Tautomeric Equilibria in Relation to Pi-Electron Delocalization

Conjugate Addition of Carbon Acids to β,γ-Unsaturated α-Keto Esters: Product Tautomerism and Applications for Asymmetric Synthesis of Benzo[a]phenazin-5-ol Derivatives

A correlation between the equilibrium ratio of tautomeric products generated by the asymmetric Michael reactions of cyclic carbon acids with β,γ-unsaturated α-keto esters and the chemical shift of the α-proton in starting nucleophilic substrates was revealed which makes equilibration predictable. New tetrahydropyran-fused benzo[a]phenazins were enantioselectively (up to 99% ee) synthesized from β,γ-unsaturated α-keto esters and benzo[a]phenazin-5-ol, a powerful anti-cancer agent sAJM589. Facile recyclability of catalyst Ia in the catalytic reactions was demonstrated.

Catalyst-Free Synthesis of Polysubstituted 5-Acylamino-1,3-Thiazoles via Hantzsch Cyclization of α-Chloroglycinates

A catalyst-free heterocyclization reaction of α-chloroglycinates with thiobenzamides or thioureas leading to 2,4-disubstituted-5-acylamino-1,3-thiazoles has been developed. The methodology provides straightforward access to valuable building blocks for pharmaceutically relevant compounds.

Photochemical Transformations of Dichloroacetamide Safeners

Dichloroacetamide safeners are commonly added to commercial chloroacetamide herbicide formulations and widely used worldwide, but their environmental fate has garnered little scrutiny as a result of their classification as "inert" ingredients. Here, we investigated the photolysis of dichloroacetamide safeners to better understand their persistence and the nature of their transformation products in surface waters. High-resolution mass spectrometry (HRMS) and nuclear magnetic resonance (NMR) spectroscopy were used to characterize photoproducts. Of the four commonly used dichloroacetamide safeners, only benoxacor undergoes direct photolysis under simulated natural sunlight ( t_1/2 ∼ 10 min). Via a photoinitiated ring closure, benoxacor initially yields a monochlorinated intermediate that degrades over longer irradiation time scales to produce two fully dechlorinated diastereomers and a tautomer, which further photodegrade over several days to a structurally related aldehyde confirmed via NMR. Dichlormid, AD-67, and furilazole were more slowly degraded by indirect photolysis in the presence of the photosensitizers nitrate, nitrite, and humic acid. Reactive entities involved in these reactions are likely hydroxyl radical and singlet oxygen based on the use of selective quenchers. These safeners also directly photolyzed under higher energy ultraviolet (UV) light, suggesting their potential transformation in engineered systems using UV for disinfection. The finding that dichloroacetamide safeners can undergo photolysis in environmental systems over relevant time scales demonstrates the importance of evaluating the fate of this class of "inert" agrochemicals.

Tautomerism in Azo and Azomethyne Dyes: When and If Theory Meets Experiment

The performance of 26 hybrid density functionals was tested against a tautomeric dataset (TautData), containing experimental information for the keto-enol tautomeric equilibrium in 16 tautomeric azodyes and Schiff bases in cyclohexane, carbon tetrachloride and acetonitrile. The results have shown that MN12-SX, BHandH and M06-2X can be used to describe the tautomeric state of the core structures in the frame of ~0.5 kcal/mol error and correctly predict the tautomeric state in respect of dominating tautomeric form. Among them MN12-SX is the best performer, although it fails to describe the nonplanarity of some of the enol tautomers. The same experimental dataset was used to develop and test a special DFT functional (TautLYP) aimed at describing the tautomeric state in azo- and azomethyne compounds in solution when nonspecific solvents are used.

Application of the Extended HOMED (Harmonic Oscillator Model of Aromaticity) Index to Simple and Tautomeric Five-Membered Heteroaromatic Cycles with C, N, O, P, and S Atoms

The geometry-based HOMA (Harmonic Oscillator Model of Aromaticity) descriptor, based on the reference compounds of different delocalizations of n- and π-electrons, can be applied to molecules possessing analogous bonds, e.g., only CC, only CN, only CO, etc. For compounds with different heteroatoms and a different number of CC, CX, XX, and XY bonds, its application leads to some discrepancies. For this reason, the structural descriptor was modified and the HOMED (Harmonic Oscillator Model of Electron Delocalization) index defined. In 2010, the HOMED index was parameterized for compounds with C, N and O atoms. For parametrization, the reference molecules of similar delocalizations of n- and π-electrons were employed. In this paper, the HOMED index was extended to compounds containing the CP, CS, NN, NP, PP, NO, NS, PO, and PS bonds. For geometrical optimization of all reference molecules and of all investigated heterocompounds, the same quantum–chemical method {B3LYP/6-311+G(d,p)} was used to eliminate errors of the HOMED estimation. For some tautomeric systems, the Gn methods were also employed to confirm tautomeric preferences. The extended HOMED index was applied to five-membered heterocycles, simple furan and thiophene, and their N and P derivatives as well as for tautomeric pyrrole and phosphole and their N and P derivatives. The effects of additional heteroatom(s) in the ring on the HOMED values for furan are parallel to those for thiophene. For pyrroles, aromaticity dictates the tautomeric preferences. An additional N atom in the ring only slightly affects the HOMED values for the favored and well delocalized NH tautomers. Significant changes take place for their rare CH forms. When intramolecular proton-transfer is considered for phosphole and its P derivatives, the PH tautomers seem to be favored only for 1,2,3-triphosphole/1,2,5-triphosphole and for 1,2,3,5-tetraphosphole. For other phospholes, the CH forms have smaller Gibbs energies than the PH isomers. For phosphazoles, the labile proton in the favored form is linked to the N atom. The PH forms have smaller HOMED indices than the NH tautomers but higher than the CH ones.

Dynamics of Oxygen-Independent Photocleavage of Blebbistatin as a One-Photon Blue or Two-Photon Near-Infrared Light-Gated Hydroxyl Radical Photocage

Development of versatile, chemically tunable photocages for photoactivated chemotherapy (PACT) represents an excellent opportunity to address the technical drawbacks of conventional photodynamic therapy (PDT) whose oxygen-dependent nature renders it inadequate in certain therapy contexts such as hypoxic tumors. As an alternative to PDT, oxygen free mechanisms to generate cytotoxic reactive oxygen species (ROS) by visible light cleavable photocages are in demand. Here, we report the detailed mechanisms by which the small molecule blebbistatin acts as a one-photon blue light-gated or two-photon near-infrared light-gated photocage to directly release a hydroxyl radical (^•OH) in the absence of oxygen. By using femtosecond transient absorption spectroscopy and chemoselective ROS fluorescent probes, we analyze the dynamics and fate of blebbistatin during photolysis under blue light. Water-dependent photochemistry reveals a critical process of water-assisted protonation and excited state intramolecular proton transfer (ESIPT) that drives the formation of short-lived intermediates, which surprisingly culminates in the release of ^•OH but not superoxide or singlet oxygen from blebbistatin. CASPT2//CASSCF calculations confirm that hydrogen bonding between water and blebbistatin underpins this process. We further determine that blue light enables blebbistatin to induce mitochondria-dependent apoptosis, an attribute conducive to PACT development. Our work demonstrates blebbistatin as a controllable photocage for ^•OH generation and provides insight into the potential development of novel PACT agents.

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC^+•), and negative ionization, called one-electron reduction (iC + e → iC^-•), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC^+• is close to that of the iC conjugate acid, and basicity of iC^-• is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC^+•, iC^-•, U, U^+•, U^-•, C, C^+•, and C^-• are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.

Open-Resonance-Assisted Hydrogen Bonds and Competing Quasiaromaticity

The delocalization of electron density upon tautomerization of a proton across a conjugated bridge can alter the strength of hydrogen bonds. This effect has been dubbed resonance-assisted hydrogen bonding (RAHB) and plays a major role in the energetics of the tautomeric equilibrium. The goal of this work was to investigate the role that π-delocalization plays in the stability of RAHBs by engaging other isomerization processes. Similarly, acid-base chemistry has received little experimental attention in studies of RAHB, and we address the role that acid-base effects play in the tautomeric equilibrium. We find that π-delocalization and the disruption of adjacent aromatic rings is the dominant effect in determining the stability of a RAHB.

Critical Role of Anions in Platinum(II) Precursors upon the Structural Motifs of Six-Membered Cycloplatinated N,N',N″-Triarylguanidines

The reactions of cis-[Pt(OAc)₂(DMSO)₂] with 2 equiv of sym N,N',N″-triarylguanidines, [ArN=C(NHAr)₂], in toluene under reflux condition for 8 h afforded six-membered cycloplatinated guanidines, [Pt{κ²(C,N)}(OAc){κ¹ N(ArN=C(NHAr)₂)}] [sym = symmetrical; Ar = 2-MeC₆H₄ (1) and 2,4-Me₂C₆H₃ (2)], in 82 and 84% yields, respectively. The salt metathesis reaction of 1 with 1 equiv of AgTFA in CH₂Cl₂ at room temperature (RT) afforded [Pt{κ²(C,N)}(TFA){κ¹ N(ArN=C(NHAr)₂)}] (3) in 94% yield. The reaction of cis-[Pt(TFA)₂(DMSO)₂] with 1 equiv of [ArN=C(NHAr)₂] in toluene under reflux condition for 8 h afforded six-membered cycloplatinated guanidines, [Pt{κ²(C,N)}(TFA)(DMSO)] [Ar = 2-MeC₆H₄ (4), 4-MeC₆H₄ (5), 2,4-Me₂C₆H₃ (6), and 2-(MeO)C₆H₄ (7)], in ≥73% yields. The reaction of trans-[PtCl₂(PhCN)₂] with 2 equiv of [ArN=C(NHAr)₂] in toluene under reflux condition for 48 h afforded trans-[PtCl₂{ArN=C(NHAr)₂}₂] [Ar = 2-MeC₆H₄ (8) and 2,4-Me₂C₆H₃ (9)] in 90 and 45% yields, respectively. Complexes 8 and 9 were separately refluxed in MeOH for 8 h to afford six-membered cycloplatinated guanidines, [Pt{κ²(C,N)}(μ-Cl)]₂ (10 and 11), in 93 and 96% yields, respectively, with concomitant formation of the respective guanidinium salts, [(ArNH)₃C]Cl, as the byproduct. Platinacycle 10 was treated with 2 equiv of AgTFA in CH₂Cl₂ at RT to afford six-membered cycloplatinated guanidine, [Pt{κ²(C,N)}(μ-TFA)]₂ (12), in 94% yield. The new compounds were characterized by analytical techniques and multinuclear NMR (¹H, ¹³C, and ¹⁹⁵Pt) spectroscopy, and further, molecular structures of 10 compounds were determined by single-crystal X-ray diffraction. The structural motif in 1·1/2CH₂Cl₂ and 3 is novel in that it contains a planar six-membered [Pt{κ²(C,N)}] unit and a nonplanar eight-membered [Pt{κ²(N,O)}] ring, wherein OAc and the guanidine ligands are linked through a N-H···O hydrogen bond. The six-membered cycloplatinated structural motifs present in 10/11·C₇H₈ and 12·CH₂Cl₂ are also unprecedented in the literature. The number and nature of solution species of new complexes were unambiguously investigated by detailed NMR studies. The critical role of anions in Pt(II) precursors upon the course of cycloplatination and thus the motifs in the products were addressed. Plausible mechanisms of cycloplatination reactions are discussed.

The influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study

Zinc cation (Zn2+) plays an important role in the chemistry of DNA base pairs. In this work, the influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine (T) is investigated by the density functional theory method. It is shown that the calculated binding energies between Zn2+ and T are exothermic in vacuum. Compared to T, Zn2+ increases the stability of tautomer T' by 28.7 kcal mol-1, promoting the intramolecular proton transfer of T. But in a micro-water environment, the attachment processes of Zn2+ to T hydrates, penta-hydrated Zn2+ to T, and penta-hydrated Zn2+ to T hydrates lead to the rearrangement of molecules and the redistribution of charges. The conventional T is still the most stable form and the influence of Zn2+ is much reduced and the proton transfer is thermodynamically unfavored. The detailed characterization is helpful to understand the genotoxicity of zinc ions.

Proton transfer triggered proton transfer: a self-assisted twin excited state intramolecular proton transfer

The double excited state intramolecular proton transfer (ESIPT) of 3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazole (bis-HPTA) has been investigated and found to undergo a new type of proton transfer.

Natural polyprenylated benzophenone: keto-enol tautomerism from density functional calculations and the AIM theory

The quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT) calculations were employed to investigate the structure and tautomeric equilibrium of epiclusianone, a polyisoprenylated benzophenone with interesting biological activities. Two different exchange-correlation functionals were employed, namely ωB97x-D and M06-2x, including implicit solvent models (benzene and DMSO). Our results for the thermodynamic properties show that the isomer in which the H atom is bonded to the oxygen away from the benzene ring is the most stable tautomer form of the epiclusianone, thus confirming previous charge density analysis from X-ray diffraction data (Martins et al. J Braz Chem Soc 18(8):1515-1523, 22).

Proton tautomerism for strong polarization switching

Ferroelectrics based on proton tautomerism are promising in low-field and above-room-temperature operations. Here seven organic ferroelectric crystals are examined to search for efficient switching of strong spontaneous polarization on proton tautomerism. Solution-grown crystals exhibit strong pinning of ferroelectric domain walls, but excellent switching performance is awakened by depinning domain walls under thermal annealing and/or repetitive bipolar pulses with a high voltage. Compared with ferroelectric polymers such as polyvinylidefluoride, the optimized polarizations are comparable or stronger in magnitude whereas the coercive fields are two orders of magnitude weaker. The polarization of croconic acid, in particular, breaks its own record for organic systems in increasing from 21 to 30 μC cm⁻² and now exceeds those of some commercial ferroelectric materials such as SrBi₂Ta₂O₉ and BaTiO₃. Optimization reduces the discrepancy of the spontaneous polarization with the results of the first-principles calculations to less than 15%. The cooperative roles of proton transfer and π-bond switching are discussed by employing the point-charge model and hydrogen-bond geometry.

Ferroelectrics based on proton tautomerism are promising in low-field and above-roomtemperature operations. Here the authors establish a procedure to optimize spontaneous polarizations, finding that the polarization in croconic acid breaks its own record for organic systems.

Entropy in multiple equilibria, theory and applications

Entropy controls the dependence of the equilibrium constants in the synthesis of host–guest composites on the occupation rc for channels of different length.

Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase

Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)_n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.

H-Bond: Τhe Chemistry-Biology H-Bridge

H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.

Resonance-Assisted Hydrogen Bonding as a Driving Force in Synthesis and a Synthon in the Design of Materials

Resonance-assisted hydrogen bonding (RAHB), a concept introduced by Gilli and co-workers in 1989, concerns a kind of intramolecular H-bonding strengthened by a conjugated π-system, usually in 6-, 8-, or 10-membered rings. This Review highlights the involvement of RAHB as a driving force in the synthesis of organic, coordination, and organometallic compounds, as a handy tool in the activation of covalent bonds, and in starting moieties for synthetic transformations. The unique roles of RAHB in molecular recognition and switches, E/Z isomeric resolution, racemization and epimerization of amino acids and chiral amino alcohols, solvatochromism, liquid-crystalline compounds, and in synthons for crystal engineering and polymer materials are also discussed. The Review can provide practical guidance for synthetic chemists that are interested in exploring and further developing RAHB-assisted synthesis and design of materials.

Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies

Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.

XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional refinement on XModeScore is also discussed.