Calculations of pKa Values of Selected Pyridinium and Its N-Oxide Ions in Water and Acetonitrile

Medicinal Chemistry of Drugs with N-Oxide Functionalities

Molecules with N-oxide functionalities are omnipresent in nature and play an important role in Medicinal Chemistry. They are synthetic or biosynthetic intermediates, prodrugs, drugs, or polymers for applications in drug development and surface engineering. Typically, the N-oxide group is critical for biomedical applications of these molecules. It may provide water solubility or decrease membrane permeability or immunogenicity. In other cases, the N-oxide has a special redox reactivity which is important for drug targeting and/or cytotoxicity. Many of the underlying mechanisms have only recently been discovered, and the number of applications of N-oxides in the healthcare field is rapidly growing. This Perspective article gives a short summary of the properties of N-oxides and their synthesis. It also provides a discussion of current applications of N-oxides in the biomedical field and explains the basic molecular mechanisms responsible for their biological activity.

Mechanisms of hydrogen evolution by six-coordinate cobalt complexes: a density functional study on the role of a redox-active pyridinyl-substituted diaminotriazine benzamidine ligand as a proton relay

The hydrogen evolution reaction is an important process for energy storage. The six-coordinate cobalt complex [CoIII(L1-)(LH)]2+ (LH = N-(4-amino-6-(pyridin-2-yl)-1,3,5-triazin-2-yl)benzamidine) was found to catalyze photocatalytic hydrogen evolution. In this work, we performed density functional calculations to obtain the reduction potentials and the proton-transfer free energy of possible intermediates to determine the preferred pathways for proton reduction. The mechanism involves the metal-based reduction of Co(III) to Co(II) before the protonation at the amidinate N on the pyridinyl-substituted diaminotriazine benzamidinate ligand L1- to form [CoII(LH)(LH)]2+. Essentially, the subsequent electron transfer is not metal-based reduction, but rather ligand-based reduction to form [CoII(LH)(LH˙1-)]1+. Through a proton-coupled electron transfer process, the cobalt hydride [CoIIH(LH)(LH2˙)]1+ is formed as the key intermediate for hydrogen evolution. As the cobalt hydride complex is coordinatively saturated, a structural change is required when the hydride on Co is coupled with the proton on pyridine. Notably, the redox-active nature of the ligand results in the low acidity of the protonated pyridine moiety of LH2˙, which impedes its function as a proton relay. Our findings suggest that separating the proton relay fragment from the electron reservoir fragment of the redox-active ligand is preferred for fully utilizing both features in catalytic H2 evolution.

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

Alkanes in Minisci-Type Reaction under Photocatalytic Conditions with Hydrogen Evolution

We report herein a protocol for the selective activation of C(sp3)-H bonds based on the interplay of two readily available organic catalysts and their successful implementation in cross-coupling azaarenes with alkanes. This Minisci-like reaction is promoted by visible light at room temperature and is free from chemical oxidants, metals, and chlorinated solvents. A wide range of substrates are compatible, including some bioactive molecules. Mechanistic studies support a dual catalytic cycle with H2 evolution.

Theoretical Study on the Alkylimino-Substituted Sulfonamides with Potential Biological Activity

Antibiotics play a key role in the fight against bacterial diseases. However, bacteria quickly learn how to minimize the effects of antibiotics and strengthen their resistance. Thus, the fight against them becomes more and more difficult and there is a constant search for new bactericidal compounds. It is important in this type of search to determine the basic properties of compounds such as pKa, hydrogen bond formation, or hydrophobicity. Here, we present the results of our in silico study of five sulfonamide derivatives differing in alkylamine substituent length. Based on our results, we propose a model of three possible pKa values for each of the studied compounds. Interestingly, the use of Muckerman's approach for pKa determination exhibits that theoretical and experimental results are in very good agreement. Intramolecular hydrogen bond formation affects pKa. The strength of the H-bond interaction increases from ethyl to butylamine and then decreases with the elongation of the alkylamine chain. The obtained partition coefficients (expressed here in the value of log P) increase with the number of carbon atoms in the alkylamine chain following Lipinski's rule of five. The presented results provide important structural, physicochemical, and thermodynamic information that allows for the understanding of the influence of some sulfonamides and their possible activity.

Hydrogen-Bonding Trends in a Bithiophene with 3- and/or 4-Pyridyl Substituents

To improve the charge-carrier transport capabilities of thin-film organic materials, the intermolecular electronic couplings in the material should be maximized. Decreasing intermolecular distance while maintaining proper orbital overlap in highly conjugated aromatic molecules has so far been a successful way to increase electronic coupling. We attempted to decrease the intermolecular distance in this study by synthesizing cocrystals of simple benzoic acid coformers and dipyridyl-2,2'-bithiophene molecules to understand how the coformer identity and pyridine N atom placement affected solid-state properties. We found that with the 5-(3-pyridyl)-5'-(4-pyridyl)-isomer, the 4-pyridyl ring interacted with electrophiles and protons more strongly. Synthesized cocrystal powders were found to have reduced average crystallite size in reference to the parent compounds. The opposite was found for the intermolecular electronic couplings, as determined via density functional theory (DFT) calculations, which were relatively large in some of the cocrystals.

Room-Temperature One-Pot Synthesis of pH-Responsive Pyridine-Functionalized Carbon Surfaces

Carbon surfaces (glassy carbon, graphite, and boron-doped diamond) were functionalized with layers composed of linked pyridinium and pyridine moieties using simple electrochemical reduction of trifluoroacetylpyridinium. The pyridinium species was generated in situ in solution by the reaction of trifluoroacetic anhydride and pyridine precursors and underwent electrochemical reduction at -1.97 V vs Fc/Fc⁺, as determined by cyclic voltammetry. The pyridine/pyridinium films were electrodeposited at room temperature, on a timescale of minutes, and were characterized using X-ray photoelectron spectroscopy. The as-prepared films have a net positive charge in aqueous solution at pH 9 and below due to the pyridinium content, confirmed by the electrochemical response of differently charged redox molecules at the functionalized surfaces. The positive charge can be enhanced further through protonation of the neutral pyridine component by controlling the solution pH. Moreover, the nitrogen-acetyl bond can be cleaved through base treatment to purposefully increase the neutral pyridine proportion of the film. This results in a surface that can be "switched" from functionally near neutral to a positive charge by treatment in basic and acidic solutions, respectively, through manipulation of the protonation state of the pyridine. The functionalization process demonstrated here is readily achievable at a fast timescale at room temperature and hence can allow for rapid screening of surface properties. Such functionalized surfaces present a means to test in isolation the specific catalytic performance of pyridinic groups toward key processes such as oxygen and CO₂ reduction.

Aliphatic C-H Functionalization Using Pyridine N-Oxides as H-Atom Abstraction Agents

The alkylation and heteroarylation of unactivated tertiary, secondary, and primary C(sp3)-H bonds was achieved by employing an acridinium photoredox catalyst along with readily available pyridine Noxides as hydrogen atom transfer (HAT) precursors under visible light. Oxygen-centered radicals, generated by single-electron oxidation of the Noxides, are the proposed key intermediates whose reactivity can be easily modified by structural adjustments. A broad range of aliphatic C-H substrates with electron-donating or -withdrawing groups as well as various olefinic radical acceptors and heteroarenes were well tolerated.

Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties

Pyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure of chlorohydrazinopyrazine, its physicochemical and cytotoxic properties, and the site and nature of interaction with DNA. The obtained results indicated that 2-chloro-3-hydrazinopyrazine (2Cl3HP) displayed the highest affinity to DNA. Cytotoxicity studies revealed that the compound did not exhibit toxicity toward human dermal keratinocytes, which supported the potential application of 2Cl3HP in clinical use. The study also attempted to establish the possible equilibria occurring in the aqueous solution and, using both theoretical and experimental methods, clearly showed the hydrophilic nature of the compound. The experimental and theoretical results of the study confirmed the quality of the compound, as well as the appropriateness of the selected set of methods for similar research.

Doping Engineering of Single-Walled Carbon Nanotubes by Nitrogen Compounds Using Basicity and Alignment

Charge transport properties in single-walled carbon nanotubes (SWCNTs) can be significantly modified through doping, tuning their electrical and thermoelectric properties. In our study, we used more than 40 nitrogen-bearing compounds as dopants and determined their impact on the material's electrical conductivity. The application of nitrogen compounds of diverse structures and electronic configurations enabled us to determine how the dopant nature affects the SWCNTs. The results reveal that the impact of these dopants can often be anticipated by considering their Hammett's constants and pK_a values. Furthermore, the empirical observations supported by first-principles calculations indicate that the doping level can be tuned not only by changing the type and the concentration of dopants but also by varying the orientation of nitrogen compounds around SWCNTs.

Improving Small Molecule pKa Prediction Using Transfer Learning With Graph Neural Networks

Enumerating protonation states and calculating microstate pK_a values of small molecules is an important yet challenging task for lead optimization and molecular modeling. Commercial and non-commercial solutions have notable limitations such as restrictive and expensive licenses, high CPU/GPU hour requirements, or the need for expert knowledge to set up and use. We present a graph neural network model that is trained on 714,906 calculated microstate pK_a predictions from molecules obtained from the ChEMBL database. The model is fine-tuned on a set of 5,994 experimental pK_a values significantly improving its performance on two challenging test sets. Combining the graph neural network model with Dimorphite-DL, an open-source program for enumerating ionization states, we have developed the open-source Python package pkasolver, which is able to generate and enumerate protonation states and calculate pK_a values with high accuracy.

Charge-State Dependence of Proton Uptake in Polyoxovanadate-alkoxide Clusters

Here, we present an investigation of the thermochemistry of proton uptake in acetonitrile across three charge states of a polyoxovanadate-alkoxide (POV-alkoxide) cluster, [V₆O₇(OMe)₁₂]ⁿ (n = 2–, 1–, and 0). The vanadium oxide assembly studied features bridging sites saturated by methoxide ligands, isolating protonation to terminal vanadyl moieties. Exposure of [V₆O₇(OMe)₁₂]ⁿ to organic acids of appropriate strength results in the protonation of a terminal V=O bond, generating the transient hydroxide-substituted POV-alkoxide cluster [V₆O₆(OH)(OMe)₁₂]ⁿ⁺¹. Evidence for this intermediate proved elusive in our initial report, but here we present the isolation of a divalent anionic cluster that features hydrogen bonding to dimethylammonium at the terminal oxo site. Degradation of the protonated species results in the formation of equimolar quantities of one-electron-oxidized and oxygen-atom-efficient complexes, [V₆O₇(OMe)₁₂]ⁿ⁺¹ and [V₆O₆(OMe)₁₂]ⁿ⁺¹. While analogous reactivity was observed across the three charge states of the cluster, a dependence on the acid strength was observed, suggesting that the oxidation state of the vanadium oxide assembly influences the basicity of the cluster surface. Spectroscopic investigations reveal sigmoidal relationships between the acid strength and cluster conversion across the redox series, allowing for determination of the proton affinity of the surface of the cluster in all three charge states. The fully reduced cluster is found to be the most basic, with higher oxidation states of the assembly possessing substantially reduced proton affinities (∼7 pK_a units per electron). These results further our understanding of the site-specific reactivity of terminal M=O bonds with protons in an organic solvent, revealing design criteria for engineering functional surfaces of metal oxide materials of relevance to energy storage and conversion.

Experimental determination of the surface basicity of polyoxovanadate-alkoxide clusters across three oxidation states reveals a charge-state dependence of proton uptake in molecular, organofunctionalized vanadium oxide assemblies.

Thermodynamics regulated organic hydride/acid pairs as novel organic hydrogen reductants

Organic hydride/acid pairs could realize transformation of N-substituted organic hydrides from hydride reductants to thermodynamics regulated hydrogen reductants on conveniently choosing suitable organic hydrides and acids with various acidities.

Rational Synthesis of Imine-Linked Fluorescent Covalent Organic Frameworks with Different pKa for pH Sensing In Vitro and In Vivo

Precise modulation of pH in living cells plays a vital role in the study of many diseases, such as cancer and rheumatoid arthritis. Here, a series of imine-linked covalent organic frameworks (COFs) were rationally designed and developed for pH sensing in tumor cells and zebrafish. Four monomers were chosen to synthesize COFs (COF₁-COF₄) with different pK_a by a simple orthogonal combination through condensation reaction. The as-obtained COFs exhibited a sensitive pH-dependent fluorescence response compared to their building blocks. Among them, COF₂ possessed a high crystallinity, excellent fluorescence, and suitable pK_a for biosensing. For bioimaging applications, COF₂ was modified with poly-d-lysine (PDL) to improve its biocompatibility and endocytosis efficiency. After that, PDL-modified COF₂ (PDL@COF₂) was used as a novel fluorescence probe with a superior linear pH response over the range from 5.0 to 8.0 due to its fully reversible protonation and deprotonation. The fluorescent PDL@COF₂ was further employed as a good candidate for pH imaging in tumor cells and zebrafish. The as-constructed environment-sensitive fluorescent COFs have greatly expanded the applications of COFs in the biological area.

Selective hydrogen bonding controls temperature response of layer-by-layer upper critical solution temperature micellar assemblies

This work establishes a correlation between the selectivity of hydrogen-bonding interactions and the functionality of micelle-containing layer-by-layer (LbL) assemblies. Specifically, we explore LbL films formed by assembly of poly(methacrylic acid) (PMAA) and upper critical solution temperature block copolymer micelles (UCSTMs) composed of poly(acrylamide-co-acrylonitrile) P(AAm-co-AN) cores and polyvinylpyrrolidone (PVP) coronae. UCSTMs had a hydrated diameter of ∼380 nm with a transition temperature between 45 and 50 °C, regardless of solution pH. Importantly, micelles were able to hydrogen-bond with PMAA, with the critical interaction pH being temperature dependent. To better understand the thermodynamic nature of these interactions, in depth studies using isothermal titration calorimetry (ITC) were conducted. ITC reveals opposite signs of enthalpies for binding of PMAA with micellar coronae vs. with the cores. Moreover, ITC indicates that pH directs the interactions of PMAA with micelles, selectively enabling binding with the micellar corona at pH 4 or with both the corona and the core at pH 3. We then explore UCSTM/PMAA LbL assemblies and show that the two distinct modes of PMAA interaction with the micelles (i.e. whether or not PMAA binds with the core) had significant effects on the film composition, structure, and functionality. Consistent with PMAA hydrogen bonding with the P(AAm-co-AN) micellar cores, a significantly higher fraction of PMAA was found within the films assembled at pH 3 compared to pH 4 by both spectroscopic ellipsometry and neutron reflectometry. Selective interaction of PMAA with PVP coronae of the assembled micelles, achieved by the emergence of partial ionization of PMAA at pH 4 was critical for preserving film functionality demonstrated as temperature-controlled swelling and release of a model small molecule, pyrene. The work done here can be applied to a multitude of assembled polymer systems in order to predict suppression/retention of their stimuli-responsive behavior.

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

Interaction energy (E_int) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (V_min).

When biomolecules meet 2-hydrazinopyrazine: from theory through experiment to molecular levels using a wide spectrum of techniques

The design of drug structures that are non-toxic, easily transported and permeable to cellular barriers is currently one of the most growing research trends. Indeed, the structural similarity of 2-hydrazinopyrazine (2HP) to pyrazinamide, which has been successfully used in anti-tuberculosis therapy, makes 2HP a promising research object. Thus, herein, a complete analysis of the structure of 2HP and its physicochemical and cytotoxic properties was performed. Calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) binding studies were conducted, which demonstrated the higher affinity of 2HP to BSA. Furthermore, cytotoxicity tests were performed, which proved that 2HP was non-toxic to human skin keratinocyte cells. Accordingly, 2HP was initially classified as a compound with potential application. Physicochemical investigations were performed using a wide range of experiments, which were supported by DFT calculations using the B3LYP functional and 6-311+G** basis set. The good correlation, high quality and correctness of the obtained parameters were proven although the data was obtained using independent techniques. Additionally, 42 tautomeric (prototrophic) forms of 2HP were found by searching the conformational hyperspace. The most energy stable 2HP conformer structure and the partial charge distribution were established. The preferred 2HP ionic forms preferred were presented, and models of the equilibrium occurring in aqueous solution were proposed. The hydrophilic character of 2HP was established based on the partition coefficient values determined by both experiment and theory. The PCM and SMD solvent models of water and n-octanol were used.

Structure, ionic forms, hydrophilic and non-cytotoxic character of 2-hydrazinopyrazine with stronger affinity to BSA than DNA were proved.

Highly efficient removal of Cu(ii) by novel dendritic polyamine–pyridine-grafted chitosan beads from complicated salty and acidic wastewaters

In this study, dendritic polyamine chitosan beads with and without 2-aminomethyl pyridine were facilely prepared and characterized. Compared to CN (without the pyridine function), more adsorption active sites, larger pores, higher nitrogen content, higher specific surface area, and higher strength could be obtained for CNP (with the pyridine function). CNP microspheres afforded a larger adsorption capacity than those obtained by CN for different pH values; further, the uptake amounts of Cu(ii) were 0.84 and 1.12 mmol g⁻¹ for CN and CNP beads, respectively, at pH 5. The CNP microspheres could scavenge Cu(ii) from highly acidic and salty solutions: the maximum simulated uptake amount of 1.93 mmol g⁻¹ at pH 5 could be achieved. Due to the strong bonding ability and weakly basic property of pyridine groups, the adsorption capacity of Cu(ii) at pH 1 was 0.75 mmol g⁻¹ in highly salty solutions, which was comparative to those obtained from the commercial pyridine chelating resin M4195 (Q_Cu(II) = 0.78 mmol g⁻¹ at pH 1). In addition, a distinct salt-promotion effect could be observed for CNP beads at both pH 5 and 1. Therefore, the prepared adsorbent CNP beads can have promising potential applications in the selective capturing of heavy metals in complex solutions with higher concentrations of H⁺ and inorganic salts, such as wastewaters from electroplating liquid and battery industries.

Dendritic polyamine chitosan (CNP) beads containing 2-aminomethyl pyridine were facilely prepared for the efficient removal of Cu(ii) ions from highly acidic and salty solutions.