Study of 7-azaindole in its first four singlet states

The molecular structure and properties of 7-azaindole in its first four singlet states were studied with a view to improving current understanding of the photophysical behavior of its C(2h) dimer. This dimer, which exhibits a double proton transfer via its two hydrogen bonds upon electronic excitation, has for 35 years been used as a model for the photophysical behavior of DNA base pairs. Electronic excitation of 7-azaindole simultaneously increases its acidity and basicity; these changes facilitate a concerted mechanism for the double proton transfer in the dimer. In this work, we found the acidity and basicity changes to occur only in its first pi,pi(*) excited singlet state.     

The molecular symmetry and electronic spectroscopy of 7-azaindole dimer: its proton-transfer channels

The potential-energy surfaces for the proton transfer in the doubly hydrogen-bonded dimer of 7-azaindole in its lowest excited electronic states were examined. The dimer with C2h symmetry in its lowest excited electronic states, 2Ag and 1Bu, undergoes concerted double-proton transfer via transition states of the same symmetry placed at energies 4.55 and 4.70 kcal/mol higher, respectively. This suggests that the activation barriers for the double-proton transfer, if any, are lower than 1 kcal/mol. Emission from the dimers resulting from the double-proton transfer involves a Stokes shift of 5605 cm(-1), as theoretically estimated from the 0-0 components of the absortion and emission transitions of the dimer. Surprisingly, however, the calculations suggest that the green emission cannot arise from the 2Ag state generated by a double-proton transfer, because this structure possesses an imaginary frequency. In the 7-azaindole dimer of Cs symmetry, the first excited electronic state, a', lies 4.9 kcal/mol below 1Bu. This excited state a' can be the starting point for single-proton transfers giving a zwitterionic form that can dissociate into the protonated and deprotonated forms of 7-azaindole, the former being electronically excited. This situation of lower symmetry is consistent with the mutational scheme proposed by Goodman [Nature (London) 378, 237 (1995)].     

A theoretical and optical spectroscopic study of the mechanism of a tautomeric transformation in the 7-azaindole dimer and the 7-azaindole complex with a water molecule

Electronic, vibrational, and electronic vibrational spectra of the 7-azaindole dimer, the 7-azaindole complex with a water molecule, and their tautomers are calculated. Transition states are considered based on the analysis of frequencies and shapes of low-frequency vibrations and the Mulliken charge redistribution. The performed quantum chemical calculation of chemical reactions enabled the determination of the structure of transition states and proton transfer conditions. It is shown that in the 7-AzI dimer the proton transfer has a character consistent with the formation of a zwitterionic form. The structure of excited states is calculated and the fluorescence spectra of the first electronic transitions that can be used as a criterion of the formation of 7-AzI tautomers as a result of chemical reactions proceeding through a proton transfer in the 7-azaindole dimer and the 7-azaindole complex with a water molecule, are interpreted.     

7—氮吲哚二体激发态双质子转移的量子化学研究

用AMl和INDO/CI方法研究了7-氮吲哚二体激发态双质子转移反应的位能面和机理,异构二体虽存在较强的分子内氢键,但基态时正常二体的能量仍比异构二体低,光照时正常二体可通过激发态质子转移变为异构二体,这是其荧光产生反常Stokes位移的原因。     

EXCITED STATE INTERACTIONS OF 7-AZAINDOLE WITH ALCOHOL AND WATER

Abstract— The fluorescence spectrum of 7-azaindole in alcohol is composed of two fluorescence bands. Effects of pH, temperature and solvent deuteration on the fluorescence spectra and quantum yields of 7-azaindole and other model compounds in ethanol and in water are reported. The long wavelength band arises from a tautomeric species formed in an adiabatic photoreaction involving double proton transfer between one molecule of 7-azaindole and one molecule of alcohol.
The fluorescence spectrum of 7-azaindole in water is composed of only one band, but the emission is weak and shows a large solvent isotope effect. The possibility of a double proton transfer reaction between 7-azaindole and water is discussed.     

Structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet: competition between N-H···N and N-H···F interactions

In the present work, we have investigated the structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet by employing resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. The R2PI spectrum of the dimer is recorded by electronic excitation of the 7-azaindole moiety, and a few low frequency intermolecular vibrations of the dimer are clearly observed in the spectrum. The electronic origin band of the dimer is red-shifted by 1278 cm(-1) from the S(1) ← S(0) origin band of 7-azaindole monomer. The presence of a single conformer of the dimer is confirmed by IR-UV and UV-UV hole-burning spectroscopic techniques. RIDIR (Resonant ion dip infrared) spectrum of the dimer shows a red-shift of 265 cm(-1) in the N-H stretching frequency with respect to that of the 7-azaindole monomer. Two planar double hydrogen bonded cyclic structures of the dimer have been predicted from DFT calculations. Comparison of experimental and theoretical N-H stretching frequencies confirms that the observed dimer is stabilized by N-H···N and C-H···N hydrogen bonding interactions. The less stable conformer with N-H···F and C-H···N interactions are not observed in the experiment. The competition between N-H···N and N-H···F interactions in the two dimeric structures are discussed from natural bond orbital (NBO) analysis. The current results demonstrate that fluorine makes a hydrogen bond of intermediate strength through cooperative interaction of another hydrogen bond (C-H···N) present in the dimer, although fluorine is believed to be very weak hydrogen bond acceptor.     

Excited-state double proton transfer of 7-azaindole dimers in a low-temperature organic glass

The excited-state double proton transfer of model DNA base pairs, 7-azaindole (7AI) dimers, is explored in a low-temperature organic glass of n-dodecane using picosecond time-resolved fluorescence spectroscopy. Reaction mechanisms are found to depend on the conformations of 7AI dimers at the moment of excitation; whereas planar conformers tautomerize rapidly (<10 ps), twisted conformers undergo double proton transfer to form tautomeric dimers on the time scale of 250 ps at 8 K. The proton transfer is found to consist of two orthogonal steps: precursor-configurational optimization and intrinsic proton transfer via tunneling. The rate is almost isotope independent at cryogenic temperatures because configurational optimization is the rate-determining step of the overall proton transfer. This optimization is assisted by lattice vibrations below 150 K or by librational motions above 150 K.     

1H and 13C NMR studies of 7-azaindole and related compounds

The ¹H and ¹³C chemical shifts, proton-proton coupling constants, and one-bond carbon-hydrogen coupling constants have been obtained for 7-azaindole, 1-methyl-7-azaindole, their corresponding methyl iodide salts, and the related compound 7-methyl-7H-pyrrolo [2,3-b]pyridine. are different from those of either 7-azaindole or 1-methyl-7-azaindole.     

Theoretical studies for excited-state tautomerization in the 7-azaindole-(CH3OH)n (n = 1 and 2) complexes in the gas phase

The excited-state tautomerization of 7-azaindole (7AI) complexes bonded with either one or two methanol molecule(s) was studied by systematic quantum mechanical calculations in the gas phases. Electronic structures and energies for the reactant, transition state (TS), and product were computed at the complete active space self-consistent field (CASSCF) levels with the second-order multireference perturbation theory (MRPT2) to consider the dynamic electron correlation. The time-dependent density functional theory (TDDFT) was also used for comparison. The excited-state double proton transfer (ESDPT) in 7AI-CH(3)OH occurs in a concerted but asynchronous mechanism. Similarly, such paths are also found in the two transition states during the excited-state triple proton transfer (ESTPT) of the 7AI-(CH(3)OH)(2) complex. In the first TS, the pyrrole ring proton first migrated to methanol, while in the second the methanol proton moved first to the pyridine ring. The CASSCF level with the MRPT2 correction showed that the former path was much preferable to the latter, and the ESDPT is much slower than the ESTPT. Additionally, the vibrational-mode enhanced tautomerization in the 7AI-(CH(3)OH)(2) complex was also studied. We found that the excitation of the low-frequency mode shortens the reaction path to increase the tautomerization rate. Overall, most TDDFT methods used in this study predicted different TS structures and barriers from the CASSCF methods with MRPT2 corrections.     

Charge-transfer pipi* excited state in the 7-azaindole dimer. A hybrid configuration interactions singles/time-dependent density functional theory description

The hybrid configuration interaction singles/time dependent density functional theory approach of Dreuw and Head-Gordon [Dreuw, A.; Head-Gordon, M. J. Am. Chem. Soc. 2004, 126, 4007] has been applied to study the potential energy landscape and accessibility of the charge-transfer pipi* excited state in the dimer of 7-azaindole, which has been traditionally considered a model for DNA base pairing. It is found that the charge-transfer pipi* excited state preferentially stabilizes the product of a single proton transfer. In this situation, the crossing between this state and the photoactive electronic state of the dimer is accessible. It is found that the charge-transfer pipi* excited state has a very steep potential energy profile with respect to any single proton-transfer coordinate and, in contrast, an extremely flat potential energy profile with respect to the stretch of the single proton-transfer complex. This is predicted to bring about a pair of rare fragments of the 7-azaindole dimer, physically separated and hence having very long lifetimes. This could have implications in the DNA base pairs of which the system is an analogue, in the form of replication errors.     

Excited-state double-proton transfer in the 7-azaindole dimer in the gas phase. 2. Cooperative nature of double-proton transfer revealed by H/D kinetic isotopic effects

The dispersed fluorescence (DF) spectra of the 7-azaindole dimer (7AI2) and deuterated dimers 7AI2-hd and 7AI2-dd, where hd and dd indicate the deuteration of an imino proton and two imino protons, have been measured in a supersonic free jet expansion. The undeuterated 7AI2-hh dimer exhibits only the tautomer fluorescence, but both the normal and tautomer fluorescence have been detected by exciting the origins of 7AI2-h*d, 7AI2-hd* and 7AI2-dd in the S1-S0 region, where h* and d* indicate the localization of the excitation on 7AI-h or 7AI-d moiety. The DF spectra indicate that 7AI2-h*d and 7AI2-hd* undergo excited-state proton/deuteron transfer (ESPDT), while excited-state double-deuteron transfer (ESDDT) occurs in 7AI2-dd. The H/D kinetic isotopic effects on ESDPT have been investigated by measuring the intensity ratios of the normal fluorescence to the tautomer fluorescence. The ESPDT rate is about 1/60th of the ESDPT rate, and the ESDDT rate is about 1/12th of the ESPDT rate, where ESPDT rate is an average of the rates for 7AI2-h*d and 7AI2-hd*. The observed H/D kinetic isotope effects imply that the ESDPT reaction of 7AI2 has a "cooperative" nature; i.e., the motion of the two moving protons strongly couples each other through the electron motions. The difference in the estimated ESPDT reaction rates, 9.8 x 10(9) and 6.9 x 109 s(-1) for 7AI2-h*d and 7AI2-hd*, respectively, is consistent with the concerted mechanism rather than the stepwise mechanism.     

Reactive force fields for proton transfer dynamics

A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I.     

The Cyclic Hydrogen‐Bonded 6‐Azaindole Trimer and its Prominent Excited‐State Triple‐Proton‐Transfer Reaction

The compound 6‐azaindole undergoes self‐assembly by formation of N(1)?H???N(6) hydrogen bonds (H bonds), forming a cyclic, triply H‐bonded trimer. The formation phenomenon is visualized by scanning tunneling microscopy. Remarkably, the H‐bonded trimer undergoes excited‐state triple proton transfer (ESTPT), resulting in a proton‐transfer tautomer emission maximized at 435 nm (325 nm of the normal emission) in cyclohexane. Computational approaches affirm the thermodynamically favorable H‐bonded trimer formation and the associated ESTPT reaction. Thus, nearly half a century after Michael Kasha discovered the double H‐bonded dimer of 7‐azaindole and its associated excited‐state double‐proton‐transfer reaction, the triply H‐bonded trimer formation of 6‐azaindole and its ESTPT reaction are demonstrated.     

Theoretical study on molecular structures, intramolecular proton transfer reaction, and solvent effects of 1-phenyl-3-methyl-4-(6-hydro-4-amino-5-sulfo-2,3-pyrazine)-pyrazole-5-one

The molecular structures and intramolecular proton transfer reaction of 1-phenyl-3-methyl-4-(6-hydro-4-amino-5-sulfo-2,3-pyrazine)-pyrazole-5-one have been investigated with both ab initio method and the density functional theory. The solvent effects are simulated using the self-consistent reaction field (SCRF) method within the framework of the polarizable continuum model (PCM). The results show that the computed geometrical parameters at the B3LYP levels are in better agreement with experimental values than those at the RHF levels, and the choice of functional in DFT plays an important role in describing the title compound. It is found that strong hydrogen bonds (O–H···N and O···H–N) exist in the title compound, and in the proton transfer process, the O–H bond is broken while the N–H bond is formed. In addition, the order of stability of the isomers remains the same in different solvents, while the barrier height of the proton transfer reaction and dipole moments for the title compound grow with the increase of the solvent polarity. Eventually, the NBO analysis shows that the strength of the hydrogen bond reduces with the increase of the solvent polarity.     

A theoretical study on excited state double proton transfer reaction of a 7-azaindole dimer: an ab initio potential energy surface and its empirical valence bond model

Double proton transfer (DPT) reaction of a 7-azaindole dimer in the first ππ* electronically excited state was studied theoretically. We investigated the reaction mechanism through constructing a full dimensional empirical valence bond potential energy function (PEF) based on potential energies evaluated by ab initio molecular orbital methods, and carrying out quantum dynamics calculations with the PEF. Potential energy surfaces of the DPT obtained at the multi-reference perturbation level of theory favors a concerted DPT mechanism, although a stepwise channel is suggested to open for an excited initial vibrational state. Reduced two dimensional quantum dynamics calculations for a reaction surface Hamiltonian of DPT coordinates were performed. Time constants of the reaction were evaluated to be on the order of picoseconds, which is consistent with experiments. On the other hand, the computed kinetic isotope effect deviates from experimental evidence, suggesting the importance of intermolecular stretching motion, which is not explicit in the present calculations for the quantum effect.     

Synthesis of pyrrolopyridines (azaindoles)

Improved, convenient, and reliable routes for the synthesis of 4-, 5-, 6-, and 7-azaindole, 7-methyl-4-azaindole, 7-methyl-6-azaindole, and the hitherto unreported 7-amino-4-azaindole are described. The syntheses have been accomplished either by significant modifications to established procedures or by new methods which afford the compounds in improved yields.     

Excited-state double proton transfer of 7-azaindole in water nanopools

The excited-state proton-transfer dynamics of 7-azaindole occurring in the water nanopools of reverse micelles has been investigated by measuring time-resolved fluorescence spectra and kinetics, as well as static absorption and emission spectra, with varying water content and isotope. 7-Azaindole molecules are found to exist in the bound-water regions of reverse micelles. The rate constant and the kinetic isotope effect of proton transfer are smaller than those in bulk water although both increase with the size of the water nanopool. The retardation of proton transfer in the bound regions is attributed to the increased free energy of prerequisite solvation to form a cyclically H-bonded 1:1 7-azaindole/water complex.     

Synthesis and reactivity of N-heterocycle-B(C6F5)3 complexes. 4. Competition between pyridine- and pyrrole-type substrates toward B(C6F5)3: structure and dynamics of 7-B(C6F5)3-7-azaindole and [7-Azaindolium]+[HOB(C6F5)3]-

Reaction between 7-azaindole and B(C6F5)3 quantitatively yields 7-(C6F5)3B-7-azaindole (4), in which B(C6F5)3 coordinates to the pyridine nitrogen of 7-azaindole, leaving the pyrrole ring unreacted even in the presence of a second equivalent of B(C6F5)3. Reaction of 7-azaindole with H2O-B(C6F5)3 initially produces [7-azaindolium]+[HOB(C6F5)3]- (5) which slowly converts to 4 releasing a H2O molecule. Pyridine removes the borane from the known complexes (C6F5)3B-pyrrole (1) and (C6F5)3B-indole (2), with formation of free pyrrole or indole, giving the more stable adduct (C6F5)3B-pyridine (3). The competition between pyridine and 7-azaindole for the coordination with B(C6F5)3 again yields 3. The molecular structures of compounds 4 and 5 have been determined both in the solid state and in solution and compared to the structures of other (C6F5)3B-N-heterocycle complexes. Two dynamic processes have been found in compound 4. Their activation parameters (DeltaH = 66 (3) kJ/mol, DeltaS = -18 (10) J/mol K and DeltaH = 76 (5) kJ/mol, DeltaS = -5 (18) J/mol K) are comparable with those of other (C6F5)3B-based adducts. The nature of the intramolecular interactions that result in such energetic barriers is discussed.     

Proton transfer of excited 7-azaindole in reverse-micellar methanol nanopools: even faster than in bulk methanol

The methanol-catalyzed double-proton transfer of photoexcited 7-azaindole in the free cores of solvation-restricted reverse micelles takes place on the time scale of 90 ps, even shorter than in bulk methanol. This anomalous rate increase with a large kinetic isotope effect of 5 experimentally proves the widely discussed two-step model for the overall reaction of solvent-mediated proton transfer. On the other hand, the molecules in the bound layers and in the headgroup layers relax in 900 and 6000 ps, respectively, without going through proton transfer. The tautomerization and the relaxation of excited 7-azaindole can be exploited to probe the nanopools of methanol reverse micelles.     

Excited-state double-proton transfer in a model DNA base pair: Resolution for stepwise and concerted mechanism controversy in the 7-azaindole dimer revealed by frequency- and time-resolved spectroscopy

The excited-state double-proton transfer (ESDPT) reaction in the dual hydrogen-bonded 7-azaindole dimer (7AI₂) in a supersonic jet expansion has been extensively studied with various laser spectroscopic methods and quantum chemistry calculations by many groups. This article reviews the results and discussions associated with stepwise and concerted mechanism controversy on ESDPT of 7AI₂ together with the excited-state dynamics associated with ESDPT.