NMR Spectroscopic Parameters of Molecular Systems with Strong Hydrogen Bonds

Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis

Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and ¹H-chemical shifts [δ(¹H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on ¹J(N-H), ¹J(O-H), ^2hJ(O-N), and δ(¹H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on ^2hJ(N-O) under the proton transfer process was investigated. ^2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(¹H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as ¹J(N-H) (¹J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of ^2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of ^2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.

Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models

To obtain detailed information about the position of hydrogen atoms in hydrogen bonds, HBs, of crystalline organic molecular compounds is not an easy task. In this work we propose a combination of ssNMR experimental data with theoretical procedures to get such information. Furthermore, the combination of experimental and theoretical models provides us with well-defined grounds to analyse the strength of π-stacking interactions between layers of hydrogen bonded molecules. Two different theoretical models were considered, both approaches being quite different. The first one is a solid-state model, so that the periodicity of a crystalline system underlies calculations of the electronic energy, the electronic density and NMR parameters. The other one is a molecular model in which molecules are taken as isolated monomers, dimers and tetramers. These two models were applied to the tizoxanide, TIZ, molecular crystal though it can widely be applied to any other molecular crystal. By the application of the quantum molecular model it was possible to learn about the way the intermolecular HBs affect the position of hydrogen atoms that belong to HBs in TIZ. This molecule has two intermolecular HBs that stabilize the structure of a basic dimer, but it also has an intramolecular HB in each monomer whose position should be optimized together with the other ones. We found that by doing this it is possible to obtain reliable results of calculations of NMR spectroscopic parameters. Working with the solid-state model we found that any local variation of the TIZ crystalline structure is correlated with the variation of the values of the NMR parameters of each nucleus. The excellent agreement between experimental and calculated chemical shifts leads to the conclusion that the N10-H10 bond distance should be (1.00 ± 0.02) Å.

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol^-1 . This value increases by ca. 1 kcal mol^-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol^-1 depending on the structure of the β-diketone in question.

Magnetic descriptors of hydrogen bonds in malonaldehyde and its derivatives

The nature of the hydrogen bond, HB, as such is still unknown, though a few of its most fundamental features has been uncovered during the last few decades. At the moment, it is possible to obtain reliable results for only a few of its broadest properties, like magnetic properties. They could give new insights into the physics underlying the strength and features of HBs. In this article we analyze the electronic origin of the NMR spectroscopic parameters of malonaldehyde, MA, and some substituted MAs. These substituted MAs are such that the H-bonds are assisted by one of two phenomena: resonance, RAHB, or charge, CAHB. We have studied the dependences of these parameters on two of the main factors which contribute the most to both phenomena, the geometrical and electronic factors, and found out how they can be used to characterize RAHB or CAHB by means of reliable theoretical calculations. We show that in the set of compounds analyzed here (i) the shielding of the proton of the H-bond can be used as a measure of the strength of the HB and (ii) the relation between the contact and non-contact mechanisms of J-couplings between donor and acceptor atoms is a reliable descriptor of whether the H-bond is resonance assisted or charge assisted.

Calculation of 15N NMR chemical shifts: Recent advances and perspectives

Recent advances in computation of ¹⁵N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections and relativistic effects. Computational aspects of ¹⁵N NMR are illustrated for the series of neutral and protonated open-chain nitrogen-containing compounds and nitrogen heterocycles, coordination and intermolecular complexes.

Intermolecular magnetic interactions in stacked DNA base pairs

The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.

Intramolecular hydrogen bonding in malonaldehyde and its radical analogues

High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA_RS, and cis-MA_RA, both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA_RA, in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA_RS, in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ^* orbital of acceptor O-H bond (n → σ^*_OH). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA_RS.

Synthesis, photoisomerization properties and thermal bleaching kinetics of pyrazolones containing 3-cyanobenzal

Through the design of molecules and the modification of structures, ten novel pyrazolone derivatives containing 3-cyanobenzal have been synthesized. They are 1-phenyl-3-methyl-4-(3-cyanobenzal)-5-hydroxypyrazole thiosemicarbazone (1)/4-methyl-3-thiosemicarbazone (2)/4-ethyl-3-thiosemicarbazone (3)/4-phenyl-3-thiosemicarbazone (4)/4-phenylsemicarbazone (5) and 1,3-diphenyl-4-(3-cyanobenzal)-5-hydroxypyrazole thiosemicarbazone (6)/4-methyl-3-thiosemicarbazone (7)/4-ethyl-3-thiosemicarbazone (8)/4-phenyl-3-thiosemicarbazone (9)/4-phenylsemicarbazone (10), in which seven compounds (1, 2, 3, 6, 7, 8 and 10) have photoisomerization behaviors. Their structures, photoisomerization properties, and first-order kinetics were investigated. The results show that the compounds 2, 3, 7 and 8 exhibit irreversible photoisomerization behaviors, the other three compounds have reversible photoisomerization behaviors under 365nm light irradiation and heat. But only 1,3-diphenyl-4-(3-cyanobenzal)-5-hydroxypyrazole 4-phenylsemicarbazone (10) exhibits good photochromic properties and fatigue resistance. Moreover, effects of various temperatures on the thermal bleaching reaction for 10 and substituent groups on the photochromic phenomenon are discussed.

Pseudo-cyclic structures of mono- and di-azaderivatives of malondialdehydes. Synthesis and conformational disentanglement by computational analyses

Mono- and diaza-derivatives of malondialdehydes, namely 3-alkyl(aryl)amino-2-arylacroleins and 1,5-dialkyl(aryl)-3-arylvinamidines are open-chain systems in which extended electron delocalization and pseudoaromaticity can be envisaged. A set of diversely functionalized compounds has been synthesized and characterized by spectroscopic data and X-ray diffractometry. Quantum-chemical calculations were performed for all possible neutral tautomers and conformers in the gas phase and compared to those in polar solvents (CHCl3, DMSO, and EtOH) at the M06-2X/6-311++G(d,p) level. Tautomeric equilibria and conformational preferences can be rationalized in terms of structural factors, which can be roughly estimated as summation or subtractions of intramolecular interactions. As expected, a key role is played by intramolecular hydrogen bonds whose strength varies from the gas phase to polar ethanol. This issue also delves into the concept of resonance-assisted H-bond, where the donor and acceptor atoms are connected by a π-conjugated system. The most stable conformers (structures a and c) possess a high degree of pseudoaromaticity as inferred from HOMA indexes and other delocalization parameters.

Intramolecular O-H···O═C hydrogen bond energy via the molecular tailoring approach to RAHB structures

A method for the calculation of the intramolecular hydrogen bond (HB) energy (EHB) by molecular tailoring approach for hydroxycarbonyl aliphatic compounds has been used for compounds with resonance-assisted hydrogen bonding (RAHB). The intramolecular hydrogen bond energies estimated for 229 structures (of 186 compounds) range from 8.2 to 26.3 kcal/mol and show correlation with the geometry descriptors of hydrogen bonds, with the calculated frequencies as well as with topological parameters obtained from the atoms in molecules (AIM) theory. These correlations differ significantly from obtained formerly for saturated nonenolizable structures and prove the special character of the resonance-assisted hydrogen-bonded systems.

Investigation of the resonance-assisted hydrogen bond in model β-diketones through localized molecular orbital analysis of the spin-spin coupling constants related to the O-H···O hydrogen bond

The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.

Estimation of the intramolecular O-H···O═C hydrogen bond energy via the molecular tailoring approach. Part I: aliphatic structures

A simple and universal method for the estimation of the intramolecular hydrogen bond (HB) energy (E(HB)) in hydroxycarbonyl aliphatic compounds is proposed by the application of the molecular tailoring approach (MTA) based on calculations at the second-order Møller-Plesset MP2 level. The calculation of EHB can be realized by the one optimization and three single point calculations of the energy for each compound with carbonyl and hydroxyl groups involved in HB. The intramolecular hydrogen bond energies estimated for 153 structures (of 102 compounds) ranged from 1.4 to 13.7 kcal/mol for systems without resonance-assisted hydrogen bonding (RAHB). To verify the method, we show the correlations of the energy (E(HB)) in six-, seven-, and eight-membered HB rings in the optimized multifunctional molecules with the usual geometry descriptors of hydrogen bonds. Moreover, topological parameters from the atoms in molecules (AIM) theory and the calculated infrared and proton NMR spectra are correlated. The effects of conjugation and π-electron delocalization, bifurcation, and cooperativity are discussed, along with the correlation between the strength and geometrical parameters of H bonding.

Computational study of interactions and nuclear magnetic shielding constants in linear chains of formamide clusters

We investigated the energetic, structural, dielectric, and nuclear magnetic shielding properties of linear n-formamide clusters, with n up to 6, to quantitatively characterize cooperative effects in model biological systems. The geometries of the complexes were optimized at the MP2 and DFT/B3LYP levels by using the pc-2 and pc-3 basis sets, while the nuclear magnetic shielding constants were calculated by employing pcS-n type basis sets, which have been optimized specifically for density functional calculations of these properties. The interaction energies show the cooperative effect, which favors the successive addition of monomers. In addition, by analyzing structural changes in the intermolecular C=O, C-N and hydrogen O⋯H bonds, as well as in the average dipole moments as cluster size increases, we found that the cooperative interaction far exceeds that expected for electrostatic interactions. Such non-pairwise-additive effects are also reflected in the changes of the nuclear magnetic shielding constants. In particular, the negativity of O shielding decreases around 23% from the monomer to the 6-formamide chain. It is possible to note the decrease in the shielding of H and in the deshielding of O as a result of their hydrogen bonding. However, the results obtained show that these variations in the extremes of formamide chains tend to zero, and the respective shielding values tend to stabilize as the number of monomers increases in the chain. Also, the cooperative effect increases in the middle of the chains, by decreasing the shielding for all atoms except that of O, which decreases its deshielding. These results could serve to guide improvements in current conventional models for simulating hydrogen bonded systems.

The analysis of NMR J-couplings of saturated and unsaturated compounds by the localized second order polarization propagator approach method

Calculations of NMR J-coupling with polarization propagators are not invariant under unitary transformations at second order level of approach, second order polarization propagator approach (SOPPA). They are only invariant at first order or random phase level of approach (RPA). We performed "localized" SOPPA (Loc-SOPPA), calculations of J-couplings applying two different schemes for the localization of molecular orbitals(LMO): Foster-Boys and Pipek-Mezey. We show here that results of such Loc-SOPPA calculations are different though not much: they are less than 6% different in the worst case. Therefore it is possible to apply them with confidence in the analysis of the transmission of different coupling mechanisms within the molecule. We are able now to get reliable information on what LMOs are the most important (and so which are not important) for a given J-coupling in a molecule. This information can then be used for selecting which are the paths that should be described with the highest possible accuracy for that J-coupling calculation. A few unsaturated compounds are analyzed: ethene, trans-difluoroethene or DiF-ethene, and imine. It is shown that different lone pairs (of p(z) or p(x/y) type) are responsible for the vicinal F-F J-coupling in DiF-ethene; and also the fact that the main LP contributor is not the same for the fermi contact and the spin-dipolar mechanisms. We also studied phosphorous containing compounds such as phosphine and cis-propylene phosphine. In both cases the analysis of the main LMO contributing to one-bond P-H coupling and through-space P-C coupling were performed. The above mentioned unsaturated molecular systems have quasiinstability problems that arise at RPA level of approach. We show here that they are mostly originated in the antibonding π∗ LMO, corresponding to the C=C or C=N double bonds. We performed the analysis of the origin of quasiinstabilities for the SD mechanism. The contribution of each kind of excitation terms to SOPPA calculations were considered, meaning the main contributions by single and double excitations. It is shown that one can get more than 97% of the total electron correlation contribution when including terms that mainly contain single excitations (though double-excitation matrix elements should still be calculated).