Computational Calculation of Equilibrium Constants: Addition to Carbonyl Compounds

Hemiacetal-based dynamic systems: a new mechanistic insight

The formation of hemiacetals from pyrazine trifluoromethylketone as a model receptor and four simple alcohols was studied by using quantum chemical calculations and NMR spectroscopy. Free energy profiles for four types of mechanistic pathways were calculated and discussed with respect to kinetic and thermodynamic measurements. We show that hemiacetal formation is facilitated by an assisted proton transfer process via a pseudo eight-membered transition state which brings the theory and experiment into close agreement. Also, a newly proposed mechanistic pathway for hemiacetal formation via a five-membered transition state leading to zwitterionic intermediates is discussed. Direct proton transfer in a pseudo four-membered transition state can be ruled out due to the high energy of transition states with respect to other mechanistic pathways. We also show that in the case of hemiacetals, water and alcohol molecules cannot account sufficiently for the H-transfer process via six-membered transition states.

The photodissociation of solvated cyclopropanone and its hydrate explored via non-adiabatic molecular dynamics using ΔSCF

The decay of cyclopropanone is a typical example of a photodecomposition process. Ethylene and carbon monoxide are formed following the excitation to the first singlet excited state through a symmetrical or asymmetrical pathway. The results obtained with non-adiabatic molecular dynamics (NAMD) using the delta self-consistent field (ΔSCF) method correspond well to previous experimental and multireference theoretical studies carried out in the gas phase. Moreover, this efficient methodology allows NAMD simulations of cyclopropanone in aqueous solution to be performed, which reveal analogue deactivation mechanisms, but a shorter lifetime and reduced photodissociation as compared to the gas-phase. The excited state dynamics of cyclopropanone hydrate, an enzyme inhibitor, in an aqueous environment are reported as well. Cyclopropanone hydrate strongly interacts with the surrounding solvent via the formation of hydrogen bonds. Excitation to the first singlet excited state shows an asymmetric pathway with cyclopropanone hydrate and propionic acid as the main photoproducts.

The lifetime and photodissociation of cyclopropanone are reduced in aqueous solution, while the excitation of solvated cyclopropanone hydrate yields a range of photoproducts.

The pH-Dependence of the Hydration of 5-Formylcytosine - an Experimental and Theoretical Study

5-Formylcytosine is an important nucleobase in epigenetic regulation, whose hydrate form has been implicated in the formation of 5-carboxycytosine as well as oligonucleotide binding events. The hydrate content of 5-formylcytosine and its uracil derivative has now been quantified using a combination of NMR and mass spectroscopic measurements as well as theoretical studies. Small amounts of hydrate can be identified for the protonated form of 5-formylcytosine and for neutral 5-formyluracil. For neutral 5-formylcytosine, however, direct detection of the hydrate was not possible due to its very low abundance. This is in full agreement with theoretical estimates.

Thermodynamic non-ideality in charge regulation of weak polyelectrolytes

Polymer ionization differs from that for their monomeric counterparts due to intramolecular correlations. Such effects are conventionally described in terms of the site-binding model that accounts for short-range interactions between neighboring sites. With an apparent equilibrium constant for each ionizable group and the nearest-neighbor energy as adjustable parameters, the site-binding method is useful to correlate experimental titration curves when the site-site interactions are insignificant at long ranges. This work aims to describe the electrostatic behavior of weak polyelectrolytes in aqueous solutions on the basis of the intrinsic equilibrium constants of the individual ionizable groups and solution conditions underlying the thermodynamic non-ideality. A molecular thermodynamic model is proposed for the protonation of weak polyelectrolytes by incorporating classical density functional theory into the site-binding model to account for the effects of the local ionic environment on both inter-chain and intra-chain correlations. By an extensive comparison of theoretical predictions with experimental titration curves, we demonstrate that the thermodynamic model is able to quantify the ionization behavior of weak polyelectrolytes over a broad range of molecular architectures and solution conditions.

Microbiological versus Chemical Reductive Sulfidation: An Experimental and Theoretical Study

Microbiological reductive sulfidation (RS) has rarely been documented, although it represents an efficient strategy for thiol formation. In this work, we reported on the sulfate-respiring bacterium Desulfovibrio sp.86 that has previously demonstrated RS activity toward the pesticide chlordecone. The purpose of this study was to assess its substrate versatility using a set of 28 carbonyls, to compare with chemical RS and to rationalize the observed trends using a dual experimental and theoretical approach. The chemical RS generally proceeds in two steps (S/O exchange using a sulfur donor like P₄S₁₀, reduction of the thione intermediate). Intriguingly, chlordecone was found to be converted into chlordecthiol following the first step. Hence, we designed a protocol and applied it to the 28 substrates to assess their propensity to be directly converted into thiols with the P₄S₁₀ treatment alone. Finally, we performed density functional theory calculations on these carbonyls and their thiocarbonyl derivatives to build a set of structural, electronic, and thermodynamic parameters. The results showed that chemical and microbiological RS probably involved two distinct mechanisms. Chemically, we observed that several carbonyls, possessing electron-withdrawing groups and/or aromatic rings, were directly transformed into thiols in the presence of P₄S₁₀. The correlation obtained with the electron affinity of the thiones led us to conclude that a probable single-electron reductive transfer occurred during the first step. We also found that Desulfovibrio sp.86 transformed a variety of aldehydes and ketones, without ever detecting thiones. No significant correlation was observed with the calculated parameters, but a relationship between aldehyde RS biotransformation and bacterial growth was observed. Differences in selectivity with chemical RS open the way for further applications in organic synthesis.

Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes

The SPARC software program and comparative density functional theory (DFT) calculations were used to investigate the aqueous phase hydration equilibrium constants (Khyd) of perfluoroalkyl aldehydes (PFAlds) and n:2 fluorotelomer aldehydes (FTAlds). Both classes are degradation products of known industrial compounds and environmental contaminants such as fluorotelomer alcohols, iodides, acrylates, phosphate esters, and other derivatives, as well as hydrofluorocarbons and hydrochlorofluorocarbons. Prior studies have generally failed to consider the hydration, and subsequent potential hydrate acidity, of these compounds, resulting in incomplete and erroneous predictions as to their environmental behavior. In the current work, DFT calculations suggest that all PFAlds will be dominantly present as the hydrated form in aqueous solution. Both SPARC and DFT calculations suggest that FTAlds will not likely be substantially hydrated in aquatic systems or in vivo. PFAld hydrates are expected to have pKa values in the range of phenols (ca. 9 to 10), whereas n:2 FTAld hydrates are expected to have pKa values ca. 2 to 3 units higher (ca. 12 to 13). In order to avoid spurious modeling predictions and a fundamental misunderstanding of their fate, the molecular and/or dissociated hydrate forms of PFAlds and FTAlds need to be explicitly considered in environmental, toxicological, and waste treatment investigations. The results of the current study will facilitate a more complete examination of the environmental fate of PFAlds and FTAlds.

Mechanistic studies on the Rh(III)-mediated amido transfer process leading to robust C-H amination with a new type of amidating reagent

Mechanistic investigations on the Cp*Rh(III)-catalyzed direct C-H amination reaction led us to reveal the new utility of 1,4,2-dioxazol-5-one and its derivatives as highly efficient amino sources. Stepwise analysis on the C-N bond-forming process showed that competitive binding of rhodium metal center to amidating reagent or substrate is closely related to the reaction efficiency. In this line, 1,4,2-dioxazol-5-ones were observed to have a strong affinity to the cationic Rh(III) giving rise to dramatically improved amidation efficiency when compared to azides. Kinetics and computational studies suggested that the high amidating reactivity of 1,4,2-dioxazol-5-one can also be attributed to the low activation energy of an imido-insertion process in addition to the high coordination ability. While the characterization of a cationic Cp*Rh(III) complex bearing an amidating reagent was achieved, its facile conversion to an amido-inserted rhodacycle allowed for a clear picture on the C-H amidation process. The newly developed amidating reagent of 1,4,2-dioxazol-5-ones was applicable to a broad range of substrates with high functional group tolerance, releasing carbon dioxide as a single byproduct. Additional attractive features of this amino source, such as they are more convenient to prepare, store, and use when compared to the corresponding azides, take a step closer toward an ideal C-H amination protocol.

Stereoselective Synthesis of Dioxolanes and Oxazolidines via a Desymmetrization Acetalization/Michael Cascade

The desymmetrization of p-quinols using a Brønsted acid catalyzed acetalization/Michael cascade was achieved in high yields and diastereoselectivities for aldehydes and imines. Use of a chiral Brønsted acid allowed for the synthesis of 1,3-dioxolane and 1,3-oxazolidine products in modest enantioselectivity.

Merging domino and redox chemistry: stereoselective access to di- and trisubstituted β,γ-unsaturated acids and esters

Merging is the game! The coupling of a domino reaction and an internal neutral redox reaction constitutes an excellent manifold for the stereoselective synthesis of di- and trisubstituted olefins featuring a malonate unit, an ester, or a free carboxylic acid as substituents at the allylic position (see scheme; MW=microwave). The reaction utilizes simple starting materials (propargyl vinyl ethers), methanol or water as solvents, and a very simple and bench-friendly protocol.

Atmospheric degradation of perfluoro-2-methyl-3-pentanone: photolysis, hydrolysis and hydration

Perfluorinated carboxylic acids are widely distributed in the environment, including remote regions, but their sources are not well understood. Perfluoropropionic acid (PFPrA, CF(3)CF(2)C(O)OH) has been observed in rainwater but the observed amounts can not be explained by currently known degradation pathways. Smog chamber studies were performed to assess the potential of photolysis of perfluoro-2-methyl-3-pentanone (PFMP, CF(3)CF(2)C(O)CF(CF(3))(2)), a commonly used fire-fighting fluid, to contribute to the observed PFPrA loadings. The photolysis of PFMP gives CF(3)CF(2)C·(O) and ·CF(CF(3))(2) radicals. A small (0.6%) but discernible yield of PFPrA was observed in smog chamber experiments by liquid chromatography-mass spectrometry offline chamber samples. The Tropospheric Ultraviolet-Visible (TUV) model was used to estimate an atmospheric lifetime of PFMP with respect to photolysis of 4-14 days depending on latitude and time of year. PFMP can undergo hydrolysis to produce PFPrA and CF(3)CFHCF(3) (HFC-227ea) in a manner analogous to the Haloform reaction. The rate of hydrolysis was measured using (19)F NMR at two different pHs and was too slow to be of importance in the atmosphere. Hydration of PFMP to give a geminal diol was investigated computationally using density functional theory. It was determined that hydration is not an important environmental fate of PFMP. The atmospheric fate of PFMP seems to be direct photolysis which, under low NO(x) conditions, gives PFPrA in a small yield. PFMP degradation contributes to, but does not appear to be the major source of, PFPrA observed in rainwater.

Probing autoinducer-2 based quorum sensing: the biological consequences of molecules unable to traverse equilibrium states

Bacteria have developed a cell-to-cell communication system, termed quorum sensing (QS), which allows for the population-dependent coordination of their behavior via the exchange of chemical signals. Autoinducer-2 (AI-2), a class of QS signals derived from 4,5-dihydroxy-2,3-pentandione (DPD), has been revealed as a universal signaling molecule in a variety of bacterial species. In spite of considerable interest, the study of putative AI-2 based QS systems remains a challenging topic in part due to the rapid interconversion between the linear and cyclic forms of DPD. Herein, we report the design and development of efficient syntheses of carbocyclic analogues of DPD, which are locked in the cyclic form. The synthetic analogues were evaluated for the modulation of AI-2-based QS in Vibrio harveyi and Salmonella typhimurium. No agonists were uncovered in either V. harveyi or S. typhimurium assay, whereas weak to moderate antagonists were found against V. harveyi. On the basis of NMR analyses and DFT calculations, the heterocyclic oxygen atom within DPD appears necessary to promote hydration at the C3 position of cyclic DPD to afford the active tetrahydroxy species. These results also shed light on the interaction between the heterocyclic oxygen atom and receptor proteins as well as the importance of the linear form and dynamic equilibrium of DPD as crucial requirements for activation of AI-2 based QS circuits.

Reactivity of mucohalic acids in water

One group of disinfection byproducts of increasing interest are the halogenated furanones, which are formed in the chlorination of drinking water. Among these halofuranones is mucochloric acid (MCA, 3,4-dichloro-5-hydroxyfuran-2(5H)-one), and mucobromic acid (MBA, 3,4-dibromo-5-hydroxyfuran-2(5H)-one). Both mucohalic acids (MXA) are direct genotoxins and potential carcinogens, with the capacity to alkylate the DNA bases guanosine, adenosine and cytosine, and they have been measured in concentrations ranging up to 700 ng/l in tap water. MCA and MBA react in basic aqueous medium to form mucoxyhalic acids (4-halo-3,5-hydroxyfuran-2(5H)-one). Since: i) this reaction may represent the first step in the abiotic decomposition of mucohalic acids, ii) mucoxyhalic acids have been proposed as possible intermediates in the reaction of MXA with DNA, a kinetic study of the reaction mechanism is of interest. Here, the following conclusions were drawn: a) At moderately basic pH, the reaction of mucohalic acids with OH(-) to form mucoxyhalic acids is kinetically significant. b) The nucleophilic attack of hydroxide ions on MXA occurs through a combination of two paths: one of them is first-order in hydroxide whereas the other is second-order and are proposed to occur through the deprotonation of the hydrate of MXA. c) The hydration constants of mucohalic acids -0.23 and 0.17 for MCA and MBA respectively - corresponds to the very significant hydrate concentrations. Since hydrates are not electrophilic, these values imply a decrease in the alkylating capacity of mucohalic acids.