Symmetry of Hydrogen Bonds: Application of NMR Method of Isotopic Perturbation and Relevance of Solvatomers

Short, strong, symmetric, low-barrier hydrogen bonds (H-bonds) are thought to be of special significance. We have been searching for symmetric H-bonds by using the NMR technique of isotopic perturbation. Various dicarboxylate monoanions, aldehyde enols, diamines, enamines, acid-base complexes, and two sterically encumbered enols have been investigated. Among all of these, we have found only one example of a symmetric H-bond, in nitromalonamide enol, and all of the others are equilibrating mixtures of tautomers. The nearly universal lack of symmetry is attributed to the presence of these H-bonded species as a mixture of solvatomers, meaning isomers (or stereoisomers or tautomers) that differ in their solvation environment. The disorder of solvation renders the two donor atoms instantaneously inequivalent, whereupon the hydrogen attaches to the less well solvated donor. We therefore conclude that there is no special significance to short, strong, symmetric, low-barrier H-bonds. Moreover, they have no heightened stability or else they would have been more prevalent.

The complete mechanism of an aldol condensation in water

The base-catalyzed aldol condensation between benzaldehyde and p-acetylbenzoic acid in water shows an inverse solvent kinetic isotope effect, k_3,D2O/k_3,H2O, of 1.33 ± 0.03. The reaction is definitely faster in D₂O. This is interpreted to mean that the rate-limiting step in a five-step mechanism is Step 5, the final elimination of hydroxide from the enolate intermediate, not the formation of that intermediate. This is the same result and the same conclusion as from earlier studies in aqueous acetonitrile and refutes a suggestion, based on computations, that the rate-limiting step would change in water. Those computations are criticized as implying impossibly large isotope effects.

Nucleophilic Addition of Enolates to 1,4-Dehydrobenzene Diradicals Derived from Enediynes: Synthesis of Functionalized Aromatics

Alkylation of aromatics and formation of a new C-C bond is usually achieved by the electrophilic attack of an activated carbon species on an electron-rich aromatic ring. Herein, we report an alternative method for alkylation of aromatics via nucleophilic addition of enolates of active methylene compounds to 1,4-dehydrobenzene diradicals derived from enediynes cyclodec-1,5-diyne-3-ene, benzo[3,4]-cyclodec-1,5-diyne-3-ene, and cyclohexeno[3,4]-cyclodec-1,5-diyne-3-ene. The benzo-substituted enediyne produces slightly higher yields of alkylation products than do the other two enediynes, but the differences are not substantial. The reaction produces a new C-C bonded aromatic alkylation product, which allows the construction of complex polyfunctional structures in a few steps. Moreover, this reaction provides solely C-arylated products, and no O-arylation products were observed.

Glossary of terms used in physical organic chemistry (IUPAC Recommendations 2021)

This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.

Malonic Anhydrides, Challenges from a Simple Structure

After many years of unsuccessful attempts, monomeric malonic anhydrides were prepared by ozonolysis of ketene dimers, a procedure validated by model studies. The structure proof relied most heavily on IR absorption at 1820 cm^-1 and a Raman band at 1947 cm^-1. Malonic anhydrides are unstable, decomposing below room temperature to a ketene plus carbon dioxide. Surprisingly, according to kinetic studies, the dimethyl derivative is slightly less unstable than the parent, and the monomethyl is the fastest to decompose, with an enthalpy of activation of only 12.6 kcal/mol. Computations rationalize this behavior in terms of a concerted [2_s + 2_a] cycloreversion that requires a more highly organized transition state, as also manifested by a negative entropy of activation.

ipso

On a substituted benzene ring the position that bears the substituent is designated as the ipso position. This Perspective presents the history behind that designation.

Comment on "Topography of the free energy landscape of Claisen-Schmidt condensation: solvent and temperature effects on the rate-controlling step" by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, , 6738

The referenced article in PCCP presents calculations of solvent kinetic isotope effects that indicate that the rate-limiting step in base-catalyzed chalcone formation in aqueous solution becomes the second enolization. This disputes our previous conclusion, based on experimental isotope effects in aqueous acetonitrile, that the rate-limiting step is the final loss of hydroxide and formation of the C-C double bond. That conclusion is here affirmed as general for any protic solvent, and it is further concluded that those calculations are flawed.

Cyclohexeno[3,4]cyclodec-1,5-diyne-3-ene: A Convenient Enediyne

Enediynes are widely studied to understand their cycloaromatization and the trapping of the resulting p-dehydrobenzene diradical. However, few model substrates are known, and they are hard to synthesize and difficult to handle. Herein we report cyclohexeno[3,4]cyclodec-1,5-diyne-3-ene as a convenient model for studying the reactivity of enediynes. It can be easily synthesized from 1,2-diethynylcyclohexene and 1,4-diiodobutane. It is a solid that is stable at room temperature. In solution the p-dehydrobenzene diradical derived from its cycloaromatization can be trapped by nucleophiles. The rate-limiting step is the cyclization, which is slightly slower than that of the parent cyclodec-1,5-diyne-3-ene but faster than that of its benzo analogue, consistent with the distances between the reacting carbon atoms.

Enthalpic and entropic contributions to the basicity of cycloalkylamines

Large-ring cycloalkylamines are slightly less basic than other cycloalkylamines such as cyclohexylamine, even though all have tetrahedral carbons and are strain-free. To understand why, enthalpy and entropy for protonation of a series of cycloalkylamines were accurately determined by isothermal titration calorimetry in 3 : 1 methanol–water. The study required resolving a discrepancy between these measurements and those in pure water. The data show that the lower basicity of large-ring cycloalkylamines is not due to enthalpy but to a more negative entropy of protonation. Computations show that this can be attributed in part to an entropy of conformational mixing, but the dominant contribution is steric hindrance to solvation, also corroborated by computation.

Large-ring cycloalkylamines are slightly less basic than other cycloalkylamines such as cyclohexylamine, even though all have tetrahedral carbons and are strain-free.

Isotopic-Perturbation NMR Study of Hydrogen-Bond Symmetry in Solution: Temperature Dependence and Comparison of OHO and ODO Hydrogen Bonds

Is a hydrogen bond symmetric, with the hydrogen centered between two donor atoms, or is it asymmetric, with the hydrogen closer to one but jumping to the other? The NMR method of isotopic perturbation has been used to distinguish these. Previous evidence from isotope shifts implies that a wide variety of dicarboxylate monanions are asymmetric, present as a rapidly equilibrating mixture of tautomers. However, calculations of hydrogen trajectories across an anharmonic potential-energy surface could reproduce the observed isotope shifts in a phthalate monoanion. Therefore, it was concluded that those isotope shifts are instead consistent with isotope-induced desymmetrization on a symmetric potential-energy surface. To distinguish between these two interpretations, the ¹⁸O-induced isotope effects on the ¹³C NMR chemical shifts of cyclohexene-1,2-dicarboxylate monoanion in chloroform-d and on the ¹⁹F NMR chemical shifts of difluoromaleate monoanion in D₂O have been investigated. In both cases the isotope effects are larger at lower temperature and also with deuterium in the hydrogen bond. It is concluded that these behaviors are consistent with the perturbation of an equilibrium between asymmetric tautomers and inconsistent with isotope-induced desymmetrization on a symmetric potential-energy surface.

Polynomial coefficients. Application to spin-spin splitting by N equivalent nuclei of spin I > 1/2

The NMR intensity pattern of a nucleus split by N identical nuclei of spin 1/2 is given by the binomial coefficients. These are conveniently obtained from Pascal's triangle, equivalent to the chemist's branching diagram. Much less well-known is the pattern from splitting by N identical nuclei of spin I > 1/2. This was originally presented in terms of multinomial coefficients, but polynomial coefficients are more convenient. These describe the number of ways that N objects can be distributed to 2I + 1 numbered boxes. They arise in the polynomial expansion and are conveniently obtained from generalizations of Pascal's triangle. Examples and predictions are given.

Approach control. Stereoelectronic origin of geometric constraints on N-to-S and N-to-O acyl shifts in peptides

Intramolecular N-to-S or N-to-O acyl shifts in peptides are of fundamental and practical importance, as they constitute the first step in protein splicing and can be used for the synthesis of thioester-modified peptides required for native chemical ligation. It has been stated that the nucleophile must be positioned anti to the carbonyl oxygen, as in a cis amide. Despite the importance of such reactions, an understanding of this geometric restriction remains obscure. Here we argue that the empirical requirement for positioning the nucleophile is a stereoelectronic effect arising from the ease of approach of the nucleophile to a carbonyl group, not ground-state destabilization. DFT calculations on model amides support our explanation and indicate a significant decrease in both the transition-state energy and the activation energy for a cis amide. However, the approach of the nucleophile must be anti not only to the carbonyl oxygen but also to the nitrogen. The direction of approach is expressed by a new, modified Bürgi-Dunitz angle. Our data shed light on the mechanisms of acyl shifts in peptides, and they explain why a cis peptide might be required for protein splicing. The further implications for acyl shits in homoserine and homocysteine peptides and for aldol condensations are also considered.

pH-Free Measurement of Relative Acidities, Including Isotope Effects

A powerful pH-free multicomponent NMR titration method can measure relative acidities, even of closely related compounds, with excellent accuracy. The history of the method is presented, along with details of its implementation and a comparison with earlier NMR titrations using a pH electrode. Many of its areas of applicability are described, especially equilibrium isotope effects. The advantages of the method, some practical considerations, and potential pitfalls are considered.

Can a secondary isotope effect be larger than a primary?

Primary and secondary (18)O equilibrium isotope effects on the acidities of a variety of Brønsted and Lewis acids centered on carbon, boron, nitrogen, and phosphorus were computed by density-functional theory. For many of these acids, the secondary isotope effect was found to be larger than the primary isotope effect. This is a counterintuitive result, because the H atom that is lost is closer to the (18)O atom that is responsible for the primary isotope effect. The relative magnitudes of the isotope effects can be associated with the vibrational frequency and zero-point energy of the X═O vibrations, which are greater than those of the X-O vibrations. However, the difference between these contributions is small, and the major responsibility for the larger secondary isotope effect comes from the moment-of-inertia factor, which depends on the position of the (18)O atom relative to the principal axes of rotation.

Comment on “The role of electrostatic induction in secondary isotope effects on acidity” by E. A. Halevi, New J. Chem., 2014, 38, 3840

We reject Halevi's interpretation and reaffirm our conclusion that secondary deuterium isotope effects on acidity are due to n–σ* delocalization.

Variable-temperature study of hydrogen-bond symmetry in cyclohexene-1,2-dicarboxylate monoanion in chloroform-d

The symmetry of the hydrogen bond in hydrogen cyclohexene-1,2-dicarboxylate monoanion was determined in chloroform using the NMR method of isotopic perturbation. As the temperature decreases, the (18)O-induced (13)C chemical-shift separations increase not only at carboxyl carbons but also at ipso (alkene) carbons. The magnitude of the ipso increase is consistent with an (18)O isotope effect on carboxylic acid acidity. Therefore it is concluded that this monoanion is a mixture of tautomers in rapid equilibrium, rather than a single symmetric structure in which a chemical-shift separation arises from coupling between a desymmetrizing vibration and anharmonic isotope-dependent vibrations, which is expected to show the opposite temperature dependence.

Hydrogen-bond symmetry in difluoromaleate monoanion

The symmetry of the hydrogen bond in hydrogen difluoromaleate monoanion is probed by X-ray crystallography and by the NMR method of isotopic perturbation in water, in two aprotic organic solvents, and in an isotropic liquid crystal. The X-ray crystal structure of potassium hydrogen difluoromaleate shows a remarkably short O-O distance of 2.41 Å and equal O-H distances of 1.206 Å, consistent with a strong and symmetric hydrogen bond. Incorporation of (18)O into one carboxyl group allows investigation of the symmetry of the H-bond in solution by the method of isotopic perturbation. The (19)F NMR spectra of the mono-(18)O-substituted monoanion in water, CD(2)Cl(2), and CD(3)CN show an AB spin system, corresponding to fluorines in different environments. The difference is attributed to the perturbation of the acidity of a carboxylic acid by (18)O, not to the mere presence of the (18)O, because the mono-(18)O dianion shows equivalent fluorines. Therefore, it is concluded that the monoanion exists as an equilibrating pair of interconverting tautomers and not as a single symmetric structure not only in water but also in organic solvents. However, in the isotropic liquid crystal phase of 4-cyanophenyl 4-heptylbenzoate, tetrabutylammonium hydrogen difluoromaleate-(18)O shows equivalent fluorines, consistent with a single symmetric structure. These results support earlier studies, which suggested that the symmetry of hydrogen bonds can be determined by the local environment.

On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective

The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water.

Are short, low-barrier hydrogen bonds unusually strong?

In a symmetric hydrogen bond (H-bond), the hydrogen atom is perfectly centered between the two donor atoms. The energy diagram for hydrogen motion is thus a single-well potential, rather than the double-well potential of a more typical H-bond, in which the hydrogen is covalently bonded to one atom and H-bonded to the other. Examples of symmetric H-bonds are often found in crystal structures, and they exhibit the distinctive feature of unusually short length: for example, the O-O distance in symmetric OHO H-bonds is found to be less than 2.5 Å. In comparison, the O-O distance in a typical asymmetric H-bond, such as ROH···OR(2), ranges from about 2.7 to 3.0 Å. In this Account, we briefly review and update our use of the method of isotopic perturbation to search for a symmetric, centered, or single-well-potential H-bond in solution. Such low-barrier H-bonds are thought to be unusually strong, owing perhaps to the resonance stabilization of two identical resonance forms [A-H···B ↔ A···H-B]. This presumptive bond strength has been invoked to explain some enzyme-catalyzed reactions. Yet in solution, a wide variety of OHO, OHN, and NHN H-bonds have all been found to be asymmetric, in double-well potentials. Examples include the monoanion of (±)-2,3-di-tert-butylsuccinic acid and a protonated tetramethylnaphthalenediamine, even though these two ions are often considered prototypes of species with strong H-bonds. In fact, all of the purported examples of strong, symmetric H-bonds have been found to exist in solution as pairs of asymmetric tautomers, in contrast to their symmetry in some crystals. The asymmetry can be attributed to the disorder of the local solvation environment, which leads to an equilibrium among solvatomers (that is, isomers that differ in solvation). If the disorder of the local environment is sufficient to break symmetry, then symmetry itself is not sufficient to stabilize the H-bond, and symmetric H-bonds do not have an enhanced stability or an unusual strength. Nor are short H-bonds unusually strong. We discuss previous evidence for "short, strong, low-barrier" H-bonds and show it to be based on ambiguous comparisons. The role of such H-bonds in enzyme-catalyzed reactions is then ascribed not to any unusual strength of the H-bond itself but to relief of "strain."

Rotation and solvation of ammonium ion

From nitrogen-15 spin-lattice relaxation times and nuclear Overhauser enhancements, the rotational correlation time (c) for (15)NH(4)(+) was determined in a series of solvents. Values of (c) range from 0.46 to 20 picoseconds. The solvent dependence of (c) cannot be explained in terms of solvent polarity, molecular dipole moment, solvent basicity, solvent dielectric relaxation, or solvent viscosity. The rapid rotation and the variation with solvent can be accounted for by a model that involves hydrogen bonding of an NH proton to more than one solvent molecule in a disordered solvation environment.

Symmetry of hydrogen bonds in solution

A classic question regarding hydrogen bonds (H-bonds) concerns their symmetry. Is the hydrogen centered or is it closer to one donor and jumping between them? These possibilities correspond to single- and double-well potentials, respectively. The NMR method of isotopic perturbation can answer this question. It is illustrated with 3-hydroxy-2-phenylpropenal and then applied to dicarboxylate monoanions. The 18O-induced 13C NMR splittings signify that their intramolecular H-bonds are asymmetric and that each species is a pair of tautomers, not a single symmetric structure, even though maleate and phthalate are symmetric in crystals. The asymmetry is seen across a wide range of solvents and a wide variety of monoanions, including 2,3-di-tert-butylsuccinate and zwitterionic phthalates. Asymmetry is also seen in monoprotonated 1,8-bis(dimethylamino)naphthalenediamines, N,N'-diaryl-6-aminofulvene-2-aldimines, and 6-hydroxy-2-formylfulvene. The asymmetry is attributed to the disorder of the local environment, establishing an equilibrium between solvatomers. The broader implications of these results regarding the role of solvation in breaking symmetry are discussed. It was prudent to confirm a secondary deuterium isotope effect (IE) on amine basicity by NMR titration of a mixture of PhCH2NH2 and PhCHDNH2. The IE is of stereoelectronic origin. It is proposed that symmetric H-bonds can be observed in crystals but not in solution because a disordered environment induces asymmetry, whereas a crystal can guarantee a symmetric environment. The implications for the controversial role of low-barrier H-bonds in enzyme-catalyzed reactions are discussed.

Nucleophilic addition to a p-benzyne derived from an enediyne: a new mechanism for halide incorporation into biomolecules

Biosynthesis of haloaromatics ordinarily occurs by electrophilic attack of an activated halogen species on an electron-rich aromatic ring. We now present the discovery of a new reaction whereby a nucleophilic halide anion can be attached even to an aromatic ring without activating substituents. We show that the enediyne cyclodeca-1,5-diyn-3-ene, in the presence of lithium halide and a weak acid, is converted to 1-halotetrahydronaphthalene. The kinetics are consistent with rate-limiting cyclization to a p-benzyne biradical that rapidly adds halide and is then protonated. This reaction has interesting mechanistic features and important implications for incorporation of halide into biomolecules.

Secondary Deuterium Isotope Effects on the Acidity of Carboxylic Acids and Phenols

Secondary deuterium isotope effects (IEs) on acidities have been accurately measured by an NMR titration method applicable to a mixture of isotopologues. Deuteration definitely decreases the acidity of carboxylic acids and phenols, by up to 0.031 in the DeltapK per D. For aliphatic acids, the IEs decrease as the site of deuteration becomes more distant from the OH, as expected, but a surprising result is that IEs in both phenol and benzoic acid do not decrease as the site of deuteration moves from ortho to meta to para. The experimental data are supported by ab initio computations, which, however, substantially overestimate the IEs. The discrepancy does not seem to be due to solvation. The IEs originate in isotope-sensitive vibrations whose frequencies and zero-point energies are lowered upon deprotonation. In the simplest case, formate, the key vibration can be recognized as the C-H stretch, which is weakened by delocalization of the oxygen lone pairs. For the aromatic acids, delocalization cannot account for the near constancy of IEs from ortho, meta, and para deuteriums, but the observed IEs are consistent with calculated vibrational frequencies and electron densities. Moreover, the ability of the frequency analysis to account for the IEs is evidence against an inductive origin.

Hydrogen-Bond Symmetry in Zwitterionic Phthalate Anions: Symmetry Breaking by Solvation

The cationic nitrogen of zwitterion 1 is located symmetrically with respect to its intramolecular OHO hydrogen bond. Incorporation of one (18)O allows investigation of the H-bond symmetry by the NMR method of isotopic perturbation. In both CD(3)OD and CD(2)Cl(2) equilibrium isotope shifts are detected at the carboxyl and ipso carbons. Therefore, 1 exists as a pair of interconverting tautomers, not as a single symmetric structure with its hydrogen centered between the two oxygens. The H-bond is instantaneously asymmetric, and there is an equilibrium between solvatomers (isomers or stereoisomers that differ in solvation). The broader implications of this result regarding the role of the local environment ("solvation") in breaking symmetry are discussed.

Stereochemistry of β-Deuterium Isotope Effects on Amine Basicity

Secondary beta-deuterium isotope effects on amine basicities are measured using a remarkably precise NMR titration method. Deuteration is found to increase the basicity of methylamine, dimethylamine, benzylamine, N,N-dimethylaniline, 2-methyl-2-azanorbornane, and pyrrolizidine. The increase in dimethylamine arises entirely from enthalpy, contrary to a previous report. The method permits a determination of intramolecular isotope effects in 1-benzyl-4-methylpiperidine and 2-benzyl-2-azanorbornane. It is found that deuteration has a larger isotope effect when either antiperiplanar or synperiplanar to a lone pair, but the synperiplanar effect is smaller, as confirmed by computations. The isotope effect is attributed to a lowered zero-point energy of a C-H bond adjacent to an amine nitrogen, arising from delocalization of either a syn or an anti lone pair, and with no detectable angle-independent inductive effect.

One-bond C-C coupling constants in ethers are not primarily determined by N-sigma delocalization

One-bond carbon-carbon coupling constants, 1JCC, were measured for a series of cyclic and acyclic ethers. Surprisingly, the dependence on COCC dihedral angle, tau, parallels cos(tau), rather than the cos(2tau) characteristic of n-sigma* delocalization. These results complement recently calculated 1JCH values in three ethers. The variations in 1J are not primarily determined by delocalization but instead are attributed to a dipolar interaction that affects electron density, perhaps via the hybridization.