H-bonding Patterns Research Articles

Investigating the effect of water on collagen triple helix stability

Collagen provides essential structural support to diverse body tissues through its unique triple helix structure. Collagen stability is crucial for proper tissue function and any disruptions in its stability can lead to various health issues. Prior research has identified multiple factors affecting collagen stability. However, despite its fundamental presence in biological systems, the influence of water remains inadequately explored. Here, we performed molecular dynamics simulations on collagen model peptides (CMPs) with varying experimental stability profiles to investigate the influence of water on collagen stability. Our simulations revealed variations in both the hydrogen bonding (H-bonding) patterns between the CMPs and surrounding water molecules, as well as the water networks formed around CMPs. We noted that water molecules form H-bonds with collagen residues which enhance its structural stability. Additionally, water molecules assemble around the collagen and form topological water networks (TWNs) through intermolecular H-bonding. These TWNs further stabilizes the collagen structure. Overall, this research provides insight into the role of water molecules in preserving the stability of the collagen triple helix.

Bisphosphonium Benzene Diimides.

The incorporation of cationic groups onto electron-poor compounds is a viable strategy for achieving potent electron acceptors, as evidenced by reports of air-stable radical forms of large aromatic diimides such as naphthalene and perylene diimides. These ions have also been observed to exhibit anion-π interaction tendencies of interest in molecular recognition applications. The benefits of phosphonium incorporation, however, have not yet been extended to the smallest benzene diimides. Here, we report that dibrominated pyromellitic diimide and mellophanic diimide both readily undergo substitution reactions with phosphine sources to yield bisphosphonium compounds. In the single crystalline form, these dications display anion-π interactions and, in the case of mellophanic diimide, the stabilization of a bromide-water H-bonding ring pattern. The reaction of these dications with chemical reductants readily provides the singly and doubly reduced redox states, which were characterized by UV-vis spectroscopy and found to exhibit intense absorptions extending into the near-IR region. Taken together, this work demonstrates that phosphonium incorporation onto congested aromatic diimide scaffolds is synthetically viable and produces unusual electron-poor compounds.

Hydrogen bonding patterns and cooperativity in polyproline II helical bundles

Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies built by α-helices and β-sheets, the most common secondary structures. However, whether HBC exists in other types of protein secondary structures such as polyproline II (PPII) helices remains unexplored. This is intriguing, since PPII systems as assembling blocks are continuously emerging across multiple fields. Here, using a combination of computational chemistry tools and molecular modeling corroborated by experimental observables, we characterize the distinct H-bonding patterns present in PPII helical bundles and establish that HBC stabilizes intermolecular PPII helices as seen in other protein assemblies such as amyloid fibrils. In addition to cooperative interactions in canonical CO···HN H-bonds, we show that analogous interactions in non-canonical CO···HαCα H-bonds are relevant in Gly-rich PPII bundles, thus compensating for the inability of glycine residues to create hydrophobic cores. Our results provide a mechanistic explanation for the assembly of these bundles.

Variation of Activation Volume as an Indicator of the Difference in Clusterization Phenomenon Induced by H-Bonding and F-Π Stacking Interactions in Enantiomers and a Racemate of Flurbiprofen.

In this paper, X-ray diffraction (XRD), differential scanning calorimetry (DSC), broadband dielectric (BDS), and Fourier transform infrared (FTIR) spectroscopy supported by molecular dynamics (MD) simulations and quantum chemical computations were applied to investigate the structural and thermal properties, molecular dynamics, and H-bonding pattern of R-, S-, and RS-flurbiprofen (FLP). Experimental data indicated various spatial molecular arrangements in crystalline forms of examined systems, which seemed to disappear in the liquid state. Surprisingly, deeper analysis of high-pressure dielectric data revealed unexpected variation in the activation volume of pure enantiomers and a racemate. MD simulations showed that it is an effect of the clusterization phenomenon and a higher population of small associates in the former samples. Moreover, theoretical consideration exposed the particular role of unspecific F-Π interactions as a driving force underlying local molecular arrangements of molecules in the liquid and the crystal lattice of R-, S-, and RS-FLP.

Photochemistry of micro-solvated benzonitrile complexes with water/ammonia bordering on the formation of icy grains

Polycyclic aromatic hydrocarbons (PAHs) act as condensation nuclei for water/ammonia molecules forming icy water clusters. In the context of small aromatic rings, we have theoretically examined complexes of benzonitrile with water/ammonia molecules in order to investigate the photochemical kinetics of the icy grain formation. First, we obtain the structure of energetically stable complexes containing different H-bonding patterns and analyze their effects in the infrared (IR) and vacuum ultraviolet (VUV) spectra, before and after ionization. Second, we evaluate the H-bonding reorientation kinetics of the complexes at low temperatures, which indicates that the process involving water occurs faster than the corresponding process involving ammonia. Finally, the thermal rate constants indicate which configurations are the most likely to be ionized under vacuum ultraviolet (VUV) irradiation. Our results are consistent with what has experimentally been observed for related complexes, and are useful as a starting point to investigate the process of the icy grains formation. This study provides insight into possible subsequent photochemical reactions occurring in the interstellar medium (ISM) or in jet-cooled molecular complexes.

Urea-Functionalized Heterocycles: Structure, Hydrogen Bonding and Applications

Ureido-heterocycles exhibiting different triple- and quadruple H-bonding patterns are useful building blocks in the construction of supramolecular polymers, self-healing materials, stimuli-responsive devices, catalysts and sensors. The heterocyclic group may provide hydrogen bond donor/acceptor sites to supplement those in the urea core, and they can also bind metals and can be modified by pH, redox reactions or irradiation. In the present review, the main structural features of these derivatives are discussed, including the effect of tautomerization and conformational isomerism on self-assembly and complex formation. Some examples of their use as building blocks in different molecular architectures and supramolecular polymers, with special emphasis on biomedical applications, are presented. The role of the heterocyclic functionality in catalytic and sensory applications is also outlined.

New Benzamides as Multi-Targeted Compounds: A Study on Synthesis, AChE and BACE1 Inhibitory Activity and Molecular Docking.

The synthesis of eleven new and previously undescribed benzamides was designed. These compounds were specifically projected as potential inhibitors of the enzymes acetylcholinesterase (AChE) and β-secretase (BACE1). N,N'-(1,4-phenylene)bis(3-methoxybenzamide) was most active against AChE, with an inhibitory concentration of AChE IC50 = 0.056 µM, while the IC50 for donepezil was 0.046 µM. This compound was also the most active against the BACE1 enzyme. The IC50 value was 9.01 µM compared to that for quercetin, with IC50 = 4.89 µM. Quantitative results identified this derivative to be the most promising. Molecular modeling was performed to elucidate the potential mechanism of action of this compound. Dynamic simulations showed that new ligands only had a limited stabilizing effect on AChE, but all clearly reduced the flexibility of the enzyme. It can, therefore, be concluded that a possible mechanism of inhibition increases the stiffness and decreases the flexibility of the enzyme, which obviously impedes its proper function. An analysis of the H-bonding patterns suggests a different mechanism (from other ligands) when interacting the most active derivative with the enzyme.

Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine-Cytosine Base Pair.

In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine-cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

Atomic-level understanding on conformational flexibility of neochlorogenic and chlorogenic acids and their inclusion complexation with β-cyclodextrin

Neochlorogenic acid (NCA) and chlorogenic acid (CGA) are positional isomers, abundant in plums and prunes. Their limited bioavailability due to instability under ambient conditions can be overcome by cyclodexrin (CD) encapsulation. Here, single-crystal X-ray diffraction combined with density functional theory (DFT) calculation has been carried out on NCA in free form (1) and in complex with β-CD (2), providing atomic-level insights into the structural flexibility and the inclusion complexation with β-CD of CGA isomers. X-ray analysis revealed that the two symmetry-independent s-cis-NCA and 0.3 water molecules form elaborated H-bond networks (1). Upon β-CD encapsulation, complex H-bond patterns are disrupted and the converted s-trans-NCA is almost entirely enclosed in the asymmetric capsular β-CD dimer (2). On the contrary, the twofold symmetry-related β-CD–s-cis-CGA dimer forms a rare [4]pseudorotaxane reported previously. DFT full-geometry optimization disclosed that both the 2:1 and 1:1 trimodal β-CD–s-trans-NCA inclusion complexes are energetically stable, as the reported s-cis-CGA complex. Furthermore, the three-dimension potential energy surface (3D PES) profiles and all the DFT-fully optimized NCA and CGA structures existing in different lattice environments showed that both the s-cis and s-trans conformers are thermodynamically stable. This study not only presents crystallographic evidence for the distinct NCA and CGA conformers, unequivocally differentiating and resolving the long-time confusing CGA nomenclature for the first time, but also highlights the prime role of CGA conformational flexibility in their pharmacological functions.

Deciphering the Properties of Nanoconfined Aqueous Solutions by Vibrational Sum Frequency Generation Spectroscopy.

When confined between walls at nanometer distances, water exhibits surprisingly different properties with reference to bare interfacial water. Based on computer simulations, we demonstrate how vibrational sum frequency generation (VSFG) spectroscopy can be used-even with very mild symmetry breaking-to discriminate multilayer water in wide slit pores from both bilayer and monolayer water confined within molecularly narrow pores. Applying the technique, the VSFG lineshapes of monolayer, bilayer, and multilayer water are found to differ in characteristic ways, which is explained by their distinct density stratifications giving rise to different H-bonding patterns in the respective solvation layers.

Isomorphous but No Dead Ringer: Contrasting the Supramolecular Binding of Tetrafluoroberyllate and Sulfate Ions by Nanojars

An extensive single-crystal X-ray crystallographic study of 11 nanojar structures (of which seven are novel) of the formula [anion⊂{cis-CuII(μ-OH)(μ-pz)}n]2– (anion = BeF42–, n = 28, 31, 32, CunBeF4; anion = SO42–, n = 28, 31, CunSO4; pz = pyrazolate, C3H3N2–) has been carried out, providing a detailed description of isomorphism and pseudopolymorphism in nanojars. The results point to a remarkable variety in the shape of the constituent [cis-CuII(μ-OH)(μ-pz)]x (Cux; x = 6, 8, 9, 10, 12 and 14) metallamacrocycles, despite only small differences in the coordination environment of the individual Cu2+ centers. The flexibility of the Cux rings and, ultimately, of the nanojar framework allows for the incarceration of different anions with slightly different dimensions in a nanojar of a given size, resulting in the formation of isomorphous structures in the case of CunBeF4 and CunSO4. Selectivity studies monitored by electrospray-ionization mass spectrometry (ESI-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) reveal that despite the virtually identical H-bonding pattern around the two anions in nanojars of a given size, SO42– is strongly preferred over BeF42–. The origins of this selectivity are discussed, along with the nature of bonding in the two isosteric anions. Lastly, the crystal structure of (Bu4N)3Be2F7(H2O)3 documents the formation of the Be2F73– ion from BeF42–.

On the Propensity of Excess Hydroxide Ions at the Alcohol Monolayer–Water Interface

Atomistic molecular dynamics simulations have been employed to study the self-ion (H+ and OH-) distribution at the interface between long-chain C16-OH alcohol (cetyl alcohol) monolayer and water. It is well known that the free air-water interface is acidic due to accumulation of the hydronium (H3O+) ions at the interface. In the present study, we have observed that contrary to the air-water interface, at the long-chain alcohol monolayer-water interface, it is the hydroxide (OH-) ion, not the hydronium ion (H3O+) that gets accumulated. By calculating the potential of mean forces, it is confirmed that there is extra stabilization for the OH- ions at the interface relative to the bulk, but no such stabilization is observed for the H3O+ ions. By analyzing the interaction of the self-ions with other constituents in the medium, it is clearly shown that the favorable interaction of the OH- ions with the alcoholic -OH groups stabilizes this ion at the interface. By calculating coordination numbers of the self-ions it is observed that around 50% water neighbors are substituted by alcoholic -OH in case of the hydroxide ion at the interface, whereas in the case of hydronium ions, only 15% water neighbors are substituted by the alcoholic -OH. The most interesting observation about the local structure and H-bonding pattern is that the hydroxide ion acts solely as the H-bond acceptor, but the hydronium ion acts only as the H-bond donor.

Stereo-Recognition of Hydrogen Bond and Its Implications for Lignin Biomimetic Synthesis.

The hydrogen bond (H-bond) is essential to stabilizing the three-dimensional biological structure such as protein, cellulose, and lignin, which are integral parts of animal and plant cells; thus, stereo-recognition of the H-bond is extremely attractive. Herein, a methodology combining the variable-temperature 1H NMR technique with the density functional theory was established to recognize the underlying H-bonding patterns in lignin diastereomers. This method successfully classified the intramolecular and intermolecular H-bonds with slope values varying between 50.2-201.5 and 221.9-655.4, respectively, from the natural logarithm of the hydroxyl proton chemical shift versus the inverse of the temperature plot. Moreover, this slope was found to be correlated with the interaction distance between the H-bond donor and acceptor. Finally, it was proposed that the stereo-preferential formation of the β-O-4 structure (erythro vs threo form) during lignin biomimetic synthesis was probably influenced by their intramolecular H-bonding patterns, thus making it easier to reach thermodynamic equilibrium.

Designing Heat-Set Gels for Crystallizing APIs at Different Temperatures: A Crystal Engineering Approach

An organic salt crystallizes through different kinds of charge-assisted hydrogen-bonded networks depending on carboxylic functionality number and the degree of amine. These H-bonded packing patterns are often robust and predictable, so one can design a supramolecular salt with a certain purpose. In some cases, two different crystalline packing patterns can be found in Primary Ammonium Dicarboxylate (PAD) salts at different temperatures. Two kinds of supramolecular bonding, namely, charge-assisted hydrogen bonding and weak van der Waals interactions stabilize the two states. A small increase in the carbon chain length in a primary amine enhances the additional van der Waals interactions with the packing so that the 2D hydrogen-bonded network (HBN) transforms into a 1D HBN at room temperature. Such van der Waals interactions can be controlled by external heat, so a temperature-dependent 1D to 2D phase change is feasible. When certain moieties, such as azo and bipyridine, are introduced into the carboxylic acid backbone, the acids become insoluble in most organic solvents, raising their melting point, and resulting in heat-set gels. In the presence of an API, temperature and solvent-dependent polymorphic crystals can be grown in the heat-set gel medium and by simply cooling down the mixture, the API crystals can be separated easily.

Structural and Biofunctional Insights into the Cyclo(Pro-Pro-Phe-Phe-) Scaffold from Experimental and In Silico Studies: Melanoma and Beyond.

Short peptides have great potential as safe and effective anticancer drug leads. Herein, the influence of short cyclic peptides containing the Pro-Pro-Phe-Phe sequence on patient-derived melanoma cells was investigated. Cyclic peptides such as cyclo(Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe-), called CLA, and cyclo(Pro-homoPro-β3homoPhe-Phe-), called P11, exert the cytotoxic and the cytostatic effects in melanoma cells, respectively. CLA was the most active peptide as it reduced the viability of melanoma cells to 50% of control at about 10 µM, whereas P11 at about 40 µM after 48 h incubation. Interestingly, a linear derivative of P11 did not induce any effect in melanoma cells confirming previous studies showing that cyclic peptides exert better biological activity compared to their linear counterparts. According to in silico predictions, cyclic tetrapeptides show a better pharmacokinetic and toxic profile to humans than CLA. Notably, the spatial structure of those peptides containing synthetic amino acids has not been explored yet. In the Cambridge Structural Database, there is only one such cyclic tetrapeptide, cyclo((R)-β2homoPhe-D-Pro-Lys-Phe-), while in the Protein Data Bank—none. Therefore, we report the first crystal structure of cyclo(Pro-Pro-β3homoPhe-Phe-), denoted as 4B8M, a close analog of P11, which is crucial for drug discovery. Comparative molecular and supramolecular analysis of both structures was performed. The DFT findings revealed that 4B8M is well interpreted in the water solution. The results of complex Hirshfeld surface investigations on the cooperativity of interatomic contacts in terms of electrostatic and energetic features are provided. In short, the enrichment ratio revealed O…H/H…O and C…H/H…C as privileged intercontacts in the crystals in relation to basic and large supramolecular H-bonding synthon patterns. Furthermore, the ability of self-assemble 4B8M leading to a nanotubular structure is also discussed.

Insights into structure and activity relationship of clinically mutated PER1 and PER2 class A β-lactamase enzymes

PER1 and PER2 are among the class A β-lactamase enzymes, which have evolved clinically to form antibiotic resistance and have significantly expanded their spectrum of activity. Hence, there is a need to study the clinical mutation responsible for such β-lactamase mediated antibiotic resistance. Alterations in catalytic centre and Ω-loop structure could be the cause of antibiotic resistance in these β-lactamase enzymes. Structural and functional alterations are caused due to mutations on or near the catalytic centre, which results in active site plasticity and are responsible for its expanded spectrum of activity in these class A β-lactamase enzymes. Multiple sequence alignment, structure, kinetic, molecular docking, MMGBSA and molecular dynamic simulation comparisons were done on 38 clinically mutated and wild class A β-lactamase enzymes. This work shows that PER1 and PER2 enzymes contains most unique mutations and have altered Ω-loop structure, which could be responsible for altering the structure-activity relationship and extending the spectrum of activity of these enzymes. Alterations in molecular docking, MMGBSA, kinetic values reveals the modification in the binding and activity of these clinically mutated enzymes with antibiotics. Further, the cause of these alterations can be revealed by active site interactions and H-bonding pattern of these enzymes with antibiotics. Met69Gln, Glu104Thr, Tyr105Trp, Met129His, Pro167Ala, Glu168Gln, Asn170His, Ile173Asp and Asp176Gln mutations were uniquely found in PER1 and PER2 enzymes. These mutations occurs at catalytic important residues and results in altered interactions with β-lactam antibiotics. Hence, these mutations could be responsible for altering the structure-activity of PER1 and PER2 enzymes. Communicated by Ramaswamy H. Sarma

Second Sphere Interactions in Amyloidogenic Diseases.

Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.

Polypeptoid-Assisted Formation of Supramolecular Architectures from Folic Acid for Targeted Cancer Therapy with Enhanced Efficacy.

In recent years, much research has focused on assemblies formed by charged polyelectrolytes via electrostatic interactions in aqueous solutions as they have the potential to be used in a variety of biomedical applications. In this study, we analyzed supramolecular architectures fabricated from poly(N-allyl glycine) modified with cysteamine (PNAG-NH2) and folic acid (FA) via electrostatic interactions. The PNAG-NH2/FA complex exhibits a reversible pH-responsive morphological transformation from vesicles (pH = 7.0) to nanofibers (pH = 5.0). Besides, we demonstrated that homopolypeptoids electrostatically interact with FA, thereby facilitating ribbon- and disk-like H-bonded FA patterns and inducing the formation of vesicle nanostructures and fiber arrays, respectively. Additionally, we systematically studied the influence of the degree of polymerization of the polymers, concentration, charge mixing ratio, and type of the polymer and the small-molecule acid on the assemblies. We show the superior stability of the polypeptoid/FA complex as compared to those based on other polymers. We established that the polypeptoid/FA complex exhibits a superior stability than those based on other polymers. By applying these beneficial properties, we encapsulated the anticancer drug doxorubicin (DOX) in the complex vesicle to obtain a pH-induced drug carrier. Cytotoxicity studies and internalization assays revealed that the DOX-loaded PNAG-NH2/FA complex vesicles display an enhanced therapeutic efficacy via typical FA-folate receptor-mediated endocytosis in vitro.

Aromaticity effect on supramolecular aggregation. Aromatic vs. cyclic monohydroxy alcohols

In this paper, the steric hindrance effect related to the presence of either a cyclic or aromatic ring on the self-association process in the series of monohydroxy alcohols (MAs), from cyclohexanemethanol to 4-cyclohexyl-1-butanol and from benzyl alcohol to 4-phenyl-1-butanol, was studied using X-Ray Diffraction (XRD), Differential Scanning Calorimetry (DSC), Fourier Transform Infrared (FTIR) spectroscopy, Broadband Dielectric Spectroscopy (BDS) and the Pendant Drop (PD) methods. Based on FTIR results, it was shown that phenyl alcohol (PhA) and cyclohexyl alcohol (CA) derivatives reveal substantial differences in the association degree, the activation energy of dissociation, and the homogeneity of supramolecular nanoassociates suggesting that the phenyl ring exerts a stronger steric impact on the self-assembling of molecules than cyclohexyl one. Additionally, XRD data revealed that phenyl moiety introduces more heterogeneity in the organization of molecules compared to the cyclic one. The changes in the self-association process of alcohols were also reflected in differences in the molecular dynamics of the H-bonded aggregates, as well as in the Kirkwood factor, defining the long-range correlation between dipoles, which were slightly higher for CAs with respect to those determined for PhAs. Unexpectedly it was also found that the surface layers of PhAs were more organized than those formed by CAs. Thus, these findings provided insight into the impact of aromaticity on the self–assembly process, H-bonding pattern, supramolecular structure, and intermolecular dynamics of the studied alcohols.

Variation in the local ordering, H-bonding pattern and molecular dynamics in the pressure densified ritonavir

In this paper, high-pressure (HP) dielectric studies on H-bonded active pharmaceutical ingredient – ritonavir indicated the narrowing of α-dispersion with compression, and consequently, a breakdown of the temperature-pressure superpositioning rule. To understand such peculiar behavior, reported so far only for a few van der Waals compounds, we performed calorimetric, structural, and infrared measurements on the pressure densified glass (as well as on ordinary glass) of the examined substance. These investigations demonstrated that variations in the structural organization of molecules and H-bonding pattern are responsible for the observed changes in the shape of the structural relaxation peak. Moreover, further isobaric HP studies at pressure 400 MPa revealed the presence of an additional secondary relaxation process (not detected at p = 0.1 MPa) in the loss spectra collected below the glass transition temperature for this compound.