Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.     

Non-standard base pairing and stacked structures in methyl xanthine clusters

We present resonant two-photon ionization and IR-UV double resonance spectra of methylated xanthine derivatives including 7-methylxanthine dimer and theobromine dimer seeded in a supersonic jet by laser desorption. For 7-methylxanthine, theophylline and theobromine monomer we assign the lowest energy tautomer based on comparison with IR-UV double resonance spectra and calculated IR frequencies. For the 7-methylxanthine dimer, we observe hydrogen bonding on the N3H position suggesting 3 possible combinations, one that is reverse Watson-Crick type and two that are reverse Hoogsteen type. For the theobromine dimer, we observe a stacked structure. For trimethylxanthine dimers we infer a stacked structure as well.     

Effect of the H-bonding on aromaticity of purine tautomers

Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F(-) and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (-14.12 and -10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to -14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N(-)···HF type are stronger by ~10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N(-)···HF energies in pyrrole and imidazole are -32.28 and -30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability.     

Conformation and tautomerism of the cimetidine molecule: a theoretical study

The cimetidine molecule conformation and tautomer stability was studied at the ab initio HF/6-31G** level and for single point energies at the MP2/6-31G** level. The most stable N3-H cimetidine tautomer was found to be more stable than the most stable N1-H tautomer by ca. 3.7 and 5.0 kcal/mol, at the HF/6-31G** and MP2/6-31G**//HF/6-31G** level, respectively. At the HF/6-31G** level, the most stable N3-H and 1-H forms are stabilized by the intramolecular N3′-H?N1 hydrogen bond and N1-H?N4′, respectively. However, when the correlation effects are included at the MP2/6-31G**//HF/6-31G** level, the most stable N3-H and N1-H tautomers appeared to be folded forms without hydrogen bonds.     

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G(d,p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G(d,p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.     

Structural and spectral studies on N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea

The crystal and molecular structure of the N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea (C₁₅H₁₃N₂OSCl, M_r=304.79) is determined by X-ray diffraction. The crystal structure is monoclinic, space group: P2₁/n, a=16.097(6), b=4.5989(2), c=19.388(7) Å and β=89.299(6)° V=1434.7(9)ų, Z=4. FTIR and NMR spectra have been characterized. The interactions of intramolecular and intermolecular hydrogen bonds have been discussed. Density functional theory (DFT) (B3LYP) methods have been used to determine the structure and energies of stable conformers. Minimum energy conformations are calculated as a function of the torsion angle θ (C13–N1–C14–N2) varied every 30°. The optimized geometry corresponding to crystal structure is the most stable conformation. This has partly been attributed to intramolecular hydrogen bonds. With the basis sets of the 6-311G* quality, the DFT calculated bond parameters and harmonic vibrations are predicted in a very good agreement with experimental data.     

Infrared spectra of 6-thioguanine tautomers. An experimental and theoretical approach

Both amino-thiol N9H and amino-thiol N7H tautomeric forms of 6-thioguanine have been identified in approximately equal abundance in infrared studies of these molecules isolated in the hydrophobic environment of an argon matrix at 12 K. The relative concentrations of the amino-thiol N9H and amino-thiol N7H ([SH, N9H]/[SH, N7H] = K(N9H-N7H) = 1.00 +/- 0.02) are estimated from the observed relative infrared absorbances. From these relative concentrations, the difference in the Gibbs free energy of these two tautomers (deltaG500(N9H-N7H) = -0.012 +/- 0.005 kJ mol(-1) have been estimated. The infrared and Raman spectra of 6-thioguanine in solid state are also discussed in terms of hydrogen bonding and stacking interactions in the crystal which are not considered in the calculation. In an effort to interpret the experimental results, ab initio calculation of the infrared spectrum has been made for the amino-thione N7H tautomer at 3-21G level. Comparison with experimental spectra is of some help in the assignment of the infrared and Raman spectra for 6-thioguanine in the solid state.     

Photochemical syn-anti isomerization reactions in N2-hydroxyisocytosines--an experimental matrix isolation and theoretical study

N2-hydroxyisocytosine and 1-methyl-N2-hydroxyisocytosine were studied using a matrix isolation technique combined with infrared absorption spectroscopy. For N2-hydroxyisocytosine isolated in an Ar matrix (at 10 K), two imino-oxo isomers, one with the hydroxyimino =N-OH group directed toward the N1-H group (the form called further anti) and the second with the =N-OH group directed toward N3-H (syn), were observed in the ratio 1.4:1. The syn isomer is converted totally to the anti form after UV (lambda > 295 nm) irradiation of the matrix. A small amount of the N(3)H-hydroxy-amino tautomer of N2-hydroxyisocytosine was also detected in the matrix. This form did not react photochemically. For 1-methyl-N2-hydroxyisocytosine, only the syn form of the imino-oxo tautomer was observed after deposition of the matrix. UV (lambda > 295 nm) irradiation induced a photoreaction converting this isomer into the anti form. After 15% of the starting material had been converted into the product, a photostationary state was achieved, and no further progress of the reaction was observed. Subsequent UV irradiation (lambda > 335 nm) caused a back reaction, leading to a disappearance of the anti form and to the recovery of the initial syn isomer. All isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-31G(d,p) level, where DFT is the density functional theory. Good agreement between the observed and predicted patterns of the spectral lines allowed for reliable identification. The experimental IR spectra were interpreted and discussed. The relative energies of the 12 isomers of N2-hydroxyisocytosine were calculated at the MP2/6-31G(d,p) and MP4//MP2/6-31G(d,p) levels. For six isomers of 1-methyl-N2-hydroxyisocytosine, the calculations were carried out at the MP2/6-31G(d,p) level. The anti form of the imino-oxo tautomer of N-hydroxyisocytosine and the syn form of the imino-oxo tautomer of 1-methyl-N2-hydroxyisocytosine were predicted to be the most stable.     

Hydrogen-bonding interactions in 2-thiophen-3-ylmalonic acid

Formation of intra- and intermolecular hydrogen bonds in 2-thiophen-3-ylmalonic acid, the precursor of a polythiophene derivative bearing two carboxylic acid groups in the side chain, have been examined by Fourier transform infrared (FTIR) spectroscopy and ab initio quantum mechanical calculations. Interactions found in the FTIR spectra recorded for the melted and solid states are in good agreement with results provided by MP2/6-31+G(d,p) calculations on monomers and dimers, respectively. Specifically, inter- and intramolecular hydrogen bonds were detected in the solid and melted states, respectively. Calculations on dimers stabilized by intermolecular hydrogen bonds exclusively and by both intra- and intermolecular interactions indicated that the former structures are significantly more stable than the latter ones, which is fully consistent with experimental observations. On the other hand, intramolecular interactions in isolated monomers are favored in the melted state, which is dominated by a thermally driven entropic process.     

UV-induced oxo --> hydroxy unimolecular proton-transfer reactions in hypoxanthine

Monomers of hypoxanthine isolated in low-temperature Ar matrixes were studied using Fourier transform infrared spectroscopy. Two most stable tautomeric forms of hypoxanthine: oxo-N(9)-H and oxo-N(7)-H as well as a very small amount of the minor hydroxy-N(9)-H tautomer were observed in Ar matrixes directly after their deposition. UV irradiation of the matrixes induced conversion of the oxo-N(9)-H and oxo-N(7)-H tautomers of the compound into the hydroxy-N(9)-H and hydroxy-N(7)-H forms, respectively. Upon exposure of the matrixes to the UV (lambda > 270 nm) light, the oxo-N(9)-H --> hydroxy-N(9)-H phototautomeric reaction dominated strongly over the oxo-N(7)-H --> hydroxy-N(7)-H phototransformation. The latter phototautomeric reaction occurred effectively when matrix-isolated hypoxanthine was irradiated with shorter-wavelength (lambda > 230 nm) UV light. Thanks to this wavelength dependency, it was possible to clearly distinguish the oxo --> hydroxy photoreaction within the N(9)-H tautomers from the analogous phototautomeric process within the N(7)-H tautomers. All of the observed isomers of hypoxanthine (substrates and products of the photoreactions) were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-31++G(d,p) level of theory.     

Hydrogen-bond interactions in hydrated 6-selenoguanine tautomers: a theoretical study

A comprehensive theoretical investigation has been performed to study the six most stable complexes of isolated, mono, and hexahydrated 6-selenoguanine tautomers. The ground state geometries are studied at the density-functional theory and Møller–Plesset Perturbation theory implementing the 6-311++G (2d, 2p) basis set. The intermolecular distances between the water molecule and the acceptor atom of 6-selenoguanine is about 0.6 Å longer for hydrogen bonds involving selenium atom. The relative Gibbs free energy of the 6-selenoguanine tautomers favors the selenone tautomer. The majority of the stable monohydrated complexes are the one in which the oxygen atom of water accepts the acidic N7-H proton while donating a proton to the carbonyl selenium atom of 6-selenoguanine; the interaction toward N7-H being stronger than that with the selenium site. The amino group planarity has been found to be increased in the hydrated complexes. The examination of molecular orbital reveals a moderate band gap between the donor and acceptor atoms of isolated and hydrated complexes. An excellent linear correlation is found to exist between electron density and laplacian of electron density with hydrogen-bond length through atoms in molecule analysis. The natural bond orbital analysis shows a maximum charge transfer of 0.060e for selenium acceptors and around 0.025e for selenium donors.     

Isomer- and species-selective infrared spectroscopy of jet-cooled 7H- and 9H-2-aminopurine and 2-aminopurine·H2O clusters

The infrared (IR) spectra of the supersonic-jet cooled 9H- and 7H-tautomers of 2-aminopurine (2AP) and of the 9H-2-aminopurine·H(2)O monohydrate clusters have been measured by mass- and species-selective IR-UV double resonance spectroscopy in the 3200-3900 cm(-1) region, covering the N-H and O-H stretching vibrations. The spectra are complemented by density functional (B3LYP and PW91) and by second-order M?ller-Plesset (MP2) calculations of the electronic energies and vibrational frequenciesof the respective 2AP tautomers and clusters. The 9H- and 7H-2-aminopurine tautomers were definitively identified by the shifts of their NH and NH(2) symmetric and asymmetric stretching frequencies and by comparison to the B3LYP/TZVP calculated IR spectra. The H-bond topologies of the two previously observed 9H-2-aminopurine·H(2)O isomers (Sinha. R. K.; et al. J. Phys. Chem. A2011, 115, 6208) are definitively identified as the "sugar-edge" isomer A and the "trans-amino-bound" isomer B by comparing their IR spectra to the calculated frequencies and IR intensities of the cluster isomers A, B, C, and D, as well as to the IR spectrum of 9H-2AP. The sugar-edge isomer A involves N9-H···OH(2) and HOH···N3 hydrogen bonds and is predicted to be the most stable form. The amino-bound isomer B involves NH(2)···OH(2) and HOH···N1 hydrogen bonds and is calculated to lie 2.5 kJ/mol above isomer A. The H-bond topology of the "cis-amino-bound" isomer C is symmetrically related to isomer B, with a hydrogen bond to the N3 of the pyrimidine group. However, it is calculated to lie 7 kJ/mol above isomer A and indeed is not observed in the supersonic jet. Isomer D involves a single H-bond to the N7 position, is predicted to be 14 kJ/mol above A and is therefore not observed.     

Calculation of vibrational spectra of linear tetrapyrroles. 3. Hydrogen-bonded hexamethylpyrromethene dimers

The structure and vibrational spectra of hexamethylpyrromethene (HMPM) have been investigated by X-ray crystallography, IR and Raman spectroscopies, and density functional theory calculations. HMPM crystallizes in the form of dimers, which are held together by bifurcated N-H(...N)(2) hydrogen bonds, involving one intramolecular and one intermolecular N-H...N interaction. The monomers are essentially planar, and the mean planes of the monomers lie approximately perpendicular to one another, so that the four N atoms in the dimer form a distorted tetrahedron. The structure of the HMPM dimer is well-reproduced by B3LYP/6-31G calculations. A comparison of the calculated geometry of the dimer with that of the monomer reveals only small changes in the N-H...N entity and the methine bridge angles upon dimerization. These are a result of weakening of the intramolecular N-H...N hydrogen bond and the formation of a more linear N-H...N intermolecular hydrogen bond. Using an empirical relation between the shift of the N-H stretching frequency of pyrrole and the enthalpy of adduct formation with bases [Nozari, M. S.; Drago, R. S. J. Am. Chem. Soc. 1970, 92, 7086-7090], estimates of the strength of the intra- and intermolecular hydrogen bonds are obtained. IR and Raman spectroscopies of HMPM and its isotopomers deuterated at the pyrrolic nitrogen atom and at the methine bridge reveal that the molecule is monomeric in nonpolar organic solvents but dimeric in a solid Ar matrix and in KBr pellets. The matrix IR spectra show a splitting of vibrational modes for the dimer, particularly those involving the N-H coordinates. Due to intrinsic deficiencies of the B3LYP/6-31G approximation, a satisfactory reproduction of these modes of the monomeric and dimeric HMPM requires specific adjustments of the NH scaling factors for the calculated force constants and, in the case of the NH out-of-plane modes of HMPM dimers, also of intra- and intermolecular coupling constants. This parametrization does not significantly affect the other calculated modes, which in general reveal a very good agreement with the experimental data.     

X-ray spectroscopy of heterocyclic biochemicals: xanthine, hypoxanthine, and caffeine

The electronic structures of the purine derivatives xanthine, hypoxanthine and caffeine have been investigated in the gas phase using C, N, and O 1s X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results have been interpreted by means of ab initio calculations using the third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Green's function and the second-order ADC method (ADC(2)) for the polarization propagator. The carbon, nitrogen and oxygen K-edge NEXAFS spectra of xanthine and caffeine are very similar, since the molecules differ only by substitution of three hydrogen atoms by methyl groups. For hypoxanthine, the electronic structure and spectra differ considerably from xanthine as the purine ring is more highly conjugated, and there is one less oxo group. Effects due to oxo-hydroxy tautomerism were not observed. However, the two oxo tautomeric forms of hypoxanthine oxo-N(9)-H and oxo-N(7)-H are populated in the gas phase, and the C 1s spectra can be simulated only by taking account of these two tautomers, with appropriate Boltzmann population ratios which we have also calculated. For xanthine and caffeine, single tautomeric forms were observed.     

Quantum chemical studies on prototautomerism of 1H‐imidazo[4,5‐c]pyridine

The structural features of the 1H‐imidazo[4,5‐c]pyridine (ICPY) tautomers and homodimers of the most stable tautomers have been studied by quantum chemical methods. FTIR and Raman spectra of the ICPY were recorded in the range of 4000–60 cm^?1 and 3500–5 cm^?1. The predominant tautomer among four possible isomers of ICPY were determined. The optimized geometries and vibrational frequencies of possible ICPY tautomers and dimers were computed by B3LYP/DFT method with 6‐311++G(d,p) and 6‐31G(d) basis sets. All vibrational frequencies assigned in detail with the help of total energy distribution (TED) and isotopic shifts. ICPY dimeric forms were also characterized according to their hydrogen bonding interactions, and it has been found that the most stable ICPY homodimer establishes moderate strong N ? H …N type hydrogen bond. ¹H NMR, ¹³C NMR, and ¹⁵N NMR properties have been calculated for all tautomeric forms using the gauge independent atomic orbital (GIAO) method. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Crystal structure of 6-[(1-methyl-4-nitroimidazol-5-yl)thio] purine

6-[(l-methyl-4-nitroimidazol-5-yl)thio] purine, is an immunosuppressant derivative of the antitumour drug, 6-mercaptopurine. Crystals are monoclinic witha = 4.488(2),b = 31.886(4), c = 8.067(2)A and β= 105.99(2)° in the space group P2₁/c. The crystal structure was solved by direct methods using diffractometer data and refined by least squares to anR- index of 0.065 for 502 observed reflections. The molecule crystallizes in the N(9)-H tautomer form, in contrast to the N(7)-H tautomer form found in crystals of 6-mercaptopurine and assume a conformation in which the substituents on the sulphur atom are directed away from imidazole moiety of the purine NCL Communication number 3313     

6‐(4‐Methoxy­benzyl­amino)­purin‐3‐ium chloride

The title compound, C₁₃H₁₄N₅O⁺·Cl⁻, belongs to the group of aromatic cytokinins. These compounds affect a variety of important physiological processes in plants and animals as well as in bacteria, including cell division, differentiation and senescence. The structure consists of a 6‐(4‐methoxy­benzyl­amino)­purinium cation and a Cl⁻ anion. The cation moiety exists as the N3‐protonated N7 tautomer. The cation contains nearly planar benzene and purine ring systems, with a dihedral angle of 77.46 (5)°. The crystal structure is stabilized by N_amino—H⋯N_purine hydrogen bonds connecting two adjacent mol­ecules, thus forming centrosymmetric dimers.     

N6‐Furfuryladenine (kinetin) hydrochloride

In the title compound, N⁶‐furfuryl­adenin‐3‐ium chloride, C₁₀H₁₀N₅O⁺·Cl⁻, the adenine moiety exists as the N3‐protonated N7–H tautomer. The orientation of the N6 substituent (furfuryl moiety) is distal to the imidazole ring of the adenine base. The dihedral angle between the adenine plane and the furfuryl ring plane is 76.1 (2)°. Three N—H⋯Cl hydrogen bonds are responsible for the formation of a supramolecular chain‐like pattern. These supramolecular chains are interconnected by C—H⋯Cl hydrogen bonds to form a hydrogen‐bonded sheet and a three‐dimensional hydrogen‐bonded network.     

Synthesis and Crystal Structure of Cis-syn Cyclobutane 1-（Carboxyethyl）thymine Dimer Monopentyl Amide Monotryptophan Methyl Ester Amide

The crystal structure of the title compound (C34H47N7O9, Mr = 697.79) has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000(8), b = 11.360(10), c = 17.841(15) , β = 97.083(14)°, V = 1810(3) 3, Z = 2, F(000) = 744, Dc = 1.280 g/cm3, μ = 0.094 mm-1, the final R = 0.0721 and wR = 0.1942 for 2479 observed reflections with I > 2σ(I). The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond (N(6)-H(6)…O(8)) introduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.     

Synthesis and Crystal Structure of （4S）-5-（2-Methoxy-2-oxoethylamino）-5-oxo-4-（3,4,5-trimethoxybenzamido） Pentanoic Acid

1 INTRODUCTION Aminopeptidase N (APN), a member of mem- brane-bound zinc-dependent exopeptidase, is known to be high expression on the brush border membran- es of the small intestine and renal proximal tubules[1]. The over-expression of APN has been involved in several pathological conditions including cancer[2], leukemia, diabetic nephropathy[3], rheumatoid arth- ritis[4], angiogenesis[5] and central nervous system di- seases, such as Alzheimer’s disease[6]. This has led to the sear…