Long distance structural consequences of H‐bonding: the case of complexes of para‐substituted phenol derivatives

H‐bonded complexes of p‐X‐PhOH/p‐X‐PhO^? with fluoride and hydrofluoric acid (X = OH, H, NO₂) were subject of optimization (by means of B3LYP/6‐311+G**) for gradually changed O···F distance from d_O···F = 4.0 Å down to (i) the distance of the proton transfer from the hydroxyl group to fluoride leading to O^?···HF interaction and (ii) fully optimized system (O^?···HF type). In this way, we simulate gradual changes of H‐bond strength estimating simultaneously the energy of interaction, E_int, energy of deformation, E_def, and the binding energy, E_tot. The obtained geometrical parameters allow us to show that H‐bond formation causes substantial changes in geometry, even at so distant parts of the system as the ring and bond length in para‐substituents (OH and NO₂). All these changes are monotonically dependent on interaction and deformation energies. Copyright © 2009 John Wiley & Sons, Ltd.     

Prediction models for the Abraham hydrogen bond donor strength: comparison of semi‐empirical,ab initio,and DFT methods

Hydrogen bonding has a great impact on the partitioning of organic compounds in biological and environmental systems as well as on the shape and functionality of macromolecules. Electronic characteristics of single molecules, localized at the H‐bond (HB) donor site, are able to estimate the donor strength in terms of the Abraham parameter A. The quantum chemically calculated properties encode electrostatic, polarizability, and charge‐transfer contributions to hydrogen bonding. A recently introduced respective approach is extended to amides with more than one H atom per donor site, and adapted to the semi‐empirical AM1 scheme. For 451 organic compounds covering acidic ? CH, ? NH? , and ? OH groups, the squared correlation coefficient is 0.95 for the Hartree–Fock and density functional theory (B3LYP) level of calculation, and 0.84 with AM1. The discussion includes separate analyses for weak, moderate, and strong HB donors, a comparison with the performance of increment methods, and opportunities for consensus modeling through the combined use of increment and quantum chemical methods. Copyright © 2011 John Wiley & Sons, Ltd.     

Identification of hydrogen bond modes in polarized Raman spectra of single crystals of α‐oxalic acid dihydrate

Polarized Raman spectra of single crystals of the α‐polymorphs of protonated and deuterated oxalic acid dihydrate were recorded. The interpretation of the spectra is assisted by periodic DFT calculations using the CRYSTAL06 program and by comparison with the infrared spectra of the polycrystalline material. The agreement between the calculated and observed band wavenumbers is fair in the case of low‐anharmonicity modes, but marked differences appear for the stretching modes that are strongly anharmonic. A very broad feature, extending between ∼2000 and 1200 cm⁻¹, is attributed to OH stretching. Notable is the topping of this feature by distinct bands that can be attributed to CO stretching, H₂O scissoring and COH bending coupled to C O stretching. The assignments are supported by isotope effects. However, deuteration does not notably affect the wavenumber limits of the broad OH stretching band, which suggests that the potential governing the proton dynamics is of the asymmetric double‐minimum type with a very low barrier. The calculated normal coordinates show a strong participation of the bending modes of water molecules in almost all internal acid motions, as well as in the external phonons. Copyright © 2009 John Wiley & Sons, Ltd.     

1H NMR study of through‐bond and through‐space effects in the hetero‐association of pyridine with alkane diols

The ¹H NMR titration method is used to investigate through‐space and through‐bond effects on the association of diols with pyridine in benzene. Alkan‐1,n‐diols (n goes from 2 to 10), DL and meso isomers of butan‐2,3‐, pentan‐2,4‐ and hexan‐2,5‐diols, two adamantane diols and a bicyclo[2.2.2]octane diol are compared with alkanols. The –CH₂OH groups of the tri‐ and bicyclic compounds behave as if they were independent, with limiting OH proton shifts (at very low concentration) and both the first and the second association constants similar to those of a primary alcohol. In contrast, the alkane diols, with n = 2–4, display unusually high limiting shifts, ranging from 1.0 to 1.5 ppm (2.1 ppm for one methyl‐substituted diol). For these diols the first dissociation constant and the sum of the OH proton shifts in the 1:1 pyridine: diol complex are enhanced. This may be attributed to small cooperative effects, implying intramolecular hydrogen bonding, for n = 3 and 4, but for n = 2 a through‐bond effect accounts for most of the increase. Substituent interaction falls off sharply for n = 5 and is practically negligible for n = 10, for which the second association constant is close to the first. A sterically hindered BiEDOT diol, 2,2′‐bis{(3,4‐ethylenedioxythienyl)‐5‐[3‐(2,2,4,4‐tetramethylpentan‐3‐ol)]} behaves like the polycyclic compounds, with the two ? C(t‐Bu)₂OH groups independent. Copyright © 2010 John Wiley & Sons, Ltd.     

Inter‐ and intramolecular hydrogen bonds in polyamines: variable‐concentration 1H‐NMR studies

Inter‐ and intramolecular hydrogen bonding play an important role in determining the arrangement, physical properties, and reactivity of a great diversity of structures in chemical and biological systems. Several aromatic nucleophilic substitutions (ANS) in nonpolar aprotic, (non‐HBD), solvents recently studied in our laboratory have demonstrated the importance of self‐association of amines by hydrogen‐bond interactions. In this paper, we describe ¹H‐NMR studies carried out at room temperature on bi‐ and polyfunctionalized amines, namely: N‐(3‐amino‐1‐propyl)morpholine (3‐APMo), histamine, 2‐guanidinobenzimidazole (2‐GB), 1,2‐diaminoethane (EDA), 3‐dimethylamino‐l‐propylamine (DMPA), and 1‐(2‐aminoethyl)piperidine (2‐AEPip). By ¹H‐NMR measurements of amine solutions at variable concentrations we have shown that 3‐APMo, histamine and 2‐GB are able to form a six‐membered ring by intramolecular hydrogen bonding, while EDA, DMPA, and 2‐AEPip form dimers by intermolecular hydrogen bonds. Likewise, variable concentration ¹H‐NMR studies allowed estimation of the corresponding equilibrium constants for the dimerization. These results are correlated with experimental kinetic results of ANS, confirming hereto the relevance of the “dimer mechanism” in reactions involving these amines. Copyright © 2011 John Wiley & Sons, Ltd.     

Difference between 1H NMR signals of primary amide protons as a simple spectral index of the amide intramolecular hydrogen bond strength

The effect of the intramolecular H‐bonding of the primary amide group on the spectral properties and reactivity of this group towards electrophiles has been studied in systematic rows of 1,2,5,6,7,8‐hexahydro‐7,7‐dimethyl‐2,5‐dioxo‐1‐R‐quinoline‐3‐carboxamides and 2‐aryliminocoumarin‐3‐carboxamides using ¹H and ¹⁵N NMR spectroscopy and the kinetics of model reactions. The upfield signal of the amide proton that is not intramolecularly H‐bonded (H^a) depends on external factors such as solvent nature and concentration. At the same time, the downfield chemical shift of the H^b proton (bonded by the intramolecular hydrogen bond) depends mostly on the strength of the intramolecular H‐bond, which is affected by such internal factor as electron nature of substituent R. The substituent's influence on the H^b proton's chemical shift is more effective in deuterochloroform medium than in DMSO‐d₆ where the intramolecular hydrogen bond is less stable. The value Δδ(H) = δ(H^b) ? δ(H^a) is suggested as a simple comparative spectral index of the intramolecular hydrogen bond strength in these and similar compounds. By contrast, the effect of R on the ¹⁵N NMR chemical shift of the amide nitrogen has turned out to be too small to estimate changes of the electron density at the nitrogen. The effect of the intramolecular H‐bond on the reactivity of the amide group is twofold. When the cleavage of the H‐bond occurs on the rate limiting step it dramatically reduces the reaction rate. In the other case, the strengthening of the H‐bond favors the reaction rate because of the increase of the electron density at the amide nitrogen. Copyright © 2011 John Wiley & Sons, Ltd.     

The effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer of 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone in methanol: A TD‐DFT study

Excited‐state intermolecular or intramolecular proton transfer (ESIPT) reaction has important potential applications in biological probes. In this paper, the effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer reaction of the 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone (MQ) dye in methanol solvent is investigated by the density functional theory and time‐dependent density functional theory approaches. Both the primary structure parameters and infrared vibrational spectra analysis of MQ and its benzo‐analogue 2‐methyl‐3‐hydroxy‐4(1H)‐benzo‐quinolone (MBQ) show that the intermolecular hydrogen bond O₁―H₂?O₃ significantly strengthens in the excited state, whereas another intermolecular hydrogen bond O₃―H₄?O₅ weakens slightly. Simulated electron absorption and fluorescence spectra are agreement with the experimental data. The noncovalent interaction analysis displays that the intermolecular hydrogen bonds of MQ are obviously stronger than that of MBQ. Additionally, the energy profile analysis via the proton transfer reaction pathway illustrates that the ESIPT reaction of MBQ is relatively harder than that of MQ. Therefore, the effect of benzo‐annelation of the MQ dye weakens the intermolecular hydrogen bond and relatively inhibits the proton transfer reaction.     

Hydrogen‐bonded complexes of sulfonamides and thioamides with DMF: FT‐IR and DFT study,NBO analysis

The structure of H‐complexes of dimethylformamide (DMF) with N‐(2,2,2‐trichloro‐1‐hydroxyethyl)‐p‐toluenesulfonamide (1), N‐[1‐(4‐chlorophenylsulfonylamino)‐2,2,2‐trichloro)ethyl]dithiooxamide (2), N,N'‐bis[2,2‐dichloro‐1‐(4‐chlorophenylsulfonylamino)‐2‐phenylethyl]ethanebis(thioamide) (3) and N,N'‐bis[2,2,2‐trichloro‐1‐(phenylsulfonylamino)ethyl]ethanebis(thioamide) (3a) as proton donors was investigated using Fourier transform infrared spectroscopy and Density Functional Theory calculations. According to calculations, the interaction of DMF with the sulfonamide and thioamide NH groups in the complexes strongly affects the intramolecular H‐bonding in 1–3. From the natural bond orbital analysis, complexation with DMF strongly decreases the energy of the intramolecular N?H · · · S = C bonds, up to their rupture. Variation of the strength of the intra‐ and intermolecular H‐bonds in the complexes is consistent with the calculated frequencies of the NH and OH stretching vibrations, and the analysis of the corresponding bands in the IR spectra allows to suggest the preferable structure of the formed H‐complexes. Copyright © 2013 John Wiley & Sons, Ltd.     

Vibrational spectral studies on charge transfer and ionic hydrogen‐bonding interactions of nonlinear optical material L‐arginine nitrate hemihydrate

The near infrared Fourier‐transform (NIR FT)‐Raman and Fourier‐transform infrared (FT‐IR) spectroscopies supported by HF/6‐31G(d) computations have been employed to derive equilibrium geometry, vibrational wavenumbers and the first hyperpolarizability of the nonlinear optical (NLO) material, L ‐arginine nitrate (LAN) hemihydrate. The reasonable NLO efficiency, predicted for the first time in this novel compound, has been confirmed by Kurtz–Perry powder second harmonic generation (SHG) experiments. The changes in the atomic charge distribution among different groups due to the presence of strong electronegative atoms and the shrinking of N O bonds of nitrate anion and C N bonds of guanidyl group have been analyzed. The splitting of the carboxylate stretching modes, blue shifting of methine vibrations and the electronic effects such as backdonation and induction on the methylene hydrogen atoms have also been examined in detail. The intense low wavenumber H‐bond Raman vibrations due to electron–phonon coupling and nonbonded interactions in making the LAN molecule NLO active have been discussed based on the vibrational spectral features. The natural bond orbital (NBO) analysis and HF computations confirm the occurrence of strong intra‐ and intermolecular N H·O and O H·O ionic hydrogen bonding between charged species providing the noncentrosymmetric structure in the LAN crystal. Copyright © 2008 John Wiley & Sons, Ltd.     

Hydrogen bond and internal rotations barrier: DFT study on heavier group‐14 analogues of formamide

A theoretical study on heavier group‐14 substituting effect on the essential property of formamide, strong hydrogen bond with water and internal rotational barrier was performed within the framework of natural bond orbital (NBO) analysis and based on the density functional theory calculation. For heavier group‐14 analogues of formamide (YHONH₂, Y = Si, Ge and Sn), the n_N–π_Y=O conjugation strength does not always reduce as Y becomes heavier, for example, silaformamide and germaformamide have similar strength of delocalization. Heavier formamides prefer being H‐bond donors to form FYO–H₂O complexes to being H‐bond acceptors to form FYH–H₂O complexes. The NEDA analysis indicates that H‐bond energies of FYO–H₂O complexes increase as moving down group 14 due to concurrently stronger charge transfer (CT) and electrostatic attraction and for the FYH–H₂O complexes H‐bond strengths are similar. The model of CTs from FYO to H₂O differs from that at FYH–H₂O complexes, which are contributed not only by aligning lone‐pair orbital of O but also by another lone‐pair orbital. At two lowest lying excited states (the triplet and S₁ excited states), formamide and its heavier analogues form double H‐bonds with H₂O molecule at the same time. The barrier heights of internal rotation become gradually low from C to Sn, formamide (15.73 kcal/mol) > silaformamide (11.73 kcal/mol) > germaformamide (9.45 kcal/mol) > stannaformamide (7.50 kcal/mol) at the CCSD(T)/aug‐cc‐pVTZ//B3LYP/cc‐pVTZ level. NBO analysis indicates that the barrier does not only come from the n_N→π*_YO conjugation, and for heavier analogues of formamide, the n_N→σ*_YO hyperconjugation effect and steric effect considerably contribute to the overall rotational barrier. Copyright © 2013 John Wiley & Sons, Ltd.     

Hydrogen‐bonded nucleophile effects in ANS: the reactions of 1‐chloro and 1‐fluoro‐2,4‐dinitrobenzene with 2‐guanidinobenzimidazole, 1‐(2‐aminoethyl)piperidine and N‐(3‐aminopropyl)morpholine in aprotic solvents

The kinetics of the reactions of 2,4‐dinitrofluorobenzene (DNFB) and 2,4‐dinitrochlorobenzene (DNClB) with 2‐guanidinobenzimidazole (2‐GB) at 40 ± 0.2 °C in dimethylsulphoxide (DMSO), toluene, and in toluene–DMSO mixtures, and with 1‐(2‐aminoethyl)piperidine (2‐AEPip) and N‐(3‐aminopropyl)morpholine (3‐APMo) in toluene at 25 ± 0.2 °C were studied under pseudo first‐order conditions. For the reactions of 2‐GB carried out in pure DMSO, the second‐order rate coefficients were independent of the amine concentration. In contrast, the reactions of 2‐GB with DNFB in toluene, showed a kinetic behaviour consistent with a base‐catalysed decomposition of the zwitterionic intermediate. These results suggest an intramolecular H‐bonding of 2‐GB in toluene, which is not present in DMSO. To confirm this interpretation the reactions were studied in DMSO–toluene mixtures. Small amounts of DMSO produce significant increase in rate that is not expected on the basis of the classical effect of a dipolar aprotic medium; the effect is consistent with the formation of a nucleophile/co‐solvent mixed aggregate. For the reactions of 3‐APMo with both substrates in toluene, the second‐order rate coefficients, k_A, show a linear dependence on the [amine]. 3‐APMo is able to form a six‐membered ring by an intramolecular H‐bond which prevents the formation of self‐aggregates. In contrast, a third order was observed in the reactions with 2‐AEPip: these results can be interpreted as a H‐bonded homo‐aggregate of the amine acting as a better nucleophile than the monomer. Most of these results can be well explained within the frame of the ‘dimer nucleophile’ mechanism. Copyright © 2010 John Wiley & Sons, Ltd.     

Thermal reaction of electron deficient 4‐oxo‐4H‐pyrazole 1,2‐dioxide with cycloheptatriene: the first examples of the formation of an endo‐[4π + 6π]‐cycloadduct and an intramolecular 1,3‐dipolar reaction leading to a heterocage

The reaction of 3,5‐bis(methoxycarbonyl)‐4‐oxo‐4H‐pyrazole 1,2‐dioxide (1a) with 1,3,5‐cycloheptatriene (2b) gave a mixture of the novel endo‐[4 + 6]‐cycloadduct (4ab), anti‐exo‐[4 + 2]‐cycloadduct (5ab), and the heterocage (6ab) derived from the intramolecular 1,3‐dipolar cycloaddition reaction of the syn‐endo‐[4 + 2]‐cycloadduct. Analogous endo‐[4 + 6] selectivity in 1,3‐dipolar cycloadditions has not been reported previously. The X‐ray analysis indicates that 6ab has a very long N_sp3–N_sp3 bond distance of 1.617(4) Å. The cycloaddition behaviour is discussed on the basis of transition‐state structures optimized at the B3LYP/6‐31G(d) level of theory, from which predictions of the peri‐, regio‐, and stereoselectivities agreed well with the experimental results. Copyright © 2012 John Wiley & Sons, Ltd.     

The effects of insertion of nitrogen atoms on the aromatic nitrogen‐containing compounds: a potential approach for designing stable radical molecular materials

The effects of insertion of nitrogen atoms on the N―H bond strength of azaphenalene and on the stability of the corresponding radicals were comprehensively investigated using density functional theory. The N―H bond dissociation enthalpy of azaphenalene is found to be strengthened in all cases, but the magnitudes are various with the replaced sites and are additive. It is correlated with the coefficient of frontier molecular orbital; that is, it is correlated with the electron density distribution of the outer electrons. The computational results explain why the product substituted with two CH groups by N atoms in the phenalenyl skeleton yielded radical easily, whereas the product replaced with six nitrogen atoms failed. In addition, the effects of insertion of nitrogen atoms in other aromatic nitrogen‐containing compounds, including carbazole, indole, and pyrrole, were also studied. All the understanding about the insertion effects of nitrogen atoms would be helpful in designing novel molecules for specific applications, such as functional materials and antioxidants. Copyright © 2011 John Wiley & Sons, Ltd.