Imino Form Research Articles

Photoreaction of neutral 9-aminoacridine in glycerol:water glass characterized by satellite holes and antiholes

Satellite holes and antiholes in the hole burned (HB) spectrum are used to determine the photoproduct of 9-aminoacridine (9AA) doped in glycerol:water (Gl:H 2O) glass with pH = 13. Although monoprotonated 9AA is the photoproduct of the imino form of neutral 9AA, antihole recovery implies that the excited state 9AA returns to original form of 9AA predominantly. Furthermore, similar satellite holes but different antihole structures are observed in the HB spectrum of 9AA doped in polyvinyl butyral film, implying that different HB mechanisms are involved.

Metal-Stabilized Rare Tautomers of Nucleobases. 6. Imino Tautomer of Adenine in a Mixed-Nucleobase Complex of Mercury(II).

(1,3-Dimethyluracil-5-yl)mercury(II), (1,3-DimeU-C5)Hg(II), reacts with the model nucleobase 9-methyladenine (9-MeA) to give the mixed-nucleobase complex [Hg(1,3-DimeU-C5)(9-MeA-N6)]NO(3).H(2)O. Hg(II) binds to the adenine via the N6 position with N1 being protonated. The neutral adenine nucleobase is therefore present in its imino form, which represents the rare tautomer form of this nucleobase. The X-ray crystal structure analysis reveals an anti orientation of the (1,3-DimeU-C5)Hg(II) entity with respect to N1 of 9-MeA and substantial differences in nucleobase geometry as compared to the amino tautomer form of 9-MeA. These differences refer to both the pyrimidine and the imidazole rings of the purine base. The possible relevance of this compound with regard to nucleobase cross-linking in DNA and nucleobase mispairing is discussed. Attempts to demonstrate mispairing between the metalated rare tautomer and "the wrong" bases 1-methylcytosine (1-MeC) and 9-ethylguanine (9-EtGH) in DMSO-d(6) proved unsuccessful due to a ligand exchange process at the heavy metal.

2‐Amino‐2‐Oxazolines, Part VIII. Calculated Molecular Properties of Tautomeric Species

AbstractThe geometries, tautomerization energies, and dipole moments of the tautomeric species of the 2‐amino‐2‐oxazoline heterocycle were calculated with full geometry optimization using semiempirical (MNDO, AM1 and PM3) and ab initio (RHF/6–31G) methods. The planar conformation of the amino form is well reproduced by the semiempirical and by the ab initio methods as compared with X‐ray structures in which this form is found. However the exocyclic nitrogen atom is pyramidalized in the semiempirical geometries whereas the ab initio method reproduces a sp2 hybridization state. The twisted conformation of the imino form is better reproduced by the ab initio calculation. All methods (semiempirical and ab initio) show a stability energy value in favour of the amino tautomer of the neutral heterocycle. On the contrary, the dominant species of the charged heterocycle is the imino tautomer, protonated on the exocyclic nitrogen atom. Molecular electrostatic potential calculations confirmed this tendency. Finally the 3D‐lipophilicity profile of the heterocycle completed the investigation of the tautomerism.

Methoxyamine-induced mutagenesis of nucleic acids. A proton NMR study of oligonucleotides containing N4-methoxycytosine paired with adenine or guanine.

We report the solution structure of two heptanucleotides each containing a central N4-methoxycytosine, in one case paired with adenine on the opposite strand and the other with guanine. For the N4-methoxycytosine adenine pair, only the imino form of the N4-methoxycytosine residue is observed and base pairing is in Watson-Crick geometry. However, rotation of the methoxy group about the N-OCH3 bond is not constrained to a particular orientation although it must be anti to the N3 of N4-methoxycytosine. The slow exchange on a proton NMR time scale between the single strand and double strand forms is attributed to the strong preference of the cis conformation of the OCH3 group in the single strand, which inhibits base pair formation. For the N4-methoxycytosine that is base paired with guanine, we observe an amino form in Watson-Crick geometry in slow exchange with a base paired imino form in wobble geometry. The amino form is predominant at low temperature whereas the imino form predominates above 313 K. We have measured the exchange rate between the two forms at 303 K and observed a value of approximately 1 S-1. The relative ratio of amino and imino forms of N4-methoxycytosine is influenced by both the base that is in front and the temperature. Our results explain the preferential replacement of dTTP by N4-methoxycytosine in primer elongation.

Intramolecular hydrogen bonding and molecular structure of 2-iminomethyl-phenol and molecular structure of iminomethyl-benzene from ab initio MO calculations

Ab initio calculations, including electron correlation (MP2), have been performed for iminomethyl-benzene and 2-iminomethyl-phenol. They indicate the existence of two (syn and anti) stable conformers of 2-iminomethyl-phenol. The principal syn conformer is characterized by considerable hydrogen bonding between the iminomethyl and hydroxy groups, accompanied by pronounced structural changes in the rest of the molecule, as compared with phenol and iminomethyl-benzene calculated at the same theoretical level. These structural changes are consistent with the notion of resonance-assisted hydrogen bonding, also observed in a series of nitrophenols and similar molecules. The anti conformer of 2-iminomethyl-phenol has 41.8 kJ mol −1 higher energy than the syn conformer. The internal rotation of iminomethyl group in 2-iminomethyl-phenol is hindered by a considerably higher barrier, 55.9 kJ mol −1, due to intramolecular hydrogen bond formation, than that in iminomethyl-benzene, 27.6 kJ mol −1, according to the calculations at the HF/6-31G ∗ level. The amino tautomer form of 2-iminomethyl-phenol has 25.0 kJ mol −1 (HF/6-31G ∗) or 30.6 kJ mol −1 (MP2(FC)/6-31G ∗) higher energy than the imino form. The energy of the structural changes as compared to iminomethyl-benzene and phenol and the energy of the intramolecular hydrogen bond formation in 2-iminomethyl-phenol was estimated to be −28.8 kJ mol −1 at the HF/6-31G ∗ level and −36.8 kJ mol −1 at the MP2(FC)/6-31G ∗ level of theory.

Methoxyamine attack on cytosine produces ambivalent base pairing properties of the modified base.

We report the solution structure of two heptanucleotides each containing a central N4-methoxycytosine, in one case with adenine on the opposite strand and in the other with guanine. For the N4-methoxycytosine-adenine pair only the imino form of the N4-methoxycytosine residue is observed and base pairing is in Watson-Crick geometry. However, rotation of the methoxy group about the N-OCH3 bond is not constrained to a particular orientation although it must be anti to the N3 of N4-methoxycytosine. The slow exchange on a proton NMR time scale between the single strand and double strand forms is attributed to the strong preference of the syn conformation of the OCH3 group in the single strand which inhibits base pair formation. For N4-methoxycytosine base paired with guanosine we observe the N4-methoxycytosine base in the amino form in Watson-Crick geometry and a slow exchange of this species with an imino form base paired in wobble geometry. The amino form is predominant at low temperature whereas the imino form predominates above 40 degrees C. Our results point to preferential replacement of dTTP by N4-methoxycytosine in primer elongation.

5-Hexylamino-1,2-benzoquinone 2-Oxime Monohydrate

In C12H18N2O2.H2O, the oximic OH group is anti (trans) to the quinoid carbonyl group, thus there are no intramolecular hydrogen bonds in the molecule. Extensive intermolecular interactions between neighbouring quinone oxime molecules and associated water molecules are observed. Bond distances are intermediate between those predicted for the 1,2-quinoneoxime and 2,5-oxime imino forms.

Matrix-Isolation FT-IR Studies and Ab-Initio Calculations of Hydrogen-Bonded Complexes of Molecules Modeling Cytosine or Isocytosine Tautomers. 2. 4-Aminopyridine and 4-Aminopyrimidine Complexes with H2O in Ar Matrixes

H-bonding interactions of the cytosine-modeling compounds 4-aminopyridine and 4-aminopyrimidine with water are investigated with the use of a combined experimental matrix-isolation FT-IR and theoretical ab-initio method. Both bases appear exclusively as the amino tautomers in low-temperature Ar matrices, in accordance with large ab-initio predicted energy differences with the rare imino forms. The most stable complex of water with 4-aminopyridine is the H-bonded N{sub 1}...HO-H structure, but the energy difference with the alternative N-H...OH{sub 2} complex is calculated to be only 6.7 kJ/mol. Both complexes are observed in the Ar matrix. In the case of 4-aminopyrimidine, the closed N-H...O-H...N{sub 3} structure containing two H-bonds is found to be significantly more stable than the singly H-bonded structures N{sub 1}...HO-H and N-H...OH{sub 2} by 8.0 and 10.2 kJ/mol, respectively. The previously suggested relation between the scaling factor for the theoretically-calculated $nu{sup b}{sub OH} mode of the H-bonded water and the proton affinity value of the proton-acceptor site in the base is developed further. 24 refs., 10 figs., 10 tabs.

Investigations on the Amidine System in Amidinobenzisothiazole Derivatives

AbstractThe amino/imino equilibrium is studied in free bases and hydrochloride salts of amidinobenzisothiazole derivatives by IR and 1H‐NMR spectroscopy. The X‐ray crystallographic analysis of two of these compounds shows that the free base exists as amino form whereas the hydrochloride as imino form.

Surface‐modified gold electrodes for electrocatalytic oxidation of NADH based on the immobilization of phenoxazine and phenothiazine derivatives on self‐assembled monolayers

AbstractSelf‐assembled monolayers of cystamine and cysteine chemisorbed on gold electrode surfaces have been used as a support for covalent immobilization of some phenoxazine and phenothiazine derivatives. The covalent attachment was achieved after previous functionalization of the free amino groups on the electrode surface with bifunctional reagents (terephthaloyl chloride and 1,6‐hexamethylene diisocyanate) able to react with the imino form of the amino group in position 3 of the phenoxazine and phenothiazine derivatives.In every case, a shift of the redox potentials between 130 and 180 mV towards more positive potentials, as well as an increase in the peak‐topeak separation between anodic and cathodic peaks was observed after covalent attachment. The surface coverages (10−11 < Γ < 10−10 mol/cm2) obtained from the cyclic voltammograms were those for a not densely packed monolayer and varied depending on the redox compound immobilized. The surface‐modified electrodes obtained were afterwards used for the electrocatalytic oxidation of NADH.UV‐vis spectroscopy was used to monitor the successive steps of surface modification using gold semitransparent electrodes. The total surface coverage of redox mediator on the electrode surface could also be calculated from the optical difference spectra between the oxidized and the reduced state obtained ‘in situ’ in a spectroelectrochemical cell.

Study of Amino-Imino Tautomerism in Derivatives of 2-, 4- and 6-Aminonicotinic Acid

13C NMR spectra of p-nitrobenzoyl 2-, 4-, and 6-aminopyridine-3-carboxylates, their hydrochlorides, trifluoroacetates and 1-benzyl derivatives were studied. As found from the chemical shifts of pyridine carbon atoms C-2, C-4 and C-6, the free bases exist in the amino form whereas hydrochlorides and 1-substituted pyridinium derivatives in the imino form. Trifluoroacetates of the 2- and 6-amino derivatives have structure similar to that of amidiniumcarboxylates (parallel hydrogen bonds and partially ionic character) whereas trifluoroacetate of the 4-amino derivative is structurally close to the corresponding hydrochloride. The found structures were confirmed by 1H NMR and IR spectroscopy.

Model studies on the structure of poly(amide oxime)s and their cyclodehydration reactions leading to poly(1,2,4‐oxadiazole)s

AbstractTo obtain an understanding of the low molecular weight character of wholly aromatic poly(1,4‐arylene acyldiamide oxime)s (PAAs) having n‐alkyloxymethyl side braches and the additional decrease in molecular weight during their cyclodehydration reaction leading to the corresponding poly(1,4‐arylene‐1,2,4‐oxadiazole)s (PAOs), tautomeric structures of poly[1,4‐phenylene‐2,5‐bis(n‐octyloxymethyl)terephthaldiamide oxime] (C8‐PAA) were 1H‐NMR‐spectroscopically investigated by using two model compounds: O,O'‐dibenzoyl terephthaldiamide oxime (H‐PAA‐M, 4) and O,O'‐dibenzoyl‐2,5‐bis(n‐octyloxymethyl) terephthaldiamide oxime (C8‐PAA‐M, 5). In solution H‐PAA‐M existed exclusively as oximino isomer, while C8‐PAA‐M consisted only of imino tautomer and C8‐PAA contained both the oximino and imino form, the former being dominant in composition. It was found that the presence of imino tautomer caused serious effects both on the low molecular weight character of C8‐PAA and on the additional decrease in molecular weight during thermal cyclodehydration to C8‐PAO, whereas the presence of oximino tautomer showed practically little effect. A discussion on the results is provided from mechanistic viewpoint. © 1993 John Wiley & Sons, Inc.

Mechanism of hydroxylamine mutagenesis: Role of tautomerism, conformation and proton exchange on base pairing between the promutagen N6 methoxyadenosine and uridine

A study of the interaction of N 6-methoxyadenosine (OMe 6A, which exists as an equilibrium mixture of amino and imino tautomers) with the potentially complementary uridine in non-aqueous medium demonstrated that only the tautomer amino-OMe 6A base pairs with uridine. The association constant, determined by 1H NMR spectroscopy, was 101 M −1 at + 30°C, an order of magnitude greater than those for autoassociation of amino-OMe 6A or uridine. Base pair formation between amino-OMe 6A and uridine led to a shift of the amino-imino equilibrium of 10% in favour of the amino species which associates with uridine, with the concomitant decrease in population of the imino form. Base pairing was accompanied by intermolecular proton exchange between the N 6-H of amino-OMe 6A and the N(3)-H of uridine. The rate constants for these exchanges, as well as for tautomeric exchange of OMe 6A in the presence of uridine, were measured by means of the saturation transfer technique. The mechanism of proton exchange is compared with, and shown to be different from, that previously observed for base pair formation between the imino tautomer of OMe 6A and cytidine (Stolarski et al., Biochemistry 26 (1987), 4332 also linked with tautomeric exchange. The resulting proposed schemes of base pairing are dependent on the conformation of the exocyclic N 6-methoxy group, and are compared and discussed with reference to published data on base pairing at the oligonucleotide duplex level, as well as known data on base pairing of the analogous promutagen N 4-methoxycytidine. The overall findings further contribute to our understanding of the dual functionality of the promutagen OMe 6A at the molecular level, and furthermore, provide an excellent model system for studying the role of tautomerism on proton exchange in base pairs.

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 N 4-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 N 4-hydroxycytosine and N 4-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 N 4-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 N 4-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 N 4-hydroxycytosine and some of its derivatives. The implications of the present study are discussed in relation to the molecular mechanisms of mutagenesis caused by NH 2OH and of enzyme (thymidylate synthase) inhibition by N 4-hydroxydeoxycytidine monophosphate.

Structure of 2-benzothiazolylhydrazones of aromatic and aliphatic aldehydes

On the basis of data of 13C and 1H NMR and IR spectroscopy, it was shown that 2-benzothiazolylhydrazones of aliphatic aldehydes were in solution as a mixture of E and Z isomers, and hydrazones of aromatic aldehydes were in solution only as E isomers. All investigated compounds existed in solution mainly in an amino tautomeric form, and the content of the imino form did not depend on the nature of the aldehyde fragment.

Tautomerism of some amino aza‐containing heterocycles

AbstractWith the aim of checking potential amino/imino tautomerism in heterocyclic series, some uv/visible spectroscopic properties of 2‐N‐(2,4,6‐trinitrophenyl)pyridine, 2‐N‐(2,4,6‐trinitrophenyl)pyrimidine and of 2‐N‐(2,4,6‐trinitrophenyl)thiazoleamine are reported and discussed. In dimethyl sulphoxide the imino tautomer of the thiazole derivatives is the more populated form, while in toluene the amino aromatic form predominates. The more populated tautomer of the pyridine and pyrimidine derivatives is the amino aromatic form in both polar and apolar solvents. For the thiazole derivatives the tautomeric equilibrium in toluene is shifted toward the imino form by adding small amounts of tetrabutylammonium bromide or of dimethyl sulphoxide. The position of the tautomeric equilibrium is quantitatively evaluated and discussed.

Thermal decomposition of aminotetrazoles: Part 1. 5-Aminotetrazole

The thermal decomposition of 5-aminotetrazole (5-AT) has been studied by thermogravimetry, thermal volumometry, DSC, DTA and EGA. Solid products of thermal decomposition have been identified by IR spectroscopy and gaseous products by IR and mass spectrometry. Theoretical considerations of thermodynamic characteristics and energies of atomic bonding in the 5-AT tautomeric forms and intermediates have been carried out by the MO SCF method in the MNDO approximation. On the basis of IR and available literature data it is shown that dehydrated 5-AT exists mainly in the imino form in the solid state. Thermal treatment leads to increasing content of the amino form. The thermal decomposition of the imino form of 5-AT starts just after melting and results in hydrogen azide and carbodiimide. The linear polymer of carbodiimide and melamine derivatives have been identified in the solid residue. Further increase of temperature in the course of linear heating leads to another route of thermal decomposition involving the amino form of 5-AT accompanied by the evolution of nitrogen. Apparent activation energies of these routes determined from non-isothermal thermogravimetric data amount to 165 and 135 kJ mol −1, respectively.

Metal-stabilized rare tautomers of nucleobases. 4. On the question of adenine tautomerization by a coordinated platinum(II)

An attempt is described and critically asssessed to use the ‘method of basicity measurements’ for estimating the effect of Pt(II) electrophiles bound to the N7 position of the model nucleobase 9-methyladenine to shift the tautomer equilibrium from the preferred 6-amino to the rare 6-imino form. The question of tautomerization of an adenine nucleobase is of biological interest with regard to the now established preference for A → T transversions as a consequence of 5′ (ApG) adduct formation of the antitumor agent Cisplatin. For this purpose, a series of model nucleobase complexes of Pt(II) with 9-methyladenine (9-MeA), 1,9-dimethyladenine (1,9-DimeA) and 6,9-dimethyladenine (6,9-DimeA), and their protonated forms have been prepared and their UV spectra at various pH values recorded. In two cases, the compounds were characterized also by X-ray analysis, cis-[Cl 2Pt(1,9-DimeAH)(NH 3)]Cl ( 2c) and Cl 3Pt(6,9-DimeAH)·H 2O ( 3a). Based on the experimentally determined p K a, values of the platinated adeninium ligands, tautomer equilibrium constants K T were calculated and found to be 10 −4.5 for [Cl 3Pt(9-MeA)] − and 10 −4.6 for cis-Cl 2Pt(NH 3)(9-MeA). These values compare with 10 −4.8 for 9-MeA. The observed shifts in favor of the rare imino tautomer on Pt binding to N7 are considered too small to unambiguously explain the observed preferential A → T transversion on the basis of an initial mispair between a platinated adenine in its imino form and an adenine in its normal amino tautomer.

Tautomerism and methylation of 2-imino-4-imidazolidinones

5-Benzylidenecreatinine and 2′-phenylglycocyamidine exist in DMSO-D6 in the imino form. In basic medium, the two compounds exhibit a dual reactivity with respect to methylating agents, forming N(2′)- and N(3)-methyl derivatives.

Mechanism of inhibition of mammalian tumor and other thymidylate synthases by N4-hydroxy-dCMP, N4-hydroxy-5-fluoro-dCMP, and related analogs

N4-Hydroxy-dCMP (N4-OH-dCMP), N4-methoxy-dCMP (N4-OMe-dCMP), and their 5-fluoro congeners (syntheses of which are described) were all slow-binding inhibitors of Ehrlich carcinoma thymidylate synthase (TS), competitive with respect to dUMP, and had differing kinetic constants describing interactions with the two TS binding sites. N4-OH-dCMP was not a substrate (no dihydrofolate produced; no tritium released with 5-3H-labeled molecule), and its inactivation of TS was methylenetetrahydrofolate-dependent, hence mechanism-based, with arrest of a step posterior to addition of cofactor and blocking abstraction of the C(5) hydrogen. Ki values for N4-OH-dCMP and its 5-fluoro analogue were in the range 10(-7) - 10(-8) M, 2-3 orders of magnitude higher for the corresponding N4-OMe analogues. The 5-methyl analogue of N4-OH-dCMP was 10(4)-fold less potent, pointing to the anti rotamer of the imino form of exocyclic N4-OH, relative to the ring N(3), as the active species. This is consistent with weaker slow-binding inhibition of the altered enzyme from 5-FdUrd-resistant, relative to parent, L1210 cells by both FdUMP and N4-OH-dCMP, suggesting interaction of both N4-OH and C(5)-F groups with the same region of the active center. Kinetic studies with purified enzyme from five sources, viz., Ehrlich carcinoma, L1210 parental, and 5-FdUrd-resistant cells, regenerating rat liver, and the tapeworm Hymenolepis diminuta, demonstrated that addition of a 5-fluoro substituent to N4-OH-dCMP increased its affinity from 2- to 20-fold for the enzyme from different sources.(ABSTRACT TRUNCATED AT 250 WORDS)