Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

Strain-Stiffening Mechanoresponse in Dynamic-Covalent Cellulose Hydrogels

Mechanical stimuli such as strain, force, and pressure are pervasive within and beyond the human body. Mechanoresponsive hydrogels have been engineered to undergo changes in their physicochemical or mechanical properties in response to such stimuli. Relevant responses can include strain-stiffening, self-healing, strain-dependent stress relaxation, and shear rate-dependent viscosity. These features are a direct result of dynamic bonds or noncovalent/physical interactions within such hydrogels. The contributions of various types of bonds and intermolecular interactions to these behaviors are important to more fully understand the resulting materials and engineer their mechanoresponsive features. Here, strain-stiffening in carboxymethylcellulose hydrogels cross-linked with pendant dynamic-covalent boronate esters using tannic acid is studied and modulated as a function of polymer concentration, temperature, and effective cross-link density. Furthermore, these materials are found to exhibit self-healing and strain-memory, as well as strain-dependent stress relaxation and shear rate-dependent changes in gel viscosity. These features are attributed to the dynamic nature of the boronate ester cross-links, interchain hydrogen bonding and bundling, or a combination of these two intermolecular interactions. This work provides insight into the interplay of such interactions in the context of mechanoresponsive behaviors, particularly informing the design of hydrogels with tunable strain-stiffening. The multiresponsive and tunable nature of this hydrogel system therefore presents a promising platform for a variety of applications.

Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline

The role of short strong hydrogen bonds (SSHBs) in ligand-target binding remains largely unexplored, thereby hindering a potentially important avenue in rational drug design. Here we investigate the interaction between the antituberculosis drug bedaquiline (Bq) and the mycobacterial ATP synthase to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity. Our ab initio molecular dynamics simulations reveal that this bond belongs to the SSHB category and accounts for a substantial fraction of the target binding free energy. We also demonstrate that the presence of an extra acidic residue, i.e., aspartic acid at position 32 (D32), found exclusively in mycobacteria, cooperatively enhances the HB strength, ensuring specificity for the mycobacterial target. Consistently, we show that the removal of D32 markedly weakens the affinity, leading to Bq resistance associated with mutations of D32 to nonacidic residues. By designing simple Bq analogs, we then explore the possibility to overcome the resistance and potentially broaden the Bq antimicrobial spectrum by making the SSHB independent of the presence of the extra acidic residue.

A Supramolecular Injectable Methacryloyl Chitosan-Tricine-Based Hydrogel with 3D Printing Potential for Tissue Engineering Applications

Printable hydrogels have attracted significant attention as versatile, tunable, and spatiotemporally controlled biomaterials for tissue engineering (TE) applications. Several chitosan-based systems are reported presenting low or no solubility in aqueous solutions at physiological pH. Herein, a novel neutrally charged, biomimetic, injectable, and cytocompatible dual-crosslinked (DC) hydrogel system based on a double functionalized chitosan (CHT) with methacryloyl and tricine moieties (CHTMA-Tricine), completely processable at physiological pH, with promising three-dimensional (3D) printing potential is presented. Tricine, an amino acid typically used in biomedicine, is capable of establishing supramolecular interactions (H-bonds) and is never explored as a hydrogel component for TE. CHTMA-Tricine hydrogels demonstrate significantly greater toughness (ranging from 656.5 ± 82.2 to 1067.5 ± 121.5 kJ m-3 ) compared to CHTMA hydrogels (ranging from 382.4 ± 44.1 to 680.8 ± 104.5 kJ m-3 ), highlighting the contribution of the supramolecular interactions for the overall reinforced 3D structure provided by tricine moieties. Cytocompatibility studies reveal that MC3T3-E1 pre-osteoblasts cells remain viable for 6 days when encapsulated in CHTMA-Tricine constructs, with semi-quantitative analysis showing ≈80% cell viability. This system's interesting viscoelastic properties allow the fabrication of multiple structures, which couple with a straightforward approach, will open doors for the design of advanced chitosan-based biomaterials through 3D bioprinting for TE.

Oxidation Chemistry of Bicarbonate and Peroxybicarbonate: Implications for Carbonate Management in Energy Storage

Carbonate formation presents a major challenge to energy storage applications based on low-temperature CO2 electrolysis and recyclable metal-air batteries. While direct electrochemical oxidation of (bi)carbonate represents a straightforward route for carbonate management, knowledge of the feasibility and mechanisms of direct oxidation is presently lacking. Herein, we report the isolation and characterization of the bis(triphenylphosphine)iminium salts of bicarbonate and peroxybicarbonate, thus enabling the examination of their oxidation chemistry. Infrared spectroelectrochemistry combined with time-resolved infrared spectroscopy reveals that the photoinduced oxidation of HCO3- by an Ir(III) photoreagent results in the generation of the short-lived bicarbonate radical in less than 50 ns. The highly acidic bicarbonate radical undergoes proton transfer with HCO3- to furnish the carbonate radical anion and H2CO3, leading to the eventual release of CO2 and H2O, thus accounting for the appearance of H2O and CO2 in both electrochemical and photochemical oxidation experiments. The back reaction of the carbonate radical subsequently oxidizes the Ir(II) photoreagent, leading to carbonate. In the absence of this back reaction, dimerization of the carbonate radical provides entry into peroxybicarbonate, which we show undergoes facile oxidation to O2 and CO2. Together, the results reported identify tangible pathways for the design of catalysts for the management of carbonate in energy storage applications.

Interaction between hydrophobic chitosan derivative and asphaltene in heavy oil to reduce viscosity of heavy oil

The high viscosity of heavy oil made it difficult to exploit and transport heavy oil in pipeline. In this research, N-[(2-hydroxy-3-trimethylammonium) propyl] O-stearoyl chitosan tetraphenylboride (sc-CTS-st) was synthesized from chitosan, 2, 3-epoxy-propyl trimethyl ammonium chloride, sodium tetraphenylboron and stearyl chloride. sc-CTS-st contains long chain saturated aliphatic hydrocarbon, hydroxyl group and benzene ring, which could be dissolved in heavy oil fully and interacted with asphaltene. At 50 °C, the viscosity of heavy oil could be reduced to 13,800 mPa·s at most, with a viscosity reduction rate of 57.54 %. SEM and XRD showed that sc-CTS-st could affect the supramolecular accumulation structure of asphaltenes. Using FT-IR, sc-CTS-st could interact with asphaltene in the form of hydrogen bonds using the polar parts of the molecule, thereby weakening the self-association between asphaltene molecules. Molecular simulation was used to demonstrate the interaction mechanism between chitosan derivatives and asphaltenes. sc-CTS-st interacted with asphaltene through chemical bonding and influenced the self-association of asphaltene molecules. In addition, the non-polar portion of sc-CTS-st molecules could form a coating on the outside of the asphaltenes stacking structure, thus shielding or reducing the polarity of the stacking structure surface.

Structural Insights into the Stability and Recognition Mechanism of the Antiquinalphos Nanobody for the Detection of Quinalphos in Foods

Nanobodies (Nbs) have great potential in immunoassays due to their exceptional physicochemical properties. With the immortal nature of Nbs and the ability to manipulate their structures using protein engineering, it will become increasingly valuable to understand what structural features of Nbs drive high stability, affinity, and selectivity. Here, we employed an anti-quinalphos Nb as a model to illustrate the structural basis of Nbs' distinctive physicochemical properties and the recognition mechanism. The results indicated that the Nb-11A-ligand complexes exhibit a "tunnel" binding mode formed by CDR1, CDR2, and FR3. The orientation and hydrophobicity of small ligands are the primary determinants of their diverse affinities to Nb-11A. In addition, the primary factors contributing to Nb-11A's limited stability at high temperatures and in organic solvents are the rearrangement of the hydrogen bonding network and the enlargement of the binding cavity. Importantly, Ala 97 and Ala 34 at the active cavity's bottom and Arg 29 and Leu 73 at its entrance play vital roles in hapten recognition, which were further confirmed by mutant Nb-F3. Thus, our findings contribute to a deeper understanding of the recognition and stability mechanisms of anti-hapten Nbs and shed new light on the rational design of novel haptens and directed evolution to produce high-performance antibodies.

Nanoconfinement enabled non-covalently decorated MXene membranes for ion-sieving

Covalent modification is commonly used to tune the channel size and functionality of 2D membranes. However, common synthesis strategies used to produce such modifications are known to disrupt the structure of the membranes. Herein, we report less intrusive yet equally effective non-covalent modifications on Ti₃C₂T_x MXene membranes by a solvent treatment, where the channels are robustly decorated by protic solvents via hydrogen bond network. The densely functionalized (-O, -F, -OH) Ti₃C₂T_x channel allows multiple hydrogen bond establishment and its sub-1-nm size induces a nanoconfinement effect to greatly strengthen these interactions by maintaining solvent-MXene distance and solvent orientation. In sub-1-nm ion sieving and separation, as-decorated membranes exhibit stable ion rejection, and proton-cation (H⁺/Mⁿ⁺) selectivity that is up to 50 times and 30 times, respectively, higher than that of pristine membranes. It demonstrates the feasibility of non-covalent methods as a broad modification alternative for nanochannels integrated in energy-, resource- and environment-related applications.

Functional System Based on Glycyrrhizic Acid Supramolecular Hydrogel: Toward Polymorph Control, Stabilization, and Controlled Release

Developments of a drug delivery system (DDS) based on a natural supramolecular hydrogel have been of wide interest due to its biocompatibility, efficacy, and adjustable performance. However, a simple and efficient design of functional hydrogel DDS based on the templated interplay of gelator and model drug is still a challenge. In this work, natural glycyrrhetinic acid (GA) gel was selected as a carrier to encapsulate the model drug pyrazinamide (PZA). It was found that the carboxyl-amide interaction at the interface of gel-drug achieved polymorph control, stabilization, and pH-responsive release. Powder X-ray diffraction confirmed that the metastable γ form of PZA was obtained from the GA gel. Spectral analysis and molecular dynamics simulation showed that the protonation at the amide-O promoted the discretization of PZA molecules in solution, resulting in the polymorphism. Furthermore, the gel-drug interplay increased the stability of the γ form significantly from 2 days to 3 months by in situ encapsulation in the GA gel. In vitro release study indicated that the GA gel achieved targeted control release of PZA due to the pH-responsiveness property of GA. This work provides a promising option for hydrogel-based DDS design combined with polymorph control and stabilization.

Interlayer spacing in pillared and grafted MCM-22 type silicas: density functional theory analysis versus experiment

Pillaring of synthetic layered crystalline silicates and aluminosilicates provides a strategy to enhance their adsorption and separation performance, and can facilitate the understanding of such behavior in more complex natural clays. We perform the first-principles density functional theory calculations for the pillaring of the pure silica polymorph of an MCM-22 type molecular sieve. Starting with a precursor material MCM-22P with fully hydroxylated layers, a pillaring agent, (EtO)₃SiR, can react with hydroxyl groups (-OH) on adjacent internal surfaces, 2(-OH) + (EtO)₃SiR + H₂O → (-O)₂SiOHR + 3EtOH, to form a pillar bridging these surfaces, or with a single hydroxyl, -OH + (EtO)₃SiR + 2H₂O → (-O)Si(OH)₂R + 3EtOH, grafting to one surface. For computational efficiency, we replace the experimental organic ligand, R, by a methyl group. We find that the interlayer spacing in MCM-22 is reduced by 2.66 Å relative to weakly bound layers in the precursor MCM-22P. Including (-O)₂SiR bridges for 50% (100%) of the hydroxyl sites in MCM-22P increases the interlayer spacing relative to MCM-22 by 2.52 Å (2.46 Å). For comparison, we also analyze the system where all -OH groups in MCM-22P are replaced by non-bridging grafted (-O)Si(OH)₂R which results in a smaller interlayer spacing expansion of 2.17 Å relative to MCM-22. Our results for the interlayer spacing in the pillared materials are compatible with experimental observations for a similar MCM-22 type material with low Al content (Si : Al = 51 : 1) of an expansion relative to MCM-22 of roughly 2.8 Å and 2.5 Å from our x-ray diffraction and scanning transmission electron microscopy analyses, respectively. The latter analysis reveals significant variation in individual layer spacings.

N-Cyano sulfilimine functional group as a nonclassical amide bond bioisostere in the design of a potent analogue to anthranilic diamide insecticide

To explore the potential of the N-cyano sulfilimine group as an amide bond isostere, a derivative of the blockbuster anthranilic diamide, chlorantramiliprole, was synthesized and evaluated with regard to its physicochemical properties, permeability, and biological activity. Given the combination of N-cyano sulfilimine chlorantraniliprole 1 and its strong hydrogen bond acceptor character, high permeability, and excellent insecticidal activity, the N-cyano sulfilimine functional group could be considered as an amide bond isostere.

Crystallographic Mapping and Tuning of Water Adsorption in Metal-Organic Frameworks Featuring Distinct Open Metal Sites

Crucial steps toward designing water sorption materials and fine-tuning their properties for specific applications include precise identification of adsorption sites and establishment of rigorous molecular-level insight into the water adsorption process. We report stepwise crystallographic mapping and density functional theory computations of adsorbed water molecules in ALP-MOF-1, a metal-organic framework decorated with distinct open metal sites and carbonyl functional groups that serve as water anchoring sites for seeding the nucleation of a complex water network. Identification of an unusual water adsorption step in ALP-MOF-1 motivated the tuning of metal ion composition to adjust water uptake. These studies provide direct evidence that the identity of the open metal sites in MOFs can dramatically affect water adsorption behavior between 0 and ∼20% RH and that multiple proximal water anchoring sites along the MOF skeleton facilitate water uptake which could be potentially useful for applications requiring rapid and energetically facile water sorption.

Intermolecular Hydrogen-Bond-Assisted Solid-State Dual-Emission Molecules with Mechanical Force-Induced Enhanced Emission

Hydrogen bonds not only play a crucial role in the life sciences but also endow molecules with fantastic physical and chemical properties, which help in the realization of their high-tech applications. This work presents an efficient strategy for achieving highly efficient solid-state dual-emission blue emitters with mechanical force-induced enhanced emission properties via intermolecular hydrogen bonds via novel pyrene-based intermediates, namely, 1,3,6,8-tetrabromo-2,7-dihydroxypyrene (1) and 1,3,6,8-tetrabromo-2-hydroxypyrene (2), prepared via hydroxylation and bromination of pyrene in high yields. Moreover, further use of a classical Pd-catalyzed coupling reaction affords new pyrene-based luminescent materials 3-5, which display high thermal stability (in range of 336-447 °C), blue emission (<463 nm), and high quantum yields in solution. Interestingly, with the monosubstituted hydroxyl (OH) or methoxy (OMe) group located at position 2 of pyrene, compounds 4a and 5 display exciting dual emission with mechanical force-induced enhanced emission properties, due to the presence of several hydrogen-bond interactions. Moreover, this series of compounds exhibits numerous advantages, for example, deeper blue emission with a narrower full width at half-maximum, a stronger steric effect, and higher hydrophilicity. Thus, these novel bromopyrene intermediates and related pyrene-based luminescent materials will pave the way for further exploration of novel organic solid-state luminescent materials for potential application in organic electronics, bioimaging, chemosensors, etc.

MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations

The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the accuracy. We present a new extrapolatable and explainable molecular representation based on bonds, angles and dihedrals that can be used to train machine learning models. The trained models can accurately predict the electronic energy and the free energy of small organic molecules with atom types C, H N and O, with a mean absolute error of 1.2 kcal mol-1. The models can be extrapolated to larger organic molecules with an average error of less than 3.7 kcal mol-1 for 10 or fewer heavy atoms, which represent a chemical space two orders of magnitude larger. The rapid energy predictions of multiple molecules, up to 7 times faster than previous ML models of similar accuracy, has been achieved by sampling geometries around the potential energy surface minima. Therefore, the input geometries do not have to be located precisely on the minima and we show that accurate density functional theory energy predictions can be made from force-field optimised geometries with a mean absolute error 2.5 kcal mol-1.

Single-Molecule Classification of Aspartic Acid and Leucine by Molecular Recognition through Hydrogen Bonding and Time-Series Analysis

Amino acid detection/identification methods are important for understanding biological systems. In this study, we developed the single-molecule measurement for investigated quantum tunneling enhancement by chemical modification and machine learning based time series analysis for develop accurate amino acid discrimination. We performed single-molecule measurement of L-aspartic Acid (Asp) and L-leucine (Leu) with mercaptoacetic acid (MAA) chemical modified nano-gap. The measured current was investigated by machine learning based time series analysis method for accurate amino acid discrimination. Compared to measurements using bare nano-gap, it is found that MAA modification improves the difference in the conductance-time profiles between Asp and Leu through the hydrogen bonding facilitated tunneling phenomena. It is also found that this method enables determination of relative concentration. even in the mixture of Asp and Leu. It improves selective analysis for amino acids, and therefore would be applicable in medicine, diagnosis, and single-molecule peptide sequencing.

Isotope Effects on Chemical Shifts in the Study of Hydrogen Bonds in Small Molecules

This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on chemical shifts can be used to elucidate the importance of either intra- or intermolecular hydrogen bonding in ionic liquids, of ammonium ions in a confined space, how isotope effects can help define dimers, trimers, etc., how isotope effects can lead to structural parameters such as distances and give information about ion pairing. Tautomerism is by advantage investigated by isotope effects on chemical shifts both in symmetric and asymmetric systems. The relationship between hydrogen bond energies and two-bond deuterium isotope effects on chemical shifts is described. Finally, theoretical calculations to obtain isotope effects on chemical shifts are looked into.

AutoSolvate: A toolkit for automating quantum chemistry design and discovery of solvated molecules

The availability of large, high-quality datasets is crucial for artificial intelligence design and discovery in chemistry. Despite the essential roles of solvents in chemistry, the rapid computational dataset generation of solution-phase molecular properties at the quantum mechanical level of theory was previously hampered by the complicated simulation procedure. Software toolkits that can automate the procedure to set up high-throughput explicit-solvent quantum chemistry (QC) calculations for arbitrary solutes and solvents in an open-source framework are still lacking. We developed AutoSolvate, an open-source toolkit, to streamline the workflow for QC calculation of explicitly solvated molecules. It automates the solvated-structure generation, force field fitting, configuration sampling, and the final extraction of microsolvated cluster structures that QC packages can readily use to predict molecular properties of interest. AutoSolvate is available through both a command line interface and a graphical user interface, making it accessible to the broader scientific community. To improve the quality of the initial structures generated by AutoSolvate, we investigated the dependence of solute-solvent closeness on solute/solvent identities and trained a machine learning model to predict the closeness and guide initial structure generation. Finally, we tested the capability of AutoSolvate for rapid dataset curation by calculating the outer-sphere reorganization energy of a large dataset of 166 redox couples, which demonstrated the promise of the AutoSolvate package for chemical discovery efforts.

C-phycocyanin decreases proliferation and migration of melanoma cells: In silico and in vitro evidences

The incidence and number of deaths caused by melanoma have been increasing in recent years, and the pigment C-phycocyanin (C-PC) appears as a possible alternative to treat this disease. So, the objective of this study was to combine in silico and in vitro analysis to understand the main anti-melanoma pathways exerted by C-PC. We evaluated the ability of C-PC to bind to the main cellular targets related in the progression of melanoma through molecular docking, and the reflection of this bind in the biological effects in the B16F10 cell line through in vitro analysis. Our results showed that C-PC was able to bind BRAF and MEK, which are related to the signal transduction pathway for proliferation and survival. There was also an interaction between C-PC and cyclin-dependent kinase 4 and 6. In vitro analysis demonstrated that C-PC decreased B16F10 cell proliferation, as observed by cell viability and mitotic index assays. C-PC also interacted with matrix metalloproteinase 2 and 9 and N-cadherin, which may have caused the decrease in cell migration observed in vitro. Besides that, C-PC interacts with VEGF, a factor responsible for regulating the proliferation and cellular invasion pathways. Finally, C-PC did not alter the cell viability of the non-tumoral melanocytes. Therefore, C-PC is a strong anti-tumor candidate for the treatment of melanoma, since it acts in different cellular pathways of melanoma, without causing damage to non-tumoral cells.

Liquid-cell transmission electron microscopy for imaging of thermosensitive recombinant polymers

Various polymers used in controlled release applications exhibit solution-based thermal responses. Unfortunately, very few characterization and imaging techniques permit resolution of individual polymers during their thermally-triggered phase transitions. Here, we demonstrate the use of temperature-ramp liquid-cell transmission electron microscopy (LCTEM) for real-time evaluation of the solution and interfacial behavior of elastinlike polypeptides (ELPs) and their self-assembled nanostructures over a temperature range incorporating their intrinsic lower critical solution temperatures (LCSTs). Individual polymers and supramolecular assemblies were discriminated dependent upon solubility states. The recombinant polymers were shown to adsorb to the silicon-nitride chip window from the buffered saline solution and desorb in a temperature-dependent manner. Silk-elastinlike protein block copolymers (SELPs) (composed of repeat peptide motifs of silk and elastin) differed from ELPs in thermal behavior. While both polymers were shown to cluster, only SELPs formed robust amyloid-like fibers upon heating.

Role of hydrogen bonding in bulk aqueous phase decomposition, complexation, and covalent hydration of pyruvic acid

The behavior of hydrogen bonding changes between the gas and aqueous phase, altering the mechanisms of various pyruvic acid processes and consequently affecting the aerosol formation in different environments.

Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase

The Asp233-Asp246 pair is highly conserved in Class A β-lactamases, which hydrolyze β-lactam antibiotics. Here, we characterize its function using CTX-M-14 β-lactamase. The D233N mutant displayed decreased activity that is substrate-dependent, with reductions in k_cat /K_m ranging from 20% for nitrocefin to 6-fold for cefotaxime. In comparison, the mutation reduced the binding of a known reversible inhibitor by 10-fold. The mutant structures showed movement of the 213-219 loop and the loss of the Thr216-Thr235 hydrogen bond, which was restored by inhibitor binding. Mutagenesis of Thr216 further highlighted its contribution to CTX-M activity. These results demonstrate the importance of the aspartate pair to CTX-M hydrolysis of substrates with bulky side chains, while suggesting increased protein flexibility as a means to evolve drug resistance.

Combined NMR and UV-Vis Spectroscopic Studies of Models for the Hydrogen Bond System in the Active Site of Photoactive Yellow Protein: H-Bond Cooperativity and Medium Effects

Intramolecular hydrogen bonds in aprotic media were studied by combined (simultaneous) NMR and UV-vis spectroscopy. The species under investigation were anionic and featured single or coupled H-bonds between, for example, carboxylic groups and phenolic oxygen atoms (COO···H···OC)^-, among phenolic oxygen atoms (CO···H···OC)^-, and hydrogen bond chains between a carboxylic group and two phenolic oxygen atoms (COO···H···(OC)···H···OC)^-. The last anion may be regarded as a small molecule model for the hydrogen bond system in the active site of wild-type photoactive yellow protein (PYP) while the others mimic the corresponding H-bonds in site-selective mutants. Proton positions in isolated hydrogen bonds and hydrogen bond chains were assessed by calculations for vacuum conditions and spectroscopically for the two media, CD₂Cl₂ and the liquefied gas mixture CDClF₂/CDF₃ at low temperatures. NMR parameters allow for the estimation of time-averaged H-bond geometries, and optical spectra give additional information about geometry distributions. Comparison of the results from the various systems revealed the effects of the formation of hydrogen bond chains and changes of medium conditions on the geometry of individual H-bonds. In particular, the proton in a hydrogen bond to a carboxylic group shifts from the phenolic oxygen atom in the system COO^-···H-OC to the carboxylic group in COO-H···(OC)^-···H-OC as a result of hydrogen bond formation to the additional phenolic donor. Increase in medium polarity may, however, induce the conversion of a structure of a type COO-H···(OC)^-···H-OC to the type COO^-···H-(OC)···H-OC. Application of these results obtained from the model systems to PYP suggests that both cooperative effects within the hydrogen bond chain and a low-polarity protein environment are prerequisites for the stabilization of negative charge on the cofactor and hence for the spectral tuning of the photoreceptor.

Molecular simulation study of 3,4-dihydroxyphenylalanine in the context of underwater adhesive design

Adhesives that can stick to multiple surface types in underwater and high moisture conditions are critical for various applications such as marine coatings, sealants, and medical devices. The analysis of natural underwater adhesives shows that L-3,4-dihydroxyphenylalanine (DOPA) and functional amyloid nanostructures are key components that contribute to the adhesive powers of these natural glues. The combination of DOPA and amyloid-forming peptides into DOPA-amyloid(-forming peptide) conjugates provides a new approach to design generic underwater adhesives. However, it remains unclear how the DOPA monomers may interact with amyloid-forming peptides and how these interactions may influence the adhesive ability of the conjugates. In this paper, we investigate the behavior of DOPA monomers, (glycine-DOPA)₃ chains, and a KLVFFAE and DOPA-glycine chain conjugate in aqueous environments using molecular simulations. The DOPA monomers do not aggregate significantly at concentrations lower than 1.0M. Simulations of (glycine-DOPA)₃ chains in water were done to examine the intra-molecular interactions of the chain, wherein we found that there were unlikely to be interactions detrimental to the adhesion process. After combining the alternating DOPA-glycine chain with the amyloid-forming peptide KLVFFAE into a single chain conjugate, we then simulated the conjugate in water and saw the possibility of both intra-chain folding and no chain folding in the conjugate.

Low barrier hydrogen bonds in protein structure and function

Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme's reaction cycle. To examine positioning and motions and test catalytic proposals, we collected "room temperature" X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI's reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI's general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure-function relationships, providing the basis for a new era of "ensemble-function" interrogation of enzymes.

Symmetry/Asymmetry of the NHN Hydrogen Bond in Protonated 1,8-Bis(dimethylamino)naphthalene

Experimental and theoretical results are presented based on vibrational spectra and motional dynamics of 1,8-bis(dimethylamino)naphthalene (DMAN) and its protonated forms (DMANH+ and the DMANH+ HSO4− complex). The studies of these compounds have been performed in the gas phase and solid-state. Spectroscopic investigations were carried out by infrared spectroscopy (IR), Raman, and incoherent inelastic neutron scattering (IINS) experimental methods. Density functional theory (DFT) and Car–Parrinello molecular dynamics (CPMD) methods were applied to support our experimental findings. The fundamental investigations of hydrogen bridge vibrations were accomplished on the basis of isotopic substitutions (NH → ND). Special attention was paid to the bridged proton dynamics in the DMANH+ complex, which was found to be affected by interactions with the HSO4− anion.

Absolute configuration of four chiral isomers of pyrisoxazole and their bioactivity

BACKGROUND

Pyrisoxazole is a fungicide that has two chiral carbon atoms and four isomers: (3S,5R)-, (3R,5S)-, (3S,5S)-, and (3R,5R)-pyrisoxazole.

RESULTS

Pure crystals of four pyrisoxazole isomers were prepared by chiral separation and single-crystal cultivation. Their absolute configurations were established by X-ray single crystal diffraction analysis. Bioassays indicated that compound (3S,5R)-pyrisoxazole showed excellent fungicidal activity with a median effective concentration (EC₅₀ ) value of 0.14 μg mL^-1 and protective activity with an EC₅₀ value of 13.29 μg mL^-1 . These values are superior to the commercial fungicides boscalid and racemic pyrisoxazole.

CONCLUSIONS

The biological activity of racemic pyrisoxazole is due almost exclusively to the isomer (3S,5R)-pyrisoxazole; the other three isomers had very low activity. © 2020 Society of Chemical Industry.

Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein

Neutron crystallography has been used to elucidate the protonation states for the enhanced green fluorescent protein, which has revolutionized imaging technologies. The structure has a deprotonated hydroxyl group in the fluorescent chromophore. Also, the protonation states of His148 and Thr203, as well as the orientation of a critical water molecule in direct contact with the chromophore, could be determined. The results demonstrate that the deprotonated hydroxyl group in the chromophore and the nitrogen atom ND1 in His148 are charged negatively and positively, respectively, forming an ion pair. The position of the two deuterium atoms in the critical water molecule appears to be displaced slightly toward the acceptor oxygen atoms according to their omit maps. This displacement implies the formation of an intriguing electrostatic potential realized inside of the protein. Our findings provide new insights into future protein design strategies along with developments in quantum chemical calculations.

Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects

Electronic and nuclear quantum effects determine the symmetry and highly downfield ¹H NMR chemical shifts of short hydrogen bonds.

Unraveling the structural and chemical features of biological short hydrogen bonds

Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.

The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.

Stereochemical Revision, Total Synthesis, and Solution State Conformation of the Complex Chlorosulfolipid Mytilipin B

Chlorosulfolipids constitute a structurally intriguing and synthetically challenging class of marine natural products that are isolated from mussels and freshwater algae. The most complex structure from this family of compounds is currently represented by Mytilipin B, isolated in 2002 from culinary mussel Mytilus galloprovincialis, whose initially proposed structure was shown to be incorrect. In this study, we present the synthesis of four diastereomers which allowed the reassignment of eight stereocenters and the stereochemical revision of Mytilipin B, along with the determination of the dominant solution-state conformation.

Hydrogen Bonds: Simple after All?

Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.

Energy Transfer to the Hydrogen Bond in the (H2O)2 + H2O Collision

Trajectory procedures are used to study the collision between the vibrationally excited H₂O and the ground-state (H₂O)₂ with particular reference to energy transfer to the hydrogen bond through the inter- and intramolecular pathways. In nearly 98% of the trajectories, energy transfer processes occur on a subpicosecond scale (≤0.7 ps). The H₂O transfers approximately three-quarters of its excitation energy to the OH stretches of the dimer. The first step of the intramolecular pathway in the dimer involves a near-resonant first overtone transition from the OH stretch to the bending mode. The energy transfer probability in the presence of the 1:2 resonance is 0.61 at 300 K. The bending mode then redistributes its energy to low-frequency intermolecular vibrations in a series of small excitation steps, with the pathway which results in the hydrogen-bonding modes gaining most of the available energy. The hydrogen bonding in ∼50% of the trajectories ruptures on vibrational excitation, leaving one quantum in the bend of the monomer fragment. In a small fraction of trajectories, the duration of collision is longer than 1 ps, during which the dimer and H₂O form a short-lived complex through a secondary hydrogen bond, which undergoes large amplitude oscillations.

Fragment-growing guided design of Keap1-Nrf2 protein-protein interaction inhibitors for targeting myocarditis

Small-molecule inhibitors that block the Keap1-Nrf2 protein-protein interactions are being intensely pursued as a new therapeutic strategy for oxidative stress-related diseases, such as cancer, diabetes, Alzheimer's disease, arteriosclerosis, inflammation and myocarditis. However, there are not enough studies on antioxidant treatments using small molecules in myocarditis. We herein provided a series of novel hydronaphthoquinones as the Keap1-Nrf2 interaction inhibitors targeting LPS-induced myocarditis both in vitro and in vivo. These compounds were designed through an in-silico fragment growing approach based on our previous reported compound, S47 (1). The new compounds were predicted to form additional hydrogen bonds with the S363 residue, leading to higher inhibitory activity. Among these new derivatives, compounds S01 and S05 emerged as inhibitors with significant biochemical potency, as determined by fluorescent anisotropy assay and confirmed by surface plasmon resonance (SPR) and differential scanning fluorimetry (DSF) assays. These inhibitors can dose-dependently protect the H9c2 cardiac cells against LPS-induced injury (100% at 2 μM and 4 μM) and effectively prolong survival or save the life of LPS-injured mice. Mechanistic studies showed that these inhibitors could release Nrf2 in H9c2 cells and LPS-inflammatory mouse models and translocate into the nucleus in a dose-response manner, which significantly increased the downstream genes (HO-1, NQO-1) and the pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), while ROS production dramatically decreased. Their protective effects and the mechanism of action were further confirmed by siNrf2 transfected experiment. Collectively, the novel hydronaphthoquinones can be used as promising lead compounds for the study of Keap1-Nrf2 protein-protein interactions and further anti-myocarditis drug development.

Dielectric Properties of a Protein Probed by Reversal of a Buried Ion Pair

Thirty years ago, Hwang and Warshel suggested that a microenvironment preorganized to stabilize an ion pair would be incapable of reorganizing to stabilize the reverse ion pair. The implications were that (1) proteins have a limited capacity to reorganize, even under the influence of strong interactions, such as those present when ionizable groups are buried in the hydrophobic interior of a protein, and (2) the inability of proteins to tolerate the reversal of buried ion pairs demonstrates the limitations inherent to continuum electrostatic models of proteins. Previously we showed that when buried individually in the interior of staphylococcal nuclease, Glu23 and Lys36 have p K_a values near pH 7, but when buried simultaneously, they establish a strong interaction of ∼5 kcal/mol and have p K_a values shifted toward more normal values. Here, using equilibrium thermodynamic measurements, crystal structures, and NMR spectroscopy experiments, we show that although the reversed, individual substitutions-Lys23 and Glu36-also have p K_a values near 7, when buried together, they neither establish a strong interaction nor promote reorganization of their microenvironment. These experiments both confirm Warshel's original hypothesis and expand it by showing that it applies to reorganization, as demonstrated by our artificial ion pairs, as well as to preorganization as is commonly argued for motifs that stabilize naturally occurring ion pairs in polar microenvironments. These data constitute a challenging benchmark useful to test the ability of structure-based algorithms to reproduce the compensation between self-energy, Coulomb and polar interactions in hydrophobic environments of proteins.

Exploring the ESIPT dynamical processes of two novel chromophores: symmetrical structure CHC and asymmetric structure CHN

The detailed ESIPT dynamical processes of CHC (symmetrical structure) and CHN (asymmetric structure) chromophores were revealed and compared using the TDDFT method at the B3LYP/6-31+G(d,p) level.

NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects). Limits for O-H···Y systems are taken as 2800 > νOH > 1800 cm-1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O-H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.

An Insight Into the Impact of Polymers on the Hydrate Conversion of Olanzapine Form I in Aqueous Suspensions

The potential of polyethyleneglycol (PEG), polyvinylpyrrolidone (PVP), and hydroxypropylcellulose (HPC) to inhibit the hydration of olanzapine (OLZ) in aqueous environments was assessed. OLZ Form I (OLZ) suspended in water (A) or in aqueous polymer solutions (2%, 0.2%, 0.02%, and 0.002%) (PEG 6000 [B], PEG 40,000 [C], HPC LF [D], or PVP K30 [E]). Filtered samples were analyzed by different techniques (X-ray powder diffraction, Fourier transform infrared spectroscopy, differential scanning calorimetry, ¹H-nuclear magnetic resonance spectroscopy). OLZ hydration showed to be faster in water than in PEG solutions, regardless of the polymer molecular weight. OLZ in D and E suspensions remained anhydrous at concentrations of 2%-0.02%. The NMR measurements revealed that all of these polymers were able to establish hydrogen bonds with the OLZ molecule and increased its saturation solubility, but only D and E showed to increase the wettability of the OLZ particles due to binding of these polymers to the surface of hydrate nuclei/first crystals OLZ crystals. This study provided an insight into the mechanisms of OLZ hydrate protection by polymers. It confirmed the advantage of using PVP K30 or HPC LF in wet granulation in concentrations as low as 0.02% to prevent formation of OLZ hydrates, due to the combined effect of H-bond ability and the strong bonding of these polymers to the surface of the crystals.

Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong

While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state ¹⁷ O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state ¹⁷ O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol^-1 , suggesting that not all LBHBs are particularly strong.