Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

The relationship between intramolecular hydrogen bonds and certain physical properties of regioselectively substituted cellulose derivatives

This article tries to provide some direct evidence about the relationship between the intramolecular hydrogen bonds in cellulose and their corresponding effect on physical properties. The formation of intramolecular hydrogen bonds has been proved to contribute directly to certain physical properties of cellulose, such as its solubility in solvents having different polarities, the relative reactivities of the hydroxyls in a repeating unit and its crystallinity, using a 6-O-methylcellulose (6MC) film that was known¹ to have intramolecular hydrogen bonds. The excellent solubility of 6MC when compared with other cellulose derivatives indicated a lack of interchain hydrogen bonds. A comparison of the relative reactivities between the C-2 and C-3 position hydroxyls in 6MC also indicates that intramolecular hydrogen bonds once formed in 6MC films are possibly maintained even after dissolution in solvents. In addition, the poor crystallinity exhibited by 6MC supports the idea that crystallization in cellulosics may be dependent more upon preferencial interchain hydrogen bonding at the C-6 position hydroxyls than upon a uniform structure such as that found in 6MC, where every structural unit is completely and regioselectively substituted, distinguishing it from other synthetic polymers such as polyolefins and polyesters. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 717–723, 1997     

Structural and energetic consequences of the formation of intramolecular hydrogen bonds

Formation of intramolecular hydrogen bonds leads to structural modifications in the whole molecule, which are discussed on the basis of B3LYP/6-31G(d,p) calculations. The energy and the structure of various hydrogen-bonded and open conformers are considered for two groups of ortho-substituted phenols–N-dimethylaminomethylphenols (Mannich bases) and N-methylbenzylideneamines (Schiff bases). The energy of intramolecular hydrogen bond formation in Mannich bases was corrected for non-bonded interactions within the molecules, based on a thermodynamic cycle. Structural data were used to estimate the fraction of the ortho-quinoid (keto) form in particular tautomers. It is shown that proton transfer in Schiff bases leads to an increase of this fraction to about 40%, while opening of the hydrogen bond in the proton transferred form increases the keto fraction to 70%.     

Effects of intramolecular hydrogen bonds on phosphorescence emission: A theoretical perspective

Importing intramolecular hydrogen bond in phosphorescent transition metal complexes has been considered one of the excellent approaches to improve the electroluminescence performance of organic light-emitting diodes in real applications. However, the relationships between such H-bond structure and phosphorescent properties have not been theoretically revealed yet. In this study, two types of intramolecular hydrogen bonds are introduced into the two classes of traditional materials, that is, Pt(II) and Ir(III) complexes ( 1a and 2a ) to completely elucidate their influence on the structures and properties by comparing with the original phosphors ( 1b and 2b ) using density functional theory/time-dependent density functional theory for the first time. A comprehensive analysis of the geometric structures, molecular orbitals, and luminescence properties (including phosphorescence emission wavelengths and radiative and nonradiative decay processes) has been carried out. Our theoretical model highlights that complexes 1a and 2a embedded with H-bonds significantly promote the phosphorescence emission band blue-shifted and restrict molecular deformations compared with the corresponding 1b and 2b , which can provide helpful guidance to regulate and design several aspects of highly efficient blue phosphorescent emitters.     

低阶煤中氢键作用的色散校正密度泛函理论研究

本研究以苯酚…苯酚、苯酚…苯、苯酚…二苯醚、苯酚…喹啉和苯甲酸…苯甲酸为对象，采用色散校正的密度泛函理论分别研究褐煤中自缔合OH、OH-π、OH-醚O、OH-N和COOH-COOH之间形成的氢键。此外，还研究了氢键供体中取代基(CH₃-、CH₃O-、OH-、NH₂-、COOH-和NO₂-)对氢键的影响。对上述复合物进行了几何优化，并计算了能量、Mulliken电荷分布及振动频率。从优化的结构中可以看出上述复合物之间都存在氢键，所有复合物中O-H键键长都比苯酚中自由羟基的长，这表明这些复合物之间存在相互作用。其中，羧酸…羧酸复合物中O-H键的键长最长。此外，通过Mulliken电荷分布可看出上述复合物之间存在电荷转移。基于振动频率分析，所有的O-H键伸缩振动都发生了红移，尤其是羧酸…羧酸和苯酚…喹啉复合物，这可为煤中羟基振动的红外光谱分析提供依据。根据键能不同氢键强度按以下顺序依次递减：COOH-COOH>OH-N > 自缔合OH≈OH-醚O > OH-π，这与振动频率的分析结果一致。此外，不同取代基对氢键作用的影响不同。     

Intramolecular C-H...Ccarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes

The anionic tripodal N-heterocyclic carbene (C3N2H3)3BH- first prepared by Fehlhammer, together with three neutral variants, (C3N2H3)3CH, (C3N2H3)3P, and (C3N2H3)3SiH, have been studied using quantum chemical methods. Isodesmic reactions are used to deduce that the phosphine-bridgehead species in particular has a large-resonance stabilization energy. All the podands undergo substantial conformational change on excitation to the lowest triplet electronic state, with effective localization of the excitation on one of the heterocyclic rings, dearomatizing it. On monoprotonation of the ground states, three of these species display intramolecular C-H...Ccarbene hydrogen bonding: The nature and strength of these interactions is explored using model (intermolecularly hydrogen-bonded) complexes, isodesmic reactions, and GIAO calculations of chemical shifts. One surprising result is that C-H...Ccarbene hydrogen bonds involving ethenic hydrogens can be almost as strong as those involving the imidazolium proton (first identified by Arduengo). The case of the monoprotonated carbon bridgehead species is in particular intriguing. It is stabilized by a competitive Ccarbene...N interaction of sufficient strength to override the C-H...Ccarbene bonding motif observed in the other structures.     

Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine

Ab initio calculations at the MP2/6‐311++G** level of theory led recently to the identification of 13 stable conformers of gaseous glycine with relative energies within 11 kcal/mol. The stability of every structure depends on subtle intramolecular effects arising from conformational changes. These intramolecular interactions are examined with the tools provided by the Atoms In Molecules (AIM) theory, which allows obtaining a wealth of quantum mechanics information from the molecular electron density ρ( r ). The analysis of the topological features of ρ( r ) on one side and the atomic properties integrated in the basins defined by the gradient vector field of the density on the other side makes possible to explore the different intramolecular effects in every conformer. The existence of intramolecular hydrogen bonds on some conformers is demonstrated, while the presence of other stabilizing interactions arising from favorable conformations is shown to explain the stability of other structures in the potential energy surface of glycine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 702–716, 2001     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Computational study of the patterns of weaker intramolecular hydrogen bonds stabilizing acylphloroglucinols

Acylphloroglucinols (ACPLs) are polyphenolic compounds derivative from phloroglucinol, characterized by the presence of at least one COR group and exhibiting a variety of biological activities, which makes them interesting for drug development possibilities. This study investigates patterns in the ways in which weaker intramolecular hydrogen bonds contribute to their conformational stabilization, considering the C? H···O H‐bonds, present in all ACPLs, and the O? H···π H‐bonds, present in ACPLs in which one or more substituents contain a π bond or system sufficiently close to a phenol OH for the H‐bond to be possible. The results in vacuo and in three different solvents (chloroform, acetonitrile, and water) show that, whereas C? H···O plays a significant roles in all these media, the role of O? H···π decreases with increasing solvent polarity. Calculations in vacuo are performed at various levels to enable performance comparisons; calculations in solution use the polarizable continuum model. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Partition potential for hydrogen bonding in formic acid dimers

The ground-state energy and density of 4 low-energy conformations of the formic acid dimer were calculated via partition density functional theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds (HBs) among all 4 dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than 1 HB. We also provide numerical confirmation of the intuitive (but unproven) observation that fragment deformation energies are larger for systems with larger binding energies.     

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.     

Structure and cooperativity of the hydrogen bonds in sodium dihydrogen triacetate

Geometry and energetics of low energy conformers of sodium dihydrogen triacetate (SDHTA) and its anion are studied using density functional theory (DFT) at the Becke, Lee‐Yang‐Parr hybrid functional (BLYP) and Becke, three‐parameter, Lee‐Yang‐Parr hybrid functional (B3LYP) levels. For both cases, two structures of comparable energy are found, which have different symmetry with respect to the two hydrogen bonds (HBs). DFT‐based Born–Oppenheimer molecular dynamics simulations are performed for SDHTA, which show that both structures are visited at room temperature conditions. The trajectory analysis further reveals that the two HBs behave anticooperative, that is, on average elongation of one HB is accompanied by a compression of the other one. This is in accord with nuclear magnetic resonance (NMR) experimental studies for a similar counter ion–dihydrogen triacetate complex. © 2012 Wiley Periodicals, Inc.     

The interaction of fluorosilanes with hydrogen fluoride clusters: strongly blue-shifted hydrogen bonds

The equilibrium structures, binding energies, and vibrational spectra of the complexes formed between hydrogen fluoride clusters (HF)_n (1≤n≤4) and the fluorosilanes SiHF₃, SiH₂F₂, and SiH₃F are investigated within the second-order Møller–Plesset perturbation theory method applying extended basis sets. It is shown that Si–FH–F halogen–hydrogen bonds are formed in the most stable open dimers, SiHF₃–HF, SiH₂F₂HF, and SiH₃FHF. No Si–HF–H hydrogen bonds occur in these dimers. Nevertheless, blue shifts of Si–H stretching frequencies are calculated. All three trimers, fluorosilane–(HF)₂, all three tetramers, fluorosilane–(HF)₃, and two of the pentamers, fluorosilane–(HF)₄, form cyclic structures with strong Si–FH–F halogen–hydrogen bonds and weak Si–HF–H contacts, the latter displaying, nevertheless, strongly blue-shifted Si–H stretching frequencies. These blue shifts are comparable in size to those of the corresponding fluoromethane–(HF)_n complexes and are with about +50 cm⁻¹ for the case n=3 among the largest ever calculated and definitely the largest for Si–H bonds. In the title complexes, the formation of the Si–FH–F halogen–hydrogen bonds induces a substantial stretching of this Si–F bond, which in turn leads to a significant contraction of the fluorosilane Si–H bond in the Si–HF–H hydrogen bond. This disposition of the fluorosilane monomers is demonstrated with the aid of suitable potential energy surface scans and appears to be a prerequisite for the formation of strongly blue-shifted hydrogen bonds.     

Identification of hydrogen bonds using quantum electrodynamics

A method for the identification of hydrogen bonds was investigated from the viewpoint of the stress tensor density proposed by Tachibana and following other works in this field. Hydrogen bonds are known to exhibit common features with ionic and covalent bonds. In quantum electrodynamics, the covalent bond has been demonstrated to display a spindle structure of the stress tensor density. Importantly, this spindle structure is also seen in the hydrogen bond, although the covalency is considerably weaker than in a typical covalent bond. Distinguishing it from the ionic bond is most imperative for the identification of the hydrogen bond. In the present study, the directionality of the hydrogen bond is investigated as the ionic bond is nearly isotropic, while the hydrogen bond exhibits the directionality. It was demonstrated that the hydrogen bond can be distinguished from the ionic bond using the angle dependence of the largest eigenvalue of the stress tensor density.     

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.     

Structure and property of the hydrogen bonding complex between triazines and water

The study of the intermolecular interactions that drive the solvation of six-membered nitrogenated aromatic rings is of particular importance since they are known to constitute key building blocks of pro- teins and nucleotides[1―5]. The investigation of the 1:1 adduct of these molecules with water will be the first step in the understanding of such interactions. These molecules possess two different proton-acceptor sites: the ring π cloud and the lone pairs of electrons on the nitrogen atoms…     

The influence of formamide (model of protein unit) on the intramolecular proton transfer in the DNA simple base guanine: A density functional theory study

For the purpose of investigating the influence of protein unit on the intramolecular proton transfer (IPT) reactions in the simple base guanine, a simple model (formamide) of peptides is designed to biological system investigations, and five complexes of formamide–guanine (FG1, FG2, FG3, FG4, and FG5) are determined at the B3LYP/6‐311++G(d,p) level of theory. For comparison, HF and MP2 methods are also used in this paper. The proton transfer (PT) reaction processes of guanine and FGs have been investigated employing the B3LYP/6‐311++G(d,p) level of theory. The selected thermodynamic and kinetic parameters, such as the activation energies (E_a), changes of enthalpy (ΔH) and changes of free energies (ΔG), as well as the equilibrium constants (K_p) for those reaction processes, have also been obtained by calculational means. The calculated results indicate that the assisted and protected effects of formamide on IPT in guanine are site‐dependent. CH1 is the lowest activation energy needed PT process no matter where the formamide molecule is located in. The activation energy of CH1 with formamide in S2 is the lowest one (153.3 KJ/mol), whereas the one of CH5 with formamide in S5 is the highest (318.3 KJ/mol). © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A DFT Study on Intramolecular Hydrogen Bond in Substituted Catechols and Their Radicals

Density functional theory(DFT)at B3LYP/6-31G(d,p) level was employed to calculate intramolecular hydrogen bond enthalpies (H1HB),O-H charge differencces,O-H bond lengths and bond orders for various substituted catechols and their radicals generated after H-abstraction.It was found that although the charge difference between hydrogen-bonded H and O played a role in determining H1HB,H1HB was mainly governed by the hydrogen bond length.As the oxygen-centedred radiocal has great tendency to form a chemical bond with the H atom,hydrogen bond lengths in catechloic radicals are systematically shorter than those in catechlos,hence,the H1HB for the former are higher than those for the latter.     

Intramolecular hydrogen bond in the hydroxycyclohexadienyl peroxy radicals

The hydroxycyclohexadienyl peroxy radicals (HO? C₆H₆? O₂) produced from the reaction of OH‐benzene adduct with O₂ were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical II_s and 4‐hydroxycyclohexadienyl peroxy radical III_s were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical II_s is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical III_s, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Interplay of intramolecular hydrogen bonds,OH orientations,and symmetry factors in the stabilization of polyhydroxybenzenes

Polyhydroxybenzenes are the parent compounds of large classes of derivatives, many of which exhibit biological activities. The study of derivatives highlights the importance of the conformation stabilizing factors of the parent compounds. To identify these factors, a systematic comparative study of polyhydroxybenzenes was carried out through a computational study of all possible structures and conformers in vacuo and in three solvents differing by their polarities and by the types of interactions with the solute molecule (water, chloroform, and acetonitrile); the results in solution are complemented by the study of adducts with explicit water molecules and, for the simpler structures, also with explicit acetonitrile molecules. The greatest conformation stabilizing effect pertains to intramolecular hydrogen bonds, with preference for consecutive H‐bonds. Uniform orientation of the phenol OH is a stabilizing factor for structures with meta OH groups. Preference for structures with meta OH and with greater symmetry increases as the medium polarity increases. The coexistence of intramolecular H‐bonds and solute–solvent intermolecular H‐bonds in water and acetonitrile solution narrows the solvent‐effect difference between conformers with and without intramolecular H‐bonds. Comparison of results from different calculation methods (HF, MP2, and DFT/B3LYP, with 6‐31G(d,p) and 6‐31++G(d,p) basis sets) shows consistency of the identified trends. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011