The effect of substitution on the intramolecular hydrogen bonding in 3‐hydroxy‐propenethial

The intramolecular hydrogen bond strength of 3‐hydroxy‐propenethial (HPT) as well as the fluoro, chloro, bromo, and methyl derivatives were investigated at the B3LYP/6‐311++G^** level of theory. Solvent‐based calculations (in water) for HPT and derivatives were also carried out. The nature of the intramolecular hydrogen bond existing within the molecular under investigation has been studied by means of the Bader theory of atoms in molecules (AIM) that is based upon the use topological properties in terms of the electron density. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Palladium‐Catalyzed Intermolecular Oxidative Coupling Reactions of (Z)‐Enamines with Isocyanides through Selective β‐C(sp2)‐H and/or C=C Bond Cleavage

Herein, two efficient palladium‐catalyzed intermolecular oxidative coupling reactions of (Z)‐enamines with isocyanides via selective β‐C(sp²)‐H and/or C=C bond cleavage have been developed, leading to controllable chemodivergent and stereoselective construction of a wide range of (E)‐β‐carbamoylenamine derivatives containing strong intramolecular hydrogen bonds. Furthermore, possible reaction pathways for these transformations are proposed on the basis of preliminary mechanism studies.     

Photolysis of α,β‐Epoxyketones: A Green Synthesis of β‐Hydroxyenones through Tandem H‐Abstraction,Ring Cleavage and Isomerisation

The photochemical behavior of various substituted epoxycarbonyl compounds consisting of more than one possible photo‐labile site (i.e. δ‐hydrogen, β‐hydrogen and epoxide ring) has been investigated. These compounds on photo‐irradiation produced the β‐hydroxyenones in an eco‐friendly green approach. Mechanistically, these photo‐transformations have been envisaged to occur via an intramolecular β‐hydrogen abstraction by the carbonyl group of benzoyl moiety to generate the 1,3‐biradical followed by epoxide ring opening that isomerizes into the photoproducts. The photolysis of the probed epoxy ketones didn’t furnish any photoproduct through δ‐hydrogen abstraction, whatsoever. This exclusive preference for β‐H abstraction over δ‐H abstraction by carbonyl group has been vindicated by the MM2 energy mini‐ mized program for the investigated photochemical substrates. The structures of these photoproducts were established from the analysis of their spectral parameters (IR, ¹H/¹³C NMR and Mass) and single crystal X‐ray crystallography data.     

Cooperative Hydrogen Bonding in Glyco–Oligoamides: DNA Minor Groove Binders in Aqueous Media

A strategy to create cooperative hydrogen‐bonding centers by using strong and directional intramolecular hydrogen‐bonding motifs that can survive in aqueous media is presented. In particular, glyco–oligoamides, a family of DNA minor groove binders, with cooperative and non‐cooperative hydrogen‐bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β‐D ‐Man‐Py‐γ‐Py‐Ind ( 1 ; Ind=indole, Man=mannose, Py=pyrrole) and β‐D ‐Tal‐Py‐γ‐Py‐Ind ( 2 ; Tal=talose), were chosen according to our design. These sugar molecules should present one‐ or two‐directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco–oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco–oligoamides with non‐cooperative hydrogen‐bonding centers, that is, β‐D ‐Glc‐Py‐γ‐Py‐Ind ( 3 ; Glc=glucose), β‐D ‐Gal‐Py‐γ‐Py‐Ind ( 4 ; Gal=galactose), and the model compounds β‐D ‐Man‐Py‐NHAc ( 5 ) and β‐D ‐Tal‐Py‐NHAc ( 6 ) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH—π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf‐thymus DNA and poly(dA‐dT)₂ by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar–oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen‐bonding and CH—π interactions are present.     

Phosphoryl group differentiating α‐amino acids from β‐ and γ‐amino acids in prebiotic peptide formation

In recent years β‐amino acids have increased their importance enormously in defining secondary structures of β‐peptides. Interest in β‐amino acids raises the question: Why and how did nature choose α‐amino acids for the central role in life? In this article we present experimental results of MS and ³¹P NMR methods on the chemical behavior of N‐phosphorylated α‐alanine, β‐alanine, and γ‐amino butyric acid in different solvents. N‐Phosphoryl α‐alanine can self‐assemble to N‐phosphopeptides either in water or in organic solvents, while no assembly was observed for β‐ or γ‐amino acids. An intramolecular carboxylic–phosphoric mixed anhydride (IMCPA) is the key structure responsible for their chemical behaviors. Relative energies and solvent effects of three isomers of IMCPA derived from α‐alanine (2a–c), with five‐membered ring, and five isomers of IMCPA derived from β‐alanine (4a–e), with six‐membered ring, were calculated with density functional theory at the B3LYP/6‐31G** level. The lower relative energy (3.2 kcal/mol in water) of 2b and lower energy barrier for its formation (16.7 kcal/mol in water) are responsible for the peptide formation from N‐phosphoryl α‐alanine. Both experimental and theoretical studies indicate that the structural difference among α‐, β‐, and γ‐amino acids can be recognized by formation of IMCPA after N‐phosphorylation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 232–241, 2003     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

2‐Amino‐5‐(3,4‐dimethoxybenzylidene)‐1‐methylimidazol‐4(5H)‐one N,N‐dimethylformamide monosolvate

The crystal structure of the title compound, C₁₃H₁₅N₃O₃·C₃H₇NO, was determined as part of a larger project focusing on creatinine derivatives as potential pharmaceuticals. The molecule is essentially planar, in part because of intramolecular hydrogen bonding. Inversion‐related pairs of molecules result from intermolecular hydrogen bonding. The π systems of 2‐amino‐5‐(3,4‐dimethoxybenzylidene)‐1‐methylimidazol‐4(5H)‐one and an inversion‐related molecule overlap slightly, indicating a small amount of π–π stacking. Bond lengths, angles and torsion angles are consistent with similar structures, except in the imidazolone ring near the doubly bonded C atom, where significant differences occur.     

Improved treatment of cyclic β‐amino acids and successful prediction of β‐peptide secondary structure using a modified force field: AMBER*C

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000     

Energy Dissipation Processes of singlet‐excited 1‐Hydroxyfluorenone and its Hydrogen‐bonded Complex with N‐methylimidazole¶

Effects of solvent, pH and hydrogen bonding with N‐methylimidazole (MIm) on the photophysical properties of 1‐hydroxyfluorenone (1HOF) have been studied. Fluorescence lifetime, fluorescence quantum yield and triplet yield measurements demonstrated that intersystem crossing was the dominant process in apolar media and its rate constant significantly diminished with increasing solvent polarity. The acceleration of internal conversion in alcohols paralleled the strength of intermolecular hydrogen bonding. The faster energy dissipation from the singlet‐excited state in cyclohexane was attributed to intramolecular hydrogen bonding. The pK_a of 1HOF decreased from 10.06 to 5.0 on light absorption, and H₃O⁺ quenched the singletexcited molecules in a practically diffusion‐controlled reaction. On addition of MIm in toluene, dual fluorescence was observed, which was attributed to reversible formation of excited hydrogen‐bonded ion pair. Rate constants for the various deactivation pathways were derived from the combined analysis of the steady‐state and the time‐resolved fluorescence results.     

Theoretical insights into the excited‐state process of 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol

In this paper, we theoretically explore the motivation and behaviors of the excited‐state intramolecular proton transfer (ESIPT) reaction for a novel white organic light‐emitting diode (WOLED) material 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol (t‐MTTH). The “atoms in molecules” (AIM) method is adopted to verify the formation and existence of the hydrogen bond O? H···N. By analyzing the excited‐state hydrogen bonding behaviors via changes in the chemical bonding and infrared (IR) vibrational spectra, we confirm that the intramolecular hydrogen bond O? H···N should be getting strengthened in the first excited state in four kinds of solvents, thus revealing the tendency of ESIPT reaction. Further, the role of charge‐transfer interaction is addressed under the frontier molecular orbitals (MOs), which depicts the nature of the electronic excited state and supports the ESIPT reaction. Also, the electron distribution confirms the ESIPT tendency once again. The scanned and optimized potential energy curves according to variational O? H coordinate in the solvents demonstrate that the proton transfer reaction should occur in the S₁ state, and the potential energy barriers along with ESIPT direction support this reaction. Based on the excited‐state behaviors reported in this work, the experimental spectral phenomenon has been reasonably explained.     

Methyl β‐d‐fructopyranoside

In methyl β‐d ‐fructopyranoside, C₇H₁₄O₆, the thermodynamically most stable methyl glycoside of the ketose d ‐fructose, the pyranose ring is close to being an ideal ²C₅ chair. The compound forms bilayers involving a complex hydrogen‐bonding pattern of five independent hydrogen bonds. Graph‐set analysis was applied to distinguish the hydrogen‐bond patterns at unary and higher level graph sets.     

Induced Folding of Protein‐Sized Foldameric β‐Sandwich Models with Core β‐Amino Acid Residues

The mimicry of protein‐sized β‐sheet structures with unnatural peptidic sequences (foldamers) is a considerable challenge. In this work, the de novo designed betabellin‐14 β‐sheet has been used as a template, and α→β residue mutations were carried out in the hydrophobic core (positions 12 and 19). β‐Residues with diverse structural properties were utilized: Homologous β³‐amino acids, (1R,2S)‐2‐aminocyclopentanecarboxylic acid (ACPC), (1R,2S)‐2‐aminocyclohexanecarboxylic acid (ACHC), (1R,2S)‐2‐aminocyclohex‐3‐enecarboxylic acid (ACEC), and (1S,2S,3R,5S)‐2‐amino‐6,6‐dimethylbicyclo[3.1.1]heptane‐3‐carboxylic acid (ABHC). Six α/β‐peptidic chains were constructed in both monomeric and disulfide‐linked dimeric forms. Structural studies based on circular dichroism spectroscopy, the analysis of NMR chemical shifts, and molecular dynamics simulations revealed that dimerization induced β‐sheet formation in the 64‐residue foldameric systems. Core replacement with (1R,2S)‐ACHC was found to be unique among the β‐amino acid building blocks studied because it was simultaneously able to maintain the interstrand hydrogen‐bonding network and to fit sterically into the hydrophobic interior of the β‐sandwich. The novel β‐sandwich model containing 25 % unnatural building blocks afforded protein‐like thermal denaturation behavior.     

Intramolecular Hydrogen Bond Reverting the Solvent Effect on Phosphorus Hyperfine Coupling Constants of β‐Phosphorylated Nitroxides

Recently, we reported a dramatic solvent effect on the phosphorus hyperfine coupling constant a_P of β‐phosphorylated six‐membered ring nitroxides, that is, approximately 25 G of difference in a_P from n‐hexane to water (Org. Biomol. Chem. 2016 , 14, —1228‐1292). In this article, we report on the effect of intramolecular hydrogen bonding (IHB) in three nitroxides exhibiting IHB between the hydroxyl and diethylphosphoryl groups and one exhibiting IHB between the hydroxyl group and the nitroxyl moiety. It is observed that for the first three nitroxides, a_P increases with increasing polarity/polarizability and hydrogen bond donor (HBD) properties of the solvent (π* and α, respectively)—in sharp contrast to the data reported in the literature—and for the last nitroxide, a_P decreases with π* and α. In fact, the occurrence of IHB induces a large strain, its suppression by hydrogen bond acceptor (HBA) solvents affords an increase in a_P.     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.     

N‐Chloro­acetyl‐β‐alanine

The β‐alanine residue of the title compound, C₅H₈ClNO₃, has a ggt folded conformation, which is mainly stabilized through intermolecular N—H⋯O=C (amide–acid) and O—H⋯O=C (acid–amide) hydrogen bonds. In addition, a cis conformation is found for the Cl—CH₂—C(=O)—NH torsion angle, which is associated with the presence of an intramolecular hydrogen bond.     

Isotopic splitting patterns in the 13C NMR spectra of some partially deuterated 1‐aryl‐2‐(phenyldiazenyl)butane‐1,3‐dione and 4‐hydroxy‐3‐(phenyldiazenyl)‐2H‐chromen‐2‐one: evidence for elucidation of tautomeric forms

Nuclear magnetic resonance spectra of synthesized azo dyes derived from aniline derivatives in reaction with benzoylacetone and 4‐hydroxycoumarin were studied in both CDCl₃ and (CD₃)₂SO (two drops of D₂O were added into solutions of dyes). All dyes showed intramolecular hydrogen bonding. Dyes derived from o‐nitro aniline in the reaction with benzoylacetone, and 4‐hydroxycoumarin showed bifurcated intramolecular hydrogen bonds. The solvent‐substrate proton exchange of dyes derived from benzoylacetone and 4‐hydroxycoumarin was examined in the presence of two drops of D₂O. Among ten dye samples, two dyes derived from benzoylacetone did not show deuteration, three dyes showed partial deuteration and five dyes showed full deuteration under similar conditions. For the partially deuterated dyes the β‐isotope effect in ¹³C splitting was investigated and was used for the determination of the predominant tautomeric form. Copyright © 2016 John Wiley & Sons, Ltd.     

β‐Carboline (norharman)

The structure of β‐carboline, also called norharman (systematic name: 9H‐pyrido[3,4‐b]indole), C₁₁H₈N₂, has been determined at 110 K. Norharman is prevalent in the environment and the human body and is of wide biological interest. The structure exhibits intermolecular N—H...N hydrogen bonding, which results in a one‐dimensional herringbone motif. The three rings of the norharman molecule collectively result in a C‐shaped curvature of 3.19 (13)° parallel to the long axis. The diffraction data show shorter pyridyl C—C bonds than those reported at the STO‐3G level of theory.     

Carbonyl–carbonyl interactions and amide π‐stacking as the directing motifs of the supramolecular assembly of ethyl N‐(2‐acetylphenyl)oxalamate in a synperiplanar conformation

The title compound, C₁₂H₁₃NO₄, is one of the few examples that exhibits a syn conformation between the amide and ester carbonyl groups of the oxalyl group. This conformation allows the engagement of the amide H atom in an intramolecular three‐centred hydrogen‐bonding S(6)S(5) motif. The compound is self‐assembled by C=O...C=O and amide–π interactions into stacked columns along the b‐axis direction. The concurrence of both interactions seems to be responsible for stabilizing the observed syn conformation between the carbonyl groups. The second dimension, along the a‐axis direction, is developed by soft C—H...O hydrogen bonding. Density functional theory (DFT) calculations at the B3LYP/6‐31G(d,p) level of theory were performed to support the experimental findings.     

On the chemistry of 5‐aryl‐2‐hydrazino‐benzo[6,7]cyclohepta[1,2‐b]pyrido[2,3‐e] pyrimidin‐4‐one

Several pyrido[2,3‐e]pyrimidine fused with other rings have been prepared by intramolecular cyclization of 5‐(4‐chlorophenyl)‐2‐hydrazino‐benzo [6,7]cyclohepta‐[1,2‐b]pyrido[2,3‐e]pyrimidine‐4‐one ( 1 ) with acids, carbon disulfide to form triazole derivatives ( 2,4 ), halo‐ketones to give triazine derivative ( 5 ), β‐ketoesters, β‐cyanoesters, and β‐diketones to yield 2‐(1‐pyrazolyl) derivatives ( 7,9,10 ), and aldehydes to form arylhydrazone derivatives ( 11a,b ) which cyclized to form triazoles ( 12a,b ). Also, acyclic N‐nucleosides are prepared by heating under reflux 2‐hydrazino‐benzo[6,7]cyclohepta[1,2‐b]pyrido[2,3‐e] pyrimidin‐4‐one ( 1 ) with xylose and glucose to give the corresponding acyclic N‐nucleosides ( 13a,b ) which are cyclized to afford the corresponding protected tetra and penta–O‐acetate C‐nucleosides ( 14a,b ). Deacetylating of the latter nucleosides afforded the free acyclic C‐nucleosides ( 15a,b ). © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:34–43, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20248