Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study

Imidazole is a five-membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non-covalent interactions involving the NH group, the pyridine-like nitrogen atom or the π-system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non-covalent interactions (e.g., hydrogen bonds and π-interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95-GD3/def2-QZVPD) for a series of model systems constructed based on analysis of available x-ray data. It is shown that for considered complexes formation of additional non-covalent interactions can only enhance the proton-donating ability of imidazole. At the same time, its proton-accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non-covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity-a small change in the length of non-covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non-covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non-covalently bound systems with its participation.

Sinefungin analogs targeting VP39 methyltransferase as potential anti-monkeypox therapeutics: a multi-step computational approach

The increasing spread of the Monkeypox virus (MPXV) presents a significant public health challenge, emphasising the urgent requirement for effective treatments. Our study focuses on the VP39 Methyltransferase enzyme of MPXV as a critical target for therapy. By utilising virtual screening, we investigated natural compounds with structural similarities to sinefungin, a broad-acting MTase inhibitor. From an initial set of 177 compounds, we identified three promising compounds-CNP0346326, CNP0343532, and CNP008361, whose binding scores were notably close to that of sinefungin. These candidates bonded strongly to the VP39 enzyme, hinting at a notable potential to impede the virus. Our rigorous computational assays, including re-docking, extended molecular dynamics simulations, and energetics analyses, validate the robustness of these interactions. The data paint a promising picture of these natural compounds as front-runners in the ongoing race to develop MPXV therapeutics and set the stage for subsequent empirical trials to refine these discoveries into actionable medical interventions.

Molecular crowding effect in Hantzch pyridine synthesis in polyethylene glycol aqueous solution

In a molecular crowding environment, the kinetics and thermodynamics differ from those in a diluted solution. Although the molecular crowding effect has been extensively investigated, its fundamental kinetics and thermodynamics remain unclear. In this study, we investigated the change in the rate constant (k) of the Hantzch pyridine reaction in a molecular crowding environment using polyethylene glycol (PEG). While the k value increased to a PEG concentration (CPEG) of 10 vol%, a decreasing trend was observed for CPEG > 20 vol%. This intriguing behavior was analyzed based on the increase in reactant activity due to volume exclusion and the decrease in water activity due to osmotic pressure. Volume exclusion and osmotic pressure had opposing effects on the reaction, which were positive for volume exclusion and negative for osmotic pressure. We found that k decreased when the negative effect of the osmotic pressure surpassed the volume exclusion effect.

Dependence of Intramolecular Hydrogen Bond on Conformational Flexibility in Linear Aminoalcohols

Intramolecular hydrogen bonds (H-bonds) are abundant in physicochemical and biological processes. The strength of such interaction is governed by a subtle balance between conformational flexibility and steric effect that are often hard to predict. Herein, using linear aminoalcohols NH2(CH2)nOH (n = 2-5) as a model system, we demonstrated the dependence of intramolecular H-bond on the backbone chain length. With sensitive photoacoustic Raman spectroscopy (PARS), the gas-phase Raman spectra of aminoalcohols were measured in both N-H and O-H stretching regions at 298 and 338 K and explained with the aid of quantum chemistry calculations. For n = 2-4, two conformers corresponding to the O-H···N intramolecular H-bond and free OH were identified, whereas for n = 5, only the free-OH conformer was identified. Compared to free OH, a striking spectral dependence was observed for the intramolecular H-bonded conformer. According to the red shift of the OH-bonded band, the strongest intramolecular H-bond yields in n = 4, but the favorable chain length to form an intramolecular hydrogen bond at room temperature was observed in n = 3, which corresponds to a six-membered-ring in 3-aminopropanol. This is in good agreement with statistical analysis from the Cambridge Structural Database (CSD) that the intramolecular hydrogen bond is preferred when the six-membered ring is formed. Furthermore, combined with the calculated thermodynamic data at the MP2/aug-cc-pVTZ//M062X/6-311++G(d,p) level, the origin of decrease in intramolecular hydrogen-bond formation was ascribed to an unfavorable negative entropy contribution when the backbone chain is further getting longer, which results in the calculated Gibbs free energy optimum changing with increasing temperature from n = 4 (0-200 K) to n = 3 (200-400 K) and to n = 2 (above 400 K). These results will provide new insight into the nature of intramolecular hydrogen bonds at the molecular level and the application of intramolecular hydrogen bonds in rational drug design and supramolecular assembly.

A molecular view of plasticization of polyvinyl alcohol

Although macromolecules such as polymers are in widespread industrial use, pure formulations rarely have precisely the properties new applications demand. Pure polymer is often too brittle and inflexible, necessitating plasticizers to soften or toughen films and bulk polymer materials. In practice, new formulations are developed by extensive trial-and-error methods, as no general molecular explanations exist for the mechanism of plasticization to aid in determining the optimal structure and concentration of plasticizers. Here, through atomistic molecular simulations augmented with advanced sampling techniques, we develop an atomic-level picture of the processes in plasticization by directly calculating free energies that govern the interaction between polymers and small-molecule plasticizers. This work focuses on the influence of two common plasticizer molecules-glycerol and sorbitol-interacting with polyvinyl alcohol (PVA), a frequently used component of polymer films. In particular, we focus on conformational and hydrogen bond structure changes induced in globules of PVA by the plasticizer molecules, with the hypothesis that hydrogen bonding plays a role in the incorporation of these plasticizers into PVA and, thus, in the observed mechanical properties. While we focus on nanoscopic systems, we observe distinct preferences in the conformational free energy that can be connected to the performance of polymer materials at laboratory and industrial scales. This work presents a new molecular perspective from which effective plasticizers can be developed and presents a firm basis from which important analyses of plasticization in complex chemical environments relevant to industry may be developed.

Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes

Where the basic units of molecular chemistry are the bonds within molecules, supramolecular chemistry is based on the interactions that occur between molecules. Understanding the "how" and "why" of the processes that govern molecular self-assembly remains an open challenge to the supramolecular community. While many interactions are readily examined in silico through electronic structure calculations, such insights may not be directly applicable to experimentalists. The practical limitations of computationally accounting for solvation is perhaps the largest bottleneck in this regard, with implicit solvation models failing to comprehensively account for the specific nature of solvent effects and explicit models incurring a prohibitively high computational cost. Since molecular recognition processes usually occur in solution, insight into the nature and effect of solvation is imperative not only for understanding these phenomena but also for the rational design of systems that exploit them.Molecular balances and supramolecular complexes have emerged as useful tools for the experimental dissection of the physicochemical basis of various noncovalent interactions, but they have historically been underexploited as a platform for the evaluation of solvent effects. Contrasting with large biological complexes, smaller synthetic model systems enable combined experimental and computational analyses, often facilitating theoretical analyses that can work in concert with experiment.Our research has focused on the development of supramolecular systems to evaluate the role of solvents in molecular recognition, and further characterize the underlying mechanisms by which molecules associate. In particular, the use of molecular balances has provided a framework to measure the magnitude of solvent effects and to examine the accuracy of solvent models. Such approaches have revealed how solvation can modulate the electronic landscape of a molecule and how competitive solvation and solvent cohesion can provide thermodynamic driving forces for association. Moreover, the use of simple model systems facilitates the interrogation and further dissection of the physicochemical origins of molecular recognition. This tandem experimental/computational approach has married less common computational techniques, like symmetry adapted perturbation theory (SAPT) and natural bonding orbital (NBO) analysis, with experimental observations to elucidate the influence of effects that are difficult to resolve experimentally (e.g., London dispersion and electron delocalization).

The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer

The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.

Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations

Cyclic peptides have the potential to bind to challenging targets, which are undruggable with small molecules, but their application is limited by low membrane permeability. Here, using a series of cyclic pentapeptides, we showed that established physicochemical criteria of permeable peptides are heavily violated. We revealed that a dominant core conformation, stabilized by amides' shielding pattern, could guide the design of novel compounds. As a result, counter-intuitive strategies, such as incorporation of polar residues, can be beneficial for permeability. We further find that core globularity is a promising descriptor, which can extend the capability of standard predictive models.

Perylene Bisimide and Naphthyl-Based Molecular Dyads: Hydrogen Bonds Driving Co-planarization and Anomalous Temperature-Response Fluorescence

The origin of the positive temperature effect in fluorescence emission of a newly designed perylene bisimide (PBI) derivative with two naphthyl units containing ortho-methoxy group (NM) at its bay positions (PBI-2NM) was elucidated. A key point is the finding of a weak hydrogen bond (<5.0 kcal mol^-1 ) between the methoxy group of the NM unit and a nearby hydrogen atom of the PBI core. It is the bonding that drives co-planarization of the different aromatic units, resulting in delocalization of the π-electrons of the compound as synthesized, inducing fluorescence quenching via intramolecular charge transfer (ICT). With increasing temperature, the co-planar structure could be distorted in part, resulting in a decreased degree of ICT, and hence leading to enhanced fluorescence emission. The unique positive temperature effect in emission induced by H-bond-driven co-planarization may pave a new avenue in designing functional molecular systems complementary to conventional methods.

Weak functional group interactions revealed through metal-free active template rotaxane synthesis

Modest functional group interactions can play important roles in molecular recognition, catalysis and self-assembly. However, weakly associated binding motifs are often difficult to characterize. Here, we report on the metal-free active template synthesis of [2]rotaxanes in one step, up to 95% yield and >100:1 rotaxane:axle selectivity, from primary amines, crown ethers and a range of C=O, C=S, S(=O)2 and P=O electrophiles. In addition to being a simple and effective route to a broad range of rotaxanes, the strategy enables 1:1 interactions of crown ethers with various functional groups to be characterized in solution and the solid state, several of which are too weak - or are disfavored compared to other binding modes - to be observed in typical host-guest complexes. The approach may be broadly applicable to the kinetic stabilization and characterization of other weak functional group interactions.