Amide NH Research Articles

Structural studies on C-amidated amino acids and peptides: function of amide group in molecular association in crystal structures of Val-Gly-NH2, Ser-Phe-NH2, Gly-Tyr-NH2 and Pro-Tyr-NH2 hydrochloride salts.

As part of a series of elucidation of the structural features of peptides caused by C-terminal alpha-amidation, the crystal structures of H-Val-Gly-NH2, H-Ser-Phe-NH2, H-Gly-Tyr-NH2, and H-Pro-Tyr-NH2 hydrochloride salts were analyzed by the X-ray diffraction method. Although respective molecules take energetically allowable torsion angles concerning the backbone and side chains, their conformations are not necessarily the same as the corresponding unamidated ones. This results from the different molecular packing requirements, rather than from different conformational features inherent in the C-amidated and -unamidated peptides. As for the molecular packing feature, each peptide tended to form a repeated structure through those hydrogen bonds in which both amide NH and O=C groups participate. The chloride ions are located between the neighboring peptides and are hydrogen-bonded to the respective amide NHs, leading to the sheet structure. The hydrogen-bonding feature of the amide group and its function in molecular packing was discussed based on the results analyzed so far.

Molecular Modeling of the 1,1-Cyclopropane- and 1,1-Cyclobutanedicarboxamide Systems. Insights into the Self-Assembly of Diamide Diacids in Water

Modeling of the following compounds bis-(N-α-amido-L-phenylalaninyl)-1,1-cyclopropane dicarboxylate, 3, and bis-(N-α-amido-L-phenylalaninyl)-1,1-cyclobutane dicarboxylate, 4, were undertaken. The study involved construction and optimization of the precursory 1,1-dicarboxaldehydes and continued stepwise via the 1,1-dicarboxamides, the bis-N-(methyl)dicarboxamides, the bis(N-α-amidoglycinyl) dicarboxylates, the bis(N-α-amido-L-alaninyl) dicarboxylates and onto the targeted bis(N-α-amido-L-phenylalaninyl) dicarboxylates. Using the X-ray crystal structure of 4 (i.e., 4X) as a guide, we found that our approach was not able to reproduce the packable conformer of 4, via the computational methods employed. Nevertheless, an enhanced understanding of the intramolecular hydrogen bonding patterns available to these systems was obtained from IR and VT-NMR studies. In summary, the conformational preferences found in the 1,1-disubstituted cycloalkanes (3 and 4) direct their respective self-assembly processes by controlling the orientation of their amide NH populations.

Dendritic Iron(II) Porphyrins as Models for Hemoglobin and Myoglobin: Specific Stabilization of O2 Complexes in Dendrimers with H-Bond-Donor Centers

Two types of dendritically functionalized iron(II) porphyrins were prepared (Scheme) and investigated in the presence of 1,2-dimethylimidazole (1,2-DiMeIm) as the axial ligand as model systems for T(tense)-state hemoglobin (Hb) and myoglobin (Mb). Equilibrium O2- and CO-binding studies were performed in toluene and aqueous phosphate buffer (pH 7). UV/VIS Titrations (Fig. 4) revealed that the two dendritic receptors 1⋅FeII-1,2-DiMeIm and 2⋅FeII-1,2-DiMeIm (Fig. 2) with secondary amide moieties in the dendritic branching undergo reversible complexation (Fig. 5) with O2 and CO in dry toluene. Whereas the CO affinity is similar to that measured for the natural receptors, the O2 affinity is greatly enhanced and exceeds that of T-state Hb by a factor of ca. 1500 (Table). The oxygenated complexes possess half-lives of several h (Fig. 6). This remarkable stability originates from both dendritic encapsulation of the iron(II) porphyrin and formation of a H-bond between bound O2 and a dendritic amide NH moiety (Fig. 11). Whereas reversible CO binding was also observed in aqueous solution (Fig. 10), the oxygenated iron(II) complexes are destabilized by the presence of H2O with respect to oxidative decay (Fig. 9), possibly as a result of the weakening of the O2⋅⋅⋅H−N H-bond by the competitive solvent. The comparison between the two dendrimers with amide branchings and ester derivative 3⋅FeII-1,2-DiMeIm (Fig. 2), which lacks H-bond donor centers in the periphery of the porphyrin, further supports the role of H-bonding in stabilizing the O2 complex against irreversible oxidation. All three derivatives bind CO reversibly and with similar affinity (Fig. 8) in dry toluene, but the oxygenated complex of 3⋅FeII-1,2-DiMeIm undergoes much more rapid oxidative decomposition (Fig. 7).

Changes in protein conformation and dynamics upon complex formation of brain-derived neurotrophic factor and its receptor: Investigation by isotope-edited Fourier transform IR spectroscopy

The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly β strands (∼53%) and relatively low contents of other secondary structures including β turns (∼16%), disordered structures (∼12%), and loops (∼18%) and is deficient in α helix. We also observe that trkB in solution contains mostly β strands (52%) and little α helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly β turns and disordered structures while the majority of the β-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to β strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H–D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand–receptor complex that is in contrast to other ligand–receptor complexes such as a cytokine–receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation. © 2002 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 67: 10–19, 2002; DOI 10.1002/bip.10038

Ca–O Binding of Poly[1-carboxylate-2-( N - t - butylcarbamoyl)ethylene- alt -ethylene] and Calcium Carbonate Composites

A novel poly(carboxylate) ligand was synthesized as a ligand for a crystalline CaCO3-organic composite. Poly[1-carboxylate-2-(N-t-butylcarbamoyl)ethylene-alt-ethylene] has a 7-membered ring with an intramolecular NH·O hydrogen bond between the carboxylate group and the neighboring amide NH proton in the anionic carboxylate form. The configuration of the polymer ligand was estimated with polymer repeat-unit models, (S,S)- or (R,R)-2-(N-t-butylcarbamoyl)-cyclohexanecarboxylic acid ((S,S)- or (R,R)-TBCA) and (S,R)- 2-(N-t-butylcarbamoyl)-cyclohexanecarboxylic acid ((S,R)-TBCA). The proton NMR spectum of the carboxylate anion of (S,S)- or (R,R)-TBCA exhibits a non-hydrogen bonded NH signal at 7.31 ppm in Me2SO-d 6. (S,R)-TBCA shows a strongly NH·O hydrogen-bonded NH signal at 8.50 ppm. The observation of one strongly NH·O hydrogen bonded NH signal at 11.3 ppm indicates that the polymer anion has a threo-form in the zigzag polymer main chain. Moreover, a polymer ligand-CaCO3 composite was synthesized. The composite was characterized by 13C cross polarization/magic angle spinning (CP/MAS) and scanning electron microscopy (SEM). The polymer ligand stabilizes the Ca–O (carboxylate) bond in the CaCO3 composite. This prevents dissociation due to pKa shifts of the NH·O hydrogen bond and controls the crystal growth toward metastable vaterite.

Inhibitory Module of Ets-1 Allosterically Regulates DNA Binding through a Dipole-facilitated Phosphate Contact

DNA binding of the transcription factor Ets-1 is negatively regulated by three inhibitory helices that lie near the ETS domain. The current model suggests that this negative regulation, termed autoinhibition, is caused by the energetic expense of a DNA-induced structural transition that includes the unfolding of one inhibitory helix. This report investigates the role of helix H1 of the ETS domain in the autoinhibition mechanism. Previous structural studies modeled the inhibitory helices packing together and connecting with helix H1, suggesting a role of this helix in the configuration of an inhibitory module. Recently, high-resolution structures of the ETS domain-DNA interface indicate that the N terminus of helix H1 directly contacts DNA. The contact, which is augmented by the macrodipole of helix H1, consists of a hydrogen bond between the amide NH of leucine 337 in helix H1 and the oxygen of a corresponding phosphate. We propose that this hydrogen bond positions helix H1 to be a link between autoinhibition and DNA binding. Four independent approaches tested this hypothesis. First, the hydrogen bond was disrupted by removal of the phosphate in a missing phosphate analysis. Second, base pairs that surround the helix H1-contacting phosphate and appear to dictate DNA backbone conformation were mutated. Next, a hydrophobic residue in helix H1 that is expected to position the N terminus of the helix was altered. Finally, a residue on the surface of helix H1 that may contact the inhibitory elements was changed. In each case DNA binding and autoinhibition was affected. Taken together, the results demonstrate the role of the dipole-facilitated phosphate contact in DNA binding. Furthermore, the findings support a model in which helix H1 links the inhibitory elements to the ETS domain. We speculate that this helix, which is conserved in all Ets proteins, provides a common route to regulation.

(α-Monofluoroalkyl)phosphonates: a class of isoacidic and “tunable” mimics of biological phosphates

In the early 1980s, Blackburn and McKenna suggested that α-fluorination might lead to phosphonates that better mimic natural phosphates. Although α-monofluorination produces phosphonates with “matching” second p K a values, the α,α-difluorinated phosphonates have received more attention in the past decade or so. Recently, reported enzyme kinetic data on the α-monofluorinated phosphonates from the O’Hagan lab and from our lab suggest that the CHF stereochemistry does affect enzyme-binding, thereby providing an additional variable that may be tuned to achieve optimal binding to an active site of interest. This asymmetry also appears in structural data from the groups of Barford/Burke and Tracey on PTP1B complexes with bound α,α-difluorinated phosphonate inhibitors. In those complexes, only one of two prochiral fluorine atoms appears to interact appreciably with the enzyme. Namely, it is thought that the pro- R (F si) fluorine is engaged in an important hydrogen bond with the Phe-182 amide NH. Available methods for the synthesis of this class of α-monofluorinated phosphonates are reviewed. A new convergent approach, developed at Nebraska, in which the potassium anion of (α-fluoro-α-phenylsulfonylmethyl)phosphonate is used to displace primary triflates is also described. This method is particularly convenient as it allows one to perform a “fluorinated phosphonate scan” of an active site of interest (in what follows, we use this expression to designate the synthesis and evaluation of a complete set of the CH 2–, CF 2– and both stereoisomeric CHF-phosphonates in an active site of interest) from a single primary triflate. The properties of the title compounds in enzyme active sites are discussed, as are possible interactions of these fluorine-containing bioisosteres with active site residues.

A polarised μ-FTIR study on a model system for nylon 6 6: implications for the nylon Brill structure

Polarised transmission FTIR microscopy studies (μ-FTIR) have been performed on a monodisperse 3-amide oligomer. The oligomer is a model compound for nylon 6 6; it has essentially the same room temperature crystal structure, and it undergoes the same high temperature transition, the Brill transition, prior to melting. However, the oligoamide forms extended chain, rather than chain-folded, crystals, and so crystals are produced that are essentially 100% crystalline, and of ∼μm–mm size. Consequently, this material is ideally suited for polarised μ-FTIR single crystal studies. The thermal polarised FTIR behaviour of this material provides definitive proof that the Brill transition does not involve major rearrangement of hydrogen bonds, since the strong parallel polarisation of both the NH stretch and amide I bands are retained right up to melting. Quantitative infrared dichroism measurements indicate that a maximum of 5° rotation of the N–H bonds about the extended chain axis occurs prior to melting. These results strongly suggests that the equivalent Brill transition in nylon 6 6 also proceeds without significant hydrogen bond rearrangement. In addition we have investigated the behaviour of designated ‘Brill’, ‘crystalline’, ‘amorphous’ and ‘fold’ bands that are present in our spectra.

Structure, stability and folding of the α-helix

Pauling first described the alpha-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 3(10)-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or alpha L C-cap motif. The kinetics of alpha-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

Sequence Determination of Reduction Potentials by Cysteinyl Hydrogen Bonds and Peptide Dipoles in [4Fe-4S] Ferredoxins

A sequence determinant of reduction potentials is reported for bacterial [4Fe-4S]-type ferredoxins. The residue that is four residues C-terminal to the fourth ligand of either cluster is generally an alanine or a cysteine. In five experimental ferredoxin structures, the cysteine has the same structural orientation relative to the nearest cluster, which is stabilized by the SH···S bond. Although such bonds are generally considered weak, indications that Fe-S redox site sulfurs are better hydrogen-bond acceptors than most sulfurs include the numerous amide NH···S bonds noted by Adman and our quantum mechanical calculations. Furthermore, electrostatic potential calculations of 11 experimental ferredoxin structures indicate that the extra cysteine decreases the reduction potential relative to an alanine by ∼60 mV, in agreement with experimental mutational studies. Moreover, the decrease in potential is due to a shift in the polar backbone stabilized by the SH···S bond rather than to the slightly polar cysteinyl side chain. Thus, these cysteines can “tune” the reduction potential, which could optimize electron flow in an electron transport chain. More generally, hydrogen bonds involving sulfur can be important in protein structure/function, and mutations causing polar backbone shifts can alter electrostatics and thus affect redox properties or even enzymatic activity of a protein.

Systematic solid-phase synthesis of linear pseudooligolysines containing multiple adjacent CH(2)NH amide bond surrogates: potential agents for gene delivery.

Solid-phase methodology was used to synthesize a series of fully reduced linear oligolysines (pseudooligolysines, abbreviated herein as PLs) containing up to five adjacent CH2NH peptide bond isosteres. The reduced peptide bonds were introduced by the reductive alkylation reaction between Fmoc-Lys-(Boc)-al and a free alpha-amine moiety on the pseudopeptidyl resin, using sodium cyanoborohydride in an acidified mixture of NMP/CH3OH (1 : 1 v/v). The oligomeric molecules, which can be regarded as polyethylene imine and spermine analogs, possess multiple positive charges under physiological conditions and form tight complexes with plasmid DNA. These characteristics and the increased resistance to hydrolysis by trypsin make these molecules potential candidates for future use as DNA carriers in gene delivery.

Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach.

The three-dimensional structures of the two L-peptides, H-CGGIRGERA-OH, called L(A), and H-CGGIRGERG-OH, called L(G), corresponding or close to the IRGERA sequence present in the C-terminal region (residues 130-135) of histone H3, and their retro-inverso analogues HO-mAreGriGGC-NH2, called RI(mA), and HO-mGreGriGGC-NH2, called RI(mG), have been studied by two-dimensional 1H NMR and molecular dynamics calculations in association with a monoclonal antibody generated against L(A). At 25 degrees C, the affinity constants of the monoclonal antibody with respect to RI(mA) and RI(mG) were 75- and 270-fold higher than those measured with the homologous L(A) and L(G) peptides, respectively. Due to the spontaneous epimerization of the mA malonic residue, RI(mA) gave rise to two sets of resonances. With regard to the NH amide region, one set was similar to that for RI(mG) while the second was similar to those for the parent L-peptides L(A) and L(G). The antibody-bound conformations of the two couples of L- and retro-inverso peptides have been analyzed using molecular modeling calculations based on the transferred NOE interproton distances. Folded structures appeared in both cases with a type II' beta-turn in the parent GGIR sequence and a type I' beta-turn in the retro-inverso reGr sequence.

Magnetic susceptibility tensor anisotropies for a lanthanide ion series in a fixed protein matrix.

The full series of lanthanide ions (except the radioactive promethium and the S-state gadolinium) has been incorporated into the C-terminal calcium binding site of the dicalcium protein calbindin D(9k). A fairly constant coordination environment is maintained throughout the series. At variance with several lanthanide complexes with small chelating ligands investigated in the past, the large protein moiety provides a large number of NMR signals whose hyperfine shifts can be exclusively ascribed to pseudocontact shifts (PCS). The chemical shifts of 1H and 15N backbone and side chain amide NH groups were accurately measured through HSQC experiments. 1097 PCS were estimated from these by subtracting the diamagnetic contributions measured on HSQC spectra of either the 4f(0) lanthanum(III) or the 4f(14) lutetium(III) derivatives and used to define a quality factor for the structure. The differences in diamagnetic chemical shifts between the two diamagnetic blanks were relatively small, although some were not negligible especially for the nuclei closest to the metal center. These differences were used as a tolerance for the PCS. The magnetic susceptibility tensor anisotropies for each paramagnetic lanthanide ion were obtained as the result of the solution structure determination performed by using the NOEs of the cerium(III) derivative and the PCS of all lanthanides simultaneously. This set of reliable magnetic data permits an experimental assessment of Bleaney's theory relative to the magnetic properties for an extended series of lanthanide complexes in solution. All of the obtained tensors show some rhombicity, as could be expected from the lack of symmetry of the protein environment. The directions of the largest magnetic susceptibility component for Ce, Pr, Nd, Sm, Tb, Dy, and Ho and of the smallest magnetic susceptibility component for Eu, Er, Tm, and Yb were found to be all within 15 degrees from their average (within 20 degrees for Sm), confirming the essential similarity of the coordination environment for all lanthanides. Bleaney's theory is in excellent qualitative agreement with the observed pattern of axial anisotropies. Its quantitative agreement is substantially better than that suggested by previous analyses performed on more limited sets of PCS data for small lanthanide complexes, the so-called crystal field parameter varying only within +/-30% from one lanthanide to another. These variations are even smaller (+/-15%) if a reasonable T(-3) correction is taken into consideration. A knowledge of magnetic susceptibility anisotropy properties of lanthanides is essential in determining the self-orienting properties of lanthanide complexes in solution when immersed in magnetic fields.

Secure Binding of Alternately Amidated Poly(acrylate) to Crystalline Calcium Carbonate by NH···O Hydrogen Bond

Alternately amidated poly(1-carboxylate-3-N-alkylamidotetramethylene)s (alkyl = t-Bu, n-Bu) were synthesized from poly(acrylic anhydride) and alkylamines as ligands for Ca(II) complexes. The anion form of the alternately amidated polycarboxylates possesses an NH···O hydrogen bond between the carboxylate oxygen and the adjacent amide NH. The reinforcement of Ca−O bond strength by the NH···O hydrogen bond, upon the mineralization of calcium carbonate, is maintained at the interface between crystalline CaCO3 and the polymer ligands because it prevents the removal of the alternately amidated poly(1-carboxylate-3-N-alkylamidotetramethylene) ligand from the crystalline CaCO3 under neutral conditions. Under the same conditions, a commercial poly(acrylate) ligand readily releases Ca(II) ion to separate from the surface of the crystal by hydrolysis with water. The binding carboxylate ligand 13C on calcium carbonate is detectable using solid-state 13C CP/MAS spectroscopy.

Structural studies on C-amidated amino acids and peptides: structures of hydrochloride salts of C-amidated Ile, Val, Thr, Ser, Met, Trp, Gln and Arg, and comparison with their C-unamidated counterparts.

To elucidate the structural features of amino acids caused by the C-terminal alpha-amidation, the crystal structures of HCl salts of C-terminal amidated Ile, Val, Thr, Ser, Met, Trp, Gln and Arg were analysed and compared with those of their C-terminal free acids. The bonding parameter of the amide group was little affected by the different chemical properties of the side chains. As for the molecular packing patterns, some structural differences were observed by the C-amidation. The Calpha-H...O hydrogen bonds and carbonyl-carbonyl interactions were more strengthened by the salt formation with HCl in C-amides than C-acids. Furthermore, there is a clear difference between the interaction patterns with Cl ions. In most C-amide crystals, Cl ions are bifurcately hydrogen-bonded to two neighbouring amide NH(2) groups and the parallel layers of the C-amides and Cl ions are alternatively formed. In the case of the carboxyl OH in C-acid crystals, however, the direct hydrogen bond with the Cl ion is not always observed and is largely dependent on the crystal packing environment. This suggests the superior hydrogen-bonding ability of NH...Cl(-) compared with OH...Cl(-). The difference in hydrogen-bonding ability between the amide and carboxyl groups is considered, based on the spatial dispositions of the hydrogen-bonding polar atoms/groups.

Involvement of Glycine 141 in Substrate Activation by Enoyl-CoA Hydratase

Raman spectroscopy has been used to investigate the structure of a substrate analogue, hexadienoyl-CoA (HD-CoA), bound to wild-type enoyl-CoA hydratase and G141P, a mutant in which a hydrogen bond to the substrate carbonyl has been removed. Raman spectra of isotopically labeled HD-CoAs, together with normal mode calculations, confirm the selective ground-state polarization of the enone fragment previously suggested to occur on binding to the wild-type enzyme [Tonge, P. J., Anderson, V. E., Fausto, R., Kim, M., Pusztai-Carey, M., and Carey, P. R. (1995) Biospectroscopy 1, 387-394]. In addition, Raman spectra of HD-CoA bound to the G141P mutant enzyme demonstrate that the hydrogen bond between the G141 amide NH group and the substrate carbonyl is critical for polarization and activity. Replacement of G141 with proline results in an approximately 10(6)-fold decrease in k(cat) and eliminates the ability of the enzyme to polarize the substrate analogue. As G141 is part of a consensus sequence in the enoyl-CoA hydratase superfamily, the results presented here provide direct evidence for the importance of the oxyanion hole in the reactions catalyzed by other family members.

Nanoconstruction of Microspheres and Microcapsules Using Proton-Induced Phase Transitions: Molecular Self-Recognition by Diamide Diacids in Water

Bis(N α -amido-L-phenylalanine)-1,1-cyclobutane dicarboxylate (5) was studied by Fourier transform infrared (FTIR) spectroscopy, variable-temperature NMR (VT-NMR), transmission electron microscopy, X-ray crystallography, Raman microscopy, and a novel imaging technique known as soft X-ray microscopy (XRM). Diamide diacid 5 was shown to self-associate into solid microspheres during a proton-induced phase transition from the solvated state to the desolvated assembled state. These diverse techniques allowed for the delineation of the molecular recognition events involved in the assembly process. X-ray crystallography revealed that 5 packs in a bundled helical array comprised of two types of intermolecular hydrogen bonds (i.e., OC=O…HN and COOH…O=CN). VT-NMR and IR measurements of 5 (1 mM in CDCl 3 ) revealed the small temperature dependence of the amide NH chemical shift (Δδ/ΔT = -1.1 ppb/K) and the availability of the free amide NH of 5 to form intermolecular hydrogen bonds. Supramolecular rodlike structures were observed during the aqueous assembly of 5 into microspheres by XRM. Raman microscopy confirmed that nearly identical bonding patterns are present in the assembled microsphere and the crystal architecture of 5. Collectively, these observations provide compelling evidence that the assembly of 5 occurs via crystalline supramolecular intermediates, which are similar in shape and have complementary bonding motifs for proper self-recognition. Competition experiments involving varying concentrations of 5 and its microcapsule-forming cyclopropane analogue 3 revealed that molecular fidelity was less important to the microsphere-forming process than the related capsule-forming process.

Dinuclear calcium complex with weakly NH...O hydrogen-bonded sulfonate ligands.

The novel intramolecularly NH...O hydrogen-bonded Ca(II)-aryl sulfonate complex, [Ca2(SO3-2-t-BuCONHC6H4)2(H2O)4]n(2-t-BuCONHC6H4SO3)2n (1), sulfonate anion, (HNEt3)(SO3-2-t-BuCONHC6H4) (2a), (PPh4)(SO3-2-t-BuCONHC6H4) (2b), (n-Bu4N)(SO3-2-t-BuCONHC6H4) (2c), and sulfonic acid, 2-t-BuCONHC6H4SO3H (3), were synthesized. The structures of 1, 2a, and 2b depict the presence of the formation of NH...O hydrogen bonds between the amide NH and S-O oxygen for a series of compounds as determined by IR and 1H NMR analyses both in the solid state and in the solution state. Thus, the NH...O hydrogen bonds with neutral amide groups are available for investigation of the electronic state of the O- anion. The combined data from the IR and 1H NMR spectra indicate that the sulfonic acid, sulfonate anion, and Ca(II) complex have a substantially weak intramolecular NH...O hydrogen bond between the SO3 oxygen and amide NH. In the detailed comparison with the intense NH...O hydrogen bonds for the carboxylate, weak NH...O hydrogen bonds for sulfonate is due to the strong conjugation of the SO3- group with the lower nucleophilicity.

Kinetics and mechanism of hydrolysis of N-amidomethylsulfonamides

The kinetics of the hydrolyses of secondary and tertiary N-amidomethylsulfonamides were studied at 50 °C. Both types of N-amidomethylsulfonamide hydrolyse through acid- and base-catalysed processes, as indicated by the pH–rate profiles. The order of reactivity for the acid-catalysed pathway implies a mechanism involving protonation of the amide followed by expulsion of a neutral amide and formation of a sulfonyliminium ion. In the base-catalysed region, compound 5c, which is substituted at both amide and sulfonamide nitrogen atoms, hydrolyses by nucleophilic attack of hydroxide ion at the amide carbonyl carbon atom to form benzoic acid and a sulfonamide. In contrast, compound 5b, which contains a sulfonamide NH group, hydrolyses to benzamide and sulfonamide products by an E1cbrev mechanism involving ionisation of the sulfonamide. Compound 5a, which contains an amide NH, also hydrolyses to sulfonamide and amide products, probably by an E2 mechanism.

IR-UV ion-depletion and fluorescence spectroscopy of 2-phenylacetamide clusters: hydration of a primary amide

Fluorescence excitation, resonant two-photon ionisation (R2PI) and IR-UV ion-depletion spectroscopy were used to study the structures of 2-phenylacetamide (2PA) and its dimer and water clusters in their S0, S1 and ionic states. The n = 1–3 hydrates have ‘daisy chain’ structures in which the water molecules link the amide NH and CO sites. The dimer is symmetric, connected ia two strong NH···OC hydrogen bonds. Hydrogen-bonded NH and OH modes of the 1:1 hydrates are strongly coupled, to the extent that the symmetric combination is almost IR forbidden. Examination and reinterpretation of previously published IR data on the 1:1 hydrates of formamide and 2-pyridone revealed similar coupling. Solvation affects the photophysics of 2PA as it does N-benzylformamide; the isolated 2PA molecule does not appear to fluoresce but its clusters do. Hydrogen bonding to the amide carbonyl group could account for this behaviour by raising the energy of the lowest amide (n,π*) states above that of the fluorescent S1 (π,π*) level.