Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes

The RNA N6-adenosine methylation, resulting in N6-methyl adenosine (m6A), is one of the most important post-transcriptional modification events in the eukaryotic transcriptome, which is dynamically regulated by methyltransferases (writers), recognition proteins (readers) and demethylases (erasers). Human has five m6A readers namely YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 that specifically recognize and bind to the methylated m6A residue of RNA through their YT521-B homology (YTH) domains, which have been involved in the pathogenesis of diabetes mellitus and its diverse complications such as diabetic nephropathy. Instead of the native N6-methylation, we herein attempted to explore the molecular effect of various non-native N6-substitutions on adenosine (A) binding behavior to YTH domains. A systematic interaction profile of 40 reported N6-substituted adenosine (x6A) mononucleotides with 5 human reader YTH domains was created computationally. Heuristic clustering of the profile divided these YTH domains and these x6A mononucleotides into two subfamilies and three classes, respectively; they represent distinct intrinsic interaction modes between the domains and mononucleotides. Statistical survey unraveled that the volume (Vg) and hydrophobicity (Hg) of N6-substituted chemical groups exhibit linear and nonlinear correlations with the binding energy (ΔGttl) of x6A mononucleotides to YTH domains, respectively; N6-substitutions with moderate size and weak polarity are favorable for the x6A binding. From the profile the N6-bromomethyl adenosine (brm6A) was identified as a potent binder of YTHDF2 YTH domain; its affinity was improved significantly by 77.2-fold from A and considerably by 19.5-fold from m6A. Structural modeling observed that the N6-bromomethyl group of brm6A is tightly packed against an aromatic cage defined by the Trp432-Trp486-Trp491 triad of YTHDF2 YTH domain. Electron-correlation analysis revealed that the bromine atom can form geometrically and energetically satisfactory halogen-π interactions with the aromatic cage, thus conferring considerable affinity and specificity to the domain-brm6A interaction.

Halogen Bonding to the π-Systems of Polycyclic Aromatics

The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.

Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts

Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using 1 H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔGX ⋅⋅⋅Ph =0 to +1.5 kJ mol-1 ). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH3 ⋅⋅⋅arene contacts (ΔGMe ⋅⋅⋅Ph =0 to -1.4 kJ mol-1 ).

Investigation of the tight binding mechanism of a new anticoagulant DD217 to factor Xa by means of molecular docking and molecular dynamics

A new promising drug candidate DD217 has been proposed recently as a potent anticoagulant acting on factor Xa (fXa) target. It exhibits the lowest concentration of doubling the prothrombin time among the known anticoagulants. In order to explain the efficacy of DD217 in terms of molecular interactions with its target we studied the hypothesis of the tight binding mechanism by means of molecular dynamics simulations and statistical analysis of the trajectory. The conducted analysis confirms the significant contributions to the MM/GBSA estimated binding free energy of the S4 pocket residues as well the crucial role of establishing the hydrogen bonds between the ligand and the backbone amides of Gly216 and Gly218 of the target. The simulation results support the hypothesis of the tight binding mechanism of DD217 to fXa.Communicated by Ramaswamy H. Sarma.

Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning

Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict optimal binding geometries and enhance stacking interactions, usually high-level quantum mechanical calculations are performed. These calculations have two major drawbacks: they are very time consuming, and solvation can only be considered using implicit solvation. Therefore, most calculations are performed in vacuum. However, recent studies have revealed a direct correlation between the desolvation penalty, vacuum stacking interactions and binding affinity, making predictions even more difficult. To overcome the drawbacks of quantum mechanical calculations, in this study we use neural networks to perform fast geometry optimizations and molecular dynamics simulations of heteroaromatics stacked with toluene in vacuum and in explicit solvation. We show that the resulting energies in vacuum are in good agreement with high-level quantum mechanical calculations. Furthermore, we show that using explicit solvation substantially influences the favored orientations of heteroaromatic rings thereby emphasizing the necessity to include solvation properties starting from the earliest phases of drug design.

Thermodynamics and Mechanism of the Membrane Permeation of Hv1 Channel Blockers

The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and the respiratory burst of phagocytes. Inhibition of Hv1 may provide therapeutic avenues for the treatment of inflammatory diseases, breast cancer, and ischemic brain damage. In this work, we investigate two prototypical Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI), and 5-chloro-2-guanidinobenzimidazole (GBIC), from an experimentally screened class of guanidine derivatives. Both compounds block proton conduction by binding the same site located on the intracellular side of the channel. However, when added to the extracellular medium, the compounds strongly differ in their ability to inhibit proton conduction, suggesting substantial differences in membrane permeability. Here, we compute the potential of mean force for each compound to permeate through the membrane using atomistic molecular dynamics simulations with the adaptive biasing force method. Our results rationalize the putative distinction between these two blockers with respect to their abilities to permeate the cellular membrane.

Alkane Shape- and Size-Recognized Selective Vapor Sorption in "Channel-Like" Crystals Based on Thiacalixarene Assemblies

Alkanes composed of C-C and C-H show a low electric polarization, and therefore, there is only very weak interaction between alkanes and adsorbents. Thus, it is difficult to separate a specific alkane from a mixture of alkanes by adsorption. Here, two activated "channel-like" crystals generated from brominated thiacalix[4]arene propyl ethers, which adopt 1,3-alternate and partial cone conformations, recognize specific alkane vapors depending on alkane-shape and -size, sorting in three-type alkane guests such as linear, branched, and cyclic alkanes. Two activated crystals, which are prepared by removal of solvent upon heating under reduced pressure, incorporate branched and/or cyclic alkane vapors by a unique "gate-opening" mechanism via a crystal transformation in the process. Linear alkane vapors do not trigger gate opening and are not taken up by the activated crystals. The shape and size molecular-recognition properties of the activated crystals promises considerable usefulness for the separation of linear, branched, and cyclic alkanes.

STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding

The use of fragments to biophysically characterize a protein binding pocket and determine the strengths of certain interactions is a computationally and experimentally commonly applied approach. Almost all drug like molecules contain at least one aromatic moiety forming stacking interactions in the binding pocket. In computational drug design, the strength of stacking and the resulting optimization of the aromatic core or moiety is usually calculated using high level quantum mechanical approaches. However, as these calculations are performed in a vacuum, solvation properties are neglected. We close this gap by using Grid Inhomogeneous Solvation Theory (GIST) to describe the properties of individual heteroaromatics and complexes and thereby estimate the desolvation penalty. In our study, we investigated the solvation free energies of heteroaromatics frequently occurring in drug design projects in complex with truncated side chains of phenylalanine, tyrosine, and tryptophan. Furthermore, we investigated the properties of drug-fragments crystallized in a fragment-based lead optimization approach investigating PDE-10-A. We do not only find good correlation for the estimated desolvation penalty and the experimental binding free energy, but our calculations also allow us to predict prominent interaction sites. We highlight the importance of including the desolvation penalty of the respective heteroaromatics in stacked complexes to explain the gain or loss in affinity of potential lead compounds.

Two-dimensional halogen-bonded organic frameworks based on the tetrabromobenzene-1,4-dicarboxylic acid building molecule

2D halogen-bonded organic frameworks were readily engineered by strong and directional effects of the primary Br⋯O and the secondary Br⋯π halogen bonding interactions from the tetrabromobenzene-1,4-dicarboxylic acid building molecule involving 100% supramolecular yields.

Halogen-sensitive solvatochromism based on a phenolic polymer of tetraphenylethene

Herein, we describe the successful preparation of a methylene-bonded tetraphenylethene polymer using a phenolic-resin synthesis protocol. Our novel phenolic polymer showed solvatochromism in response to halogenated organic solvents. Solvatochromism is induced by halogen/π interactions between the polymer and the organic halide.

Herein, we describe novel phenolic polymer showed solvatochromism in response to halogenated organic solvents through halogen/π interactions.

Separation of halogenated benzenes enabled by investigation of halogen-π interactions with carbon materials

We report the existence of bimodal interactions, the π–π and halogen–π interactions, between the halogenated benzenes and aromatic materials.

The halogen–π (X–π) interaction is an intermolecular interaction between the electron-poor region of bonded halogen atoms and aromatic rings. We report an experimental evaluation of the halogen–π (X–π) interaction using liquid chromatography with carbon-material coated columns providing strong π interactions in the normal phase mode. A C₇₀-fullerene (C70)-coated column showed higher retentions for halogenated benzenes as the number of halogen substitutions increased as a result of X–π interactions. In addition, the strength of the X–π interaction increased in the order of F < Cl < Br < I. Changes to the UV absorption of C70 and the brominated benzenes suggested that the intermolecular interaction changed from the π–π interaction to X–π interaction as the number of bromo substitutions increased. Computer simulations also showed that the difference in dipole moments among structural isomers affected the strength of the π–π interaction. Furthermore, we concluded from small peak shifts in ¹H NMR and from computer simulations that the orbital interaction contributes to the X–π interactions. Finally, we succeeded in the one-pot separation of all isomers of brominated benzenes using the C70-coated column by optimizing the mobile phase conditions.

How Significant Are Unusual Protein-Ligand Interactions? Insights from Database Mining

We present a new approach to derive interaction propensities of protein-ligand atom pairs from mining of the Protein Data Bank. To ensure solid statistics, we use a line-of-sight contact filter and normalize the observed frequency of hits by a statistical null model based on exposed surface areas of atom types in the protein-ligand binding site. This allows us to investigate which intermolecular interactions and geometries are found more often than expected by chance in protein-ligand complexes. We focus our study on some of the unusual interactions that were postulated to be favorable, including σ-hole bonding of halogen and sulfur atoms, weak hydrogen bonding with fluorine as acceptor, and different types of dipolar interactions. Our results confirm some and challenge other common assumptions on these interactions and highlight other contact types that are yet underexplored in structure-based drug design.

Hydration of Aromatic Heterocycles as an Adversary of π-Stacking

Hydration is one of the key players in the protein-ligand binding process. It not only influences the binding process per se, but also the drug's absorption, distribution, metabolism, and excretion properties. To gain insights into the hydration of aromatic cores, the solvation thermodynamics of 40 aromatic mono- and bicyclic systems, frequently occurring in medicinal chemistry, are investigated. Thermodynamics is analyzed with two different methods: grid inhomogeneous solvation theory (GIST) and thermodynamic integration (TI). Our results agree well with previously published experimental and computational solvation free energies. The influence of adding heteroatoms to aromatic systems and how the position of these heteroatoms impacts the compound's interactions with water is studied. The solvation free energies of these heteroaromatics are highly correlated to their gas phase interaction energies with benzene: compounds showing a high interaction energy also have a high solvation free energy value. Therefore, replacing a compound with one having a higher gas phase interaction energy might not result in the expected improvement in affinity. The desolvation costs counteract the higher stacking interactions, hence weakening or even inverting the expected gain in binding free energy.

Quantum Monte Carlo Study of the Water Dimer Binding Energy and Halogen-π Interactions

Halogen-π systems are involved with competition between halogen bonding and π-interaction. Using the diffusion quantum Monte Carlo (DMC) method, we compare the interaction of benzene with diatomic halogens (X₂: Cl₂/Br₂) with the typical hydrogen bonding in the water dimer, taking into account explicit correlations of up to three bodies. The benzene-Cl₂/Br₂ binding energies (13.07 ± 0.42/16.62 ± 0.02 kJ/mol) attributed to both halogen bonding and dispersion are smaller than but comparable to the typical hydrogen bonding in the water dimer binding energy (20.88 ± 0.27 kJ/mol). All of the above values are in good agreement with those from the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)) results at the complete basis set limit (benzene-Cl₂/Br₂: 12.78/16.17 kJ/mol; water dimer: 21.0 kJ/mol).

Lone pair⋯π interaction versus σ-hole appearance in metal-bonded halogens

Three complexes of N-(2,5-diluorophenyl)-2-pyrazine carboxamide and ZnX₂ have been synthesized. The crystal structures reveal that in all three coordination compounds, metal-bound halides have interacted with π systems through a negative electrostatic region.

Halogen and Hydrogen Bonding Interplay in the Crystal Packing of Halometallocenes

This paper focuses in the influence of halogen atoms in the design and structural control of the crystal packing of Group VIII halogenated metallocenes. The study is based on the present knowledge on new types of intermolecular contacts such as halogen (X⋯X, C-X⋯H, C-X⋯π), π⋯π, and C-H⋯π interactions. The presence of novel C-H⋯M interactions is also discussed. Crystal packings are analysed after database search on this family of compounds. Results are supported by ab initio calculations on electrostatic charge distributions; Hirshfeld analysis is also used to predict the types of contacts to be expected in the molecules. Special attention is given to the competition among hydrogen and halogen interactions, mainly its influence on the nature and geometric orientations of the different supramolecular motifs. Supramolecular arrangements of halogenated metallocenes and Group IV di-halogenated bent metallocenes are also compared and discussed. Analysis supports halogen bonds as the predominant interactions in defining the crystal packing of bromine and iodine 1,1′-halometallocenes.

Site specificity of halogen bonding involving aromatic acceptors

Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.

Halogen-π Interactions between Benzene and X2/CX4 (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)

Various types of interactions between halogen (X) and π moiety (X-π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X₂ and CX₄ (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Møller-Plesset second-order perturbation theory (MP2), and various flavors of density functional theory (DFT) methods, we study complexes of benzene (Bz) with halogen-containing molecules X₂ and CX₄ (X = Cl/Br) and analyze various components of the interaction energy using symmetry adapted perturbation theory (SAPT). As for the lowest energy conformers (S1), X₂-Bz is found to have the T-shaped structure where the electropositive X atom-end of X₂ is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX₄-Bz has the stacked structure. In addition to this CX₄-Bz (S1), other low energy conformers of X₂-Bz (S2/S3) and CX₄-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X₂-Bz (S1), whereas the deviations are relatively small for CX₄-Bz where the dispersion is more important. The halogen bond shows highly anisotropic electron density around halogen atoms and the DFT results are very sensitive to basis set. The unsatisfactory performance of many density functionals could be mainly due to less accurate exchange. This is evidenced from the good performance by the dispersion corrected hybrid and double hybrid functionals. B2GP-PLYP-D3 and PBE0-TS(Tkatchenko-Scheffler)/D3 are well suited to describe the X-π interactions adequately, close to the CCSD(T)/CBS binding energies (within ∼1 kJ/mol). This understanding would be useful to study diverse X-π interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers.

Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F)

Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.

Exploring the role of a single water molecule in the tropospheric reaction of glycolaldehyde with an OH radical: a mechanistic and kinetics study

This work reveals that though a single-water molecule decelerates the atmospheric reaction between the glycolaldehyde and OH radical, however, it facilitates the cis–​trans interconversion along the hydrogen-abstraction pathways.

A series of lanthanide complexes with different N-donor ligands: synthesis, structures, thermal properties and luminescence behaviors

Complexes 1 and 2 are stitched together via Cl–π and hydrogen bonding interactions to form 1D, 2D, 3D supramolecular structures, while complexes 3 and 4 are packed together by Cl–Cl, π–π, and hydrogen bonding interactions to form 1D, 2D structures.

Dispersive interactions in solution complexes

Dispersive interactions are known to play a major role in molecular associations in the gas phase and in the solid state. In solution, however, their significance has been disputed in recent years on the basis of several arguments. A major problem until now has been the separation of dispersive and hydrophobic effects, which are both maximized in water due the low polarizability of this most important medium. Analyses of complexes between porphyrins and systematically varied substrates in water have allowed us to discriminate dispersive from hydrophobic effects, as the latter turned out to be negligible for complexations with flat surfaces such as porphyrins. Also, for the first time, it has become possible to obtain binding free energy increments ΔΔG for a multitude of organic residues including halogen, amide, amino, ether, carbonyl, ester, nitro, sulfur, unsatured, and cyclopropane groups, which turned out to be additive. Binding contributions for saturated residues are unmeasurably small, with ΔΔG > 1 kJ/mol, but they increase to, e.g., ΔΔG = 5 kJ/mol for a nitro group, a value not far from, e.g., that of a stacking pyridine ring. Stacking interactions of heteroarenes with porphyrins depend essentially on the size of the arenes, in line with polarizabilities, and seem to be rather independent of the position of nitrogen within the rings. Measurements of halogen derivatives indicate that complexes with porphyrins, cyclodextrins, and pillarenes as hosts in different media consistently show increasing stability from fluorine to iodine as the substituent. This, and the observed sequence with other substrates, is in line with the expected increase in dispersive forces with increasing polarizability. Induced dipoles, which also would increase with polarizability, can be ruled out as providing the driving source in view of the data with halides: the observed stability sequence is opposite the change of electronegativity from fluorine to iodine. The same holds for the solvent effect observed in ethanol-water mixtures. Dispersive contributions vary not only with the polarizability of the used media but also with the interacting receptor sites; it has been shown that for cucurbiturils the polarizability inside the cavity is extremely low, which also explains why hydrophobic effects are maximized with these hosts. Complexations with other known host compounds, however, such as those between cryptands or cavitands with, e.g., noble gases, bear the signature of dominating dispersive forces. Some recent examples illustrate that such van der Waals forces can also play an important role in complexations with proteins. Again, a clue for this is the increase in ΔG for inhibitor binding by 7 kJ/mol for, e.g., a bromine in comparison to a fluorine derivative.

Halogen and Hydrogen Bonding Benzothiophene Diol Derivatives: A Study Using ab initio Calculations and X-Ray Crystal Structure Measurements

The aim of this study is to describe and compare the supramolecular interactions, in the solid state, of chloro-, bromo-, and iodobenzothiophene diols. The compounds were obtained through organo-catalyzed reactions starting from 3-substituted halobenzothiophene carbaldehydes. Energies of the noncovalent interactions were obtained by density functional theory calculations. Bond distances and angles were found to be in accordance with those determined by X-ray structure analysis. anti-Bromobenzothiophene derivatives showed strong halogen⋅⋅⋅π interactions between bromine and the heterocyclic phenyl ring, corresponding to an energy of 7.5 kcal mol(-1). syn-Bromo and syn-iodo derivatives appeared to be isostructural, showing X⋅⋅⋅O (carbonyl) interactions, π stacking, and formation of extended hydrogen bonding networks. In contrast, the chloro derivatives displayed no halogen bonding interactions.

σ-Hole⋯π and lone pair⋯π interactions in benzylic halides

Depending on the relative orientation of the halogen atom and the phenyl ring, the benzylic halides studied show “classical” halogen⋯π bonds as well as intramolecular interactions without σ-hole participation based on n → π* (LP⋯π) interactions.

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

Correctly ranking compounds according to their computed relative binding affinities will be of great value for decision making in the lead optimization phase of industrial drug discovery. However, the performance of existing computationally demanding binding free energy calculation methods in this context is largely unknown. We analyzed the performance of the molecular mechanics continuum solvent, the linear interaction energy (LIE), and the thermodynamic integration (TI) approach for three sets of compounds from industrial lead optimization projects. The data sets pose challenges typical for this early stage of drug discovery. None of the methods was sufficiently predictive when applied out of the box without considering these challenges. Detailed investigations of failures revealed critical points that are essential for good binding free energy predictions. When data set-specific features were considered accordingly, predictions valuable for lead optimization could be obtained for all approaches but LIE. Our findings lead to clear recommendations for when to use which of the above approaches. Our findings also stress the important role of expert knowledge in this process, not least for estimating the accuracy of prediction results by TI, using indicators such as the size and chemical structure of exchanged groups and the statistical error in the predictions. Such knowledge will be invaluable when it comes to the question which of the TI results can be trusted for decision making.

Exploring water catalysis in the reaction of thioformic acid with hydroxyl radical: a global reaction route mapping perspective

Hydrogen abstraction pathways, in the gas-phase reaction of tautomers of thioformic acid (TFA), TFA(thiol), and TFA(thione), with hydroxyl radical in the presence and absence of single water molecule acting as a catalyst, is investigated with high-level quantum mechanical calculations at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p), CCSD(T)/6-311++G(d,p)//DFT/BHandHLYP/6-311++G(d,p), and DFT/B3LYP/6-311++G(2df,2p) levels of the theory. A systematic and automated search of the potential energy surface (PES) for the reaction pathways is performed using the global reaction route mapping (GRRM) method that employs an uphill walking technique to search prereaction complexes and transition states. The computations reveal significant lowering of the PES and substantial reduction in the activation energy for the hydrogen abstraction pathway in the presence of water, thereby proving water as an efficient catalyst in the reaction of both the TFA tautomers with OH radical. The hydrogen-bonding interactions are observed to be responsible for the large catalytic effect of water. Notably, in the case of TFA(thiol), formyl hydrogen abstraction is observed to be kinetically more favorable, while acidic hydrogen abstraction is observed to be thermodynamically more feasible. Interestingly, in the case of TFA(thione), reaction pathways involving only formyl hydrogen abstraction were observed to be feasible. The water-catalyzed hydrogen abstraction reaction of TFA with hydroxyl radical, investigated in this work, can provide significant insights into the corresponding reaction in the biological systems.

Heteroaromatic π-stacking energy landscapes

In this study we investigate π-stacking interactions of a variety of aromatic heterocycles with benzene using dispersion corrected density functional theory. We calculate extensive potential energy surfaces for parallel-displaced interaction geometries. We find that dispersion contributes significantly to the interaction energy and is complemented by a varying degree of electrostatic interactions. We identify geometric preferences and minimum interaction energies for a set of 13 5- and 6-membered aromatic heterocycles frequently encountered in small drug-like molecules. We demonstrate that the electrostatic properties of these systems are a key determinant for their orientational preferences. The results of this study can be applied in lead optimization for the improvement of stacking interactions, as it provides detailed energy landscapes for a wide range of coplanar heteroaromatic geometries. These energy landscapes can serve as a guide for ring replacement in structure-based drug design.

Acid-catalyzed nucleophilic additions to carbonyl groups: is the accepted mechanism the rule or an exception?

The transesterification reaction, and in particular the methanolysis of ethyl acetate with sulfuric acid as catalyst, is used as a model reaction to study the acid-catalyzed nucleophilic addition to a carbonyl group. Continuum solvation methods (SMD and IEF-PCM) and the MPWB1K functional are used. The reaction mechanism is studied in methanol and in acetonitrile as solvents. Our results indicate that the acid-catalyzed addition mechanism is stepwise, and the transition state (TS) is a contact ion-pair. The counteranion of the acid catalyst remains in the reaction site playing an important role in the TS of this reaction. Changes in the reaction kinetics and the ionic/nonionic nature of the TS with the ionizing ability of the solvent and the strength of the acid catalyst are explored. Additional calculations at the CBS-Q3 level of theory reinforce the conclusions of this paper. The results obtained allow the generalization of important ideas regarding the mechanism of the nucleophilic addition to carbonyl groups.