Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site.

A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.

Conjugated donor-acceptor substituted systems involving the 1,3-indandione-derived electron accepting moieties.

Conjugated donor-acceptor molecules are the focus of research owing to their unusual photo- and electro-physical properties. At the same time, several unusual features of these compounds are difficult to explain or predict. Here we present our results on the synthesis, X-ray structures and D-NMR spectra providing a deeper insight into the conjugation within the derivatives involving the 1,3-indandione-derived series of compounds with varying electron acceptor strength and conjugating bridge length. The X-ray structures show the presence of several intermolecular short contacts strongly affecting the molecular geometries. In solution, the coalescence temperatures corresponding to the rotation of the phenylamino moiety of all derivatives do not exceed 246 K indicating the unhindered rotation at room temperature. Using B3LYP/aug-cc-pVDZ, the calculated model chemistry barriers to rotation, dipole moments and first hyperpolarizabilities are within experimental error. We conclude that neglecting the electron donating properties of bridges themselves and internal rotation about the single bonds taking part in conjugation can result, for instance, in misinterpretation of their room temperature NMR spectra and overestimation of the computed molecular dipole moments by more than 5 D.

Simultaneous Estimation of Two Coupled Hydrogen Bond Geometries from Pairs of Entangled NMR Parameters: The Test Case of 4-Hydroxypyridine Anion.

The computational method for estimating the geometry of two coupled hydrogen bonds with geometries close to linear using a pair of spectral NMR parameters was proposed. The method was developed based on the quantum-chemical investigation of 61 complexes with two hydrogen bonds formed by oxygen and nitrogen atoms of the 4-hydroxypyridine anion with OH groups of substituted methanols. The main idea of the method is as follows: from the NMR chemical shifts of nuclei of atoms forming the 4-hydroxylpyridine anion, we select such pairs, whose values can be used for simultaneous determination of the geometry of two hydrogen bonds, despite the fact that every NMR parameter is sensitive to the geometry of each of the hydrogen bonds. For these parameters, two-dimensional maps of dependencies of NMR chemical shifts on interatomic distances in two hydrogen bonds were constructed. It is shown that, in addition to chemical shifts of the nitrogen atom and quaternary carbon, which are experimentally difficult to obtain, chemical shifts of the carbons and protons of the CH groups can be used. The performance of the proposed method was evaluated computationally as well on three additional complexes with substituted alcohols. It was found that, for all considered cases, hydrogen bond geometries estimated using two-dimensional correlations differed from those directly calculated by quantum-chemical methods by not more than 0.04 Å.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7 + O3 Complex in Solution.

The front cover artwork is provided by the groups of Prof. Ehud Pines (BGU, Israel) and Dr. Benjamin Fingerhut (MBI, Berlin). The image shows a scientist integrating experiments with theory for resolving the structural diffusion of the aqueous proton in acetonitrile providing a novel view on the Grotthuss mechanism. Read the full text of the Article at 10.1002/cphc.202001046.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7+ O3 Complex in Solution.

Infrared (IR) absorption in the 1000-3700 cm-1 range and 1 H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7+ O3, in acetonitrile. The core H7+ O3 motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H7+ O3 structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H7+ O3 in the OH stretch region, which reaffirms the assignment of the H7+ O3 spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H7+ O3 structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H7+ O3 structures may support proton transport within larger water solvates.

Hindered rotational barriers in conjugated donor-acceptor substituted systems: calculations vs. experiments.

Quantum mechanical calculations of barriers to rotation within push-pull π-conjugated molecules involving strong electron donors (D) and acceptors (A) using the generally accepted approach fail to reproduce the experimental barriers determined by temperature-dependent NMR spectra. On the examples of seven derivatives of this type with substituents of varying electron donating and accepting strength, we find that determination of one of the rotational barriers, for instance, that of the acceptor substituent, requires not only the energy calculation of the respective transition state of this substituent, but also the transition state of the donor and the transition state involving both donor and acceptor substituents. Calculations of the rotation barriers using B3LYP and APFD functionals considering three transition states produce the results with mean absolute deviations from 10 experimental barriers of 0.28-0.19 kcal mol-1 depending on the basis set.

Dipole moments of conjugated donor-acceptor substituted systems: calculations vs. experiments.

We find that quantum mechanical calculations using B3LYP/aug-cc-pVTZ model chemistry involving anharmonic correction on simple conjugated organic compounds without rotating moieties provide the dipole moment values and molecular geometries with high accuracy. In the presence of one or two conjugated electron donating or accepting substituents capable of hindered rotation, the calculated dipole moments reproduce the experimental results equally well only in the cases when the experiments were done at the temperatures at which rotation of substituents remains hindered. In order to reproduce the experimental dipole moments determined at higher temperatures, a model assuming free (unhindered) rotation should be applied. In these cases, the contribution of each rotamer is equal and using anharmonic correction is not necessary. The APFD functional produces similar results and the M062X functional yields larger deviations from the experimental data. The other methods, like HF and MP2, are the least accurate with the basis sets usually employed for interpreting the experimental data.

2H-Indazole Tautomers Stabilized by Intra- and Intermolecular Hydrogen Bonds.

2-[(2H-Indazol-3-yl)methylene]-1H-indene-1,3(2H)-dione 6 and (E)-2-[(2H-indazol-3-yl)methylene]-2,3-dihydro-1H-inden-1-one 7 have been synthesized. In the crystal, the NH hydrogen atom of 6 is disordered between the N(1) and N(2) atoms with the population ratio of 0.69:0.31. Molecule 7 crystallizes in two tautomeric polymorphs: 7-1H tautomer (yellow) and 7-2H tautomer (red). Both 6 and 7 form centrosymmetric dimers in the crystal with the monomeric units linked by C═O···H···N bifurcated hydrogen bonds in 6 and N-H···N hydrogen bonds in 7. According to 1H and 13C NMR data, in DMSO-d6 solution, the 6-1H tautomer predominates, whereas in less polar CDCl3 or CD2Cl2, the 6-2H tautomer is stabilized by a strong N-H···O═C intramolecular hydrogen bond. Compound 7 in dimethyl sulfoxide (DMSO) or ethanol solutions exists in the form of 7-1H and 7-2H tautomers. On the example of the 7-2H tautomer, it was shown for the first time that the 2H tautomers of 3-substituted indazoles can be stabilized by an intermolecular hydrogen bond and may remain in aprotic solvents almost indefinitely. However, in the open air or in water, fast 2H → 1H tautomerization occurs. As follows from density functional theory calculations, the high stability of the 2H form in solution is due to the formation of centrosymmetric dimers, which are more stable than the corresponding dimers of the 1H tautomer.

Crystal structure determination of rac-11'-(1-acetyl-1H-indazol-3-yl)-11',11a'-di-hydro-10'H,17'H-spiro-[indene-2,18'-[5a,16b]methano-tri-indeno[1,2-b:1',2'-d:2'',1''-g]oxocine]-1,3,10',12',17'(10a'H)-penta-one aceto-nitrile 1.5-solvate.

The title compound, C46H26N2O7·1.5CH3CN, is the aldol condensation product of bindone with indazole-3-carbaldehyde followed by double inter-molecular cyclization. The asymmetric unit, which has monoclinic P21/c symmetry, contains two independent mol-ecules of the title compound and three aceto-nitrile mol-ecules. The title mol-ecule comprises a central eight-membered ring, which contains an enol-ester, from which five arms extend. The arms exhibit inter-molecular inter-actions within the crystal lattice between mol-ecules of the title compound and with co-crystallized solvent mol-ecules (aceto-nitrile).

Photoinduced Intramolecular Bifurcate Hydrogen Bond: Unusual Mutual Influence of the Components.

A series of 7-hydroxy-2-methylidene-2,3-dihydro-1H-inden-1-ones with 2-pyrrolyl (3), 4-dimethylaminophenyl (4), 4-nitrophenyl (5), and carboxyl group (6) as substituents at the exocyclic double bond was synthesized in the form of the E-isomers (4-6) or predominantly as the Z-isomer (3) which in solution is converted to the E-isomer. The synthesized compounds and their model analogues were studied by NMR spectroscopy, X-ray analysis, and MP2 theoretical calculations. The E-isomers having intramolecular O-H···O═C hydrogen bond are converted by UV irradiation to the Z-isomers having bifurcated O-H···O···H-X hydrogen bond. Unexpected shortening (and, thus, strengthening) of the O-H···O═C component of the bifurcated hydrogen bond upon the formation of the C═O···H-X hydrogen bond was found experimentally, proved theoretically (MP2), and explained by a roundabout interaction of the H-donor (HX) and H-acceptor (C═O) via the system of conjugated bonds.

Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations.

The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρBCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the 1H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρBCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρBCP and V parameters and the hydrogen bond energies obtained from empirical 1H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

Hydrogen Bonding in Bis(6-amino-1,3-dimethyluracil-5-yl)-methane Derivatives: Dynamic NMR and DFT Evaluation.

Three bis(6-amino-1,3-dimethyluracil-5-yl)-methane derivatives were studied experimentally by variable-temperature (1)H NMR in polar aprotic solutions (CD2Cl2, C5D5N, C2D2Cl4) and computationally by DFT. The unusual for diarylmethanes coplanar conformation of dimethyluracil rings of each molecule is held by a pair of unequal intramolecular N-H···O hydrogen bonds. We show the presence of two dynamic processes involving breakage/formation of these bonds. First, it is two independent NH2 group rotations, each coupled to nitrogen inversion. Second, it is uracil ring rotations (ring flips). The thermodynamic parameters (ΔH(‡), ΔS(‡), and ΔG(‡)) of both processes were estimated by the full line shape analysis of NMR signals and also by DFT calculations. We demonstrate that, though the ring flips exchange pairs of NH protons, the two processes are not coupled: during the ring flip NH2 groups do not rotate, and during the NH2 rotation the rings do not necessarily rotate. Unlike in many other diarylmethanes, the ring flips in the studied compounds are happening stepwise; i.e., the configuration when both rings are "in flight" at the same time is energetically unfavorable (small degree of "cog wheel effect"). The signs of the ΔS(‡) values indicate that the molecular flexibility increases during the NH2 rotations, but decreases during the ring flips.

Molecular Structure and Photoinduced Intramolecular Hydrogen Bonding in 2-Pyrrolylmethylidene Cycloalkanones.

The structures of pyrrolylmethylidene derivatives of 2,3-dihydro-1H-inden-1-one (3), 3,4-dihydro-naphthalen-1(2H)-one (4), and cycloalkanones (5-7) were studied for the first time in the solid state and solution by NMR, IR, and UV spectroscopies supported by DFT quantum mechanical calculations. It was shown that all studied compounds except cycloheptanone derivative 7 both in crystal and in solution exist in the form of dimers where single E or E,E configuration with respect to the exocyclic C═C bond is stabilized by intermolecular hydrogen bonds N-H···O═C. UV irradiation at a wavelength of 365 nm of MeCN or DMSO solutions of 3-6 results, depending on the exposition time and solvent, partial to complete isomerization to the Z or Z,E isomers (in the case of 6, also the Z,Z isomer). The NMR and IR spectroscopy data show the existence of a strong intramolecular hydrogen bond N-H···O═C in the Z moieties of isomerized compounds. The studied compounds are protonated by trifluoroacetic acid at the carbonyl oxygen, in spite of the reverse order of basicity and nucleophilicity of the carbonyl group and the pyrrole ring. Investigation of the behavior of compound 6 with respect to acetate and fluoride anions allows one to consider it as a potential fluoride sensor.

Keto-enol tautomerism of phenindione and its derivatives: an NMR and density functional theory (DFT) reinvestigation.

Keto-enol tautomerism of phenindione (2-phenyl-1,3-indandione) and of its 4-phenyl-substituted derivatives was reinvestigated by NMR, supported by density functional theory (DFT) quantum-mechanical calculations. The calculated data quantitatively confirmed the stabilization in DMSO solution of the enol form by a strong hydrogen bond. The symmetry of the NMR spectra of the enol forms was explained by a fast proton transfer between carbonyl oxygen atoms, which is facilitated by the formation of a strong ionic complex of the enol form and an anion. It was shown that keto-enol tautomerization also proceeds with the participation of a similar complex between an anion and the diketo form of 2-phenyl-1,3-indandione.

Intra- and intermolecular hydrogen bonds in pyrrolylindandione derivatives and their interaction with fluoride and acetate: possible anion sensing properties.

The series of push-pull compounds containing the pyrrole ring as a donor and the 1,3-indandione derived moieties as the acceptor unit were synthesized, and strong intramolecular hydrogen bonding in their molecules was studied. In the presence of fluoride and acetate anions their solutions undergo color changes. It was shown by NMR, UV-vis, and quantum chemical calculations including AIM analysis that all these compounds undergo solvent-assisted rupture of the intramolecular hydrogen bond followed by the formation of a strong intermolecular hydrogen bond with fluoride and acetate anions which finally abstract a proton from the pyrrole ring. The insensitivity of the studied compounds to other anions (Cl, Br, HSO4, PF6) is consequence of the instability of the corresponding hydrogen-bonded complexes.

C(Ar)-H···O hydrogen bonds in substituted isobenzofuranone derivatives: geometric, topological, and NMR characterization.

Substituted isobenzofuranone derivatives 1a-3a and bindone 4 are characterized by the presence of an intramolecular C(Ar)-H···O hydrogen bond in the crystal (X-ray), solution ((1)H NMR and specific and nonspecific IEF-PCM solvation model combined with MP2 and B3LYP methods), and gas (MP2 and B3LYP) phases. According to geometric and AIM criteria, the C(Ar)-H···O interaction weakens in 1a-3a (independent of substituent nature) and in 4 with the change in media in the following order: gas phase > CHCl(3) solution > DMSO solution > crystal. The maximum value of hydrogen bond energy is 4.6 kcal/mol for 1a-3a and 5.6 kcal/mol for 4. Both in crystals and in solutions, hydrogen bond strength increases in the order 1a < 2a < 3a with the rising electronegativity of the ring substituents (H < OMe < Cl). The best method for calculating (1)H NMR chemical shifts (δ(calcd) - δ(expl) < 0.7 ppm) of hydrogen bonded and nonbonded protons in 1a-3a and 1b-3b (isomers without hydrogen bonds) is the GIAO method at the B3LYP level with the 6-31G** and 6-311G** basis sets. For the C-H moiety involved in the hydrogen bond, the increase of the spin-spin coupling constant (1)J((13)C-(1)H) by about 7.5 Hz is in good agreement with calculations for C-H bond shortening and for blue shifts of C-H stretching vibrations (by 55-75 cm(-1)).

Aromatic C-H...O interactions in a series of bindone analogues. NMR and quantum mechanical study.

The aromatic C-H...O hydrogen bonding within the series of the structurally relative indenone derivatives has been studied. The presence of the hydrogen bonds is corroborated by the large low-field chemical shifts of the protons involved in the hydrogen bond observed experimentally and reproduced by quantum mechanical calculations. Further confirmation is provided by analysis of the orbital overlap coefficients, (13)C NMR chemical shifts, and one-bond spin-spin coupling constants J((13)C-(1)H). The relationship between molecular geometry and (1)H NMR chemical shifts of involved protons has a complex nature, but the C-H...O distance is the principal factor.

Dynamic of the fluorescence of the complex Zn++/bis-N-carbazolyl-distyrylbenzene.

The discrimination between similar concentrations of the different metal ions is one of the important roles of fluorescent sensors. Here we present the study of the fluorescence dynamic of the chromophore bis-N-carbazolyl-distyrylbenzene (BCDSB) in acetonitrile/water (mmol/L), doped with metal ions such as K+; Ca++; Mg++; Zn++(10 micromol/L). BCDSB has the fluorescence with lambda(max) at 448 nm by excitation at lambda(exc) = 378 nm, lifetime 1.089 ns: quantum yield of the fluorescence is 0.68. With continuation of irradiation fluorescence quenching has been registered for all investigated metal ions. However, in the presence of Zn++ oscillation of the intensity was observed. The energy activation of the oscillation as much as 15 kcal/mol was estimated. We believe, that the specificity of the complex Zn++/BCDSB, is in an asymmetrical structure, formed via binding sites of Zn++ with the electron-enriched binding sites of the BCDSB, excited in n(pi)* state. This asymmetrical complex structure can cause the photoinduced structural fluctuation in the complex coordination.