Tautomerization Barrier Research Articles

Improving a Methane C-H Activation Complex by Metal and Ligand Alterations from Computational Results.

We present results for a series of complexes derived from a titanium complex capable of activating C-H bonds under mild conditions (PNP)Ti═CHtBu(CH2tBu), where PNP = N[2-PiPr2-4-methylphenyl]2-. In addition to the initial activation of methane, a tautomerization reaction to a terminal methylidene is also explored due to methylidene's potential use as a synthetic starting point. Analogous complexes with other low-cost 3d transition metals were studied, such as scandium, titanium, vanadium, and chromium as both isoelectronic and isocharged complexes. Our results predict that V(IV) and V(V) complexes are promising for methane C-H bond activation. The V(V) complex has a low rate-determining barrier for methane activation, specifically 16.6 kcal/mol, which is approximately 12 kcal/mol less than that for the Ti complex, as well as having a moderate tautomerization barrier of 29.8 kcal/mol, while the V(IV) complex has a methane activation barrier of 19.0 kcal/mol and a tautomerization barrier of 31.1 kcal/mol. Scandium and chromium complexes are much poorer for C-H bond activation; scandium has very high barriers, while chromium strongly overstabilizes the alkylidene intermediate, potentially stopping the further reaction. In addition to the original PNP ligand, some of the most promising ligands from a previous work were tested, although (as shown previously) modification of the ligand does not typically have large effects on the activity of the system. Our best ligand modification improves the performance of the V(V) complex via the substitution of the nitrogen in PNP by phosphorus, which reduces the tautomerization barrier by 5 to 24.4 kcal/mol.

Tautomerism of cytosine, cytidine, and deoxycytidine: Proton transfer through water bridges

AbstractAltogether six tautomers of cytosine and three tautomers of cytidine and deoxycytidine are studied theoretically in the gas phase and in a microhydrated environment. Their structures are optimized at MP2/6–31 + G(d,p) level. The relative energies of the isolated and the hydrated tautomers included the correction to higher correlation energy terms evaluated at the SCS‐MP2, MP4, and CCSD(T) levels. The free energies at 298 K and higher temperatures are based on the above‐mentioned relative energies and temperature‐dependent enthalpy terms and entropies evaluated at the MP2/6–31 + G(d,p) level. Theoretical predictions for the coexistence of five species for cytosine in the gas phase (canonical, trans‐ and cis‐enol‐amino, trans‐ and cis‐imino‐oxo forms) fully agree with recent experimental results. Five‐hydrated cytosine tautomeric forms of are investigated at CPCM/SCS‐MP2/6–31 + G(d,p) level to evaluate the interconversion barriers between them and to explain the coexistence, experimentally proven, of two amino‐oxo and one imino‐oxo tautomers of cytosine in aqueous solution. The presence of coordinated water molecules acting as a catalyst make the tautomerization processes quite easier. It appeared clear from the obtained data that the influence of the hydrogen‐bonded water molecules as well as the introduction of solvent effects in reducing the height of the tautomerization barriers for these five‐hydrated systems is quite substantial. Similar results are obtained for the tri‐hydrated cytidine and the 2‐deoxycytidine tautomeric forms. In aqueous solution of cytidine, syn‐ and syn‐clinal‐conformers оf the amino‐oxo tautomer should coexist with small amounts of syn‐ and syn‐clinal conformers оf imino‐oxo tautomer. For 2‐deoxycytidine an equilibrium has been found to exist between the syn‐ and anti‐conformers of the amino‐oxo and the imino‐oxo tautomers. The water‐assisted proton transfer reactions released through asynchronous concerted mechanism and the conformation of the sugar ring in nucleosides does not change during the tautomerization.

A theoretical study of the valence tautomerism of 1H-pyrazolium-4-olates (X = O) and related compounds (X = S, Se, NH): relative stabilities, protonation effects, and tautomerization barriers

The valence isomerism of a series of heterocyclic mesomeric betaines (HMBs) belonging to class 5, called pseudo-semi-conjugated HMBs, has been studied theoretically both the neutral and the protonated species. These HMBs are 1H-pyrazol-2-ium-4-olates and related compounds where the oxygen atom has been replaced by S, Se atoms, and an NH group. The main conclusion of the present work is that the ring/open valence tautomerism is possible both for neutral and protonated although it has never been observed experimentally.

Interstellar Enolization-Acetaldehyde (CH3 CHO) and Vinyl Alcohol (H2 CCH(OH)) as a Case Study.

Owing to the unique conditions in cold molecular clouds, enols-the thermodynamically less stable tautomers of aldehydes and ketones-do not undergo tautomerization to their more stable tautomers in the gas phase because they cannot overcome tautomerization barriers at the low temperatures. Laboratory studies of interstellar analog ices have demonstrated the formation of several keto-enol tautomer pairs in astrochemically relevant ice mixtures over the last years. However, so far only one of them, acetaldehyde-vinyl alcohol, has been detected in deep space. Due to their reactivity with electrophiles, enols can play a crucial role in our understanding of the molecular complexity in the interstellar medium and in comets and meteorites. To study the enolization of aldehydes in interstellar ices by interaction with galactic cosmic rays (GCRs), we irradiated acetaldehyde ices with energetic electrons as proxies of secondary electrons generated in the track of GCRs while penetrating interstellar ices. The results indicate that GCRs can induce enolization of acetaldehyde and that intra- as well as intermolecular processes are relevant. Therefore, enols should be ubiquitous in the interstellar medium and could be searched for using radio telescopes such as ALMA. Once enols are detected and abundances are established, they can serve as tracers for the non-equilibrium chemistry in interstellar ices thus eventually constraining fundamental reaction mechanisms deep inside interstellar ices.

The C5‐substituent effects on the formic acid‐assisted tautomerization of protonated cytosine: A lower isomerization barrier and potential biological importance

AbstractThe continuous oxidative products of 5‐methylcytosine are called the “three new DNA bases.” When it comes to 5‐formylcytosine and 5‐carboxylcytosine, the electron densities at N3 sites of both bases tend to be decreased due to the presence of the electron withdrawing groups of CHO and COOH. The vital steps for mutations of DNA are tautomerism in nucleotide bases. Although there are great deal of studies on the protonated new DNA bases in photophysical and photochemical reactivity, the relationship of pKa at N3 position with the intermolecular tautomerization barrier is seldom reported. The C5 atom of cytosine is substituted by the CH3, HOCH2, CHO, and COOH, and their isomerization barriers in the presence of HCOOH have nearly linear relationship with the pKa at N3 positions of these bases. The solvent water affects the activation free energies of these paths, and yet their isomerization mechanisms are still more favorable in aqueous solution. Meantime, the rate constants could be calculated by the conventional transition state theory with Wigner's tunneling correction. The corrected rate constant for these paths is very consistent with uncorrected results. Finally, the product and reaction complexes are in a fast tautomerism equilibrium, which is a synchronous double proton transfer mechanism. The product complexes may further dissociated into the monomers. These researches may give a chemical basis for differentiating 5‐fCyt and 5‐caCyt from Cyt, 5‐MeCyt, and 5‐HCyt in the protein‐DNA interactions which might be used for selective recognition.

CH⋯O H-bond mediated tautomerization of 2-methyl-1,3-cyclohexanedione: A combined IR spectroscopic and theoretical study

Molecular association and its impact on the keto-enol tautomerization of 2-methyl-1,3-cyclohexanedione (MCHD) have been investigated in low temperature argon matrix and thin solid film. The system exists exclusively in diketo tautomeric form in argon matrix. The CH⋯O H-bonded homodimers of the diketo tautomer are produced by annealing the matrix at 28 K. No trace of the keto-enol tautomer is observed in matrix isolated homodimers in the temperature range of 8–28 K. However, tautomeric conversion initiates in a thin film of pure diketo tautomer when the temperature of the film is raised to ~170 K. Transition state calculations on the monomeric and dimeric MCHD demonstrate that CH⋯O H-bond formations between diketo tautomers play a vital role in lowering the tautomerization barrier. However, the extent of CH⋯O H-bonded dimer formation in matrix isolation, as well as extent of tautomerization in the neat sample are found to be smaller than that for the previously reported 1,3-cyclohexanedione (CHD) under similar experimental conditions (J. Phys. Chem. A 2012, 116, 3836–3845). Electronic structure calculations suggest that formation of the CH⋯O H-bonded dimer is less feasible in presence of the bulky 2-methyl groups of MCHD, as compared to CHD. Additionally, the transition state geometry of the dimeric keto-enol product of MCHD, as compared to the same for CHD, is more strained and offers a weaker CH---O H-bond that contributes to lesser tautomeric conversion in the former.

Cryogenic ion spectroscopy of adenine complexes containing alkali metal cations.

Cryogenic ion spectroscopy was used to characterize adenine complexes containing alkali metal cations (M+A, M = Cs, Rb, K, Na, and Li) produced by electrospray ionization. The ultraviolet (UV) photodissociation spectra of the complexes stored in a cryogenic ion trap exhibited well-resolved vibronic bands near their origin bands of the S0-S1 transition. The UV-UV hole-burning and infrared ion-dip spectra showed that all the M+A ions in the ion trap were single isomers of M+A7a, where the M+ ion was not bound to canonical 9H-adenine (A9) but bound to a rare tautomer, 7H-adenine (A7). Density functional theory calculations showed lower tautomerization barriers for M+A9 than for bare A9 in aqueous solution. We suggest that M+ ions not only play a catalytic role in the tautomerization of A9 to A7 but also increase the tautomerization yield by forming stable M+A7a isomers.

Synthesis, DFT computations and antimicrobial activity of a Schiff base derived from 2-hydroxynaphthaldehyde: Remarkable solvent effect

A new Schiff base bearing sulfonamide group was synthesized and characterized by spectroscopic techniques. Its spectroscopic properties were investigated through density functional theory (DFT/B3LYP) method with the 6−311++G(d,p) basis set theoretically and the zwitterion ⇌ enol tautomerization was studied using IEF-PCM approximation. The thermodynamic (entropy, enthalpy and Gibbs free energy changes) and energetic quantities of the zwitterion ⇌ enol tautomerization indicate that the migration of single proton between zwitterion ⇌ enol tautomer’s is unfavored for both directions in all phases. During the change from the water phase to the gas phase, the tautomeric energy barrier increases for the proton transfer reaction from the zwitterion form to the enol form, while the barrier decreases from the enol form to the zwitterion form.On the other hand, experimental studies (UV–vis. and NMR spectroscopies) release that there are two tautomeric species which are the zwitterion form in polar and the enol form in apolar solvents for the soluted compound. Furthermore, the antibacterial effect of the compound was investigated in two different solvents (DMSO and THF) to demonstrate the effect of dominant tautomeric species. The results indicate that the solution in which the enol form is dominant than the zwitterionic form has more antimicrobial efficiency for all bacterial species.

The destabilization of hydrogen bonds in an external E-field for improved switch performance.

The effect of an electric field on a recently proposed molecular switch based on a quinone analogue was investigated using next-generation quantum theory of atoms in molecules (QTAIM) methodology. The reversal of a homogenous external electric field was demonstrated to improve the "OFF" functioning of the switch. This was achieved by destabilization of the H atom participating in the tautomerization process along the hydrogen bond that defines the switch. The "ON" functioning of the switch, from the position of the tautomerization barrier, is also improved by the reversal of the homogenous external electric field: this result was previously inaccessible. The "ON" and "OFF" functioning of the switch was visualized in terms of the response of the most preferred directions of motion of the electronic charge density to the applied external field. All measures from QTAIM and the stress tensor provide consistent results for the factors affecting the "ON" and "OFF" switch performance. Our analysis therefore demonstrates use for future design of molecular electronic devices. © 2019 Wiley Periodicals, Inc.

Quinone‐based switches for candidate building blocks of molecular junctions with QTAIM and the stress tensor

AbstractThe current work investigates candidate building blocks based on molecular junctions from hydrogen transfer tautomerization in the benzoquinone‐like core of an azophenine molecule with QTAIM and the recently introduced stress tensor trajectory analysis. We find that in particular the stress tensor trajectories are well suited to describe the mechanism of the switching process. The effects of an Fe‐dopant atom coordinated to the quinone ring, as well as F and Cl substitution of different ring‐hydrogens, are investigated and the new QTAIM and stress tensor analysis is used to draw conclusions on the effectiveness of such molecules as molecular switches in nanosized electronic circuits. We find that the coordinated Fe‐dopant greatly improves the switching properties, both in terms of the tautomerization barrier that has to be crossed in the switching process and the expected conductance behavior, while the effects of hydrogen substitution are more subtle. The absence of the Fe‐dopant atom led to impaired functioning of the switch “OFF” mechanism as well as coinciding with the formation of closed‐shell H—H bond critical points that indicated a strained or electron deficient environment. Our analysis demonstrates promise for future use in design of molecular electronic devices.

Quantum tunneling in real space: Tautomerization of single porphycene molecules on the (111) surface of Cu, Ag, and Au.

Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis tautomerization rate is much higher than on Cu(111), indicating a significantly smaller tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.

Analyzing and Tuning the Energetic Landscape of H2Pc Tautomerization

We present a detailed analysis of the energetic landscape of phthalocyanine (H2Pc) tautomerization on Ag(111), i.e., the switching of protons between different sites in the molecular frame, which is induced and measured by a low-temperature scanning tunneling microscope (STM). We demonstrate that tautomerization of this molecule is preferentially triggered by the excitation of the N–H stretching mode. Interestingly, a step-like increase of the tautomerization rate is observed at a bias voltage that corresponds to the second harmonic of this vibrational mode, which we attribute to the crossover from quantum tunneling through the tautomerization barrier to an excitation over the barrier. This hypothesis is supported by the analysis of four modified versions of H2Pc, produced by single silver atom manipulation and/or deprotonation of the pristine H2Pc molecule. Depending on the particular modification, the step-like increase varies strongly, spanning the entire range from further enhancement to almost comple...

Tautomerization and Dissociation of Molecular Peptide Radical Cations.

Radical-mediated dissociations of peptide radical cations have intriguing unimolecular gas phase chemistry, with cleavages of almost every bond of the peptide backbone and amino acid side chains in a competitive and apparently "stochastic" manner. Challenges of unraveling mechanistic details are related to complex tautomerizations prior to dissociations. Recent conjunctions of experimental and theoretical investigations have revealed the existence of non-interconvertible isobaric tautomers with a variety of radical-site-specific initial structures, generated from dissociative electron transfer of ternary metal-ligand-peptide complexes. Their reactivity is influenced by the tautomerization barriers, perturbing the nature, location, or number of radical and charge site(s), which also determine the energetics and dynamics of the subsequent radical-mediated dissociatons. The competitive radical- and charge-induced dissociations are extremely dependent on charge density. Charge sequesting can reduce the charge densities on the peptide backbone and hence enhance the flexibility of structural rearrangement. Analysing the structures of precursors, intermediates and products has led to the discovery of many novel radical migration prior to peptide backbone and/or side chain fragmentations. Upon these successes, scientists will be able tobuild peptide cationicanalogues/tautomers having a variety of well-defined radical sites.

Quantum chemical study of tautomerism in 2-[(4-phenylthiazol-2-yl)hydrazonomethyl]phenol

The relative stabilities of five tautomers of 2-[(4-phenylthiazol-2-yl)hydrazonomethyl]phenol were calculated at the B3LYP/6–311+G(d,p) and MP2/6–311+G(d,p) levels of theory. The possible tautomeric transformations were also analyzed at the same level taking into account the solvent effect with the integral equation formalism polarizable continuum model (IEF-PCM) using three different solvents. The enol-hydrazo-thiazole (T1) form has been found to be the predominant tautomer, and the tautomers follow the stability pattern: enol-hydrazo-thiazole (T1)>enol-imine-thiazoline (T2)>keto-hydrazo-thiazoline (T4)>keto-amine-thiazole (T5)>enol-azo-thiazole (T3). The tautomeric barrier heights for T1 ⇌ T2, T1 ⇌ T3 and T4 ⇌ T5 reactions are very high in both the forward and reverse directions. In the case of T1 ⇌ T5 and T2 ⇌ T4 tautomerizations, the forward proton transfer is not possible because of large barrier height. According to the B3LYP results of the reverse reactions, only the proton transfer in the gas phase and in chloroform is allowed for T1 ⇌ T5 while it is found to be barrierless for T2 ⇌ T4. However, the MP2 computations show that the reverse T1 ⇌ T5 reaction impossible for all cases while the reverse T2 ⇌ T4 reaction needs very low energy. These results are also corroborated by the thermodynamic parameters obtained at the B3LYP/6–311+G(d,p) level. The barrier energy height increases with the increasing polarity of the solvent in general, however, the trend is not observed for all cases.

Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective.

The one-step tautomerization processes of uracil and its radical cation and radical anion have been investigated in the light of the reaction force and reaction electronic flux (REF) formalisms. The relative energies of the different tautomers as well as the corresponding tautomerization barriers have been obtained through the use of the G4 high-level ab initio method and by means of B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d, p) calculations. Systematically, the enol radical cations are more stable in relative terms than the neutral, due to the higher ionization energy of the diketo forms with respect to the enolic ones. Conversely, the enol radical anions, with the only exception of the 2-keto-N1 anion, are found to be less stable than the neutral. The effects of the ionization are also sizable on the tautomerization barriers although this effect also depends on the particular tautomerization process. The reaction force analysis shows that all reactions are mainly activated through structural rearrangements that initiate the electronic activity. This electronic activity is monitored along the reaction coordinate through the REF that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer.

Keto-enol tautomerization of a peptide group with proton transfer through a water bridge

Calculations were performed for structures of the keto and enol forms of dipeptide N-glycylglycine and its complexes with water molecules using the quantum-chemical B3LYP/6-31+G** method. The barrier for the reactions of the dipeptide’s keto-enol tautomerization that proceed by the mechanism of intramolecular proton transfer and proton transfer through water molecules connecting the oxygen and nitrogen atoms of the (-CONH-) peptide group was calculated. It was found that the barrier of the keto-enol tautomerization reaction with proton transfer by an exchange mechanism through water molecules is decreased halved compared to direct intramolecular transfer. It was shown that addition of a second water molecule in the transfer chain leads to linearization of the H-bonds bridges and increases hydrogen bonding between the peptide group and water molecules, but has virtually no influence on the calculated value of the keto-enol tautomerization barrier of about 20 kcal/mol. The structures of the transition states of the reaction indicate that the transfer of protons along the H-bonds chain is in both cases concerted but asynchronous. The order of the protons translocations along the water bridge is explained on the basis of NBO analysis of the relative strength of H-bonds in the transfer chain when the proton involved in the strongest H-bond is transferred first.

Reactive intermediates in (4)He nanodroplets: infrared laser Stark spectroscopy of dihydroxycarbene.

Singlet dihydroxycarbene (HOC̈OH) is produced via pyrolytic decomposition of oxalic acid, captured by helium nanodroplets, and probed with infrared laser Stark spectroscopy. Rovibrational bands in the OH stretch region are assigned to either trans,trans- or trans,cis-rotamers on the basis of symmetry type, nuclear spin statistical weights, and comparisons to electronic structure theory calculations. Stark spectroscopy provides the inertial components of the permanent electric dipole moments for these rotamers. The dipole components for trans, trans- and trans, cis-rotamers are (μa, μb) = (0.00, 0.68(6)) and (1.63(3), 1.50(5)), respectively. The infrared spectra lack evidence for the higher energy cis,cis-rotamer, which is consistent with a previously proposed pyrolytic decomposition mechanism of oxalic acid and computations of HOC̈OH torsional interconversion and tautomerization barriers.

Decarbonylation of the 2-Hydroxypyridine Radical Cation: A Computational Study

The potential energy surface (PES) for the dissociation of the 2-hydroxypyridine (2-HP) radical cation was determined from G3//B3LYP calculations, including the loss of CO, HCN, and HNC. The formation of the 1Hpyrrole radical cation by decarbonylation through a more stable tautomer, the 2-pyridone (2-PY) radical cation, was the most favorable dissociation pathway. Kinetic analysis by the Rice-Ramsperger-Kassel-Marcus model calculations was carried out based on the obtained PES. It is proposed that the dissociation occurs after a rapid tautomerization to 2-PY + , and that most of the ions generated by ionization of 2-HP have the structure of 2PY + at equilibrium above the tautomerization barrier.

Ionization-induced tautomerization in cytosine and effect of solvation.

The recent observation of excitation-induced tautomerization in gas-phase cytosine motivated us to investigate the possibility of facile tautomerization in ionized cytosine and the effect of solvation on the tautomerization barriers. The tautomerization mechanisms were characterized at the density functional theory (DFT)/ωB97X-D and coupled-cluster singles and doubles (CCSD) levels of theory. Vertical and adiabatic ionization energies (VIEs and AIEs, respectively) of the tautomers of cytosine and the microsolvated species were calculated with the equation-of-motion ionization-potential coupled-cluster (EOM-IP-CCSD) method. We observed that, in microsolvated cytosine, the solvatochromic shifts of the VIEs can be both blue- and red-shifted depending on the tautomers. This is explained by the analysis of the charge-dipole interactions between the cytosine and water molecules. We noticed that, upon ionization, gas-phase tautomerization barriers are reduced by 0-4 kcal/mol, whereas microsolvated (with one water) tautomerization barriers are reduced by 4-5 kcal/mol. We also investigated the tautomerization process in solvation using a continuum model with one active water molecule in the quantum mechanical region. We noticed that, even though bulk solvation has a significant effect on ionization energies, its effect on the ionization-induced tautomerization barrier is minimal.

Effects of sulfur-deficient defect and water on rearrangements of formamide on pyrite (100) surface.

The efficient formation of HCN/HNC from formamide (FM) combining the advantages of water-assistance, self-catalyzed reactions, and the mineral surfaces was investigated. Periodic density functional theory calculations with plane-wave pseudopotential basis sets were performed to study the interaction of FM with pyrite (100) ideal and defect surfaces. Effects of sulfur vacancy defect and water on tautomerization and rearrangement barriers of FM on the (100) surface were evaluated. Calculated results show that FM adsorbs more strongly on the defect surface than on the ideal surface, with the lowest adsorption energy on the defect surface being -22 kcal/mol. The energy barriers for rearrangements of FM on these two surfaces being close to each other suggests that the adsorptions on the surfaces have small effects on the energy barriers. The energy barriers for formimic acid isomer formations are 44.5 and 46.0 kcal/mol, and those of aminohydroxymethylene formations are 72.6 and 71.9 kcal/mol on the ideal and defect surfaces, respectively. A reduction of ∼30 kcal/mol in tautomerization energy barriers is observed in water-assisted process on the defect surface. Because this reduction is close to that of the gas-phase reactions, the catalytic effect is clearly due to the presence of water molecule instead of the interaction with the surface. In this case, the pyrite surfaces with the ability to accumulate reactive species only play the role of connecting bridges between the two steps of the proposed reaction mechanism: the water-assisted rearrangement and the self-catalyzed dehydration.