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.     

Directing-protecting groups for carbohydrates. Design, conformational study, synthesis and application to regioselective functionalization

A novel concept of regioselective transformation of secondary hydroxyl groups in carbohydrates is presented. First, the relative reactivity of the free hydroxyl groups of onoprotected d-glucose derivatives was assessed using acetylation as a model reaction. As a result, acylation of these polyols gave a mixture of monosubstituted products in which the 3-O functionalized derivatives predominated. Novel hydrogen bond acceptor protecting groups were next designed to modulate the 4-OH and 3-OH reactivity in the hope to mediate higher regioselective transformations. A molecular modeling study later validated by spectroscopic analysis predicted additional intramolecular hydrogen bonds between the hydroxyl groups and pyridyl-containing protecting groups. Taking advantage of this induced hydrogen bond network, we achieved regioselective acetylation of the hydroxyl group at position 3 without protecting any secondary hydroxyl groups of the carbohydrate moiety. This designed protecting/directing group increased the nucleophilicity and the steric hindrance of position 3. As a result, optimization of the reaction conditions enabled the monoacetylation (not affected by steric hindrance) of 6-O-protected glucopyranosides at position 3 and selective silylation (affected by steric hindrance) of position 2 in high isolated yields and regioselectivities. This result certainly opens doors to the regioselective open glycosylation of carbohydrates.     

Investigations into the effectiveness of deuterium as a "protecting group" for C-H bonds in radical reactions involving hydrogen atom transfer

Competition experiments have been carried out to determine the extent to which deuterium can be used as a protecting group for carbon-hydrogen bonds in radical-based intramolecular hydrogen atom transfer processes.     

几种二醇与非质子溶剂相互作用的红外光谱研究

测定了1，2-乙二醇、1，2-丙二醇、1，4-丁二醇和1，6-己二醇在CCl4中分别与十几种非质子溶剂相互作用的红外光谱，通过考察频率位移的变化，定量地研究了二醇分子内氢键与分子间氢键的协同效应．在四氯化碳介质中，乙二醇、1，2-丙二醇和1，4-丁二醇体系中存在明显的氢键协同效应。利用红外光谱数据，估算了常温下二醇分子内缔体与非质子溶剂的交叉缔合常数，其数值大于一元正链醇与相应溶剂的交叉缔合常数．     

Normal coordinate analysis of bilirubin vibrational spectra: Effects of intramolecular hydrogen bonding

Normal coordinate analyses are presented for half-bilirubin molecules. Calculations for the AB pyrromethenone include intramolecular hydrogen bonds, while those for the CD chromophore exclude intramolecular hydrogen bonds. Valence force-field parameters have been optimized to correlate closely with the IR and Raman spectra of the target molecules. The results of the calculations are compared with the spectra of bilirubin IXa and various model compounds in the solid state and solution.     

Synthesis of kinetically stabilized 1,2-dihydrodisilenes

Kinetically stabilized 1,2-dihydrodisilenes were successfully synthesized and isolated by the introduction of sterically protecting bulky aryl groups. These 1,2-dihydrodisilenes exhibit distinct Si═Si double-bond character in both solution and the solid state. The Si-H bonds in these 1,2-dihydrodisilenes exhibit higher s character than those of typical σ(4),λ(4)-hydrosilanes. Moderate heating of these 1,2-dihydrodisilenes in solution resulted in their isomerization to the corresponding trihydrodisilanes, with an intramolecular hydrogen migration as the rate-determining step.     

Rate of enolate formation is not very sensitive to the hydrogen bonding ability of donors to carboxyl oxygen lone pair acceptors; a ramification of the principle of non-perfect synchronization for general-base-catalyzed enolate formation

Two series of structures (1 and 2) possessing intramolecular hydrogen bonds to the lone-pair electrons of carbonyl oxygens have been examined to reveal the influence of the pK(a) of the hydrogen-bond donor on the rate of general-base-catalyzed enolate formation. The geometry of the hydrogen bonds is well accepted to be appropriate for intramolecular hydrogen-bond formation. Yet, as revealed by Br?nsted plots, both series show very little dependence of the rate of enolate formation on the hydrogen-bond donor ability. The intramolecular hydrogen bonds give rate enhancements only on the order of 10-100-fold, and corrected Br?nsted alpha-values are slightly below 0.1. The results can be understood by interpreting them in light of the Principle of Non-Perfect Synchronization. The results are consistent with the proton transfer occurring through an asynchronous transition state with the developing negative charge localized on carbon. We postulate that catalysts of enolate formation will be most effective if the binding groups are focused on stabilizing negative charge that is forming on the enolate carbon rather than on the enolate oxygen.     

Conformational isomerism of chlorophenylthioureas and intramolecular N---H … Cl hydrogen bonds: IR spectra of N---H stretching vibrations

The vN---H regions of the IR spectra of thioureas with chlorophenyl (ClPh) groups and those with halophenyl groups were measured in dilute CCl₄ solution. The observed vN---H bands were classified into eight groups according to the wavenumbers and the two substituent groups. The suggested conformational states and the formation of intramolecular N---H … Cl hydrogen bonds in these compounds were discussed in comparison with those of the urea analogs. It was found that these thiourea derivatives are more stable in the cis form than the urea analogs and that thioureas with o-ClPh groups form fewer intramolecular N---H … Cl hydrogen bonds than do the urea analogs.     

Analytical terahertz spectroscopy.

Recent progress in analytical terahertz (THz) spectroscopy is reviewed with illustrative examples showing that it is an effective method for detecting and identifying intermolecular interactions in chemical compounds, such as hydrogen bonds. The unique and characteristic properties of THz waves, their significance to both science and industry, and the bases of one of the successful fields of analytical THz spectroscopy, namely THz time-domain spectroscopy and THz imaging for chemical analysis, are described. Preliminary quantitative studies are presented to show the potential of THz spectroscopy for the detection and identification of intermolecular hydrogen bonds in unknown mixture samples. The selective detection of intramolecular hydrogen bonds and the detection of intramolecular interactions in ice are also introduced. Some brief remarks are provided on future developments, the main issues, and the prospects for analytical THz spectroscopy.     

Correlation between the reactivity and spectroscopic properties of N‐substituted secondary thioamides. New intramolecular N···H+···N binding approach and proton complexes based on thioamide ligation

On the basis of a comparison of chemical shifts and wavenumbers of several secondary thioamides and amides having monocationic substituents attached to thiocarbamoyl or carbamoyl groups by a polymethylene chain, new intramolecular unconventional N···H⁺···N hydrogen bonding effects were discovered. It is argued that the CH₂—N rotation is hindered and two ⁺H···NHCH₃ non‐equivalent protons occur in a proton spectrum of hydrochloride 1a (at 10.68 and 2.77 ppm, respectively) instead of two ⁺NH₂CH₃ protons. Presumably, the above steric factors inhibit the acidic hydrolysis of 1a (stabilized by strong intramolecular N···H⁺···N hydrogen bonds) to an amide and prevent intramolecular cyclization of 2a (stabilized by strong intramolecular neutral–neutral N···HN hydrogen bonds) to a cyclic amidine. Postulation of additional dihydrogen bond formation is helpful in understanding the spectroscopic differences of 4 and 5 . The above new bonding is also compared with intramolecular N···H—N⁺ hydrogen bonds in primary amine salts 7 and 8 . In contrast to 3 , a cooperative hydrogen bonded system is observed in 9 and 10 . The weak hydrogen bonds in 7 – 10 facilitate the hydrolysis and cyclization reactions of secondary thioamides. The spectroscopic data for secondary (thio)amides are especially useful for characterizing the electronic situation at the (thio)carbamoyl nitrogen atoms and they are perfectly correlated with the reactivity. Examples of chelation of protons by thioamides ( 11 and 12 ), which contain strongly electron‐donating pyrimidine groups, are presented to show the contribution of dihydrogen bonding in the protonation reaction similar to 1 and 4 . Copyright © 2003 John Wiley & Sons, Ltd.     

Structural characteristics of phenol formaldehyde novolak resin depending on polycondensation type using molecular simulation

Phenol formaldehyde novolak resins have various structures depending on the polycondensation types. Their structures were characterized using molecular mechanics and molecular dynamics. Dimer, tetramer, hexamer, octamer, and decamer of the resins with the ortho–ortho, ortho–para, and para–para sequences were calculated. The ortho–ortho resins have the structural characteristics of intramolecular hydrogen bonds between hydroxyl groups of the adjacent phenolic units. For the ortho–para and para–para resins, the intramolecular hydrogen bonds are formed mainly between hydroxyl groups of the backbone phenolic units. The para–para resins also have intramolecular hydrogen bonds between hydroxyl groups of the branched phenolic units. A factor determining the structural characteristics of the resins was found to be the geometry of the basic unit (dimer). The order of the end‐to‐end distances between hydrogen atoms on the para‐position of the basic units of the resins is ortho–ortho resin < ortho–para resin < para–para resin. The calculational results were found to be consistent with the gel permeation chromatography (GPC) analysis. Copyright © 2001 John Wiley & Sons, Ltd.     

The influence of intramolecular hydrogen bonding on the structure and E ↔ Z photoisomerization of urocanic acid derivatives

The molecular structures and E ? Z photoisomerization reactions of methyl urocanate and several urocanamides were investigated. All of the Z isomers possess intramolecular hydrogen bonds. The intramolecular hydrogen bonds may influence the efficiency of photoisomerization but do not totally inhibit its occurrence. The relative energies of the electronic absorption of the E and Z isomers depends on the mode of hydrogen bonding and are accurately predicted in the case of methyl urocanate using INDO/S-CI calculations. The solvent dependence of the absorption spectra of methyl urocanate can be related to the effects of inter- and intramolecular hydrogen bonding.     

Biodegradable gemini surfactants. Correlation of area per surfactant molecule with surfactant structure

Values of the area per surfactant molecule of various single chain and gemini quaternary ammonium surfactants containing biodegradable amide and ester groups are obtained from the surface tension measurements and they are mutually compared. It was found that surfactant molecules with the ester group in their structure occupy smaller area at the air/water interface than the corresponding molecules with the amide group, mainly due to the higher conformational flexibility of ester groups. In decreasing the area per surfactant molecule value, hydrogen bonding (both inter- and intramolecular) plays a significant role when amide groups are present in the spacer of a gemini molecule. They must be separated by a polymethylene chain or a flexible group such as cyclohexane which is short enough to allow intramolecular hydrogen bonds. The flexible cyclohexane group with the amide group in single chain surfactants may lead to the formation of intermolecular hydrogen bonds among surfactant molecules which also results in the reduction of the area per surfactant molecule.     

Explanation of Ionic Sequences in Various Phenomena. IV. General Method for Determination of the Type of Bonding in Polymers; Bonds in Ovalbumin,Ribonuclease, Collagen,Hemoglobin, and Starch Determined

Abstract

The salting-out or -in of hydrocarbons, uncharged nitrogen bases, and acids containing polarized hydroxyl groups give different cationic sequences. Also various ionic groups have different solubility sequences. Such neutral or electrostatically charged groups are attached to polymers and are involved as forces which hold together aggregates or helicies in inter- or intramolecular interactions. In aqueous solutions, the addition of various salts can destroy or produce these inter- or intramolecular interactions. Consequently, by applying the ionic solubility sequences, the observed salting-in and -out sequences of low molecular weight molecules, and other solubility criteria to the destruction or formation of such polymer interactions, it is possible to determine the major force or forces which are involved in holding the aggregate or helix together. Such forces involve hydrophobic bonds, hydrogen bonds between neutral bases, hydrogen bonds involving polarized hydroxyl groups, ionic bonds, and/or repulsive forces between electrostatically charged groups. The method is applied to the salting-out of ovalbumin, the destruction of the α-helix of ribonuclease, the collagen-gelatin transformation, the dissociation of hemoglobin, and the retrogradation and solubilization of starch. These five examples involve all the secondary forces considered. The method should find wide applicability because it can be applied to any method of physical measurement involving ionic solutions.     

Intra- and intermolecular hydrogen bonds in alkyl and silyl ethers: experimental and theoretical analysis

We have investigated the electronic impact of the R protecting group (TBS or PMB) in the conformational equilibrium of alpha-methyl substituted alcohols 1 (R = TBS) and 2 (R = PMB). The conformational analysis and (1)H NMR experiments for alcohols 1 and 2 reflect the tendency for the existence of hydrogen-bonded conformations. The intrinsic low basicity of silyl ethers does not affect the capacity of the oxygen attached to the silicon atom in forming intramolecular hydrogen bonds. We showed that the extents of the hydrogen bonds in silyl and alkyl ethers are determined by several properties, such as orbital interactions, lone pair hybridizations, and lone pair energies, and not just by the electronic occupancy of the donor atom. The populational analysis of NBO allowed understanding the intra- and intermolecular hydrogen bonds between the OH group and oxygen bonded to silicon as well as to alkyl ethers, concluding that there are distinct lone pair contributions.     

Recognition of Hydrophilic Cyclic Compounds by a Water-Soluble Cavitand

A water-soluble deep cavitand bearing amides on the upper rim and trimethyl ammonium groups on the feet was synthesized. The open-ended cavity is stabilized by the intramolecular hydrogen bonds formed between the adjacent amides, and the introduction of trimethylammonium imparts to the cavitand good solubility in water. The cavitand exhibits high binding affinity and selectivity to hydrophilic molecules in water. With certain guests, such as cyclohexyl alcohols, amines and acids, the recognition involves the synergistic action of hydrogen bonding with hydrophobic effects. The binding phenomena are interpreted in terms of a fixed solvent cage presented by the host to the guest.     

The molecular and crystal structure of tert-butyl Nalpha-tert-butoxycarbonyl-L-(S-trityl)cysteinate and the conformation-stabilizing function of weak intermolecular bonding

The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A and C...C ca. 3.7 A, respectively. The first type of interaction links phenyl H-atoms and carbonyl groups. The second type of interaction is formed between a methyl group of the tert-butyl fragment and a trityl phenyl ring. The resulting molecular conformation in the crystal is very close to an ab initio minimum energy conformer of the isolated molecule. The extended C5 conformation of the main peptide chain is the same and there is slight discrepancy in the disposition of trityl phenyl rings. Their small dislocation creates the possibility of forming the entire network above of extensive, specific, weak intermolecular interactions; these constrain the molecule and permit it to retain the minimum energy C5 conformation of its main chain in the solid state. In contrast, in n-hexane solution, where such specific interactions cannot occur, only a small population of the molecules adopts the extended C5 conformation.     

Solvent-exposed backbone loosens the hydration shell of soluble folded proteins

The hydration shell of a soluble folded protein is not uniform: its tightness, marked by the mobility of interfacial water, is site dependent and modulates the propensity for protein associations. We found that the most pronounced interfacial dehydration propensity for representative folds is promoted by solvent-exposed intramolecular hydrogen bonds that are incompletely shielded from water attack. These bonds are poorly wrapped by surrounding nonpolar groups from the side chains and their dehydration is energetically favored.     

Structure and intramolecular hydrogen bonds in Bis(trifluoromethylsulfonylamino)methane and N-[(trifluoromethylsulfonyl)aminomethyl]acetamide

Bis(trifluoromethylsulfonylamino)methane in an inert medium exists as an equilibrium mixture of monomeric forms with various types of intramolecular hydrogen bonds, whose population depends on the polarity of the medium. The energetically most favorable form is a symmetrical form containing two N-H...O=S bonds. Less stable are the isomer with two N-H...F-C bonds and the unsymmetrical isomer with two different hydrogen bonds. N-[(Trifluoromethylsulfonyl)aminomethyl]acetamide contains one intramolecular intramolecular N-H...O=C hydrogen bond and preserves ability for self-association.     

Hydrogen-bonding effects in calix

The synthesis and spectroscopic characterization of self-assembling calix[4]arene based capsules 1a.1a and 1b.1b are described. These compounds feature four urea substituents at the upper rims and four secondary amide fragments at the lower rims that can participate in inter- and intramolecular hydrogen bonding in apolar solution. Communication between the calixarene rims in 1a, b influences the self-assembled cavity's size and shape. Specifically. dimerization results in a perfect cone conformation of the calixarene skeleton in 1a, b and stabilizes a seam of intramolecular amide C=O...H-N hydrogen bonds at the lower rim. This seam is cycloenantiomeric, with either clockwise or counterclockwise arrangements of the head-to-tail amides. Complexation of Na+-cation breaks hydrogen bonds at the lower rim but maintains the capsular assembly. Encapsulation properties of 1a.1a and 1b.1b were studied in nonpolar solvents and their binary mixtures as well as through heterodimerization experiments. The presence of amide groups at the lower rim causes notable differences in the capsule's binding affinities when compared to the corresponding tetraester capsules 1c.1c and 1d.1d. In the monomeric state calixarenes 1a, b are in a pinched cone conformation. The solid state X-ray crystallographic studies with monomeric 1a reveal only two intramolecular C=O...H-N hydrogen bonds between the adjacent amides at the lower rim, and an extensive network of intermolecular hydrogen bonds between urea groups at the upper rim.