Role of pK a in establishing the crystal structures of six hydrogen-bonded compounds of 4-methylquinoline with different isomers of chloro- and nitro-substituted benzoic acids

The structures of the six hydrogen-bonded 1:1 compounds of 4-methylquinoline (C10H9N) with chloro- and nitro-substituted benzoic acids (C7H4ClNO4), namely, 4-methylquinolinium 2-chloro-4-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (I), 4-methylquinoline–2-chloro-5-nitrobenzoic acid (1/1), C10H9N·C7H4ClNO4, (II), 4-methylquinolinium 2-chloro-6-nitrobenzoate, C10H9.63N0.63+·C7H3.37ClNO4 0.63−, (III), 4-methylquinolinium 3-chloro-2-nitrobenzoate, C10H9.54N0.54+·C7H3.46ClNO4 0.54−, (IV), 4-methylquinolinium 4-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (V), and 4-methylquinolinium 5-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, have been determined at 185–190 K. In each compound, the acid and base molecules are linked by a short hydrogen bond between a carboxy (or carboxylate) O atom and an N atom of the base. The O...N distances are 2.5652 (14), 2.556 (3), 2.5485 (13), 2.5364 (13), 2.5568 (13) and 2.5252 (11) Å, respectively, for compounds (I)–(VI). In the hydrogen-bonded acid–base units of (III) and (IV), the H atoms are each disordered over two positions with O site:N site occupancies of 0.37 (3):0.63 (3) and 0.46 (3):0.54 (4), respectively, for (III) and (IV). The H atoms in the hydrogen-bonded units of (I), (V) and (VI) are located at the N-atom site, while the H atom in (II) is located at the O-atom site. In all the crystals of (I)–(VI), π–π stacking interactions between the quinoline ring systems and C—H...O hydrogen bonds are observed. Similar layer structures are constructed in (IV)–(VI) through these interactions together with π–π interactions between the benzene rings of the adjacent acid molecules. A short Cl...Cl contact and an N—O...π interaction are present in (I), while a C—H...Cl hydrogen bond and a π–π interaction between the benzene ring of the acid molecule and the quinoline ring system in (II), and a C—H...π interaction in (III) are observed. Hirshfeld surfaces for the title compounds mapped over d norm and shape index were generated to visualize the weak intermolecular interactions.

Synthesis, structure and magnetocaloric properties of a new two-dimensional gadolinium(III) coordination polymer based on azobenzene-2,2′,3,3′-tetracarboxylic acid

A new Gd3+ coordination polymer (CP), namely, poly[diaqua[μ4-1′-carboxy-3,3′-(diazene-1,2-diyl)dibenzene-1,2,2′-tricarboxylato]gadolinium(III)], [Gd(C16H7N2O8)(H2O)2] n , (I), has been synthesized hydrothermally from Gd(NO3)3·6H2O and azobenzene-2,2′,3,3′-tetracarboxylic acid (H4abtc). The target solid has been characterized by single-crystal and powder X-ray diffraction, elemental analysis, IR spectroscopy and susceptibility measurements. CP (I) crystallizes in the monoclinic space group C2/c. The structure features a 4-connected topology in which Gd3+ ions are connected by carboxylate groups into a linear chain along the monoclinic symmetry direction. Adjacent one-dimensional aggregates are bridged by Habtc3− ligands to form a two-dimensional CP in the (10-1) plane. A very short hydrogen bond [O...O = 2.4393 (4) Å] links neighbouring layers into a three-dimensional network. A magnetic study revealed antiferromagnetic Gd...Gd coupling within the chain direction. CP (I) displays a significant magnetocaloric effect (MCE), with a maximum −ΔS m of 27.26 J kg−1 K−1 for ΔH = 7 T at 3.0 K. As the MCE in (I) exceeds that of the commercial magnetic refrigerant GGG (Gd3Ga5O12, −ΔS m = 24 J kg−1 K−1, ΔH = 30 kG), CP (I) can be regarded as a potential cryogenic material for low-temperature magnetic refrigeration.

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

A new role of low barrier hydrogen bond in mediating protein stability by small molecules

Low barrier hydrogen bond (LBHB) is a special type of hydrogen bond which occurs where two heteroatoms with similar pKa values share a single proton resulting in an unusually strong and short hydrogen bond. LBHBs in protein play important roles in enzyme catalysis and maintaining protein structural integrity but its other biochemical roles are unknown. Here we report a novel function of LBHB in selectively inducing tubulin protein degradation. A tubulin inhibitor, 3-(3-Phenoxybenzyl) amino-β-carboline (PAC), promotes selective degradation of αβ-tubulin heterodimers by binding to the colchicine site of β-tubulin. Biochemical studies have revealed that PAC specifically destabilizes tubulin, making it prone to aggregation that then predisposes it to ubiquitinylation and then degradation. Structural activity analyses have indicated that the destabilization is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a LBHB. In contrast, another two tubulin inhibitors only forming normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. Most importantly, we screened for compounds capable of forming LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimers degradation in a PAC-like manner as expected. Our study has identified a novel approach for designing tubulin degraders, providing a unique example of LBHB function and suggests that designing small molecules to form LBHBs with protein residues resulting in the highly specific degradation of a target protein could be a new strategy for drug development.

Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca2+ Biosensor

Ratiometric indicators with long emission wavelengths are highly preferred in modern bioimaging and life sciences. Herein, we elucidated the working mechanism of a standalone red fluorescent protein (FP)-based Ca2+ biosensor, REX-GECO1, using a series of spectroscopic and computational methods. Upon 480 nm photoexcitation, the Ca2+-free biosensor chromophore becomes trapped in an excited dark state. Binding with Ca2+ switches the route to ultrafast excited-state proton transfer through a short hydrogen bond to an adjacent Glu80 residue, which is key for the biosensor’s functionality. Inspired by the 2D-fluorescence map, REX-GECO1 for Ca2+ imaging in the ionomycin-treated human HeLa cells was achieved for the first time with a red/green emission ratio change (ΔR/R0) of ~300%, outperforming many FRET- and single FP-based indicators. These spectroscopy-driven discoveries enable targeted design for the next-generation biosensors with larger dynamic range and longer emission wavelengths.

A quantum crystallographic approach to short hydrogen bonds

Mapped electron density and ab initio modelling reveal how H-atom position and molecular environment tune short hydrogen bond characteristics and properties.

The KDEL trafficking receptor exploits pH to tune the strength of an unusual short hydrogen bond

The endoplasmic reticulum (ER) is the main site of protein synthesis in eukaryotic cells and requires a high concentration of luminal chaperones to function. During protein synthesis, ER luminal chaperones are swept along the secretory pathway and must be retrieved to maintain cell viability. ER protein retrieval is achieved by the KDEL receptor, which recognises a C-terminal Lys-Asp-Glu-Leu (KDEL) sequence. Recognition of ER proteins by the KDEL receptor is pH dependent, with binding occurring under acidic conditions in the Golgi and release under conditions of higher pH in the ER. Recent crystal structures of the KDEL receptor in the apo and peptide bound state suggested that peptide binding drives the formation of a short-hydrogen bond that locks the KDEL sequence in the receptor and activates the receptor for COPI binding in the cytoplasm. Using quantum mechanical calculations we demonstrate that the strength of this short hydrogen bond is reinforced following protonation of a nearby histidine, providing a conceptual link between receptor protonation and KDEL peptide binding. Protonation also controls the water networks adjacent to the peptide binding site, leading to a conformational change that ultimately allows the receptor-complex to be recognized by the COPI system.

Crystal structures of four isomeric hydrogen-bonded co-crystals of 6-methylquinoline with 2-chloro-4-nitrobenzoic acid, 2-chloro-5-nitrobenzoic acid, 3-chloro-2-nitrobenzoic acid and 4-chloro-2-nitrobenzoic acid

The structures of the four isomeric compounds of 6-methylquinoline with chloro- and nitro-substituted benzoic acids, C7H4ClNO4·C10H9N, namely, 2-chloro-4-nitrobenzoic acid–6-methylquinoline (1/1), (I), 2-chloro-5-nitrobenzoic acid–6-methylquinoline (1/1), (II), 3-chloro-2-nitrobenzoic acid–6-methylquinoline (1/1), (III), and 4-chloro-2-nitrobenzoic acid–6-methylquinoline (1/1), (IV), have been determined at 185–190 K. In each compound, the acid and base molecules are linked by a short hydrogen bond between a carboxyl O atom and an N atom of the base. The O...N distances are 2.5452 (12), 2.6569 (13), 2.5640 (17) and 2.514 (2) Å, respectively, for compounds (I)–(IV). In the hydrogen-bonded acid–base units of (I), (III) and (IV), the H atoms are each disordered over two positions with O site:N site occupancies of 0.65 (3):0.35 (3), 0.59 (4):0.41 (4) and 0.48 (5):0.52 (5), respectively, for (I), (III) and (IV). The H atom in the hydrogen-bonded unit of (II) is located at the O-atom site. In all of the crystals of (I)–(IV), π–π interactions between the quinoline ring system and the benzene ring of the acid molecule are observed. In addition, a π–π interaction between the benzene rings of adjacent acid molecules and a C—H...O hydrogen bond are observed in the crystal of (I), and C—H...O hydrogen bonds and O...Cl contacts occur in the crystals of (III) and (IV). These intermolecular interactions connect the acid and base molecules, forming a layer structure parallel to the bc plane in (I), a column along the a-axis direction in (II), a layer parallel to the ab plane in (III) and a three-dimensional network in (IV). Hirshfeld surfaces for the title compounds mapped over d norm and shape index were generated to visualize the weak intermolecular interactions.

Unusual Spectroscopic and Electric Field Sensitivity of a Chromophore with Short Hydrogen Bond: GFP and PYP as Model Systems

<p> Short hydrogen bonds, with heavy-atom distances less than 2.7 Å, are believed to exhibit proton delocalization and their possible role in catalysis has been widely debated. While spectroscopic and/or structural methods are usually employed to study the degree of proton delocalization, ambiguities still arise and no direct information on the corresponding potential energy surface is obtained. Here we apply an external electric field to perturb the short hydrogen bond(s) within a collection of green fluorescent protein S65T/H148D variants and photoactive yellow protein mutants, where the chromophore participates in the short hydrogen bond(s) and serves as an optical probe of the proton position. As the proton is charged, its position may shift in response to the external electric field, and the chromophore’s electronic absorption can thus reflect the ease of proton transfer. The results suggest that low-barrier hydrogen bonds are not present within these proteins even when proton affinities between donor and acceptor are closely matched. Exploiting the chromophores as pre-calibrated electrostatic probes, the covalency of short hydrogen bonds as a non-electrostatic component was also revealed. No clear evidence was found for a possible contribution of unusually large polarizabilities of short hydrogen bonds due to proton delocalization; a theoretical framework for this interesting phenomenon is developed.<br></p>