Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO-PM3 methods

Molecular structure, spectroscopic properties, NLO, HOMO-LUMO and NBO analyses of 6-hydroxy-3(2H)-pyridazinone

The molecular structure and relative stabilities of the six possible isomers of 6-hydroxy-3(2H)-pyridazinone (DHP) in the gas phase and in solutions of different polarities are predicted using the B3LYP/6-311++G(d,p) method. The oxo-hydroxo isomer is the most stable form in the gas phase and in solution. These results agree with our reported X-ray structure. The effect of solvents on the spectroscopic properties of the most stable isomer has been studied using the polarized continuum method (PCM) at the same level of theory. The vibrational spectra of the compound studied are calculated and compared with the experimentally measured FTIR spectra. The electronic spectra in gas phase and in solution were calculated using the TD-DFT method. The most intense absorption band is predicted at 312.4 nm and belongs mainly to a π→π(*) transition. In polar solvents, this spectral band undergoes a hypsochromic shift. Two stable dimer forms were calculated at same level of theory. Dimer A is more stable than dimer B, by 6.66 kcal mol(-1). The former is stabilized by stronger O-H⋯O H-bonds compared to the weaker N-H⋯O interactions in the latter. The effect of these H-bonding interactions on the molecular structure and vibrational spectra of these compounds are predicted. NBO analyses were carried out to investigate the stabilization energy of various inter- and intramolecular charge transfer interactions within the systems studied.

Computations of 36 tautomer/isomer equilibria of different lactams

Gas-phase energies of 36 tautomer/isomer pairs of 18 six-membered N-heterocyclic compounds were computed quantum chemically. Among the considered B3LYP, BH&HLYP, BH&HLYP(G), and PW6B95 DFT functionals, the latter two provide accurate tautomer/isomer pair energies with root-mean-square deviations (rmsd) relative to experiments of 0.2 and 0.3 kcal/mol, respectively. Since only few (namely five) experimental data are available, 15 tautomer/isomer pair energies were computed with the very precise QCISD(T)(quadruple-ζ) method serving as reference. Relative to this reference the PW6B95 DFT functional is slightly superior to the BH&HLYP(G) functional, yielding an rmsd of 0.7 and 0.8 kcal/mol, respectively. In contrast to BH&HLYP(G), the PW6B95 DFT functional yields also accurate tautomer/isomer pair energies if zwitterionic structures are involved. The tautomer/isomer pair states possess different amounts of aromaticity. This is characterized by nucleus-independent chemical shift (NICS) values. The tautomer/isomer pair reference energies, from which the energies computed with PW6B95 are subtracted, correlate linearly with the corresponding differences in the NICS values. This correlation is used to construct a correction term for the pair energies computed with PW6B95, yielding tautomer/isomer pair energies with rmsd of 0.3 kcal/mol with respect to the more CPU time demanding QCISD(T)(quadruple-ζ) method.

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett-Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pK(T) and pK(a). Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pK(T) values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pK(a) effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.

Electron crystallography on polymorphic organics

Organic materials, such as non-linear optical active compounds (1-(2-furyl)-3-(4-aminophenyl)-2-propene-1-one (FBAPPO) and 1-(2-furyl)-3-(4-benzamidophenyl)-2-propene-1-one (FAPPO)), polymeric materials like the metal coordinated polyelectrolyte (Fe(II) [ditopic bis-terpyridin] (MEPE)) or polymorphic materials (e.g. Cu-phthalocyanine), which do not crystallize big enough for single crystal x-ray structure analysis have been investigated by electron diffraction (ED) at 100 and 300 kV acceleration voltage. Sample preparation (direct crystallization, ultra sonication, ultra microtomy), diffraction strategies (selected area diffraction, nano diffraction, use of double-tilt rotation holder), data collection and data processing as well as structure solution strategies have been chosen dependent on the different requirements of the compounds under investigation. Structure analysis was carried out by simulation using ab initio quantum-mechanical methods like density functional theory (DFT), semi-empirical approach (MNDO/AM1/PM3) and force field packing energy calculations (DREIDING). The structure models resulting from simulation were refined kinematically as rigid bodies. Subsequently, refinements by multi-slice least squares (MSLS) procedures taking dynamical scattering into account were performed. The described combination of different methods which was used successfully on crystallizable materials is also adaptable to insoluble organic materials (e.g. pigments) and polymorphic systems.

Orthogonal dipolar interactions between amide carbonyl groups

Orthogonal dipolar interactions between amide C=O bond dipoles are commonly found in crystal structures of small molecules, proteins, and protein-ligand complexes. We herein present the experimental quantification of such interactions by employing a model system based on a molecular torsion balance. Application of a thermodynamic double-mutant cycle allows for the determination of the incremental energetic contributions attributed to the dipolar contact between 2 amide C=O groups. The stabilizing free interaction enthalpies in various apolar and polar solvents amount to -2.73 kJ mol(-1) and lie in the same range as aromatic-aromatic C-H...pi and pi-pi interactions. High-level intermolecular perturbation theory (IMPT) calculations on an orthogonal acetamide/N-acetylpyrrole complex in the gas phase at optimized contact distance predict a favorable interaction energy of -9.71 kJ mol(-1). The attractive dipolar contacts reported herein provide a promising tool for small-molecule crystal design and the enhancement of ligand-protein interactions during lead optimization in medicinal chemistry.

Reaction paths of tautomerization between hydroxypyridines and pyridones

Tautomerization paths of 2(and 4)-hydroxypyridine (called here HP) to 2(and 4)-pyridone (called here PY) with water molecules were investigated by the use of density functional theory calculations. Potential energies were compared for a number of water molecules. The 2-HP molecule was found to be isomerized most readily and concertedly to the 2-PY one via proton relays with two water molecules. The reaction pattern is invariant even when outer water molecules are added. The 4-HP(H(2)O)(n) --> 4-PY(H(2)O)(n) reaction model did not give small activation energies. However, a reaction of (4-HP)(2)(H(2)O)(2) --> (4-PY)(2)(H(2)O)(2) was found to occur readily through a transient ion-pair intermediate. The conversion processes of (2-PY)(2) to the tautomerization reacting system were discussed. The hydrogen-bond directionality regulates the tautomerization paths.

pH-Dependent Electronic and Spectroscopic Properties of Pyridoxine (Vitamin B6)

The key electronic and spectroscopic properties of vitamin B(6) (pyridoxine) and some of its main charged and protonated/deprotonated species are explored using hybrid density functional theory (DFT) methods including polarized solvation models. It is found that the dominant species at low pH is the N(1)-protonated form and, at high pH, the O(3)(')-deprotonated compound. Computed and experimental UV-spectra for these species (experimental spectra recorded at pH 1.7 and 11.1, respectively) show a very close resemblance. At pH 4.3, the protonated species dominates, but with onset of the zwitterionic oxo form which is also the dominant species at neutral pH. The computational studies furthermore show that neither a polarized continuum model of the polar aqueous solvent or explicit hydrogen bonding through additional water molecules are sufficient to describe accurately the spectrum at physiological pH. Instead, Na(+) and Cl(-) counterions were required to give a blue-shift of approximately 0.15 eV.

Tautomeric equilibria of pyridoxal-5'-phosphate (vitamin B6) and 3-hydroxypyridine derivatives: a theoretical study of solvation effects

The tautomeric equilibria of a series of 3-hydroxypyridine derivatives including pyridoxal-5'-phosphate (PLP), the active form of vitamin B(6), have been studied using density functional calculations (B3LYP/6-311+G//B3LYP/6-31G) in the gas phase and in different solvents. Three different approaches, namely continuum, discrete, and hybrid (combined discrete/SCRF), were employed to investigate the effects of solvation on the tautomeric equilibria. In all cases, the neutral hydroxy form is significantly more stable than the zwitterionic oxo form (by 43-56 kJ mol(-)(1)) in the gas phase. The tautomeric energies reduce substantially in the presence of a polarizable dielectric medium. However, the neutral form is calculated to be the dominant form in nonpolar and aprotic polar solvents. On the other hand, a reversal of tautomeric equilibrium, in favor of the zwitterionic form, is predicted in an aqueous medium. This study highlights the role of both water molecules and bulk solvent effect in influencing the tautomeric equilibria of the PLP related compounds. A combination of explicit microsolvation and continuum reaction field is required to account fully for the energetic effect of aqueous solvation. The tautomeric free energy differences (deltaG(298)) of PLP in the gas phase and in aprotic polar (epsilon = 40) and aqueous media are predicted to be 47, 22, and -29 kJ mol(-)(1), respectively.

Tautomeric equilibrium of pyridoxine in water. Thermodynamic characterization by 13C and 15N nuclear magnetic resonance

A remarkable temperature dependence on the 13C NMR and 15N NMR chemical shifts of pyridoxine in water (pH = 7.0) has been observed. C-3, C-6, and N-1 were the most sensitive nuclei to the temperature effect. This dependence has been explained on the basis of an equilibrium shift thermally induced between the neutral and the dipolar form of this molecule. The thermodynamic characterization of tautomeric equilibria that interconvert quickly on the NMR time scale can be carried out from the observed average 13C NMR and 15N NMR chemical shifts at different temperatures (5-90 degrees C). We have developed a new method for the estimation of the thermodynamic parameters of a given equilibrium by fitting the experimental data to a theoretical curve. This new method allows us to improve the fitting results on our previously proposed methodology. We show that there are linear correlations between the average chemical shifts obtained from different nuclei at the same temperature. This indicates that the parameters of the pure forms are related among them. We have carried out a simultaneous multiple function curve fitting of all data obtained from the most sensitive signals together using these linear correlations as restricted conditions in order to diminish the number of independent parameters to fit. To test the new methodology, we have studied the thermodynamics of the tautomeric equilibrium of pyridoxine in water. We have obtained delta H degree values ranging from -23.6 +/- 1.3 to -25.8 +/- 1.7 kJ/mol for this equilibrium depending on the used data set. This kind of methodology has, among others, the following advantages: It allows the use of a great number of experimental points from different signals in the fitting process, it yields very precise and accurate values of the tautomeric process, and it allows the resolution of the problem with only 13C NMR data in some cases saving NMR time.

Structure and conformation of N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine. A theoretical ab initio study

Optimal molecular geometries and molecular energies were obtained for N4-hydroxycytosine and its 5-fluoro congener with the use of the theoretical ab initio quantum mechanical calculations within the Self Consistent Field method corrected for the electron correlation effects by the second-order Many Body Perturbation Theory (SCF + MBPT(2)). The 6-31G Gaussian basis set was employed. Several tautomeric and rotameric forms were considered. For N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine the imino tautomer (in the conformation syn relatively to the N3-nitrogen atom) appeared to be the most stable form. The imino tautomer of N4-hydroxy-cytosine in the anti rotameric form is by 12.8 kJ mol-1 less stable than the imino-syn form. The 5-fluoro substituent raises the energy difference between the syn and anti rotamers up to 38.5 kJ mol-1. The potential energy barrier for the syn-anti rotation in the imino form of N4-hydroxycytosine is estimated to be about 180 kJ/mol. The results presented in this paper suggest that the syn-imino and anti-imino forms can be treated as two structural isomers that do not interconvert at temperatures relevant to biochemical conditions. The theoretical results also show that the amino tautomeric forms do not compete with the imino forms in the gas-phase and in non-polar and weakly-polar environment. In a polar environment (e.g., in aqueous solutions), however, one may expect an increased population of the amino forms. Qualitatively, the results of the present study agree well with the available experimental and theoretical data for N4-hydroxycytosine and some of its derivatives. The implications of the present study are discussed in relation to the molecular mechanisms of mutagenesis caused by NH2OH and of enzyme (thymidylate synthase) inhibition by N4-hydroxydeoxycytidine monophosphate.