PMC:4264129 / 114572-129688 JSON TXT

Annnotations TAB JSON ListView MergeView

2_test

{"project":"2_test","denotations":[{"id":"25353178-22957541-52044501","span":{"begin":555,"end":557},"obj":"22957541"},{"id":"25353178-17342702-52044502","span":{"begin":9054,"end":9057},"obj":"17342702"},{"id":"25353178-17342702-52044503","span":{"begin":9848,"end":9851},"obj":"17342702"},{"id":"25353178-18077350-52044504","span":{"begin":13587,"end":13590},"obj":"18077350"},{"id":"T10616","span":{"begin":555,"end":557},"obj":"22957541"},{"id":"T49817","span":{"begin":9054,"end":9057},"obj":"17342702"},{"id":"T98481","span":{"begin":9848,"end":9851},"obj":"17342702"},{"id":"T30179","span":{"begin":13587,"end":13590},"obj":"18077350"}],"text":"3.2.2. α-Substituted Carboxylic Acids\nα-OH and α-keto acids. The prototype for the hydroxy acids is glycolic acid (α-OH acetic acid). Whereas the O–H…O= type intramolecular H-bond is easily reachable through the formation of the H–O–C–C=O five-member ring in the case of the syn conformation for the carboxylic group (see Figure 5), the HO…H–OC=O bond is also conceivable if the carboxylic group adopts the anti form. On the basis of the reported OH stretching frequency of 3585 cm−1 in comparison with 3682–3684 cm−1 in ethanol and methanol, Gu et al., [41] concluded that the red-shift can be attributed to the formation of the structure, where the α-OH is the hydrogen-bond donor to the O= atom of the syn –COOH group. No in-solution study has been found for this molecule.\nLactic acid (α-OH propionic acid). Borba et al. [170] obtained the FT-IR spectrum for lactic acid in argon and xenon matrices. By performing B3LYP/6-311++G** and MP2/6-31++G** gas-phase calculations, four conformers were identified with observable (\u003e1%) populations. About 92% of the conformers (T = 298 K) adopt an eclipsed O=C–C–O moiety, where the alcohol hydrogen is in a weak H-bond with the carbonyl oxygen. Relatively strong intramolecular H-bond is formed between the carboxylic hydrogen and the alcohol oxygen, when the carboxylic group takes the anti conformation. It is remarkable that the relative energy including zero point vibrational contribution for the conformer with anti –COOH group was calculated at 10–11.4 kJ/mol using the B3LYP/6-311++G(d,p) and MP2/6-31++G(d,p) levels of theory. This value is much smaller than 21.3 kJ/mol calculated by Nagy [79] at the CCSD(T)/CBS level for the syn-anti conformational energy difference for acetic acid. The large energy difference, beyond the likely basis set effects, would indicate the considerable stabilization of an anti –COOH group in an intramolecular H-bond. The analysis in [170] was limited to the gas phase, no in-solution calculations were performed.\nPyruvic acid (α-keto propionic acid) is the simplest α-keto carboxylic acid presenting the s-cis/s-trans conformational isomerism. This type of structural variation emerges for systems with a double bond-single bond-double bond (DSD) substructure (Figure 7). Dyllick-Brenzinger et al. [27] concluded from gas-phase microwave studies that the molecule adopts the O=C–C=O s-trans form in its most stable conformation, and there is an intramolecular H-bond between the keto oxygen and the hydrogen of the carboxylic group in its anti conformation. Theoretical studies by Yang et al., [171] confirmed this conclusion.\nIn a recent study of DSD molecules by Nagy and Sarver [117], the above, s-trans/anti –COOH conformation was found as the most stable structure optimized at the B97D/aug-cc-pvtz level in the gas phase. In-solution structural studies were performed by applying the continuum solvent models (IEF-PCM) and by specifying explicit dichloromethane and water solvents in MC/FEP simulations. The solvation favors the syn –COOH form both for the s-cis and s-trans conformers in comparison with the s-trans/anti –COOH species. The solvent effect is, however, still not enough for stabilizing any syn –COOH structure in dichloromethane, but it is enough in water, where the s-trans/syn –COOH form is more stable by 2.2–4.6 kJ/mol than the s-trans/anti –COOH structure.\nFigure 7 below shows some remarkable differences in the pair-energy distribution functions for simple acids. The common conformation is syn for a –COOH group without substituents on the aliphatic chain (11). The syn acetic acid generates a well-resolved maximum-minimum pedf in the −38 to −17 kJ/mol interaction energy range. It must include solute-water interactions with donor waters to the carboxylic oxygens and when the O–H…O (water) bond is formed with the carboxylic hydrogen. This is the most common pattern for –COOH…water intermolecular interactions. It is noteworthy that the three types of interactions overlap in the pedf, creating a single maximum.\nThe anti conformation for the acetic acid carboxylic group (12) results in a split maximum. The difference is characteristic, but no study has pointed out yet what interactions belong to the energy range −43 to −33 kJ/mol, and what intermolecular interactions can be characterized by E = −33 to −21 kJ/mol. Since the overall pedf is not resolved at E = −33 kJ, the “weaker” representative of the stronger interactions still extend beyond −33 kJ, leading to a second elevation of the pedf.\nThe general shape of the pedf for the s-cis propenic acid (13) is very similar to that of the syn acetic acid. The small differences, less high peak and minimum shifted toward the less negative E value, may not be significant under the simulation conditions in [117]. If it is still significant, it may indicate the effect of the one-carbon-longer chain with a double bond cis to the carbonyl oxygen.\nPyruvic acid (14) again presents a split pedf. The two doubly bonded oxygens mutually affect the charges for each other. No such charge redistribution takes place for the other three structures, thus the α-keto group characteristically modifies the pedf for an aliphatic carboxylic acid. The keto group is a strong H-bond acceptor site, still the first maximum of the pedf is presumably assignable to the C(carboxylic)=O…H (water) intermolecular H-bonds. There are interaction energies for the anti acetic acid in the same range, where no competing C=O group exists for this simple acid. An opposite assignment would lead to the conclusion that the hydration of the carboxylic group for pyruvic acid has to be shifted toward an unreasonably low energy range of −27 to −15 kJ/mol.\nFigure 7 Solute-water pair-energy distribution functions for syn acetic acid (11); anti acetic acid (12); s-cis propenic acid (13); and s-trans pyruvic acid (14) with structures shown in Figure 5. All these results refer to neutral monomeric pyruvic acid (5%–16% dissociate if forms 0.1–1 molar aqueous solution). IEF-PCM/B97D/aug-cc-pvtz optimizations in dichloromethane and water found that a species composed of two s-trans/syn –COOH monomers is the most stable dimeric form with equal geometries for the monomer constituents. Calculations of the potential of mean force curves for the dimerization of pyruvic acid indicate sensitive differences in the pmf whether only monomer charges or solute-solute polarized charges were also used. Charges in the latter case were derived on the basis of the in-solution MEP for the dimer. The dimeric fraction was calculated to be nearly 100% when the solute-solute polarized charges were gradually considered in the C(carboxyl)…C(carboxyl) separation range of 384–484 pm. However, using monomer charges all way down, 51% was calculated for the degree of association in dichloromethane, and only a shallow minimum was obtained in the C…C separation range of 350–650 pm in aqueous solution which corresponds to a low level of solute association [117].\nα-Halogen acids. The prototype in this case is α-fluoroacetic acid. Chermahini et al., [172] found four local-energy-minimum structures for this molecule in the gas phase by ab initio and DFT calculations. All molecules show slightly distorted CS symmetry, thus the heavy atoms are almost co-planar. In the four molecules, F eclipses the =O or the hydroxyl oxygen, both in the syn and anti carboxyl conformations. The only arrangement where an intramolecular H-bond can be formed is when the F eclipses the hydroxy oxygen of the anti –COOH group. In the most stable conformation, the FCC=O torsion angle is 0° with syn carboxylic group. The second most stable form is when the FCC=O torsion angle is 180°. The corresponding MP2/6-311++G** relative energy is 1.7 kJ/mol, and the transition state energy is about 10 kJ/mol. The internally H-bonded conformer (FCCO(H) = 0°) with an anti carboxylic group is higher in energy than the most stable structure by 5.4 kJ/mol at the MP2 level. The F…H distance was not reported.\nFluoroacetic acid readily assumes a dimeric form in the gas phase having a syn carboxylic conformation. The basis set superposition error corrected dimerization energies were calculated at 47–59 kJ/mol. The dimer with FCC=O about 0° is more stable than the conformer with FCCO(H) of about 0°. The relative energies are 1.8 kJ/mol at the MP2 level. No in-solution studies have been found.\nα-Amino acids. Since this family includes the natural α-amino acids, there is an extremely large number of publications available in the literature. This review will survey only the simplest representatives of the family and investigate whether another α-substituent, such as a hydoxymethyl group in serine or a α-hydroxyethyl group in threonine, will remarkably modify the intramolecular hydrogen-bond pattern. This problem emerges only in the gas phase, because natural α-amino acids take a zwitterionic form in aqueous solution.\nThe simplest molecule of this family is glycine, α-amino acetic acid. In a high-level ab initio study, Kasalová [173] calculated the geometry of the two lowest energy conformers of free glycine. The geometries were in good agreement with conformations obtained experimentally and also listed in the paper. The lowest energy structure has CS symmetry (Gly I), and two, presumably weak intramolecular N–H…O= bonds should exist in this conformation. No H…O distances were provided in the paper. The H-bond is supposed to be weak, because the NH2 group is a weak H-bond donor. The group is, however, a strong hydrogen-bond acceptor. In the second most stable conformation, Gly II, there is an O–H…N hydrogen bond, which is formed feasibly with the anti carboxylic group. Considerably smaller relative energies were calculated for the second stable glycin conformer in former calculations (see a compilation in [173]) because the formation of the hydrogen bond must reduce the internal energy increase due to the syn to anti transformation of the –COOH group.\nThe structure is zwitterionic in aqueous solution, which can be derived from both gas-phase conformations. The mechanism of the formation could be, however, interesting. Nagaoka et al., [174] studied the intramolecular proton transfer from the neutral form with anti –COOH group into the zwitterion in aqueous solution through molecular dynamics simulations. The authors applied a reactive potential energy function developed on the basis of the empirical valence bond method. The free energy change through the proton transfer was calculated by means of the FEP method. The zwitterion was found to be more stable than the neutral form by 35.4 ± 6.1 kJ/mol at T = 300 K. The activation free energy in the process zwitterion to neutral form is 70.4 ± 5.7 kJ/mol. Both values are in good agreement with available experimental values. Tuñón et al., [175] performed a QM/MM molecular dynamics simulation for the intramolecular proton transfer in aqueous solution. The QM part was considered by an (unspecified) DFT functional and the basis set was of double-ξ quality + polarization functions. The overall 2000 fs long simulation protocol indicated the proton transfer in the 250–300 fs time range. The authors predicted that the activation energy may not be too large. In fact, using the computational results of Nagaoka, the activation free energy, starting from the neutral form should be about 35 kJ/mol, which is really not a too large value for a tautomeric reorganization. For example, Lunazzi at al. [176] found a tautomeric proton relocation feasible for triazoles with experimentally measured activation free energies in the range 40–60 kJ/mol.\nHowever, Tortonda et al., [177] considered the “good” estimate for the barrier obtained by Nagaoka to be a consequence of the HF parameterization of the reaction potential. It was stated that such parameterization severely overestimates the activation barrier for this process. Furthermore, the experimental barrier height, in the opinion of Tortonda et al., refers to the interconverison of the in-solution Gly I to Gly II conformations rather than for the Gly II to zwitterions process. The Gly II conformer optimized at the MP2/6-31+G** level in continuum dielectric water solvent model is more stable than the Gly I species by 11.2 kJ/mol [178]. Since the lifetime of Gly II is very small and the Gly I to Gly II conformational change requires a non-negligible barrier of about 46 kJ/mol [175], Tortonda et al., [177] attributed the experimental barrier to the zwitterion formation from Gly I rather than from Gly II. If a water molecule forms a doubly H-bonded bridge between the H2N and HOC=O sites for Gly II, the calculated barrier is 65.1 kJ/mol [178]. Then these authors predicted that an intermolecular proton transfer in the indicated arrangement would be unlikely. Nevertheless, the formation of the zwitterion through intermolecular protonation of the neutral amine in Gly I, where the nitrogen lone-pair could instead accept a proton from a neighboring water molecule, remained as a possibility. This would correspond to the Tsuchida-Yamabe mechanism, discussed in Section 3.1.\nCorrect modeling of the dissolution of serine (α-amino, β-hydroxy propionic acid) in water is a delicate theoretical problem. Gronert and O’Hair [179] theoretically derived 51 serine conformers, and concluded that only a few of them are of small-relative-energy species. In a gas-phase study using the LA-MB-FTMW technique, which combines laser ablation (LA) with molecular beam Fourier transform microwave spectroscopy (MB-FTMW), Blanco et al., [180] identified seven conformers with observable populations. The lowest-energy conformer was similar to Gly I for glycine, with an additional O–H…NH2 H-bond by the alcohol hydroxy. In the second lowest energy structure, the anti carboxylic group forms a H-bond to the amine, and the alcohol OH acts as a proton donor to the carbonyl oxygen and behaves as a proton acceptor in a N–H…O bond. The substructure resembles Gly II of glycine. Two low-energy structures of Gronert and O’Hair were selected by Tortonda et al., [177] for in-solution studies. For the easier comparison, the H-bond pattern will be characterized as that for the gas-phase glycine and coded as ser (Gly I) and ser (Gly II). The most stable gas-phase serin conformer at the DFT/B3PW91/6-31+G** level is ser (Gly II). This conformer is more stable in enthalpy by 0.9 kJ/mol than ser (Gly I), where the β-OH is only H-bond donor to the nitrogen atom. In solution, the β-OH is only a H-bond acceptor from H–N in ser (Gly II) and is not involved in any intramolecular H-bond in ser (Gly I). Accordingly, the enthalpy of ser (Gly I) relative to ser (Gly II) increases to 15.6 kcal/mol. The zwitterion is more stable in enthalpy than the neutral ser (Gly II) by 8.4 kJ/mol in aqueous solution. The OH group in the zwitterion is free to form intermolecular H-bonds with the solvent. Taking the computational results together, the conclusion was that an intramolecular proton transfer from the ser (Gly II) conformer into the zwitterionic serine species is preferred."}

NEUROSES

PMC:4264129 / 114572-129688 JSONTXT

Annnotations TAB JSON ListView MergeView

2_test

NEUROSES

PMC:4264129 / 114572-129688 JSON TXT