculated for the intertransformation reactions between different conformers are very low (below approximately 6 kcal/mol) such that the intertransformation reactions between different conformers are very fast so that the concentration distribution of the system can quickly reach the thermodynamic equilibration during the process of binding with a protein. The calculated phenomenological pKa of 3.66 is in good agreement with the experimental pKa of 3.9 reported in literature, suggesting that the computational predictions resulted from this study are reasonable.

Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers

The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.

Structure-and-mechanism-based design and discovery of therapeutics for cocaine overdose and addiction

(-)-Cocaine is a widely abused drug and there is currently no available anti-cocaine therapeutic. Promising agents, such as anti-cocaine catalytic antibodies and high-activity mutants of human butyrylcholinesterase (BChE), for therapeutic treatment of cocaine overdose have been developed through structure-and-mechanism-based design and discovery. In particular, a unique computational design strategy based on the modeling and simulation of the rate-determining transition state has been developed and used to design and discover desirable high-activity mutants of BChE. One of the discovered high-activity mutants of BChE has a approximately 456-fold improved catalytic efficiency against (-)-cocaine. The encouraging outcome of the structure-and-mechanism-based design and discovery effort demonstrates that the unique computational design approach based on transition state modeling and simulation is promising for rational enzyme redesign and drug discovery. The general approach of the structure-and-mechanism-based design and discovery may be used to design high-activity mutants of any enzyme or catalytic antibody.

First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution

The absolute pKa values of 24 representative amine compounds, including cocaine, nicotine, 10 neurotransmitters, and 12 anilines, in aqueous solution were calculated by performing first-principles electronic structure calculations that account for the solvent effects using four different solvation models, i.e., the surface and volume polarization for electrostatic interaction (SVPE) model, the standard polarizable continuum model (PCM), the integral equation formalism for the polarizable continuum model (IEFPCM), and the conductor-like screening solvation model (COSMO). Within the examined computational methods, the calculations using the SVPE model lead to the absolute pKa values with the smallest root-mean-square-deviation (rmsd) value (1.18). When the SVPE model was replaced by the PCM, IEFPCM, and COSMO, the rmsd value of the calculated absolute pKa values became 3.21, 2.72, and 3.08, respectively. All types of calculated pKa values linearly correlate with the experimental pKa values very well. With the empirical corrections using the linear correlation relationships, the theoretical pKa values are much closer to the corresponding experimental data and the rmsd values become 0.51-0.83. The smallest rmsd value (0.51) is also associated with the SVPE model. All of the results suggest that the first-principles electronic structure calculations using the SVPE model are a reliable approach to the pKa prediction for the amine compounds.

Theoretical studies of the transition-state structures and free energy barriers for base-catalyzed hydrolysis of amides

The transition-state structures and free energy barriers for the rate-determining step (i.e. the formation of a tetrahedral intermediate) of base-catalyzed hydrolysis of a series of amides in aqueous solution have been studied by performing first-principle electronic structure calculations using a hybrid supermolecule-polarizable continuum approach. The calculated results and a revisit of recently reported experimental proton inventory data reveal that the favorable transition-state structure optimized for the tetrahedral intermediate formation of hydroxide ion-catalyzed hydrolysis of formamide may have three solvating water molecules remaining on the attacking hydroxide oxygen and two additional water molecules attached to the carbonyl oxygen of formamide. The calculated results have also demonstrated interesting substituent effects on the optimized transition-state geometries, on the transition-state stabilization, and on the calculated free energy barriers for the base-catalyzed hydrolysis of amides. When some or all of the hydrogen atoms of formamide are replaced by methyl groups, the total number of water molecules hydrogen-bonding with the attacking hydroxide in the transition state decreases from three for formamide to two for N-methylacetamide, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). The larger substituents of the amide hinder the solvent water molecules approaching the attacking hydroxide oxygen in the transition state and, therefore, destabilize the transition-state structure and increase the free energy barrier. By using the optimized most favorable transition-state structures, the calculated free energy barriers, i.e., 21.6 (or 21.7), 22.7, 23.1, and 26.0 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively, are in good agreement with the available experimental free energy barriers, i.e., 21.2, 21.5, 22.6, and 24.1 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively.

New formulation and implementation for volume polarization in dielectric continuum theory

In the use of dielectric continuum theory to model bulk solvation effects on the electronic structure and properties of a solute, volume polarization contributions due to quantum mechanical penetration of the solute charge density outside the cavity nominally enclosing it are known to be significant. This work provides a new formulation and implementation of methods for solution of the requisite Poisson equation. In previous formulations the determination of the surface polarization contribution required evaluation of the difficult to calculate electric field generated by the volume polarization. It is shown that this problematic quantity can be eliminated in favor of other more easily evaluated quantities. That formal advance also opens the way for a more efficient apparatus to be implemented for calculation of the direct contribution of volume polarization to the solvation energy. The new formulation and its practical implementation are described, and illustrative numerical results are given for several neutral and ionic solutes to study the convergence and precision in practice.

Solvent effect on concertedness of the transition state in the hydrolysis of p-nitrophenyl acetate

[reaction: see text]. The reaction pathway for the alkaline hydrolysis of p-nitrophenyl acetate is investigated using density functional theory. It is shown that solvent plays an indispensable role in shaping the concerted transition state. The concertedness of this transition state is supported by good agreement with the measured kinetic isotope effects.

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.

Ab Initio Study of the Complexes of Halogen-Containing Molecules RX (X=Cl, Br, and I) and NH3: Towards Understanding the Nature of Halogen Bonding and the Electron-Accepting Propensities of Covalently Bonded Halogen Atoms

Ab initio calculations have been performed on a series of complexes formed between halogen-containing molecules and ammonia to gain a deeper insight into the nature of halogen bonding. It appears that the dihalogen molecules form the strongest halogen-bonded complexes with ammonia, followed by HOX; the charge-transfer-type contribution has been demonstrated to dominate the halogen bonding in these complexes. For the complexes involving carbon-bound halogen molecules, our calculations clearly indicate that electrostatic interactions are mainly responsible for their binding energies. Whereas the halogen-bond strength is significantly enhanced by progressive fluorine substitution, the substitution of a hydrogen atom by a methyl group in the CH(3)X...NH(3) complex weakened the halogen bonding. Moreover, remote substituent effects have also been noted in the complexes of halobenzenes with different para substituents. The influence of the hybridization state of the carbon atom bonded to the halogen atom has also been examined and the results reveal that halogen-bond strengths decrease in the order HC triple bond CX > H(2)C=CHX approximately O=CHX approximately C(6)H(5)X > CH(3)X. In addition, several excellent linear correlations have been established between the interaction energies and both the amount of charge transfer and the electrostatic potentials corresponding to an electron density of 0.002 au along the R-X axis; these correlations provide good models with which to evaluate the electron-accepting abilities of the covalently bonded halogen atoms. Finally, some positively charged halogen-bonded systems have been investigated and the effect of the charge has been discussed.

Reaction Pathways and Free Energy Barriers for Alkaline Hydrolysis of Insecticide 2-Trimethylammonioethyl Methylphosphonofluoridate and Related Organophosphorus Compounds: Electrostatic and Steric Effects

Reaction pathways and free energy barriers for alkaline hydrolysis of the highly neurotoxic insecticide 2-trimethylammonioethyl methylphosphonofluoridate and related organophosphorus compounds were studied by performing first-principles electronic structure calculations on representative methylphosphonofluoridates, (RO)CH3P(O)F, in which R = CH2CH2N+(CH3)3, CH3, CH2CH2C(CH3)3, CH2CH2CH(CH3)2, CH(CH3)CH2N+(CH3)3, and CH(CH3)CH2N(CH3)2. The dominant reaction pathway was found to be associated with a transition state in which the attacking nucleophile OH- and the leaving group F- are positioned on opposite sides of the plane formed by the three remaining atoms attached to the phosphorus in order to minimize the electrostatic repulsion between these two groups. The free energy barriers calculated for the rate-determining step of the dominant pathway are 12.5 kcal/mol when R = CH2CH2N+(CH3)3, 15.5 kcal/mol when R = CH3, 17.9 kcal/mol when R = CH2CH2C(CH3)3, 16.5 kcal/mol when R = CH2CH2CH(CH3)2, 13.4 kcal/mol when R = CH(CH3)CH2N+(CH3)3, and 18.7 kcal/mol when R = CH(CH(3))CH(2)N(CH(3))(2). The calculated free energy barriers are in good agreement with available experimentally derived activation free energies, i.e. 14.7 kcal/mol when R = CH(3), 13.4 kcal/mol when R = CH2CH2N+(CH3)3, and 13.9 kcal/mol when R = CH(CH3)CH2N+(CH3)3. A detailed analysis of the calculated energetic results and available experimental data suggests that the net charge of the molecule (M) being hydrolyzed is a prominent factor affecting the free energy barrier (DeltaG) for the alkaline hydrolysis of phosphodiesters, phosphonofluoridates, and related organophosphorus compounds. The electrostatic interactions between the attacking nucleophile OH- and the molecule M being hydrolyzed favor such an order of the free energy barrier: DeltaG(M(+)+OH-) < DeltaG(M0+OH-) < DeltaG(M(-)+OH-), where M+, M0, and M- represent the cationic, neutral, and anionic molecules, respectively. The change of the substituent R in (RO)CH(3)P(O)F from CH3 to CH2CH2N+(CH3)3 is associated with both the electrostatic and steric effects on the free energy barrier, but the electrostatic effect dominates the substituent shift of the free energy barrier. This helps to better understand why the alkaline hydrolysis of (RO)CH3P(O)F with R = CH2CH2N+(CH3)3 and CH(CH3)CH2N+(CH3)3 is significantly faster than that with R = CH3. The effect of electrostatic interaction also helps to understand why the rate constants for the alkaline hydrolysis of phosphodiesters, such as intramolecular second messenger adenosine 3',5'-phosphate (cAMP), are generally smaller than those for the alkaline hydrolysis of the phosphonofluoridates and related phosphotriesters.