Anionic Tautomers Research Articles

Stable Parent Anions of Dopamine and Adrenaline: A New Form of Neurotransmitters.

Previously, dopamine and adrenaline were only known to exist in three closed-shell forms: neutral molecules (including zwitterions), protonated cations, and deprotonated anions. In the present work, stable open-shell parent anions of dopamine and adrenaline were generated in the gas phase and characterized by a combination of anion photoelectron spectroscopy and calculations. These anions were formed as a result of an enol-keto-type tautomerization initiated by the attachment of excess electrons. Calculations showed that hydrogen atoms on the hydroxyl groups of dopamine and adrenaline migrated to adjacent carbon atoms under the influence of the additional electron, breaking the aromaticity of the benzene ring and resulting in the formation of the rare anionic tautomers. We speculate that the secondary electrons generated in scenarios such as radiotherapy could produce the anions reported in this work, providing a potential new depletion channel of these molecules in vivo.

Modeling of stability and properties of anionic and cationic tautomers of the 3-hydroxypyridin-4-one system

DFT, MP2, CBS-APNO, G4 and CCSD(T) calculations were performed for anionic and cationic tautomers of 3-hydroxypyridin-4-one molecule, a parent molecular system for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. Performed calculations show that the 3-hydroxypyridin-4-one’s anion exists in the structure with one hydroxyl group (in the meta position to the nitrogen atom in the ring) and protonated nitrogen atom. Such a “protection” of the OCCO by protonation of one oxygen atom should weaken potentially strong metal ion binding properties of studied system. In the case of 3-hydroxypyridin-4-one’s cation, the most stable is the structure in which all hetero atoms, two oxygens and the nitrogen atoms, are protonated. Properties of anionic and cationic tautomers were studied using several aromaticity indices (HOMA, NICS, PDI, Iring, MCI KMCI) and population analyses (AIM, NBO and GAPT methods). The AIM methodology was also used for determination of hydrogen bond properties and integration of atomic energies. Results served by these methods were used to explain the energetical orders of anionic and cationic tautomers. Changes in atomic charges upon protonation and deprotonation are also discussed.

Computational Study of Proton Transfer in Tautomers of 3- and 5-Hydroxypyrazole Assisted by Water.

The tautomerism of 3- and 5-hydroxypyrazole is studied at the B3LYP, CCSD and G3B3 computational levels, including the gas phase, PCM-water effects, and proton transfer assisted by water molecules. To understand the propensity of tautomerization, hydrogen-bond acidity and basicity of neutral species is approached by means of correlations between donor/acceptor ability and H-bond interaction energies. Tautomerism processes are highly dependent on the solvent environment, and a significant reduction of the transition barriers upon solvation is seen. In addition, the inclusion of a single water molecule to assist proton transfer decreases the barriers between tautomers. Although the second water molecule further reduces those barriers, its effect is less appreciable than the first one. Neutral species present more stable minima than anionic and cationic species, but relatively similar transition barriers to anionic tautomers.

A Quantum-Chemical Study of Tautomeric Equilibria of Fluorescein Dyes in DMSO

We evaluated the relative thermodynamic stability of various molecular and anionic tautomers of fluorescein, its 2,4,5,7-tetrabromo derivative (eosin), and also sulfofluorescein, 4'- and 5'-amino-fluoresceins, and 2,4,5,7-tetranitrofluorescein in DMSO, based on a quantum-chemical investigation; in some cases the calculations were performed for gas phase and aqueous solutions. These results, obtained for 39 structures (15 of which were studied by quantum-chemical methods for the first time) generally agree with the previously published experimental data.

Spectroscopical properties of a DTAF-labeled hydrophilic–hydrophobic copolymer in water and surfactant micelles

Emulsion copolymerization of hydrophilic α-tert-butoxy-ω-vinylbenzyl-polyglycidol macromonomer with styrene yields core–shell microspheres and a water-soluble copolymer fraction. This copolymer has a higher content of hydrophilic polyglycidol attested by 1H NMR. Further information is acquired by labeling the copolymer with 5-(4,6-dichlorotriazinyl)aminofluorescein (DTAF) and making absorption and fluorescence studies. The acquired data on aqueous solution of labeled copolymer without (L) and with micelles of dodecyltrimethylammonium chloride (LD), sodium dodecylsulfate (LS) and hexaethyleneglycol mono n-dodecyl ether (LE) reveal that the dianionic and anionic tautomers of the DTAF-label are apparent and concordant with the recorded spectrophotometric pKa values. The emission intensities, quantum yields and lifetimes obey the sequence LE < LS < L < LD. They are along with the increasingly deprotonated forms of the fluorophore and unveil that the micelle-label interactions depend on the surfactant.

Combinatorial-computational-chemoinformatics (C3) approach to finding and analyzing low-energy tautomers.

Finding the most stable tautomer or a set of low-energy tautomers of molecules is critical in many aspects of molecular modelling or virtual screening experiments. Enumeration of low-energy tautomers of neutral molecules in the gas-phase or typical solvents can be performed by applying available organic chemistry knowledge. This kind of enumeration is implemented in a number of software packages and it is relatively reliable. However, in esoteric cases such as charged molecules in uncommon, non-aqueous solvents there is simply not enough available knowledge to make reliable predictions of low energy tautomers. Over the last few years we have been developing an approach to address the latter problem and we successfully applied it to discover the most stable anionic tautomers of nucleic acid bases that might be involved in the process of DNA damage by low-energy electrons and in charge transfer through DNA. The approach involves three steps: (1) combinatorial generation of a library of tautomers, (2) energy-based screening of the library using electronic structure methods, and (3) analysis of the information generated in step (2). In steps 1–3 we employ combinatorial, computational and chemoinformatics techniques, respectively. Therefore, this hybrid approach is named “Combinatorial*Computational*Chemoinformatics”, or just abbreviated as C3 (or C-cube) approach. This article summarizes our developments and most interesting methodological aspects of the C3 approach. It can serve as an example how to identify the most stable tautomers of molecular systems for which common chemical knowledge had not been sufficient to make definite predictions.

Conformational and Substitution Effects on the Electron Distribution in a Series of Anthocyanidins

Density functional theory (DFT) and polarizable continuum solvation model (PCM) calculations have been applied to the study of the acid/base and prototropic equilibria of anthocyanidins. The results indicate that, excluding pelargonidin, the most favored neutral tautomers in solution are deprotonated at C4'. With the same exception, deprotonations at C5 and C4' characterize the most stable anionic tautomers in solution. The equilibrium population of tautomers is mainly modified along the series by the substitution pattern on the B-ring. Electron densities, analyzed within the formalism of the quantum theory of atoms in molecules (QTAIM), indicate that the electron distribution of cations, neutral forms, and anions is not well described by the Lewis structures usually employed to represent them.

Theoretical Study on the Relative Energies of Anionic Pterin Tautomers

Abstract Pterins exist as several tautomeric forms and behave as weak acids in aqueous solutions. Therefore, several acidbase equilibria may be present. For several pterin derivatives, the range of the experimental pKa lies in the range 6-8. The anionic form of the lactam structure is the only structure considered in the literature to represent the chemistry of pterins in alkaline solution. In the present study, density functional theory calculations were used to determine the relative energies of various anionic tautomers of pterin present in aqueous solution which may play a role in chemical and biological systems.

Solvation free energies of molecules. The most stable anionic tautomers of uracil.

Anionic states of nucleic acid bases are suspected to play a role in the radiation damage processes of DNA. Our recent studies suggested that the excess electron attachment to the nucleic acid bases can stabilize some rare tautomers, i.e. imine-enamine tautomers and other tautomers with a proton being transferred from nitrogen sites to carbon sites (with respect to the canonical tautomer). So far, these new anionic tautomers have been characterized by the gas-phase electronic structure calculations and photoelectron spectroscopy experiments. In the current contribution we explore the effect of water solvation on the stability of the new anionic tautomers of uracil. The accurate free energies of solvation are calculated in a two step approach. The major contribution was calculated using the classical free-energy perturbation adiabatic-charging approach, where it is assumed that the solvated molecule has the charge distribution given by the polarizable continuum model. In the second step the free energy of solvation is refined by taking into account the real, average solvent charge distribution. This is done using our accelerated QM/MM simulations, where the QM energy of the solute is calculated in the mean potential averaged over many MD steps. We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer.

Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine

Recently, we reported the discovery of adiabatically bound anions of guanine that might be involved in the processes of DNA damage by low-energy electrons and in charge transfer through DNA. These anions correspond to some tautomers that have been ignored thus far. They were identified using a hybrid quantum mechanical-combinatorial approach in which an energy-based screening was performed on the library of 499 tautomers with their relative energies calculated with quantum chemistry methods. In the current study, we analyze the adiabatically bound anions of guanine in two aspects: (1) the geometries and excess electron distributions are analyzed and compared with anions of the most stable neutrals to identify the sources of stability; (2) the chemical space of guanine tautomers is explored to verify if these new tautomers are contained in a particular subspace of the tautomeric space. The first task involves the development of novel approaches-the quantum chemical data like electron density, orbital, and information on its bonding/antibonding character are coded into holograms and analyzed using chemoinformatics techniques. The second task is completed using substructure analysis and clustering techniques performed on molecules represented by 2D fingerprints. The major conclusion is that the high stability of adiabatically bound anions originates from the bonding character of the pi orbital occupied by the excess electron. This compensates for the antibonding character that usually causes significant buckling of the ring. Also, the excess electron is more homogenously distributed over both rings than in the case of anions of the most stable neutral species. In terms of 2D substructure, the most stable anionic tautomers generally have additional hydrogen atoms at C8 and/or C2 and they do not have hydrogen atoms attached to C4, C5, and C6. They also form an "island of stability" in the tautomeric space of guanine.

Adiabatically Bound Valence Anions of Guanine

It is believed that guanine, a basic component of DNA and RNA, has the smallest affinity to an excess electron among all nucleic acid bases. Our experimental and computational findings indicate, however, that many so far neglected tautomers of guanine support adiabatically bound anionic states in the gas phase. The computed values of electron vertical detachment energy for the most stable anionic tautomers are within a broad range of the dominant feature of the photoelectron spectrum. We suggest that guanine might be the strongest excess electron acceptor among nucleic acid bases. Thus it might be critical to radiobiological damage of DNA and it might contribute to those chemical transformations of DNA that proceed through bound anionic states.

Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid bases

Anionic states of nucleic acid bases (NABs) are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated NAB parent anions probed mostly dipole-bound states, which are not present in condensed phase environments. Recently, we demonstrated that very rare tautomers of uracil (U), cytosine (C), adenine (A), and guanine (G), which are obtained from canonical tautomers through N-to-C proton transfers, support valence anionic states. Here we report the photoelectron spectrum of the final member of the NABs series: the valence state of the thymine (T) anion. Additionally, we summarized the work of all five NABs. All of the newfound anionic tautomers of the NABs may be formed via dissociative electron attachment followed by hydrogen atom reattachment to a carbon atom. Furthermore, these unusual tautomers may affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike dipole bound states, could exist in condensed phases and may be relevant to radiobiological damage.

Bound anionic states of adenine.

Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the newfound anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike the dipole-bound state, could exist in condensed phases and might be relevant to radiobiological damage. The discovery of these valence anionic states of adenine was facilitated by the development of (i) an experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a combinatorial/quantum chemical approach for identification of the most stable tautomers of organic molecules.

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).

Computational Studies of Nucleophilic Attack and Protonation of Electron-Deficient Benzoheterocycle Triosmium Clusters

The density functional theory method has been applied to gain insights into the regioselectivity of nucleophilic attack and protonation of electron-deficient benzoheterocycle triosmium clusters. We report our computational results on the reaction of the green 46-electron triosmium clusters Os3(CO)(9)(mu3-eta2-(LH))(mu-H) (L = benzoxazole, 1a; benzothiazole, 1b; dihydroquinoline, 1c; 1,3-dehydroindoline, 1d; 4H-3,1-benzoxazine, 1e) with hydride (H-) and proton (H+) in order to elucidate factors affecting the observed differences in the structure of the kinetic products of these reactions. Transition-state calculations for the interconversion of the anionic tautomers resulting from H- attack on the clusters 1a-e show that the activation energies of these anionic clusters are considerably lower than the previously reported barriers for related neutral clusters. Calculations also reveal that the structures of the kinetic products resulting from sequential H-/H+ attack are determined by the protonation process.

“On the complexation of allopurinol with β-cyclodextrin”

NMR diffusion coefficient measurements and PM3 theoretical calculations were employed in the study of the inclusion complexation of allopurinol with β-cyclodextrin (β-CD) at pH 6.5 and 10.0. Experimental findings revealed an increase in the association constant from 16 to 30 M−1 as a consequence of guest deprotonation. PM3 quantum-mechanical calculations were performed to investigate the complexation process between β-CD and allopurinol, considering the most stable neutral and anionic tautomers of the guest. The binding energies obtained from the computational study were in agreement with the experimental observations, indicating that the anionic complex was more stable than the neutral one. Such unusual behavior was related to hydrogen bonding interactions between β-CD and the anionic guest, leading to the increase of the association constant as a consequence of guest deprotonation.

Finding Adiabatically Bound Anions of Guanine through a Combinatorial Computational Approach

In summary, guanine supports many adiabatically bound valence anions, which result from enamine-imine transformations of the most stable neutral tautomers. These stable anionic tautomers have been found using combinatorial-computational prescreening at the B3LYP level of theory followed by CCSD(T)/aug-cc-pVDZ calculations. The new anionic tautomers contradict a common opinion that guanine has the lowest electron affinity among nucleobases. The new anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom. They might affect the structure and properties of DNA and RNA exposed to low-energy electrons. Chemical transformations of DNA triggered by the new anionic tautomers will be explored in our future studies.

Stabilization of Very Rare Tautomers of 1-Methylcytosine by an Excess Electron

We characterized valence anionic states of 1-methylcytosine using various electronic structure methods. We found that the most stable valence anion is related to neither the canonical amino-oxo nor a rare imino-oxo tautomer, in which a proton is transferred from the N4 to N3 atom. Instead, it is related to an imino-oxo tautomer, in which the C5 atom is protonated. This anion is characterized by an electron vertical detachment energy (VDE) of 2.12 eV and it is more stable than the anion based on the canonical tautomer by 1.0 kcal/mol. The latter is characterized by a VDE of 0.31 eV. Another unusual low-lying imino-oxo tautomer with a VDE of 3.60 eV has the C6 atom protonated and is 3.6 kcal/mol less stable than the anion of the canonical tautomer. All these anionic states are adiabatically unbound with respect to the canonical amino-oxo neutral, with the instability of 5.8 kcal/mol for the most stable valence anion. The mechanism of formation of anionic tautomers with carbon atoms protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to the C5 or C6 atom. The six-member ring structure of anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Indeed the neutral systems collapse without a barrier to a linear or a bicyclo structure, which might be viewed as lesions to DNA or RNA. Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated.

Stabilization of very rare tautomers of uracil by an excess electron

We characterized valence-type and dipole-bound anionic states of uracil using various electronic structure methods. We found that the most stable anion is related to neither the canonical 2,4-dioxo nor a rare imino-hydroxy tautomer. Instead, it is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion is characterized by an electron vertical detachment energy (VDE) of 1267 meV and it is adiabatically stable with respect to the canonical neutral by 3.93 kcal mol(-1). It is also more stable by 2.32 and 5.10 kcal mol(-1) than the dipole-bound and valence anion, respectively, of the canonical tautomer. The VDE values for the former and the latter are 73 and 506 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2499 meV has a proton transferred from N3H to C5. It is less stable than the neutral canonical tautomer by 1.38 kcal mol(-1). The mechanism of formation of anionic tautomers with the carbon C5 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of anionic tautomers with carbon atoms protonated might be unstable upon an excess electron detachment. Indeed, the neutral systems resulting from electron detachment from anionic tautomers with carbon atoms protonated evolve along barrier-free decomposition pathways to a linear or a bicyclo structure, which might be viewed as lesions to RNA. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral and the two most stable tautomers have carbon atoms protonated.

Quantum-chemical modeling of the tautomeric equilibria of modified anionic nucleic acid bases

The results of semiempirical quantum chemical calculations performed on the tautomeric forms of four modified anionic nucleic acid bases, i.e. the anions of the 1-methyl-5-hydroxyuracil, 1- methyl-5-hydroxycytosine, 9-methyl-8-hydroxyadenine, and 9-methyl-8-hydroxyguanine, allow prediction of the mutagenically most active forms of these compounds. Preliminary calculations on base pairs between modified and normal bases indicate strong bonding to the most stable anionic tautomers of modified bases.