PMC:4264129 / 85743-138925 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4264129","sourcedb":"PMC","sourceid":"4264129","source_url":"http://www.ncbi.nlm.nih.gov/pmc/4264129","text":"3.2. 5-Member Rings\nThis is a large family of small organic molecules where an intramolecular H-bond is supposed to exist, although AIM analyses may sometimes point out its absence. Nonetheless, close H…Y distances have been calculated and experimentally found in the gas phase for a number of such structures. A schematic structure for 2-Cl ethanol, as a prototype with a five-member ring is shown in Figure 1. Schemes for a gauche and the all-trans conformations for 1,2-ethanediol, as well as a similar pair of the zwitterionic β alanine are provided in Figure 2. Gauche conformers for 2-aminoethanol and 2-NO2-ethanol (the latter forms a six-member ring in the internally H-bonded structure) with and without intramolecular H-bonds are shown Figure 3.\n\n3.2.1. 1,2-Disubstituted Ethanes and Derivatives\n1,2-Dihydroxy ethane (1,2-ethanediol). This molecule has been studied experimentally in the gas phase, organic solvents, in water, and theoretically both in the gas phase and in aqueous solution. A detailed summary of the conformational issue can be found in [22]. A concise summary is provided below.\nOn the basis of gas-phase electron diffraction results of Bastiensen [137] and the Hedberg group [30], microwave spectroscopy results of Caminati and Corbelli [138] and IR studies by Frei et al., [139] and Takeuchi and Tasumi [140], the 1,2-dihydroxy ethane (1,2-ethanediol, ethylene glycol) is a mixture of two main conformers, tG+g− and g+G+g− in the gas phase with intramolecular H-bonds. Capital G refers to the gauche arrangement of the OCCO moiety, t and g+ refer to the free trans and gauche hydrogen in the HOCC moiety, respectively, whereas g− stands for the internally bound other hydrogen atom, which is in an electrostatically favored position. However, no (3, −1) BCP was found for this arrangement [6,7]. Quantum chemical studies by Nagy et al., [42,43] and Cramer and Truhlar [44] also found these two conformers as the most stable ones in the gas phase. Cramer and Truhlar obtained their relative energies at the high (MP2/cc-pvtz + CCSD(T)/cc-pvdz-MP2/cc-pvdz) theoretical level. The “+” and “–” superscripts follow the code in this article.\nKrueger and Mattee [141] interpreted the structural results on the basis of temperature dependence of the fundamental OH stretching bands in carbon tetrachloride so that the OCCO gauche, G conformation is overwhelming in organic solvent with one or two intramolecular hydrogen bonds. Pachler and Wessels [142] also found the G arrangement the predominate for 1,2-dihydroxy ethane in solution with up to 20% OCCO trans fraction in different organic solvents with low dielectric constants and 12% trans conformer in D2O-solution.\nNagy et al., [42,43] predicted a 99.5% G fraction on the basis of ab initio MP2/6-31G* + MC simulations, considering, however, only five G and one T conformers. There are altogether ten stable conformations for this molecule: six G and four T. Consideration of the missing 3T and 1G conformations would likely increase the overall T fraction. Such MC free energy perturbation calculations were, however, extremely time consuming in the first half of the 1990’s. Overall, the studies predicted about 67% and 33% conformers without and with an intramolecular H-bond in solution, respectively, thus the short H…Y distance in the gas phase was mostly eliminated upon interactions with water molecules.\nCramer and Truhlar [44] studied all ten conformers using a continuum solvent approach. They successfully predicted about 12% for the OCCO T conformation, and predicted 36%–54% tG+g− conformer in the equilibrium solution as compared with 56% in the gas phase. Thus their results correspond to a major in-solution conformation with a favorably close O–H…O arrangement. Altogether 73%–84% of the conformers were found with arrangements favorable for an intramolecular H-bond. The deviation between the structure-predictions in this study and those above indicates the possible underestimation of the significance of the solute-solvent intermolecular H-bonds by continuum solvent methods. Hooft et al., [143] studied the conformational problem by means of explicit–solvent molecular dynamics simulations and utilized the GROMOS force field. They predicted a G:T = 67:33 ratio and altogether 31% for conformers with a possible intramolecular H-bond.\nThe three investigations result in rather diverse results. Nonetheless, there is a unanimous conclusion that the OCCO moiety takes predominantly the G arrangement in solution, similar to that in the gas phase. Cramer and Truhlar found about 12% T conformation in good agreement with the experiment. The T fraction was under and overestimated in the other two investigations. The three studies differ mainly in predicting the fractions of conformers regarding the O–H…O substructure. Nagy et al., and Hooft et al., predicted the majority of structures with fairly large H…Y separation, Cramer and Truhlar found the opposite.\nIn a very thorough analysis by Petterson et al. [144], the G vs. T conformation problem was interpreted from a new perspective. After reviewing many former experimental studies, the authors discussed their own NMR results for the solution of 1,2-ethanediol in DMSO-d6 and CDCl3. They concluded that the OCCO gauche conformers (G) are prevailing, but their fraction strongly depends on the in-solution OCCO torsion angle. Nevertheless, the reason for the G preference for 1,2-ethanediol and 2-fluoroethanol (see below) is the well known “gauche effect” noticed for several 1,2-disusbstituted ethane derivatives, and the possible intermolecular H-bond is not a decisive factor to stabilize the G form. Accordingly, the intramolecular H-bond may or may not be maintained in aqueous solution for a G conformer, whereas the OCCO gauche arrangement remains predominant.\nGubskaya and Kusalik [145] performed MD simulations with 1,2-ethanediol molar fractions of X = 0.03, 0.1, 0.3, and 0.8 in ethanediol:water mixtures. The molar fraction in the experiment by Pachler and Wessels [142] was about 0.08. Gubskaya and Kusalik found sensitive dependence of the conformer population on the concentration of the system. Comparison is reasonable only up to X = 0.3, since X = 0.8 corresponds to a solution where the organic portion should be considered as the solvent.\nThe population of the OCCO trans (T) conformation was calculated at 56% with X = 0.03, but no T was found at X = 0.1 Interpolating the T population to the experimental X = 0.08 composition, where the finding was 12% T, the agreement is quite good. The total gauche fraction in dilute solution has contributions from two different OCCO gauche structures. Although the torsion angles are ± 62.5° for G' and G, they must not be optical antipodes since their populations are 8.7% and 35.3%, respectively. This author could not determine the torsion angles for the hydroxy hydrogens, so it was not clear whether any of the G' and G conformers would refer to a tG+g+ or a tG+t conformation without an intramolecular hydrogen. Nonetheless, one may conclude that 44% of the solutes maintain some gauche conformation allowing for the existence of structures with an intramolecular H-bond in aqueous solution. Since the calculated compositions are highly concentration dependent, it is difficult to compare these results with the three others above, where the simulation conditions modeled an infinitely dilute solution.\n1,2-Ethanediol is a substructure in sugars. The length of this review does not allow a deeper structure analysis for sugars. Nevertheless, for assignment of the OH conformations relative to the rest of these molecules by, e.g., NMR investigations [146], the above theoretical conclusions could be very helpful.\nA better sugar-substructure model for tetroses, pentoses, etc., would be glycerol. Glycerol (1,2,3-propanetriol) exhibits, however, a very complicated conformational equilibrium with 126 possible conformers, with or without intramolecular H-bonds in the gas phase. Bastiensen [137] studied the structure by electron diffraction, and found the αα and αγ conformers as the major species. The symbols α, β, and γ refer to the heavy atom torsional positions, irrespective of the hydroxy-hydrogens positions (see [137,147]). He concluded that there are two intramolecular H-bonds for glycerol, which have three hydrogen-bond donor (and acceptor) OH groups. Gas-phase studies by Jeong et al., [147] at the M06-2X level and by Callam et al., [148] at the G2(MP2) and CBS-QB3 levels deviate slightly regarding the conformer composition at T = 298 K. The most populated conformer is the αγ structure followed by αα or γγ. The free energies differ by less than 1.4 kJ/mol for the two most stable species by the different methods, thus the results are fairly method and basis set dependent. In aqueous solution, the theoretically predicted fractions with the six back-bone combinations of the individual α, β, and γ torsions are in better agreement with the experimental NMR results of Van Koningsveld [149] at the SMD M06-2Z/cc-pvtz level by Jeong et al., than when Callam et al., (see above) applied the SM5.42//HF/6-31G* approximation. Nonetheless, both groups of authors used continuum dielectric solvent models without explicitly considering water molecules in the first solvation sphere. Accordingly, Jeong et al. found five conformers within a 0.7 kJ/mol range for relative free energies. For these structures two intramolecular H-bonds are maintained.\nIn a recent MD simulation, Egorov et al., [150] studied 5.1 and 7.6 molar aqueous solutions of glycerol and neat glycerol. These solutions cannot be considered as dilute ones. Not surprisingly, the conclusion is that the typical glycerol hydrogen-bond network still exists even in the less concentrated solution (5.1 molar, of about 40 wt % glycerol). About 25% of the solutes occur in a structure similar to that in pure liquid glycerol, ca. 25% takes the water-solvated monomeric form, and about 50% of the glycerols form hydrogen-bonded strings. This study also cannot answer the question whether the two intramolecular H-bonds, generally assigned to the most stable gas-phase conformers, would become partially or entirely disrupted in dilute aqueous solutions. Correct characterization of the hydrogen-bond pattern for the latter system could be interesting from a medical point of view. The sugar level in blood, basically an aqueous solution, should be below about 0.005 mol/L for a healthy person. Although MD/MC simulations can be performed generally only on the 0.01–0.1 mol/L scale as a dilute solution, such studies still could provide useful information regarding the conformations of glycerol in highly dilute aqueous solutions.\n1,2-Ethanediol monoethers. Cyclic ethers have been demonstrated as strong H-bond acceptors in ether…water dimers from theoretical calculations [151]. The 1,2-ethanediol vinyl-ether takes an intramolecularly H-bonded OCCO gauche conformation in the gas phase, as found by Marstokk and Møllendal [24]. The methyl-ether was calculated by Gil et al., [152] as forming an intramolecular H-bond in the gas phase, which is maintained in CCl4 solution. Krueger and Mettee, who came to the conclusion on the basis of experiments conducted in dilute carbon tetrachloride solution [141].\nTafazzoli and Jalili [153] studied the conformational behavior of the 1,2-ethanediol monomethyl-ether (2-methoxyethanol) through Monte Carlo simulations in aqueous solution. They used the 12–6–1 intermolecular pair potential and the TIP4P water model in conjunction with a flexible COCCOH skeleton. The authors concluded that there are 1.73 solute-solvent H-bonds, on average, in aqueous solution with a single solute, and the water molecules favorably form H-bonds between the two oxygen atoms of the solute molecule. Using the FEP method, the potential of mean force curve was obtained in the range of 300 to 820 pm for the centers of the C–C bonds of two solutes in a water box. A double-minimum character of the pmf indicated contact and solvent separated solute associations with mainly solute…water H-bonds even in the contact-pair form.\n2-Aminoethanol (ethanolamine). Penn and Curl investigated the molecular structure by microwave spectroscopy in the gas-phase [154]. The prevalent conformation is OCCN gauche with an O–H…N intramolecular H-bond. Because of the basic character of the amino group (pKa = 9.5), it becomes protonated as a primary amine when dissolved in water. The protonation stops at 1%–3% for 0.1–1 molar solutions and the pH increases to 11–12. Thus the neutral form should be chosen for theoretical consideration as the major in-water component. IEF-PCM/B97D/aug-cc-pvtz studies [64] predict 89% gauche conformation with the intramolecular O–H…N bond, and 7% and 4% for the gauche and trans conformations, respectively, without this bond. However, when the relative solvation free energies were calculated via the MC/FEP procedure, the predicted OCCN trans:gauche (without H-bond):gauche (with H-bond) ratios change to about 92:6:2, indicating 98% of the conformers without an intramolecular H-bond in aqueous solution. Although in other reported cases the population orders have been generally maintained when the two solvation free energy calculations were applied, the results became essentially different in this case.\nBy considering the solute-solvent pair-energy distribution function (pedf) from MC simulations utilizing the explicit solvent model for water (Figure 6 for two 2-aminoethanol gauche conformers) the predicted number of H-bonds with the solvent, nHB, is considerably larger for the gauche conformer without than with the intramolecular H-bond. The value of nHB in an interaction energy range can be calculated by the integration of the pedf for the range.\nFigure 6 Solute-water pair-energy distribution functions for 2-aminoethanol and 2-NO2-ethanol with (HB) and without (NHB) an intramolecular H-bond: H2NetOH HB (7); H2NetOH NHB (8); O2NetOH HB (9); O2NetOH NHB (10). Structure numbers from Figure 3. The HB conformer has no clearly-developed maximum-minimum shape, only an inflection point appears at E = −20 kJ/mol. Moreover, the pedf starts at about 7 kJ/mol less negative energy than the NHB curve, indicating that even the strongest solute-water interaction energy is remarkably weaker than that for the no-HB (NHB) gauche conformer. The pedf for the NHB conformer shows a double-minimum structure. The first minimum at E = −25 kJ/mol is the upper limit for the strong O–H…O (water) hydrogen bond formation. The second minimum appears at E = −17 kJ/mol. The energy range of −25 to −17 kJ covers the weaker O–H…O (water) interactions and has contributions mainly due to the H (water)…N intermolecular H-bonds. Starting at −17 kJ/mol, the two curves run fairly close to each other. This energy interaction range has been interpreted to result mainly contributions involving the N–H…O (water) weak intermolecular H-bonds, which are available for both gauche conformers. The pedf has not been indicated for the trans form, which is even more favorably hydrated. For this conformer, the polar sites are fully opened to interactions with the solvent environment.\nIn contrast to the above MC/FEP results, Gubskaya and Kusalik [145] found no trans conformer with solute molar fraction of 0.03 in MD simulations (see details above for 1,2-ethanediol). The trans fraction suddenly increases, however, to 66% with X = 0.1, and disappears again with X = 0.3. If these results are correct, then the composition is largely concentration dependent for the aqueous 2-aminoethanol solutions. Da Silva et al., [155] found no trans conformer in infinitely dilute aqueous solution, where the gauche form maintained the intramolecular H-bond on the basis of MD simulations at 298 and 333 K. The same conclusion was drawn utilizing simulation results for the 10% (X = 0.1) ethanolamine solution model. López-Rendón et al., [156] also predicted the internally bound gauche ethanolamine conformation by MD simulations at two different solute concentrations. Even the more dilute solution, X = 0.25 is too concentrated for reasonable comparisons with studies above.\nFor exploring the possibility of the formation of an intermolecularly H-bonded dimer with one or perhaps two O–H…N bonds in aqueous solution, a pmf was calculated in the C…C separation range of 324–1184 pm for two solutes [64]. Two all-trans 2NH2-ethanol molecules were allowed to approach each other in steps of 20 pm, and the deviation in free energy from the reference separation was calculated at +/− 10 pm by means of the FEP method. A shallow minimum was calculated in the 350–650 pm range. By integration of the R2exp(−G(R)/RT curve (G(R) = 0 at C…C = 1184 pm) only 10% of the solutes take an associated structure up to C…C = 654 pm, without exhibiting solute-solute intermolecular hydrogen bond(s) in an about 0.22 molar aqueous solution with solute molar fraction of X = 0.004. The MD simulations results by da Silva et al. [155] also suggest that ethanolamine dimer formation in aqueous solution is very limited. This is in contrast to the prediction of Haufa and Czarnecki [157] regarding intersolute H-bonds, in, however, a much denser solution with X = 0.6 for the solute.\nIn an early experiment, Omura and Shimanouchi [158] recorded the Raman spectra of 2-aminoethanol in aqueous solution at pH = 0 and 12.6. The solute is neutral at the larger pH. The authors found both OCCN gauche and trans conformers, although they could not determine the conformer ratio. NMR studies by Smith et al., [159] pointed out that the OCCN G fraction stays in the range of 80%–84% when X, the solute’s molar fraction changes as 0.03, 0.1, and 0.3. These experimental results are in sharp contrast to the MD prediction from [144], where 66% T (and accordingly 34% G at most) was found at X = 0.1. Thus the experiments in [158,159] are in accord as much that there are both G and T fractions in the aqueous solution for 2-aminoethanol. The predicted G fraction is 80%–84% up to X = 0.3 for the solute.\nThe protonated structure becomes the major form of 2-aminoethanol in aqueous solution, if the pH is about 7.4 or lower. Omura and Shimanouchi [158] predicted predominantly the OCCN G conformation for the +H3NCH2CH2OH species at pH = 0, where an intramolecular H-bond exists in the N–H+…O form [89]. 92% G conformation was predicted by Smith et al., [159] upon NMR analysis of the G vs. T problem for the hydrochloride salt of 2-aminoethanol. These experiments may be considered as studies on a substructure of norepinephrine, a small molecule involved in important biological processes. The conformational equilibrium is a central problem in this species, and because of the presence of an aryl group on the C–C chain two, non-equivalent G structures exist as will be discussed in Subsection 3.3.1.\nEthylenediamine (2-aminoethylamine). There is an equilibrium of two neutral conformers separated in energy by about 1.3 kJ/mol in the gas phase [160]. Both structures possess a weak intramolecular N–H…N hydrogen bond, which becomes feasible by the gauche NCCN arrangement with torsion angles of 63 ± 2°. pH dependent structure analysis was performed by Omura and Shimanouchi [158], who recorded the Raman spectra in aqueous solution at pH of 3.5, 8.4, and 13.6 The molecule is a strong base, which exists in the neutral form at pH = 13.6. At pH = 8.4, most molecules take the monoprotonated form, which is the prevalent protonation state at the physiological pH of 7.4. At pH = 3.5, the dicationic form is the typical species. Despite the repulsion of the two cationic sites in the OCCN gauche conformation, the Raman spectra was interpreted as indicating both gauche and trans conformations for all three protonation states of ethylenediamine. No quantitative prediction of the gauche:trans ratio has been provided by the authors, however, for any protonation state of the solute.\nThe IEF-PCM/B97D/aug-cc-pvtz optimized (+H)NCCN torsion angles for the gauche form are 56.4° and 51.1° in water and chloroform, respectively [89]. The torsion angle is about 180° for the trans conformer in both solvents. The solvation favors the trans conformation, but the internal free energy is much more negative for the gauche form in both solvents. As a result, the gauche form with an intramolecular H-bond of the form N–H+…N is the prevalent conformation in both solvents by a relative free energy of at least 11 kJ/mol.\nGubskaya and Kusalik [145] found about 67% of the trans form with a solute molar fraction of 0.03 for the neutral conformer, which must be the dominant protonation form if the solute dissolves in pure water. A MC/FEP pmf study for the dicationic species by Boudon and Wipff [161] indicates the preference of the all-trans conformation without the possibility of an intramolecular H-bond in aqueous solution.\nTable 1 summarizes the applied experimental methods and theoretical calculations for resolving the conformer equilibrium problem for X–CH2–CH2-Y systems (X, Y = OH, NH2). The table compares studies for the three 1,2-disubstituted ethane derivatives mostly referred to in this review.\nijms-15-19562-t001_Table 1 Table 1 Comprehensive summary of the applied experimental and theoretical methods for the conformational equilibria of some 1,2-disubstituted ethane derivatives in aqueous solution. a Theor. Ref.: Theoretical reference; b Exp. Ref.: Experimental reference; c Eint: Intramolecular energy; d ZPE/Gth: Zero point vibrational energy + thermal Gibbs correction at T = 298 K; e Cont. Solv.: Continuum solvent; f MC/FEP: Free energy perturbation method through Monte Carlo simulations; g MD/FEP: Free energy perturbation method through molecular dynamics simulations; h +: The “+” sign indicates that ZPE/Gth was calculated; and i FF for reference [156] means force field. 2-Halogen ethanol. 2-F and 2-Cl ethanol adopt the OCCX (X = F, Cl) gauche structure and develop O–H…X intramolecular H-bonds in the gas phase, at least on the basis of the distant criterion and according to electron diffraction and microwave spectroscopy results [29,162]. The two structures were recently studied theoretically by Nagy [15] both in the gas phase and in solution. The calculated gas-phase geometric parameters were in good agreement with the experimental ones. In chloroform and aqueous solution, the calculated OCCF gauche fraction of about 88%–98% reproduced well the experimental values of 95%–98% by Pachler and Wessels [142]. The internal H-bond remains in CCl4, whereas nearly equal populations were calculated for the OCCF gauche fractions with and without the intramolecular H-bond in aqueous solution. In the article of Petterson et al. [144], the authors argue in favor of the gauche conformation due to the generally preferable “gauche effect” and do not consider the possibly only very weak O–H…F bond as a structure determining factor. No experimental conformational composition has been found for 2-Cl ethanol in solution. The calculated gauche OCCCl fraction was about 92% in chloroform, which decreased to 51%–86% in aqueous solution depending on whether the IEF-PCM or the FEP/MC method was used. The increasing fraction for the trans conformation (14%–49%) and the disruption of the intramolecular H-bond must be related to the explicit consideration of the water molecules.\n2,2,2-Trifluroethanol (TFE). This compound has a remarkable effect in modifying the secondary structure of proteins as a co-solvent in TFE/water mixtures utilized in NMR studies [163] or toward stabilizing intramolecular H-bonds with carbohydrates [164]. The molecule has two main conformations, with HOCC gauche or trans positions. In the gauche conformation, an O–H…F intramolecular H-bond is feasible, similar to that for 2F-ethanol. In an early gas electron-diffraction experiment the vague results due to technical difficulties prevented the identification of the gauche and/or trans conformation [165]. The microwave spectrum and the OH rotational dynamics for the gauche conformer were studied by Xu et al. [166]. Durig and Larsen [167] recorded the far- and mid-IR, as well as the Raman spectra for this molecule in the gas phase. By fitting a torsion potential curve for the hydroxy hydrogen rotation to the experimental data, they predicted that the trans conformer is higher in enthalpy than the gauche structure only by 19 cm−1 (0.2 kJ/mol). Senent et al., [16] overviewed a number of former gas-phase experiments and found that the results uniformly assign the gauche conformation to the most stable species in the gas phase. Regarding a second form as a trans conformation, if it exists at all in the gas phase, the predicted relative energies scatter in a wide 19–1161 cm−1 (0.2–13.9 kJ/mol) energy range.\nNeat liquid was studied by Radnai et al., [168] and Bakó at al., [169] by performing X-ray and neutron diffraction studies. From the latter study, the gauche:trans ratio is 60:40 in neat liquid and the TFE molecules have about 1.6 H-bonded neighbors. TFE forms both cyclic dimers and so-called gel structures with 3–4 intermolecularly H-bonded species, involving both gauche and trans TFE conformers.\nWhereas experimental results are available for the gas phase molecule and for the neat liquid, no experimental or theoretical study has been found regarding the structure of TFE in aqueous solution. The closest relationship can be revealed by the paper of Senent et al. [16], who calculated TFE monohydrates. The zero-point enthalpy difference for the isolated gauche and trans TFE conformers is 6.8 kJ/mol at the MP2/cc-pvdz level in favor of the gauche form. Monohydrate relative enthalpies at 0 K were calculated with optimized geometries for the complexes. The isomeric structure, where the water molecule forms a bridge between the O–H group and one of the F atoms of the gauche TFE, acts as a H-bond donor to F and corresponds to a H-bond acceptor to the OH group, is the most stable arrangement. AIM analysis found two BCP’s and one RCP for this species, which is a counterpart of the 1,2-ethanediol monohydrate identified by Klein [6].\nIn other three monohydrates, where the water is an acceptor to the trans (O)H, or is a donor to the gauche or trans OH, the enthalpy is higher than the most stable one by 9.3–16.1 kJ at the indicated theoretical level. All these structures form an intermolecular H-bond as confirmed by one BCP for each of them. The trans monohydrates are always higher in enthalpy than the gauche counterparts. Since the lowest two differ by 9.3 kJ, by more than the non-hydrated gauche and trans TFE do, the calculations make a hint that the solvation in bulk water could still favor the gauche conformation, but the possible presence of the trans form may not be ruled out.\n2-NO2 ethanol. Although the internally bound structure should form a six-member ring (Figure 3), it is more consistent to discuss this molecule next to the other 2-substituted ethanols. The NO2 group is a weak H-bond acceptor, still the prevailing species of 2-NO2 ethanol is the OCCN gauche arrangement. The gas-phase microwave spectrum by Marstokk and Møllendal [25] was interpreted by hypothesizing an intramolecular H-bond. Theoretical calculations found that the conformation, which allows for the formation of an O–H…O(N) H-bond in the gas phase, is maintained in chloroform and also dominates the in-aqueous solution conformer composition [64].\nThe water-solute pair-energy distribution functions for two OCCN gauche conformations, possibly with and without an intramolecular H-bond, are shown in Figure 6. For the HB structure, there is only an inflection point at E = −17 kJ/mol, indicating the upper limit of the interactions with the more strongly bound water molecules, which may be act as donors in intermolecular H-bonds to the outer oxygen of the NO2 group in structure 9 (Figure 3) The pedf for the NHB structure (10) is a well-developed maximum-minimum curve up to E = −12 kJ/mol. This shape indicates H-bonds between the freed alcohol OH and the acceptor water molecule(s). The pedfs always show distributions because the thermal disordering does not allow the maintenance of the strongest O (water)…H–O intermolecular bond. The strongest interaction is represented by the onset value of the pedf, E = −30 kJ/mol in this case.\n2-NC ethanol (2-isocyanoethanol). Only gas-phase studies have been found for the molecule by Møllendal et al. [26]. Out of five considered conformers, the OCCN gauche structure is the most stable with an (O)H…N distance of 256 pm. The authors characterize this interaction as stabilizing the conformation electrostatically when compared to the two OCCN trans forms and two other gauche conformations having the intramolecular H-bond disrupted\n\n3.2.2. 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.\n\n3.2.3. Ortho Phenols and Naphthols\nIn this subsection, both 5- and 6-member rings for forming intramolecular H-bonds will be considered in connection to the phenolic (naphtholic) OH. This author considers comparison of ortho phenols more important than strictly maintaining the categorization by the number of ring members. The only noteworthy difference being that the O–H…X bond angles could deviate.\nCompilations for experimental O–H vibrational frequencies of ortho phenols measured in the gas phase or in dilute solutions of low-dielectric-constant solvents [181,182,183] suggest that the O–H…X intramolecular H-bond exists in these phases. Appearance of this bond in aqueous solution is a more complicated question.\n2-OH phenol (catechol). By interpreting the gas-phase microwave spectrum, Caminati et al., [184] concluded that the structure forms an intramolecular H-bond. However, Mandado et al., [7] did not find a (3, –1) BCP and a related H-bond in their AIM analysis using the B3LYP/6-311++G** electron charge density. Reynolds [185] calculated the relative free energy of the catechol conformers and found that the O–H…O structure with a H-bond (HB) is preferred in comparison to the H–O…O–H disrupted H-bond (DHB) form in aqueous solution.\n2-OH benzylalcohol. Kumar et al., [186] recorded the UV, IR and microwave absorption spectra in a supersonic jet. A single conformation was identified, where the phenolic OH is a donor in the intramolecular H-bond to the alcohol oxygen. The authors also assume the existence of a weak O–H…π interaction between the alcohol OH and the aromatic ring on the basis of a second minimum in the spectrum. The two types of intramolecular hydrogen bonds were assigned to absorption in the RIDIR spectrum at 3494 cm−1 (O–H…O) and at 3636 cm−1 (O–H…π). The minima were reproduced at the M05/cc-pvtz level. A quite different theoretical spectrum was predicted for the conformer where the alcohol OH is the proton donor to the phenolic O. This local-minimum-energy structure is higher in energy than the global minimum by 10.5 kJ/mol at the M05/aug-cc-pvtz level after zero-point energy correction. No solvent effect study was provided.\nSimplerer et al., [181] compared the phenolic OH IR-frequencies for ortho substituted phenols in dilute CCl4 solutions. The experimentally observed red-shift of 202 cm−1 for the OH frequency in the 2-OH benzylalcohol methyl ether compared with the pure phenol supports the model that there must be a strong O–H…O intramolecular H-bond in 2-OH benzylalcohol and in their derivatives.\n2-Halogen phenol. The gas-phase electron diffraction experiment predicts a mixture of HB and DHB structures for 2-F phenol [187], with preference for the HB structure. 2-Cl phenol forms an intramolecular H-bond in the gas phase and both ortho-halogen phenols maintain a HB structure in dilute solutions of low-dielectric-constant solvents [181,182,183]. Recent theoretical studies by Nagy [15,64] confirm this finding: the HB structure is almost exclusive either with a 2-F or a 2-Cl substituent in CCl4, and the DHB 2-F phenol fraction was estimated at less than 10% in chloroform. In aqueous solution, the hydration itself favors the H–O…X (X = F, Cl) DHB structure, but the total relative free energy is still favorable for the HB conformers by about 3–5 kJ/mol, corresponding to at least of 80% HB structure in the equilibrium composition [15].\n2-NH2 phenol. The term “aminophenol” may be used in a more general sense as regarding the species when the –NH2 group is a substituent on the benzene ring for a phenol, or resides on an alkyl substituent connecting to a benzene ring bearing one, two, etc., OH substituent(s). This latter group will be discussed as β-substituted ethylamines in the next section.\nProbably due to the high melting point of 174 °C for 2NH2-phenol, no experimental gas-phase study has been found in the literature. The neutral (non-zwitterionic) form of 2NH2-phenol was studied by Nagy [64] in the gas phase, chloroform and water solvents. In principle, there can exist two intramolecular H-bonds for this molecule, namely O–H…N and N–H…O. The so-called aniline-type-NH2 group, as a benzene-ring substituent, is much less basic than an amino group on a saturated chain. The calculated free energy difference is almost zero in the gas phase for the two types of the intramolecular H-bonds. In both solvents the N–H…O bond was found to prevail, although the calculated relative free energies strongly depend on the applied level of theory and the manner of calculating the solvent effects.\n2-NO2 phenol. Despite the weak hydrogen-bond acceptor character of the –NO2 group, the authors of the gas-phase electron diffraction study [188] convincingly argue in favor of the O–H…O(NO) intramolecular H-bond for the isolated molecule. The six-member ring can be conveniently formed. The optimized H…O and O–H…O H-bond parameters calculated at the B97D/aug-cc-pvtz level [64] agree with the experimental values within their respective certainties.\nBoth in chloroform and water, the theoretical calculations predict a negligible fraction for the DHB conformation with a disrupted intermolecular H-bond. The calculated O–H stretching frequency for the H-bond donor group deviates only by 2 cm−1 from the experimental value. The good agreement was considered as an indication of the need for high-level, IEF-PCM/B97D/aug-cc-pvtz geometry optimizations for exploring the relative free energies between HB and DHB conformers in solutions.\n2-COOH phenol. The intramolecular H-bond is formed within a six-member ring including the phenolic OH. The molecule may be considered as a β-hydroxy carboxylic acid, as well. Accordingly, it will be compared with the saturated β-hydroxy carboxylic acids in the next section.\nThe molecule can adopt several conformations, although only one of them is highly populated and was assigned in IR experiments. The spectrum was recorded by Fiedler et al., [189] in tetrachloride solution and indicated a strong intramolecular H-bond. The deviation of the OH stretching frequency from that in phenol was 395 cm−1. The theoretically calculated deviation is 359 cm−1 at the B3LYP/6-311+G(d,p) level. The lowest-energy conformer is planar, the phenolic OH is a H-bond donor to the carbonyl oxygen of the syn carboxylic group. The =O…H distance and the =O…H–O bond angle were calculated at 176 pm and 145°, respectively. The second-most-stable conformer is higher in energy by 14.3 kJ/mol, where the phenolic OH is the H-bond donor to the syn carboxylic OH. Similar conclusions were drawn by Yahagi et al., [190] by interpreting the gas-phase IR frequencies of the phenolic OH.\nIn a former calculation by Nagy et al. [45], the two conformers above were found also to be the most stable with MP2/6-31G*//HF/6-31G* energy separation of 13.7 kJ/mol and free energy difference of 12.1 kJ/mol at T = 298 K. All other conformers are much higher in free energy, supporting the estimate of Fiedler that the population of the lowest-energy form is 99.7%.\nNagy et al., also investigated if the intramolecular H-bond would be maintained in aqueous solution by performing NpT MC/FEP simulations using the OPLS pair-potential. Comparing the two stable conformers, the solvation itself would favor the conformation with an H–O(carboxyl)…H–O(phenol) bond by 6.1 kJ/mol, but the total relative free energy is still 6.0 kJ/mol in favor of the =O…H–O(phenol) form. Even much larger solvent effect, 30.0 kJ/mol, was calculated in favor of the conformer when the phenolic OH rotates by 180°, thus when the phenolic group is free for hydration. However, the total relative free energy still remains too high by 17.4 kJ/mol at this new geometry when is compared with the most stable one. In conclusion, the conformer most stable in the gas phase with =O…H–O intramolecular H-bond remains as the predominant species in solution, although 8% second-stable form is also expectable in comparison with its gas-phase population calculated at about 1%.\n1-NO and 2-NO naphthols. Ivanova and Enchev [191] performed in-solution experimental and theoretical studies for these molecules. Using NMR spectroscopy in CHCl3 and DMSO solvents, they found that both structures exist only in the tautomeric =N–O–H oxime form at an observable fraction. This suggests that the relevant structures correspond to 1,2-naphthoquinone monooximes. The theoretical studies at the MP4(SDTQ)/6-31G*//6-31G* level augmented with PCM solvent calculations found an equilibrium between the syn and anti oximes, although the preferences are different by the two solvents. H-bonds are only possible in the syn oxime conformation with the neighboring quinone oxygen. This conformer is favored for the 1-syn-oxime-2-naphthoquinone (1-NO-2-naphthol) in both solvents, although the anti oxime was also found experimentally and predicted theoretically. For the 2-oxime-1-naphthoquinone (2-NO-1-naphthol), the authors found experimentally that only the anti oxime form exists in solution, in contrast to prior experimental results. 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