Directing Foldamer Self-Assembly with a Cyclopropanoyl Cap

The rational design of self-assembling organic materials is extremely challenging due to the difficulty in precisely predicting solid-state architectures from first principles, especially if synthons are conformationally flexible. A tractable model system to study self-assembly was constructed by appending cyclopropanoyl caps to the N termini of helical α/β-peptide foldamers, designed to form both N−H⋅⋅⋅O and C^α−H⋅⋅⋅O hydrogen bonds, which then rapidly self-assembled to form foldectures (foldamer architectures). Through a combined analytical and computational investigation, cyclopropanoyl capping was observed to markedly enhance self-assembly in recalcitrant substrates and direct the formation of a single intermolecular N−H⋅⋅⋅O/C^α−H⋅⋅⋅O bonding motif in single crystals, regardless of peptide sequence or foldamer conformation. In contrast to previous studies, foldamer constituents of single crystals and foldectures assumed different secondary structures and different molecular packing modes, despite a conserved N−H⋅⋅⋅O/C^α−H⋅⋅⋅O bonding motif. DFT calculations validated the experimental results by showing that the N−H⋅⋅⋅O/C^α−H⋅⋅⋅O interaction created by the cap was sufficiently attractive to influence self-assembly. This versatile strategy to harness secondary noncovalent interactions in the rational design of self-assembling organic materials will allow for the exploration of new substrates and speed up the development of novel applications within this increasingly important class of materials.     

Spectroscopic and Crystallographic Characterization of the R3N+−C−H⋅⋅⋅X Interaction

As appreciation for nonclassical hydrogen bonds has progressively increased, so have efforts to characterize these interesting interactions. Whereas several kinds of C−H hydrogen bonds have been well-studied, much less is known about the R₃N⁺−C−H⋅⋅⋅X variety. Herein, we present crystallographic and spectroscopic evidence for the existence of these interactions, with special relevance to Selectfluor chemistry. Of particular note is the propensity for Lewis bases to engage in nonclassical hydrogen bonding over halogen bonding with the electrophilic F atom of Selectfluor. Further, the first examples of ¹H NMR experiments detailing R₃N⁺−C−H⋅⋅⋅X (X=O, N) hydrogen bonds are described.     

Hydrogen-Bonded Complexes of Fluorophenylacetylenes: To Fluoresce or Not?

The hydrogen-bonded complexes of fluorophenylacetylenesexhibit unusual and interesting fluorescence turn ON/OFF behaviour following excitation to ¹ππ* (S₁) state. The fluorescence switching behaviour can be realized by (i) “change in the intermolecular structure, (ii) change in the position of fluorine substitution and (iii) change in the hydrogen bonding partner or a combination thereof. Experiments indicate that the ≡C−H⋅⋅⋅X (X=O, N) hydrogen bonding with the acetylenic group plays a pivotal role in this switching behaviour. Intriguingly, weaker ≡C−H⋅⋅⋅X hydrogen bonding leads to fluorescence OFF state, which is turned ON by stronger hydrogen bonding. The observed fluorescence this switching behaviour is rationalized on the basis of a phenomenological model which suggests a coupling between the initially excited S₁ state and a dark S_n state in the Franck-Condon region with limited window controlled by the ≡C−H⋅⋅⋅X hydrogen bonding as a crucial parameter. Such fluorescence switching behaviour in hydrogen-bonded complexes is unprecedented and these intriguing results hopefully will stimulate theoreticians to test ′state of the art′ theories to explain these observations in a consistent manner.     

Interactions of Pyridine-Based Organic Cations as Structure-Determining Factors in Perovskite-Related Compounds AxPb(II)yBrz

We have synthesised and characterised 21 new ternary Pb(II) bromides with 16 different pyridine-based organic cations by single crystal XRD measurements. The dominating composition is APbBr₃ with 10 representatives, but also 6 examples for APb₂Br₅ were found. The systematic variation of topological aspects of the organic cations allowed conclusions on the influence of N−H⋅⋅⋅Br hydrogen bridges on the connectivity and bonding situation of the Pb−Br polyhedra. Additionally, it turned out, that further weak ionic interactions can have an influence, if the formation of N−H⋅⋅⋅Br hydrogen bridges is hindered by steric effects. In general, the high versatility of the dominating PbBr₆ octahedra, and in some cases higher or lower coordination numbers, allows conclusions on the parameters that influence pattern and extent of the N−H⋅⋅⋅Br bridges as the strongest structure-determining factor. Type and extent of N−H⋅⋅⋅Br bridges have also an impact on the distortion of the PbBr₆ octahedra ranging from nearly regular PbBr₆ octahedra to 2+2+2 and 1+2+2+1 patterns with significant lone pair activity. Finally, the connectivity mode of the octahedra relates to formation and strength of hydrogen bonds.     

The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib)

The simplest non-proteinogenic amino acid α-aminoisobutyric acid (Aib), an analogue of glycine and alanine, has been vaporized by laser ablation and probed by high-resolution Fourier transform microwave spectroscopic techniques. Comparison of the experimental rotational and ¹⁴N nuclear quadrupole constants with that predicted ab initio has allowed the identification of three conformers of Aib exhibiting three types of hydrogen-bond interactions I (NH⋅⋅⋅O=C, cis-COOH), II (OH⋅⋅⋅N, trans-COOH), and III (N−H⋅⋅⋅O−H, cis-COOH) within the amino acid backbone. The observation of conformer III, not detected previously for related proteinogenic amino acids with a nonpolar side chain in a supersonic expansion, indicates that the presence of the methyl groups should restrict the conformational relaxation from conformer Aib-III to Aib-I. For conformer Aib-II, the rotational spectra of the ¹³C isotopomers reveal a tunneling motion arising from the two equivalent methyl groups in the molecule. The observation of a single spectrum at the midpoint between those predicted for the two ¹³C of the methyl groups has been explained by considering a double-minimum potential function with a low-energy interconversion barrier for a large amplitude internal motion. This singular fact has been corroborated by the anomalous centrifugal distortion effects determined in conformer Aib-II.     

Cover Feature: An Exploration of the Hydrogen Bond Donor Ability of Ammonia (ChemPhysChem 20/2023)

Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N−H⋅⋅⋅O hydrogen bond. Experimental reports of N−H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH₃)₂, S(CH₃)₂, and Se(CH₃)₂. The formation of the 1 : 1 complex has been monitored in the N−H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.     

Competition Between Intra- and Intermolecular Hydrogen Bonding: o-Anisic Acid⋅⋅⋅Formic Acid Heterodimer

Four conformers of the heterodimer o-anisic acid–formic acid, formed in a supersonic expansion, have been probed by Fourier transform microwave spectroscopy. Two of these forms have the typical double intermolecular hydrogen-bond cyclic structure. The other two show the o-anisic acid moiety bearing a trans-COOH arrangement supported by an intramolecular O−H⋅⋅⋅O bond to the neighbor methoxy group. In these conformers, formic acid interacts with o-anisic acid mainly through an intermolecular O−H⋅⋅⋅O hydrogen bond either to the O−H or to the C=O moieties, reinforced by other weak interactions. Surprisingly, the most abundant conformer in the supersonic expansion is the complex in which the o-anisic acid is in trans arrangement with the formic acid interacting with the O−H group. Such a trans-COOH arrangement in which the intramolecular hydrogen bond dominates over the usually observed double intermolecular hydrogen bond interaction has never been observed previously in an acid–acid dimer.     

An Experimental Exploration of C−H⋅⋅⋅X Hydrogen Bond in [CHCl3−X(CH3)2] Complexes (X=O,S, and Se)

Among the conglomeration of hydrogen bond donors, the C−H group is prevalent in chemistry and biology. In the present work, CHCl₃ has been selected as the hydrogen bond donor and are X(CH₃)₂ are the hydrogen bond acceptors. Formation of C−H⋅⋅⋅X hydrogen bond under the matrix isolation condition is confirmed by the observation of red-shift in the C−H stretching frequency of CHCl₃ and comparison with the simulated spectra. Stabilisation energy of all the three complexes is almost equal although the observed red-shift for the C−H⋅⋅⋅O complex is less compared to the C−H⋅⋅⋅S/Se complexes. The nature and origin of the hydrogen bond have been delineated using Natural Bond Orbital, Atoms in Molecules, Non-Covalent Interaction analyses, and Energy Decomposition Analysis. Charge transfer is found to be proportional to the observed red-shift. This work provides the first impression of C−H⋅⋅⋅Se hydrogen bond and its comparison with C−H⋅⋅⋅O/S hydrogen bond interaction under experimental condition.     

Confinement inside a Crystalline Sponge Induces Pyrrole To Form N−H⋅⋅⋅π Bonded Tetramers

Based on the DFT-level-calculated molecular volume (V_mol) of pyrrole and its liquid density, pyrrole manifests the highest liquid density coefficient LD_c (defined as [V_mol×density ×0.6023]/FW) value of 0.7. Normal liquids have LD_c <0.63. This very high LD_c is due to the strong N−H⋅⋅⋅π interactions in solution, and hence pyrrole can be considered to be a pseudo-crystalline liquid. When trapped inside the confined space of a crystalline sponge, a reorientation of the N−H⋅⋅⋅π interaction is observed leading to specific cyclic N−H⋅⋅⋅π tetramers and N−H⋅⋅⋅π dimers, as verified by single-crystal X-ray crystallographic and computational methods. These tetramers are of the same size as four pyrrole molecules in the solid-state of pyrrole, yet the cyclic N−H⋅⋅⋅π intermolecular interactions are circularly oriented instead of being in the linear zigzag structure found in the X-ray structure of a solid pyrrole. The confinement thus acts as an external driving force for tetramer formation.     

Gas-Phase Conformational Map of the Amino Acid Isovaline

Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and ¹⁴N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N−H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H−O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.     

Ultrafast Vibrational Dynamics of Membrane‐Bound Peptides at the Lipid Bilayer/Water Interface

Vibrational energy transfer (VET) of proteins at cell membrane plays critical roles in controlling the protein functionalities, but its detection is very challenging. By using a surface‐sensitive femtosecond time‐resolved sum‐frequency generation vibrational spectroscopy with infrared pump, the detection of the ultrafast VET in proteins at cell membrane has finally become possible. The vibrational relaxation time of the N−H groups is determined to be 1.70(±0.05) ps for the α‐helix located in the hydrophobic core of the lipid bilayer and 0.9(±0.05) ps for the membrane‐bound β‐sheet structure. The N−H groups with strong hydrogen bonding gain faster relaxation time. By pumping the amide A band and probing amide I band, the vibrational relaxation from N−H mode to C=O mode through two pathways (direct coupling and through intermediate states) is revealed. The ratio of the pathways depends on the NH⋅⋅⋅O=C hydrogen‐bonding strength. Strong hydrogen bonding favors the coupling through intermediate states.     

Sapphyrin Supramolecules through C−H⋅⋅⋅S and C−H⋅⋅⋅Se Hydrogen Bonds—First Structural Characterization of meso- Arylsapphyrins Bearing Heteroatoms

An unprecedented coupling reaction of heteroatom-containing tripyrranes leads to the formation of core-modified sapphyrins 1 and 2 , which self-assemble in the solid state to form supramolecular ladders. Weak C−H⋅⋅⋅S and C−H⋅⋅⋅Se hydrogen-bonding interactions in addition to C−H⋅⋅⋅N hydrogen bonds are responsible for the observed structures.     

Incommensurate Phase in Λ-cobalt (III) Sepulchrate Trinitrate Governed by Highly Competitive N−H⋅⋅⋅O and C−H⋅⋅⋅O Hydrogen Bond Networks**

Phase transitions in molecular crystals are often determined by intermolecular interactions. The cage complex of [Co(C₁₂H₃₀N₈)]³⁺ ⋅ 3 NO₃⁻ is reported to undergo a disorder-order phase transition at T_c1 ≈133 K upon cooling. Temperature-dependent neutron and synchrotron diffraction experiments revealed satellite reflections in addition to main reflections in the diffraction patterns below T_c1. The modulation wave vector varies as function of temperature and locks in at T_c3≈98 K. Here, we demonstrate that the crystal symmetry lowers from hexagonal to monoclinic in the incommensurately modulated phases in T_c1<T<T_c3. Distinctive levels of competitions: trade-off between longer N−H⋅⋅⋅O and shorter C−H⋅⋅⋅O hydrogen bonds; steric constraints to dense C−H⋅⋅⋅O bonds give rise to pronounced modulation of the basic structure. Severely frustrated crystal packing in the incommensurate phase is precursor to optimal balance of intermolecular interactions in the lock-in phase.     

Structures and Reactivities of Cocrystals Involving Diboronic Acids and Bipyridines: In Situ Linker Reaction and 1D-to-2D Dimensionality Change via Crystal-to-Crystal Photodimerization

Cocrystallizations of diboronic acids [1,3-benzenediboronic acid (1,3-bdba), 1,4-benzenediboronic acid (1,4-bdba) and 4,4’-biphenyldiboronic acid (4,4’-bphdba)] and bipyridines [1,2-bis(4-pyridyl)ethylene (bpe) and 1,2-bis(4-pyridyl)ethane (bpeta)] generated the hydrogen-bonded 1 : 2 cocrystals [(1,4-bdba)(bpe)₂] (1), [(1,4-bdba)(bpeta)₂] (2), [(1,3-bdba)(bpe)₂(H₂O)₂] (3) and [(1,3-bdba)(bpeta)₂(H₂O)] (4), wherein 1,3-bdba involved hydrated assemblies. The linear extended 4,4’-bphdba exhibited the formation of 1 : 1 cocrystals [(4,4'-bphdba)(bpe)] (5) and [(4,4'-bphdba-me)(bpeta)] (6). For 6, a hemiester was generated by an in-situ linker transformation. Single-crystal X-ray diffraction revealed all structures to be sustained by B(O)−H⋅⋅⋅N, B(O)−H⋅⋅⋅O, O_w−H⋅⋅⋅O, O_w−H⋅⋅⋅N, C−H⋅⋅⋅O, C−H⋅⋅⋅N, π⋅⋅⋅π, and C−H⋅⋅⋅π interactions. The cocrystals comprise 1D, 2D, and 3D hydrogen-bonded frameworks with components that display reactivities upon cocrystal formation and within the solids. In 1 and 3, the C=C bonds of the bpe molecules undergo a [2+2] photodimerization. UV radiation of each compound resulted in quantitative conversion of bpe into cyclobutane tpcb. The reactivity involving 1 occurred via 1D-to-2D single-crystal-to-single-crystal (SCSC) transformation. Our work supports the feasibility of the diboronic acids as formidable structural and reactivity building blocks for cocrystal construction.     

Helical supramolecular assembly of N2,N2′‐bis[3‐(morpholin‐4‐yl)propyl]‐N1,N1′‐(1,2‐phenylene)dioxalamide dimethyl sulfoxide monosolvate

In the title compound, C₂₄H₃₆N₆O₆·C₂H₆OS, the carbonyl groups are in an antiperiplanar conformation, with O=C—C=O torsion angles of 178.59 (15) and −172.08 (16)°. An intramolecular hydrogen‐bonding pattern is depicted by four N—H...O interactions, which form two adjacent S(5)S(5) motifs, and an N—H...N interaction, which forms an S(6) ring motif. Intermolecular N—H...O hydrogen bonding and C—H...O soft interactions allow the formation of a meso‐helix. The title compound is the first example of a helical 1,2‐phenylenedioxalamide. The oxalamide traps one molecule of dimethyl sulfoxide through N—H...O hydrogen bonding. C—H...O soft interactions give rise to the two‐dimensional structure.     

Conformational Equilibria of 2-Methoxypyridine⋅⋅⋅CO2: Cooperative and Competitive Tetrel and Weak Hydrogen Bonds

The rotational spectrum of 2-methoxypyridine⋅⋅⋅CO₂ was recorded and analysed employing a cavity-based Fourier transform microwave spectrometer, complemented with quantum chemical calculations which predicted three possible isomers within energies less than 1000 cm⁻¹. The two most stable isomers were observed in the pulsed jet, which are stabilized by a network of C⋅⋅⋅N/O tetrel and C−H⋅⋅⋅O weak hydrogen bonds. The relative population ratio of the two detected isomers was estimated to be N_I/N_II≈2.5. The competition and cooperation of the present non-covalent interactions in both isomers are discussed within the framework of Bader's quantum theory of atoms in molecules and Johnson's non-covalent interaction analyses. The study shows, that when looking for CO₂ adsorbents, one might prefer candidates with multiple interactions in one site over candidates with few but strong interactions.     

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Low-barrier hydrogen bond (LBHB) involvement in enzyme catalysis is examined by analysis of experimental nuclear and electron densities of a model compound for the catalytic triad in serine proteases (shown schematically), which is based on a cocrystal of betaine, imidazole, and picric acid. The three short, strong N−H⋅⋅⋅O hydrogen bonds in the structure have varying degrees of covalent bonding contributions suggesting a gradual transition to the LBHB situation.     

Stabilization and Structure of the cis Tautomer of a Free‐Base Porphyrin

Single‐crystal X‐ray analysis of the β‐heptakis(trifluoromethyl)‐meso ‐tetrakis(p ‐fluorophenyl)porphyrin, H₂[(CF₃)₇TpFPP], has revealed the first example of a stable cis tautomer of a free‐base porphyrin, the long‐postulated intermediate of porphyrin tautomerism. The stability of the unique molecule appears to reflect a dual origin: a strongly saddled porphyrin skeleton, which alleviates electrostatic repulsion between the two NH protons, and two polarization‐enhanced, transannular N−H⋅⋅⋅O−H⋅⋅⋅N hydrogen bond chains, each involving a molecule of water. DFT calculations suggest that the observed tautomer has a lower energy than the alternative, doubly hydrated trans tautomer by some 8.3 kcal mol⁻¹. A fascinating prospect thus exists that H₂[(CF₃)₇TpFPP]⋅2 H₂O and cognate structures may act as supramolecular synthons, which, given their chirality, may even be amenable to resolution into optically pure enantiomers.     

Halogen versus Hydrogen Bonding in Binary Cocrystals: Novel Conformation a Coformer with [2+2] Photoreactivity of Criss-Crossed C=C Bonds

A series of cocrystals involving the hydrogen- and halogen-bond donor coformers catechol ( cat ) and 1,2-diiodotetrafluorobenzene ( 1,2-di-I-tFb ), respectively, is reported. Each coformer forms a cocrystal with each of the three symmetric bipyridines trans-1,2-bis(n-pyridyl)ethylene ( n , n′ -bpe , where: n=n′=2, 3, 4). Four novel cocrystals ( cat ) ⋅ ( 3,3′-bpe ), 2( 1,2-di-I-tFb ) ⋅ ( 2,2′-bpe ), 2( 1,2-di-I-tFb ) ⋅ ( 3,3′-bpe ), and ( 1,2-di-I-tFb ) ⋅ ( 4,4′-bpe ) comprise components that assemble by either O−H⋅⋅⋅N hydrogen bonds ( cat ) or N⋅⋅⋅I halogen bonds ( 1,2-di-I-tFb ). In ( cat ) ⋅ ( 3,3′-bpe ), cat acts as a template to support an intermolecular [2+2] photocycloaddition of 3,3′-bpe . The reactivity occurs via a one-dimensional (1D) hydrogen-bonded tape with stacked and criss-crossed olefins that react stereoselectively and quantitatively to form rctt-tetrakis(3-pyridyl)cyclobutane ( 3,3′-tpcb ). The reactivity of the criss-crossed olefins is facilitated by a hitherto not reported cis-gauche conformation adopted by cat . The stereochemistry of 3,3′-tpcb is confirmed in the cocrystal 2( cat ) ⋅ ( 3,3′-tpcb ).