Hydrogen bonding and molecular assemblies (original) (raw)
Related papers
Intramolecular hydrogen bonding in derivatives of 3-amino-propenethial
International Journal of Quantum Chemistry, 2009
We have examined the intramolecular hydrogen bonding behavior of simple 0and y-amino acid derivatives as a prelude to efforts to design unnatural polyamides that will adopt compact and specific folding patterns analogous to those of a-amino acid polymers (proteins). We postulate that the desired folding behavior will be most likely if intramolecular hydrogen bonds are unfavorable between nearest neighbor amide groups on the polymer backbone. Previous work from other laboratories and our own has shown that this criterion applies to a-amino acid polymers. Variable-temperature FT-IR data reported here for p-alanine derivatives in methylene chloride indicate that nearest neighbor hydrogen bonding is unfavorable for this type of residue as well. FT-IR and N M R data for y-amino butyric acid derivatives, however, show that nearest neighbor hydrogen bonding is favorable. For two of the diamides discussed here, thermodynamic parameters have been determined for hydrogen-bond-mediated folding via variable-temperature FT-IR measurements. These AHo and ASo values should provide useful benchmarks for molecular mechanics programs.
This paper describes the conformational characteristics of a nonproteinogenic γ-aminobenzoic acid (γ-Abz), investigated experimentally as well as theoretically. The single crystal X-ray diffraction analysis of the model system Boc-γ-Abz-NHMe (1) revealed the existence of an unusual βstrand-like molecular structure. The two weak unconventional C−H···O intramolecular hydrogen-bonds, i.e., main-chain to main-chain: C β i+1 −H···OC i+1 and main-chain to side-chain C δ i+1 −H···OC i interactions, evidently stabilize the f lat molecular topology. The favorable antiparallel β-strand mimics are held together by a network of cross-strand N−H···O intermolecular hydrogen bonds. Interestingly, the noncovalent β-sheet-like duplexes facilitate the fabrication of offset face-to-face aromatic−aromatic interactions, whereas the dimers of dimers are aligned edge-to-edge. The two-dimensional 1 H NMR ROESY experiment ascertained the extraordinary stability of the rigid β-strand template and molecular self-assembly in a nonpolar environment. The ab initio molecular modeling substantiated the crystal molecular structure as the minimum energy conformer along with weak C−H···O intramolecular hydrogen bonds. The solidstate Fourier transform infrared spectral analysis sustained the participation of both amide-NHs in intermolecular hydrogen bonding. The highly ordered supramolecular architecture, engendered from a single preorganized molecular component, exploited a variety of strong as well as weak stabilizing forces as varied as N−H···O, C−H···O, Ar···Ar, and van der Waals and/or hydrophobic interactions.
Characterizing the Cooperativity in H-Bonded Amino Structures †
The Journal of Physical Chemistry A, 2007
Density functional theory calculations were used to examine the effect of H-bond cooperativity on the magnitude of the NMR chemical shifts and spin-spin coupling constants in a C 4h -symmetric G-quartet and in structures consisting of six cyanamide monomers. These included two ring structures (a planar C 6h -symmetric structure and a nonplanar S 6 -symmetric structure) and two linear chain structures (a fully optimized planar C s -symmetric chain and a planar chain structure where all intra-and intermolecular parameters were constrained to be identical). The NMR parameters were computed for the G-quartet and cyanamide structures, as well as for shorter fragments derived from these assemblies without reoptimization. In the ring structures and the chain with identical monomers, the intra-and intermolecular geometries of the cyanamides were identical, thereby allowing the study of cooperative effects in the absence of geometry changes. The magnitude of the | 1 J NH | coupling, 1 H and 15 N chemical shifts of the H-bonding amino N-H group, and the | h2 J NN | H-bond coupling increased, whereas the size of the | 1 J NH | coupling of the non-H-bonded amino N-H bonds of the first amino group in the chain, which are roughly perpendicular to the H-bonding network, decreased in magnitude when H-bonding monomers were progressively added to extending ring or chain structures. These effects are attributed to electron redistribution induced by the presence of the nearby H-bonding guanine or cyanamide molecules. † Part of the "Supporting Information Available: Cartesian coordinates of the B3LYP/6-311++G(d,p) optimized geometries of the G-quartet and the cyanamide ring and chain structures (Table S1A-E); contributions to the 1 J N2H21 and 1 J N2H22 coupling constants computed for the G-quartet and the cyanamide ring and chain structures -E); contributions to the h2 J NN coupling constants -E); and 15 N2, 1 H21, and 1 H22 chemical shifts . NBO charges in the guanine monomer and dimer . show the 1 J N1H1 and h3 J N1C6 coupling constants in the G-quartet. show the 1 J N2H2 and h2 J NN coupling constants in the C 6h -symmetric cyanamide ring structure, computed with B3LYP/ aug-cc-pVDZ-su2. This material is available free of charge via the Internet at http://pubs.acs.org.
Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids
Communications Chemistry
The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid Nacetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, synand anti-. In the syn-conformer the O-H group is oriented at~60 ∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the-COOH groups adopt an anti-conformation. However, when Nacetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to~60%.
Supramolecular self-assembly based on directed hydrogen bonding
Macromolecular Symposia, 1994
A series of hydrogen-bonding monomers has been constructed and shown to form discrete aggregates both in solution and in the solid state. 1. SELF-ASSEMBLY W SOLUTION The process of self-assembly involves the non-covalent interaction of two or more molecular subunits to form well-defined aggregates. The size, shape and makeup of the aggregates will be determined by the chemical information present on each molecule in the form of the interacting groups; their nature, number and orientation (Refs. 1-2) In nature, examples of self-assembled structures are widespread. The enormous complexity inherent and necessary in biological structures cannot be reached by individual biosynthetically derived units but requires the association of many units. For example, the viral coat proteins of the tobacco mosaic virus spontaneously self-organize (Ref. 3) into a 34 unit, twelayered disc which in turn assembles into an elongated helical aggregate around a strand of RNA. The principal
The Magnitude of [C−H···O] Hydrogen Bonding in Molecular and Supramolecular Assemblies
Journal of the American Chemical Society, 2001
Ab initio calculations at the MP2/6-311++G** level on model systems (N-methylpyridinium complexes of dimethyl ether and dimethyl phosphate anion) provide quantitative measures of the large stabilization energies that arise from [C-H‚‚‚O] contacts in charged systems. These attractive interactions control (i) the self-assembly of bipyridinium-based catenanes and rotaxanes in solution, (ii) the self-organization of left-handed Z-DNA with alternating [dC-dG] sequences in the solid state, and (iii) the binding of pyridinium derivatives with single-and double-stranded DNA. Slightly attractive interactions occur between the donor ether and phosphate moieties and a neutral pyridine molecule in the gas phase. Electrostatic potential and solvation calculations demonstrate that [C-H‚‚‚O] interactions which involve a cationic [C-H] donor are dominated by electrostatic terms.
Journal of Heterocyclic Chemistry, 2001
A supramolecular assembly formed between phthalimide and 2-guanidinobenzimidazole, containing a short 2.692(4)Å N-H ... N hydrogen bond, is reported. The crystal structure of this species was determined by both X-ray and neutron diffraction. The diffraction data reveal that the proton involved in the short hydrogen bond has been transferred from the phthalimide to the guanidinobenzimidazole to form an ion pair. There is also an interesting stacking interaction between the atoms involved in the short hydrogen bond and the π system of a phthalimide molecule that is approximately 3.3 Å away. The structure is compared with the structure of a similar assembly formed between 4-nitrophthalimide and 2-guanidinobenzimidazole. † Dedicated to Professor Jerald S. Bradshaw, a fine chemist and good friend of LFL
On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules
Journal of Molecular Biology, 1998
Crystallographic studies of duplex DNA have indicated that opposing exocyclic amino groups may form close NHÁ Á ÁN contacts. To study the nature of such interactions, we have examined the database of small molecule, high-resolution crystal structures for more accurate examples of this type of unconventional interaction. We have found cases where the amino groups in guanine and adenine bases accept hydrogen bonds from conventional donors, such as amino or hydroxyl groups. More frequently, the purine amino group was found to contact closely electropositive C-H groups. Searches of the nucleic acid structural databases also yielded several examples where the purine amino group is contacted by hydrogen bond donors in macromolecules. Ab initio calculations indicate that the hydrogen ±amino contact is improved energetically when the amino group moves from the conventional geometry, where all atoms are co-planar with the base, to one in which the hydrogen atoms lie out of the plane and the nitrogen is at the apex of a pyramid, resulting in polarization of the amino group. The combined structural and theoretical data suggest that the amino group is¯exible, and can accommodate close contacts, because the resulting polarization permits electropositive atoms to approach the amino group nitrogen more closely than expected for their conventional van der Waals radii. The¯exibility of the amino group may permit particular DNA conformations that enforce hydrogen ±amino contacts to optimize favorable stacking interactions, and it may play a role in the recognition of nucleosides. We speculate that the amino group can accept hydrogen bonds under special circumstances in macromolecules, and that this ability might play a mechanistic role in catalytic processes such as deamination or amino transfer.