Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.     

Dynamics of a network of hydrogen bonds upon water electrocrystallization

Computer simulation is employed to study the dynamics of a network of hydrogen bonds and the structural properties of water placed between graphene layers. The presence of the graphene walls has been shown to substantially affect the water phase diagram. Glass transition processes are observed in the system, and liquid water completely passes to an amorphous state. Moreover, it has been established that the imposition of an external electric field with strength E ≥ 0.5 V/Å on the system subjected to increased pressure results in structural ordering of water. It has been found that water located between graphene layers is transformed into Ic cubic ice. The electrocrystallization of water has been shown to substantially change the dynamics of the network of hydrogen bonds.     

Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

The effect the number of chitosan monomer units CTS_n (n = 1–5), the protonation of chitosan dimers, and the interaction between CTS_n (n = 1–3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS_n is 2n ? 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.     

Comparison of various types of hydrogen bonds involving aromatic amino acids

Ab initio calculations are used to compare the abilities of the aromatic groups of the Phe, Tyr, Trp, and His amino acids (modeled respectively by benzene, phenol, indole, and imidazole) to form H-bonds of three different types. Strongest of all are the conventional H-bonds (e.g., OH..O and OH..N). His forms the strongest such H-bond, followed by Tyr, and then by Trp. Whereas OH..phi bonds formed by the approach of a proton donor to the pi electron cloud above the aromatic system are somewhat weaker, they nonetheless represent an important class of stabilizing interactions. The strengths of H-bonds in this category follow the trend Trp > His > Tyr approximately Phe. CH.O interactions are weaker still, and only those involving His and Trp are strong enough to make significant contributions to protein structure. A protonated residue such as HisH(+) makes for a very powerful proton donor, such that even its CH..O H-bonds are stronger than the conventional H-bonds formed by neutral groups.     

The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

Conformer independent heterodimerisation of linear arrays using three hydrogen bonds

5-Membered heterocycles are employed to give a conformer independent DDA array of hydrogen bonds, resulting in enhanced binding affinity to a complementary AAD array in comparison to a DDA array employing a 6-membered ring.     

A scheme estimating the energy of intramolecular hydrogen bonds in diols

The relative energies of conformers of 1,2-ethanediol, 1,3-propanediol, and 1,4-butanediol are split into a sum of five different terms including the intramolecular OH?O interaction. This scheme allows to estimate the energy of the O-H?O intramolecular hydrogen bond of the tGG′g and gGG′g conformers of 1,3-propanediol, the g′GG′Gt and g′GG′Gg conformers of 1,4-butanediol, and the energy of the non-bonded O-H?O interaction in the g′Gt, g′Gg and g′Gg′ conformers of 1,2-ethanediol. This scheme provides pure hydrogen bond energies without assuming the geometry and/or electronic features to be constant between the conformation having a IHB and a reference conformation. The fitted energies show a perfect linear correlation with the corresponding r(H?O)⁻¹ values. QTAIM atomic electron population and energies of the donor hydrogen calculated along the H-O-C-C internal rotation are found to be linearly correlated. These linear correlations display small changes at the BCP formation in 1,3-propanediol.     

Simultaneous generation of different types of ion pairs upon charge-transfer excitation of a donor-acceptor complex revealed by ultrafast transient absorption spectroscopy

The excited-state dynamics of the methylperylene/tetracyanoethylene (MPe/TCNE) donor-acceptor complex has been investigated in various solvents using femtosecond transient absorption spectroscopy. The transient spectra reveal the formation of two types of ion pairs: The first (IP1), constituting the major fraction of the total ion-pair population, is characterized by a broad and red-shifted absorption spectrum compared to that of the free MPe cation and by a subpicosecond lifetime, whereas the second (IP2) has a spectrum closer to that of MPe cation and a lifetime of a few picoseconds. A substantial polarization anisotropy was observed with IP1 but not with IP2, indicating a relatively well-defined structure for the former. The reaction scheme that best accounts for the observed dynamics and its solvent dependence involves the simultaneous excitation of complexes that differ by their electronic coupling. The more coupled complexes have a high absorption coefficient and thus yield IP1, which undergoes ultrafast charge recombination, whereas the less coupled complexes have a lower probability to be excited and lead to the longer-lived IP2.     

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.     

Evaluation of the bond energy terms for the various types of boron-nitrogen bonds

Summary We have determined a series of bond energy terms in compounds containing dative, single, double and/or triple boron-nitrogen bonds. We describe various interesting applications based on these bond energy terms namely the determination of enthalpies of atomization and stabilization energies. More particularly, the conventional ring strain energies of three- and four-membered small ring containing boron and nitrogen atoms could be determined and the aromaticity of borazine, reexamined.Dedicated to Professor Alberte Pullman     

Effect of solvent upon CH...O hydrogen bonds with implications for protein folding

The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.     

Tuning the interaction energy of hydrogen bonds: the effect of the substituent

The effect of the substituent R in the hydrogen bonding properties of FH···FR (R = H, Al, Li, Cl and CCH) complexes has been studied by theoretical calculations. The dependency of the interaction energy with the hydrogen bond distance and R is explained in terms of the topologies of the electron density and the electrostatic potential. A simple model of the hydrogen bond interaction energy, which can be assimilated to an interaction potential, is defined in terms of a stabilizing mutual polarization of the monomers and an overall destabilizing contribution associated with the electron density reorganization when the overlap of the closed shells is large enough. This model shows an excellent agreement with the ab initio interaction energies and is common for all the analyzed complexes. The substituent effect is represented in the model by a single parameter that can be calculated from the electron distribution in the acceptor atom region. The perturbation in the hydrogen bonding interaction induced by the change of R presents a close similarity with that produced by an external electric field of the same order of magnitude than those found in crystalline solids, indicating that both perturbations should play a significant and similar role on the properties of hydrogen bonds in condensed matter.     

Integrated intensity of continuous absorption in infrared spectra of complexes with medium-strong and strong hydrogen bonds

A simple, nongraphical and reproducible method of separation of the complex absorption due to strong hydrogen bonds from that due to the skeleton is proposed. The method has been tested on 17 complexes of pyridine N-oxide, triphenylphosphine oxide and DMSO-d₆ with dichloroacetic acid in dry dichloromethane and acetonitrile. The integrated intensity (A_CPA) and the centre of gravity (mathtype1) of complex absorption due to protonic vibration were measured and correlated with pK_a values of bases and chemical shifts of the hydrogen-bonded protons (δ), and discussed with respect to hydrogen bond strength variations. TheA^CPA values vary from 17.5 to 46 x 10⁴ cm mmol^-1 and were reproducible to within ± 1 x 10⁴ cm mmol⁻¹ (5-15 %). A nonlinear correlation between A_CPA and (mathtype2) has been found in wide region of data; (mathtype3) varies from 500 to 2300 cm⁻¹. A gradual proton transfer has been considered from the acid to pyridine N-oxides via strengthening intermolecular H-bonds, AH⋯ON, and further via weakening interionic H-bonds, A⁻⋯ HON⁺. The obtained correlations suggest that variations of hydrogen bond strength caused similar changes of A_CPA and (mathtype4) both in molecular (A–H⋯B) and ionic (A⁻⋯H–B⁺) species.     

Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules

Physical properties of over 8000 intramolecular hydrogen bonds (iHBs), including 2901 ones of the types OH···O, OH···N, NH···O and OH···C, in 4244 conformers of the DNA-related molecules (four canonical 2'-deoxyribonucleotides, 1,2-dideoxyribose-5-phosphate, and 2-deoxy-D-ribose in its furanose, pyranose and linear forms) have been investigated using quantum theory of atoms in molecules (QTAIM) and vibrational analysis. It has been found that for all iHBs with positive red-shift of the proton donating group stretching frequency the shift value correlates with ρ(cp)-the electron charge density at the (3,-1)-type bond critical point. Combining QTAIM and spectroscopic data new relationships for estimation of OH···O, OH···N, NH···O and OH···C iHB enthalpy of formation (kcal mol(-1)) with RMS error below 0.8 kcal mol(-1) have been established: E(OH···O) = -3.09 + 239·ρ(cp), E(OH···N) = 1.72 + 142·ρ(cp), E(NH···O) = -2.03 + 225·ρ(cp), E(OH···C) = -0.29 + 288·ρ(cp), where ρ(cp) is in e a(0)(-3) (a(0)- the Bohr radius). It has been shown that XHY iHBs with red-shift values over 40 cm(-1) are characterized by the following minimal values of the XHY angle, ρ(cp) and nubla(2)ρ(cp): 112°, 0.005 e a(0)(-3) and 0.016 e a(0)(-5), respectively. New relationships have been used to reveal the strongest iHBs in canonical 2'-deoxy- and ribonucleosides and the O(5')H···N(3) H-bond in ribonucleoside guanosine was found to have the maximum energy (8.1 kcal mol(-1)).     

Effect of hydrogen bonds on the amorphous phase of a polymer as determined by atomistic molecular modelling

Molecular simulations of poly(vinyl phenol) were performed to study the effect of hydrogen bonds. Three conformations were constructed and their structure was validated in terms of the solubility parameter and gyration radius. Amorphousness was confirmed by calculating the X-ray pattern and pair correlation function. Isotropy of the structure was verified using the bond-orientational correlation function for backbone, phenyl rings, and O–H groups forming hydrogen bonds. Glass transition temperature was calculated using a stepwise change on temperature at constant pressure. The values were found to be comparable to experimental data and were consistent with poly(styrene) simulations published in the literature. The percentage of hydrogen bonds found in the model, 63%, was in good agreement with previous semi-quantitative evaluation by FTIR spectroscopy.     

Stability of hydrogen bonds upon polymerization and color transition of diacetylenes: An FTIR spectroscopy study

FTIR spectra (400–7500 cm⁻¹) have been recorded for polycrystalline films and single crystals of the diacetylene 4BCMU in the monomer, blue and red polymer states, and of 3BCMU monomer. Particular attention was paid to the amide bands associated to the urethanes in the side groups, which form one-dimensional H-bond linear chains quite similar to those found in peptides and proteins. The positions and strengths of these absorptions are practically unchanged by polymerization or blue to red polymer color transition. This suggests that the H-bond linear chains are the main constitutive interactions in these crystals, and that the conjugated parts must and do “adapt” to the unchanged H-bond lines. No evidence of side group disordering was observed at the irreversible blue to red transition in poly-4BCMU crystal.     

Transition from moderate to strong hydrogen bonds: its identification and physical bases in the case of O-H...O intramolecular hydrogen bonds

A systematic investigation aimed at identifying the transition from moderate (M) to strong (S) hydrogen bonds (HBs) and the physical bases of the main geometry-based HB strength classifications reported in the literature has been undertaken using the quantum theory of atoms in molecules (QTAIM). Correlations between the Laplacian of the electron density (rho) at the O...H hydrogen bond critical points (HBCPs), nabla2rhohb, specifically between the more intuitive parameter Lhb = -nabla2rhohb and other QTAIM parameters, have also been explored. The transition from MHBs to SHBs has been identified as the minimum (maximum) in the geometric dependence of Lhb (nabla2rhohb). For O-H...O intramolecular (IM) HBs (including resonance-assisted HBs), the transition is obtained, in a truly remarkable agreement with the existing geometry-based HB strength classifications, when the O...O (O...H) distance is approximately 2.51 ( approximately 1.55) A and when the ratio of the potential energy density (|Vhb|) to the kinetic energy density (Ghb) approximately 1.3. Accordingly, the ranges of the |Vhb|/Ghb ratios are >2-1.3 and 1.3-1 for, respectively, SHBs and MHBs. When the O...O distance is not a genuine indicator of HB strength, the |Vhb|/Ghb ratio and other parameters should be considered to characterize the strength of the HBs. Rationalizations have been provided by way of decoding the physical bases of the transition in terms of the properties of rho and the mechanical characteristics of the interactions that created the HBCPs. Lhb was found to correlate, with a very high degree of fidelity, with at least three parameters (in addition to O...O and O...H distances and the IMHB energy), Vhb/Ghb, Hhb/rhohb (the ratio of the total energy density, Hhb, to the electron density, rhohb (the so-called bond degree parameter)), and deltahb(O,H) (the delocalization index), demonstrating the importance and utility of Lhb (nabla2rhohb) for the study of HB interactions. A new refined energetics-based classification of O-H...O IMHB strengths has been advanced. The approach taken in this investigation can be extended to other HB systems.