Short Hydrogen Bond Research Articles

Systematic Computational Approaches on Biosorption of Fluoride on Chitin: Crossover from Conventional to Short and Strong Hydrogen Bonds

Systematic Computational Approaches on Biosorption of Fluoride on Chitin: Crossover from Conventional to Short and Strong Hydrogen Bonds

Synthesis, characterization and photophysical properties of phthalimide-pyrazole compounds: Effect of the substituent in the pyrazole ring on the crystal structures

Four phthalimide-pyrazole derivative compounds (L1 = H, L2 = NO2, L3 = Br, and L4 = I) were synthesized and fully characterized. Single crystals of each compound were obtained, and their conformational and supramolecular structures were analyzed. The four crystal structures (L1 to L4) are stabilized by different intermolecular interactions and therefore have different characteristics from each other. L1 is dominated by long-range Van der Waals forces and not by short hydrogen bonds. On the other hand, L2 packs into a molecular sheet along the b and c axes. L3 and L4 have a common monoclinic structure (P21/c) and thus allow stabilization of the respective compounds by halogen-halogen interactions (Br–Br, I–I) and σ-hole effects. In all compounds, these interactions, whether Van der Waals forces, π‧‧‧‧π stacking or halogen bonds, are responsible for their packing and molecular stability. Therefore, it was concluded that the substituent on the pyrazole ring is the determining factor in their crystallization. In addition, photophysical and theoretical studies showed that the compounds exhibit emission in the presence of DCM, acetonitrile (MeCN), and DMSO, primarily due to the HOMO-LUMO orbitals in the phthalimide ring.

The Fate of the Formic Acid Proton on the Anatase TiO2(101) Surface

AbstractAs a prototype adsorption reaction of gas Brønsted acid on oxides, we study the adsorption of formic acid on anatase. We perform infrared spectroscopy measurements of adsorbed HCOOH and HCOOD on TiO2 nanopowders, from 13 K up to room temperature in an ultra‐high vacuum chamber. We assign the IR signals via computed spectra from nuclear quantum dynamics simulations using our divide‐and‐conquer semiclassical ab initio molecular dynamics method. The acid proton forms an extraordinarily short and strong hydrogen bond with the surface oxygen. The strength of this hydrogen bond, that compares to H bonds in ice at high pressures, is at the root of a substantial redshift with respect to the typical free OH stretching frequency, which eludes its straightforward detection.

Structural, mechanical, electronic, vibrational properties and hydrogen bonding of a novel energetic ionic 5, 5'-dinitroamino-3, 3'-azo-oxadiazole 4, 7-diaminopyridazino [4, 5-c] furoxan salt.

The structure, mechanical, electronic, vibration, and hydrogen bonding properties of a novel high-energy and low-sensitivity 5, 5'-dinitroamino-3, 3'-azo-oxadiazole 4, 7-diaminopyridazino [4, 5-c] furoxan salt have been studied by density functional theory. The calculated vibrational properties show that the low-frequency mode is mainly contributed by the vibration of the -NO2 group, and the high-frequency mode is mainly contributed by the vibration of the -NH2 group and the N7-H3 bond which protonates the cation. In addition, it is analyzed that the first bond to break may be the N-NO2 bond. The calculated hydrogen bond properties indicate that the hydrogen bond between water molecules and cations is N7-H3… O5 (1.563Å), which is the shortest hydrogen bond among all hydrogen bonds. The presence of this exceptionally short hydrogen bond renders the N7-H3 and H6-O5 bonds resistant to disruption at high frequencies, underscoring the pivotal role of hydrogen bonding in stabilizing the structure of energetic materials. Given the absence of experimental and theoretical data on the electronic, mechanical, and vibrational properties of the material thus far, our calculations offer valuable theoretical insights into the ionic salts of high energy and low sensitivity. All calculations have been carried out based on density functional theory (DFT) and implemented in the CASTEP code. The mode-conserving pseudopotential is utilized to describe the plane wave expansion function, while the PBE functional within the generalized gradient approximation (GGA) is employed to characterize the exchange-correlation interaction. Additionally, dispersion correction is applied using Grimme's DFT-D method.

Hydrogen Bonds and In situ Photoinduced Metallic Bi0/Ni0 Accelerating Z-Scheme Charge Transfer of BiOBr@NiFe-LDH for Highly Efficient Photocatalysis.

For heterojunction system, the lack of stable interfacial driving force and definite charge transfer channel makes the charge separation and transfer efficiency unsatisfactory. The photoreaction mechanism occurring at the interface also receives less attention. Herein, a 2D/2D Z-scheme junction BiOBr@NiFe-LDH with large-area contact featured by short interface hydrogen bonds and strong interfacial electric field (IEF) is synthesized, and in situ photoinduced metallic species assisting charge transfer mechanism is demonstrated. The hydrogen bonds between O atoms from BiOBr and H atoms from NiFe-LDH induce a significant interfacial charge redistribution, establishing a robust IEF. Notably, during photocatalytic reaction, Bi0 and Ni0 are in situ performed in heterojunction, which separately act as electron transport mediator and electron trap to further accelerate charge transfer efficiency up to 71.2 %. Theoretical calculations further demonstrate that the existence of Bi0 strengthens the IEF. Therefore, high-speed spatial charge separation is realized in Bi0/BiOBr@Ni0/NiFe-LDH, leading to a prominent photocatalytic activity with a tetracycline removal ratio of 88.3 % within 7 min under visible-light irradiation and the presence of persulfate, far exceeding majority of photocatalysts reported previously. This study provides valid insights for designing hydrogen bonding heterojunction systems, and advances mechanistic understanding on in situ photoreaction at interfaces.

Hydrogen Bonds and In situ Photoinduced Metallic Bi0/Ni0 Accelerating Z‐Scheme Charge Transfer of BiOBr@NiFe‐LDH for Highly Efficient Photocatalysis

AbstractFor heterojunction system, the lack of stable interfacial driving force and definite charge transfer channel makes the charge separation and transfer efficiency unsatisfactory. The photoreaction mechanism occurring at the interface also receives less attention. Herein, a 2D/2D Z‐scheme junction BiOBr@NiFe‐LDH with large‐area contact featured by short interface hydrogen bonds and strong interfacial electric field (IEF) is synthesized, and in situ photoinduced metallic species assisting charge transfer mechanism is demonstrated. The hydrogen bonds between O atoms from BiOBr and H atoms from NiFe‐LDH induce a significant interfacial charge redistribution, establishing a robust IEF. Notably, during photocatalytic reaction, Bi0 and Ni0 are in situ performed in heterojunction, which separately act as electron transport mediator and electron trap to further accelerate charge transfer efficiency up to 71.2 %. Theoretical calculations further demonstrate that the existence of Bi0 strengthens the IEF. Therefore, high‐speed spatial charge separation is realized in Bi0/BiOBr@Ni0/NiFe‐LDH, leading to a prominent photocatalytic activity with a tetracycline removal ratio of 88.3 % within 7 min under visible‐light irradiation and the presence of persulfate, far exceeding majority of photocatalysts reported previously. This study provides valid insights for designing hydrogen bonding heterojunction systems, and advances mechanistic understanding on in situ photoreaction at interfaces.

The Fate of the Formic Acid Proton on the Anatase TiO2(101) Surface.

As a prototype adsorption reaction of gas Brønsted acid on oxides, we study the adsorption of formic acid on anatase. We perform infrared spectroscopy measurements of adsorbed HCOOH and HCOOD on TiO2 nanopowders, from 13 K up to room temperature in an ultra-high vacuum chamber. We assign the IR signals via computed spectra from nuclear quantum dynamics simulations using our divide-and-conquer semiclassical ab initio molecular dynamics method. The acid proton forms an extraordinarily short and strong hydrogen bond with the surface oxygen. The strength of this hydrogen bond, that compares to H bonds in ice at high pressures, is at the root of a substantial redshift with respect to the typical free OH stretching frequency, which eludes its straightforward detection.

Very Strong Hydrogen Bond in Nitrophthalic Cocrystals.

This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB. The four synthesized complexes were studied by experimental X-ray, IR, and Raman methods, as well as theoretical Car-Parrinello Molecular Dynamics (CP-MD) and Density Functional Theory (DFT) simulations. By variation of the steric repulsion and basicity of the complex' components, a very short intramolecular hydrogen bond was achieved. The potential energy curves calculated by the DFT method were characterized by a low barrier (0.7 and 0.9 kcal/mol) on proton transfer in the OHN intermolecular hydrogen bond for 3-nitrophthalic acid with either 2,4,6-collidine or N,N-dimethyl-4-pyridinamine cocrystals. Moreover, the CP-MD simulations exposed very strong bridging proton dynamics in the intermolecular hydrogen bonds. The accomplished crystallographic and spectroscopic studies indicate that the OHO intramolecular hydrogen bond in 4-nitrophthalic cocrystals is VSHB. The influence of a strong steric effect on the geometry of the studied cocrystals and the stretching vibration bands of the carboxyl and carboxylate groups was elaborated.

Supramolecular hydrogen-bonded networks formed from copper(II) carboxylate dimers.

The well-known copper carboxylate dimer, with four carboxylate ligands extending outwards towards the corners of a square, has been employed to generate a series of crystalline compounds. In particular, this work centres on the use of the 4-hydroxybenzoate anion (Hhba-) and its deprotonated phenolate form 4-oxidobenzoate (hba2-) to obtain complexes with the general formula [Cu2(Hhba)4-x(hba)xL2-y]x-, where L is an axial coligand (including solvent molecules), x = 0, 1 or 2, and y = 0 or 1. In some cases, short hydrogen bonds result in complexes which may be represented as [Cu2(Hhba)2(H0.5hba)2L2]-. The main focus of the investigation is on the formation of a variety of extended networks through hydrogen bonding and, in some crystals, coordinate bonds when bridging coligands (L) are employed. Crystals of [Cu2(Hhba)4(dioxane)2]·4(dioxane) consist of the expected Cu dimer with the Hhba- anions forming hydrogen bonds to 1,4-dioxane molecules which block network formation. In the case of crystals of composition [Et4N][Cu2(Hhba)2(H0.5hba)2(CH3OH)(H2O)]·2(dioxane), Li[Cu2(Hhba)2(H0.5hba)2(H2O)2]·3(dioxane)·4H2O and [Cu2(Hhba)2(H0.5hba)2(H0.5DABCO)2]·3CH3OH (DABCO is 1,4-diazabicyclo[2.2.2]octane), square-grid hydrogen-bonded networks are generated in which the complex serves as one type of 4-connecting node, whilst a second 4-connecting node is a hydrogen-bonding motif assembled from four phenol/phenolate groups. Another two-dimensional (2D) network based upon a related square-grid structure is formed in the case of [Et4N]2[Cu2(Hhba)2(hba)2(dioxane)2][Cu2(Hhba)4(dioxane)(H2O)]·CH3OH. In [Cu2(Hhba)4(H2O)2]·2(Et4NNO3), a square-grid structure is again apparent, but, in this case, a pair of nitrate anions, along with four phenolic groups and a pair of water molecules, combine to form a second type of 4-connecting node. When 1,8-bis(dimethylamino)naphthalene (bdn, `proton sponge') is used as a base, another square-grid network is generated, i.e. [Hbdn]2[Cu2(Hhba)2(hba)2(H2O)2]·3(dioxane)·H2O, but with only the copper dimer complex serving as a 4-connecting node. Complex three-dimensional networks are formed in [Cu2(Hhba)4(O-bipy)]·H2O and [Cu2(Hhba)4(O-bipy)2]·2(dioxane), where the potentially bridging 4,4'-bipyridine N,N'-dioxide (O-bipy) ligand is employed. Rare cases of mixed carboxylate copper dimer complexes were obtained in the cases of [Cu2(Hhba)3(OAc)(dioxane)]·3.5(dioxane) and [Cu2(Hhba)2(OAc)2(DABCO)2]·10(dioxane), with each structure possessing a 2D network structure. The final compound reported is a simple hydrogen-bonded chain of composition (H0.5DABCO)(H1.5hba), formed from the reaction of H2hba and DABCO.

Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method.

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of l-pyroglutamine-ammonium, comparing it with the related nonfluorescent amino acid l-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthermore, due to its inherent low computational cost, this method allows for a better sampling of the nonradiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials, and non-aromatic proteins.

Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site.

A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.

Kristjánite, KNa2H(SO4)2, a new fumarolic mineral from Iceland containing the [SO4–H–SO4]3– anion in the crystal structure

Abstract Kristjánite, KNa2H(SO4)2, is a new mineral (IMA2022–131) found in a high-temperature fumarole on Fimmvörðuháls, Iceland. It is monoclinic, P21/n, a = 6.9625(1), b = 9.9953(1), c = 11.0928(2) (Å), β = 105.637(2)° and V = 743.40(2) Å3. Kristjánite forms colourless transparent crystals up to ~100 μm in size in compact aggregates with metathénardite, belomarinaite, aphthitalite, ivsite and an unknown mineral with tentative composition K2NaH(SO4)2, or grows in white globules of smaller grains on their surface. The eight strongest maxima in a powder X-ray diffraction diagram are [d, Å (Intensity)] 4.37 (59), 3.65 (32), 3.48 (78), 3.36 (100), 3.18 (76), 2.83 (43), 2.73 (38) and 2.405 (23). The mineral represents a novel crystal structure type. In it, K is coordinated by eight O atoms, and two symmetrically independent Na atoms by seven O atoms. Two symmetrically independent S atoms are in tetrahedral coordination by O atoms. A close to linear, very short hydrogen bond (2.44 Å), connects the two to a SO4–H–SO4 dimer. K and Na coordination polyhedra share vertices, edges and even faces forming with sulfate tetrahedra a tight structure with narrow [100] channels lined on two opposite sides by hydrogen bonds.

L-Cysteine oxalates with dimeric and trimeric cations

Single crystals of two new compounds, (l-CysH···l-Cys)(HC2O4) (I) and (l-CysH···l-Cys···l-CysH)(HC2O4)2·0.5H2O (II), were obtained. Crystal structures were solved and refined using single-crystal X-ray diffraction, and compared with the previously known orthorhombic and monoclinic modifications of the simple salt (l-CysH)(HC2O4). Compound (I) crystallizes in the triclinic crystal system (space group P1, Z=2) and contains (l-CysH···l-Cys) dimeric cations with very short O···O interatomic distance of 2.434(2) Å. Hydrogen oxalate anions form head-to-tail type chains with very short hydrogen bonds, characterized by O···O distances of 2.422(2) Å and 2.417(3) Å. The crystal lattice of (II) is monoclinic with the space group C2, Z=4. It contains a new type of cation, that has never been observed before for cysteine salts, i.e. trimeric (l-CysH···l-Cys···l-CysH) cation. Protonated l-cysteinium cations are connected to the zwitterionic l-cysteine moiety through the same oxygen atom of the carboxylate group via hydrogen bonds, with O···O distances of 2.6410(18) Å and 2.4888(19) Å. Similar to the structure (I), the hydrogen oxalate anions form head-to-tail type chains linked by short hydrogen bonds with O···O distances of 2.4369(17) Å and 2.4330(17) Å, respectively. The crystals were characterized by IR and Raman spectroscopy. The batches obtained on crystallization were also characterized by X-ray powder diffraction, in order to check the phase purity of all the sample.

Augmentation of inductive effects through short range intramolecular hydrogen bonds for the improvement of cooperativity of trimeric rosettes

Three key design elements improve the binding strength of trimeric rosettes: the direction of hydrogen bonds, the addition of groups with inductive effects, and the presence of ambifunctional intramolecular hydrogen bonds between the substituents.

Identification of natural antimicrobial peptides mimetic to inhibit Ca2+ influx DDX3X activity for blocking dengue viral infectivity.

Viruses are microscopic biological entities that can quickly invade and multiply in a living organism. Each year, over 36,000 people die and nearly 400 million are infected with the dengue virus (DENV). Despite dengue being an endemic disease, no targeted and effective antiviral peptide resource is available against the dengue species. Antiviral peptides (AVPs) have shown tremendous ability to fight against different viruses. Accelerating antiviral drug discovery is crucial, particularly for RNA viruses. DDX3X, a vital cell component, supports viral translation and interacts with TRPV4, regulating viral RNA metabolism and infectivity. Its diverse signaling pathway makes it a potential therapeutic target. Our study focuses on inhibiting viral RNA translation by blocking the activity of the target gene and the TRPV4-mediated Ca2+ cation channel. Six major proteins from camel milk were first extracted and split with the enzyme pepsin. The antiviral properties were then analyzed using online bioinformatics programs, including AVPpred, Meta-iAVP, AMPfun, and ENNAVIA. The stability of the complex was assessed using MD simulation, MM/GBSA, and principal component analysis. Cytotoxicity evaluations were conducted using COPid and ToxinPred. The top ten AVPs, determined by optimal scores, were selected and saved for docking studies with the GalaxyPepDock tools. Bioinformatics analyses revealed that the peptides had very short hydrogen bond distances (1.8 to 3.6Å) near the active site of the target protein. Approximately 76% of the peptide residues were 5-11 amino acids long. Additionally, the identified peptide candidates exhibited desirable properties for potential therapeutic agents, including a net positive charge, moderate toxicity, hydrophilicity, and selectivity. In conclusion, this computational study provides promising insights for discovering peptide-based therapeutic agents against DENV.

Regioselective N-sulfonylation of 3-(methylthio)-1H-1,2,4-triazol-5-amine: Spectroscopic, thermal, crystal structure, and anticancer studies

We described a regioselective synthesis of two 1-(arylsulfonyl)-1H-1,2,4-triazol-5-amines 17 with good yields through a triethylamine-mediated N-sulfonylation reaction of 1H-1,2,4-triazol-5-amine 15 with arylsulfonyl chlorides 16 in dichloromethane at ambient temperature for 3 h. The N-heterocyclic sulfonamides 17 were characterized by spectroscopy, mass spectrometry, thermal analysis, and single crystal X-ray diffraction (SC-XRD). The SC-XRD analysis showed that compounds 17a and 17b have layered molecular structures, which are assembled through short hydrogen bonds involving N-H‧‧‧N, N-H‧‧‧O, C-H‧‧‧O, and C-H‧‧‧π, and interconnected by π‧‧‧π stacking interactions. For the two triazoles, electrostatic forces are the dominant attracting force within the molecular sheets, while dispersion forces play a more predominant role between the sheets. The packing arrangements were studied by crystallographic analysis and complementarily through computational calculations. Finally, these sulfonamides 17a and 17b demonstrated the most promising in vitro anticancer activity against the SNB-75 and UO-31 cell lines associated with the central nervous system and renal cancer, exhibiting moderate growth inhibition percentages of 18.7 % and 27.2 %, respectively.

Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond.

Multiple proton transfer (PT) controllable by external stimuli plays a crucial role in fundamental chemistry, biological activity, and material science. However, in crystalline systems, controlling multiple PT, which results in a distinct protonation state, remains challenging. In this study, we developed a novel tridentate ligand and iron(II) complex with a short hydrogen bond (HB) that exhibits a PT-coupled spin transition (PCST). Single-crystal X-ray and neutron diffraction measurements revealed that the positions of the two protons in the complex can be controlled by temperature and photoirradiation based on the thermal- and photoinduced PCST. The obtained results suggest that designing molecules that form short HBs is a promising approach for developing multiple PT systems in crystals.

Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds

There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.

Resistance profiles for the investigational neuraminidase inhibitor AV5080 in influenza A and B viruses

Neuraminidase inhibitors (NAIs) are recommended for influenza treatment and prevention worldwide. The most widely prescribed NAI is oral oseltamivir, while inhaled zanamivir is less commonly used. Using phenotypic neuraminidase (NA) enzymatic assays and molecular modeling approaches, we examined the ability of the investigational orally-dosed NAI AV5080 to inhibit viruses of the influenza A(H1N1)pdm09, A(H3N2), A(H5N1), and A(H7N9) subtypes and the influenza B/Victoria- and B/Yamagata-lineages containing NA substitutions conferring oseltamivir or zanamivir resistance including: NA-R292K, NA-E119G/V, NA-H274Y, NA-I122L/N, and NA-R150K. Broadly, AV5080 showed enhanced in vitro efficacy when compared with oseltamivir and/or zanamivir. Reduced AV5080 inhibition was determined for influenza A viruses with NA-E119G and NA-R292K, and for B/Victoria-lineage viruses with NA-I122N/L and B/Yamagata-lineage virus with NA-R150K. Molecular modeling suggested loss of the short hydrogen bond to the carboxyl group of AV5080 affected inhibition of NA-R292K viruses, whereas loss of the salt bridge with the guanidine group of AV5080 affected inhibition of NA-E119G. The resistance profiles and predicted binding modes of AV5080 and zanamivir are most similar, but dissimilar to those of oseltamivir, in part because of a guanidine moiety compensatory binding effect. Overall, our data suggests that AV5080 is a promising orally-dosed NAI that exhibited similar or superior in vitro efficacy against viruses with reduced or highly reduced inhibition phenotypes with respect to currently approved NAIs.

Experimental charge density and topological analysis of tetraaquabis(hydrogenmaleato)nickel(II): a comparison with Hirshfeld atom refinement.

Experimental charge density analysis is conducted on the coordination compound tetraaquabis(hydrogenmaleato)nickel(II), which exhibits a short intramolecular hydrogen bond. Through topological analysis, the nature of Ni-O bonds is concluded to be intermediate between ionic and covalent, but mainly presenting an ionic character, while the short hydrogen bond is classified as covalent in nature. The compound was also analysed after Hirshfeld atom refinement performed using NoSpherA2. A topological analysis was conducted on the molecular wavefunction and the results are compared with those obtained from experiment. In general, there is good agreement between the refinements, and the chemical bonds involving H atoms are in better agreement with what is expected from neutron data after HAR than they are after multipole refinement.