Importance of tautomerism in drugs

Structural and FTIR spectroscopic studies of matrix-isolated 3-thio-1,2,4-triazole complexes with carbon dioxide. The UV-induced formation of thiol⋯CO2 complexes

Matrix isolation FTIR spectroscopy was combined with quantum chemical calculations to characterize complexes of 3-thio-1,2,4-triazole (ST) with carbon dioxide. Geometries of the possible 1 : 1 and 1 : 2 complexes were optimized at the DFT (B3LYPD3) level of theory with the 6-311++G(3df,3pd) basis set. The computational results show that ST interacts specifically with carbon dioxide through different hydrogen bond and van der Waals interactions. For the 1 : 1 complexes of the most abundant ST thione tautomer, four stable minima, STn⋯CO2, have been located on the potential energy surface. In contrast, for the ST thiol tautomer, three STl⋯CO2 structures were optimized. Experimentally, the two most stable 1 : 1 complexes of STn with CO2, characterized by the presence of the N-H⋯O hydrogen bridge and an additional S6⋯C10 interaction, were identified in solid argon upon deposition. Annealing of the matrix at 32 K proved that one 1 : 2 structure is also present, resulting from the addition of a second CO2 molecule to the 1 : 1 complexes. The laser irradiation at λ = 270 nm, apart from generating the thiol tautomer of ST, also leads to the formation of three thiol⋯CO2 complexes. Furthermore, the presence of CO2 in the argon matrix was found to influence the efficiency of the UV-induced thione-thiol tautomerization, though to a lesser extent than nitrogen. This suggests that while CO2 forms stronger intermolecular interactions with ST, its impact on tautomerization kinetics is less pronounced, highlighting the nuanced role of specific gas-phase interactions in modulating photochemical transformations in low-temperature matrices. The findings presented in this work not only enhance the fundamental understanding of weak intermolecular interactions but also provide new insights into the role of CO2-specific effects in photochemical and structural transformations of heterocycles.

Solvent polarity effect on photophysical properties of some aromatic azo dyes with focus on tautomeric and toxicity competition

Edible dyes have become an essential part of modern life, widely appreciated for their safety and effectiveness in food coloring. Given the fundamental role of hydrogen bonding in chemical and biological systems, this study explores the photophysical properties of three commonly used aromatic azo food dyes-Ponceau 4R, Sunset Yellow, and Tartrazine-across both isotropic solvents and anisotropic environments. To better understand their environmental interactions in ground and excited states, the influence of media polarity on these dyes was also explored. The study further evaluated the applicability of the Kamlet-Abboud-Taft polarity scale in capturing these effects. The results highlight the crucial role of hydrogen bonding in facilitating azo-hydrazone tautomerization and enhancing structural resonance. Additionally, the toxicity of these dyes on kidney cells was assessed using the MTT assay, revealing that Ponceau 4R exhibits notable toxicity, primarily due to solute-solvent interactions. Notably, the hydrazone tautomeric form was identified as the predominant species in this dye.

Terahertz Spectroscopy and Density Functional Theory for Non-Destructive Analysis of Anticoagulant Warfarin

Pharmaceutical quality control plays a critical role in safeguarding patient safety and ensuring therapeutic efficacy. However, conventional analytical methods are often hindered by laborious procedures and complex chemical preparation requirements. This study presents a rapid, non-destructive pharmaceutical analysis approach by introducing terahertz spectroscopy for the dual-parametric detection of the anticoagulant warfarin. Characteristic absorption peaks of warfarin within the 4-10 THz range were experimentally identified and theoretically resolved through density functional theory calculations, employing both single-molecule and unit cell models. Furthermore, three strong absorption peaks were selected to construct multivariate regression models correlating spectral parameters (peak intensity and area) with warfarin weight, achieving a detection limit of 0.641 mg within a 5 min analytical workflow. This approach enables simultaneous molecular fingerprint identification and quantitative determination without chemical modification, meeting the requirements for the rapid screening of active pharmaceutical ingredients.

Fast and Accurate Prediction of Tautomer Ratios in Aqueous Solution via a Siamese Neural Network

Tautomerization plays a critical role in chemical and biological processes, influencing molecular stability, reactivity, biological activity, and ADME-Tox properties. Many drug-like molecules exist in multiple tautomeric states in aqueous solution, complicating the study of protein-ligand interactions. Rapid and accurate prediction of tautomer ratios and identification of predominant species are therefore crucial in computational drug discovery. In this study, we introduce sPhysNet-Taut, a deep learning model fine-tuned on experimental data using a Siamese neural network architecture. This model directly predicts tautomer ratios in aqueous solution based on MMFF94-optimized molecular geometries. On experimental test sets, sPhysNet-Taut achieves state-of-the-art performance with root-mean-square error (RMSE) of 1.9 kcal/mol on the 100-tautomers set and 1.0 kcal/mol on the SAMPL2 challenge, outperforming all other methods. It also provides superior ranking power for tautomer pairs on multiple test sets. Our results demonstrate that fine-tuning on experimental data significantly enhances model performance compared to training from scratch. This work not only offers a valuable deep learning model for predicting tautomer ratios but also presents a protocol for modeling pairwise data. To promote usability, we have developed an accessible tool that predicts stable tautomeric states in aqueous solution by enumerating all possible tautomeric states and ranking them using our model. The source code and web server are freely accessible at https://github.com/xiaolinpan/sPhysNet-Taut and https://yzhang.hpc.nyu.edu/tautomer.

Nanoscale Manipulation of Single-Molecule Conformational Transition through Vibrational Excitation

Controlling molecular actions on demand is a critical step toward developing single-molecule functional devices. Such control can be achieved by manipulating the interactions between individual molecules and their nanoscale environment. In this study, we demonstrate the conformational transition of a single pyrrolidine molecule adsorbed on a Cu(100) surface, driven by vibrational excitation through tunneling electrons using scanning tunneling microscopy. We identify multiple transition pathways between two structural states, each governed by distinct vibrational modes. The nuclear motions corresponding to these modes are elucidated through density functional theory calculations. By leveraging fundamental forces, including van der Waals interactions, dipole-dipole interactions, and steric hindrance, we precisely tune the molecule-environment coupling. This tuning enables the modulation of vibrational energies, adjustment of transition probabilities, and selection of the lowest-energy transition pathway. Our findings highlight how tunable force fields in a nanoscale cavity can govern molecular conformational transitions, providing a pathway to engineer molecule-environment interactions for targeted molecular functionalities.

Tautomeric Conflicts in Forty Small-Molecule Databases

We have analyzed 40 different databases ranging in size from a few thousand to nearly 100 million molecules, comprising a total of over 210 million structures, for their tautomeric conflicts. A tautomeric conflict is defined as an occurrence of two or more structures within a data set identified by the tautomeric rules applied as being tautomers of each other. We tested a total of 119 detailed tautomeric transform rules expressed as SMIRKS, out of which 79 yielded at least one conflict. These transformations include three types of tautomerism: prototropic, ring-chain, and valence tautomerism. The databases analyzed spanned a wide variety of types including large aggregating databases, drug collections, and structure collections based on experimental data. All databases analyzed showed intra-database tautomeric conflicts. The conflict rates as percentage of the database were typically in the few tenths of a percent range, which for the largest databases amounts to >100,000 cases per database.

Formation, Selective Encapsulation, and Tautomerization Control of Isoindolone Utilizing Guanidinium Sulfonate Frameworks

Herein we report the use of tetrakis (guanidinium) pyrenetetrasulfonate (G4PYR) and bis (guanidinium) 1,5-napthalene disulfonate (G2NDS) to catalyze the cyclization of 2-cyanobenzamide (1) to isoindolone (2). Moreover, we demonstrate the remarkable selectivity of these guanidinium organosulfonate hosts in encapsulating 2 over 1. By thoroughly investigating the intramolecular cyclization reaction, we determined that guanidinium and the organosulfonate moiety acts as the catalyst in this process. Additionally, 2 is selectively encapsulated, even in mixtures of other structurally similar heterocycles like indole. Furthermore, the tautomeric state of 2 (amino isoindolone (2-A) and imino isoindolinone forms (2-I)) can be controlled by utilizing different guanidinium organosulfonate frameworks.

Growth "self-inhibition" of irbesartan desmotrope: surface intra-annular tautomer inter-conversion is the culprit

The newly discovered growth self-inhibition phenomenon of tautomeric crystals is now generalized to the demostrope (form B) of irbesartan that displays intra-annular tautomerism in neutral aqueous solutions. The dynamic intra-annular tautomer inter-conversion on the surface is the key factor. Our findings provide implications for producing and engineering tautomeric materials.

Modern Alchemical Free Energy Methods for Drug Discovery Explained

This Perspective provides a contextual explanation of the current state-of-the-art alchemical free energy methods and their role in drug discovery as well as highlights select emerging technologies. The narrative attempts to answer basic questions about what goes on "under the hood" in free energy simulations and provide general guidelines for how to run simulations and analyze the results. It is the hope that this work will provide a valuable introduction to students and scientists in the field.

Proton tautomerism and stereoisomerism in 5-[(dimethylamino)methylidene]-4-[3/4-(trifluoromethylphenyl)amino]-1,3-thiazol-2(5H)-ones: synthesis, crystal structure and spectroscopic studies

5-[(Dimethylamino)methylidene]-4-{[3-(trifluoromethyl)phenyl]amino}-1,3-thiazol-2(5H)-one and the [4-(trifluoromethyl)phenyl]amino derivative, both C13H12F3N3OS, with the trifluoromethyl group substituted at the arene ring at the meta and para positions, were synthesized to study the structural changes associated with proton tautomerism of the amidine system. The studied compounds were found to be in the amine tautomeric form in both the solid and the liquid (dimethyl sulfoxide solutions) phase. In both isomers, the [(trifluoromethyl)phenyl]amino residue assumes a synperiplanar conformation with respect to the thiazolone system, while the 5-[(dimethylamino)methylidene] residue adopts the Z configuration. Density functional theory (DFT) calculations correctly predicted that the synperiplanar arrangement is favoured in both isomers. In the crystal, the whole independent molecule of the para compound is disordered over two alternative positions, with occupancy factors of 0.926 (3) and 0.074 (3).

Biomineralization and Properties of Guanine Crystals

Guanine crystals with unique optical properties in organisms have been extensively studied and the biomineralization principles of guanine are being established. This review summarizes the fundamental physicochemical properties (solubility, tautomers, bands, and refractivity), polymorphs, morphology of biological and synthetic forms, and the reported biomineralization principles of guanine (selective recrystallization of amorphous precursor, preassembled scaffolds, additives, twinning, hypoxanthine doping, fluorescence, and assembly). The biomineralization principles of guanine will be helpful for the synthesis of guanine crystals with excellent properties and the design of functional organic materials for drugs, dyes, organic semiconductors, etc.