Theoretical investigation of the structure and acid–base properties of potential 2-thiolumazine tautomeric forms using the AM1 semiempirical method

The relative stabilities of potential tautomers, in both gas and aqueous phases, have been calculated taking into account the entropy effects over the tautomeric equilibria, in order to determine the structure and acid–base properties of the most stable tautomers of 2-thiolumazine in different pH conditions. In each medium, the tautomer with the lowest energy must be the most representative form at the corresponding pH. Knowledge of the effect of the medium in the tautomerization energies allows us to evaluate the possible effect of the medium on the molecular stability. Clearly, the results show that in the gas phase the basicity of the potential donor atoms is N5<N8<O4<S2<N1<N3, and in the aqueous phase S2<(O4N5)<N8<N1<N3, with the higher basicity of N3 and N1 being common to the two phases. In the aqueous phase, the sulfur atom is usually found in the thiol form, whereas the oxygen atom is in the keto form only in the most stable species. Moreover the acid–base character of 2-thiolumazine in aqueous solution has been evaluated from the corresponding AM1 thermodynamic parameters. The results agree well with the experimental data. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-002-0094-9Electronic Supplementary Material available.     

Specific interactions of isoguanine with the neutral and deprotonated carboxylic group of amino acids: results of model quantum chemical calculations

The MNDO/H quantum chemical calculations performed in order to estimate energetic features of the isoguanine (isoGua) prototropic tautomers complexes with acetic acid and its carboxylate-ion (models of neutral and deprotonated forms of amino acid carboxylic group) demonstrate ability of the latter to induce the N9H-->N7H tautomeric transition in the base, being characteristic to other purine bases as well. By contrast, the neutral carboxylic group forms the most stable complex with the ground-state isoGua tautomer N3HN9H.     

Azaguanine: A Theoretical Study of Its Tautomerism and Protonation in the Gas Phase and Aqueous Solution

The tautomerism and protonation of 8-azaguanine (azaG) have been studied by means of ab initio methods, both in the gas phase and in aqueous solution. An elimination procedure to choose the most stable tautomeric forms, based on AM1 and HF/6–31G* energies, has been applied. Tautomers azaG(1,9), azaG(1,7) and azaG(9,15) have been selected and their energies calculated at MP2/6–311++G**//HF/6–31G* level. Self-consistent reaction field IPCM, based on polarizable continuum model (PCM), has been applied to study the solvent effects. The stability order in the gas phase is azaG(1,7) = azag(1,9) > azaG(9,15), whereas in solution the order becomes azaG(1,7) > azaG(1,9) > azaG(9,15), the latter being just 0.76 kcal/mol over azaG(1,7). The calculations of proton affinities allowed to unambiguously determine the preferred sites of protonation of these species.     

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study

In the present work, the influence of Cu⁺ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine–guanine, hypoxanthine–adenine, hypoxanthine–cytosine, hypoxanthine–thymine and hypoxanthine–hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu⁺ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu⁺ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu⁺ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses.

Communicated by Ramaswamy H. Sarma     

Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine

Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pK_a of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes.     

Tautomeric energetics of xanthine oxidase substrates: xanthine, 2-oxo-6-methylpurine, and lumazine

The stability of the tautomers of each of the three important substrates of xanthine oxidase, xanthine, 2-oxo-6-methylpurine, and lumazine, was examined by quantum mechanical calculations. The geometries of these tautomers were optimized at the AM1, Hartree-Fock (HF/6-31G), and hybrid Hartree-Fock/density functional theory (B3LYP/6-31G(d)) levels of theory. The single point energies of some of the more stable tautomers for each of the substrates were calculated at the B3LYP/6-311 +G(2d,p) level of theory. The Conductor Polarized Continuum Model (CPCM) was used to evaluate the solvent effects on the relative stabilities of these tautomers. The calculations clearly identify the lowest energy tautomeric form for xanthine and lumazine. On the other hand, there appear to be three tautomers for 2-oxo-6-methylpurine, with only minor energetic differences in vacuo. In water, however, only one of them predominates. The lowest energy tautomers presumably represent the predominant tautomeric forms at the molybdenum center of xanthine oxidase during catalysis. Implications of these computational results are discussed in the context of enzyme catalysis.     

Superoxide- and 1,1-Diphenyl-2-picrylhydrazyl Radical-scavenging Activities of Soyasaponin β g Related to Gallic Acid

Soyasaponin β g at 1 mM had 8% scavenging activity for O₂ ^-, and 25 μM β scavenged 20.9% for the DPPH radical (IC₅₀: 63.8 μM). In the soyasaponin β g-gallic acid system, synerigistic effects were observed at a low level of gallic acid concentration. The spin density distribution calculated by the MNDO/AM1 method showed unpaired electron localization on the carbons at C-4 and C-6, and on the ketone group at C-4 of the DDMP moiety. Furthermore, for soyasaponin β g, the MNDO/AM1 method gave an ionization potential of 8.38 eV, electron affinity of 1.16 eV and Mulliken electronegativity of 4.77 eV. Based on this evidence, the synergistic antiradical effects of the soyasaponin β g-gallic acid system are assumed to involve two-electron reduction from gallic acid.     

The role of CS<Subscript>2</Subscript> in CS<Subscript>2</Subscript>/NMP mixed solvent in weakening the hydrogen bond of OH–N in coal: a DFT investigation

The interaction processes of trace amounts of N-methyl-2-pyrrolidinone (NMP), CS₂/NMP (1:1 by volume) and pure NMP solvent with the hydrogen bond of OH?N in coal were constructed and simulated by density functional theory methods. The distances and bond orders between the main related atoms, and the hydrogen bond energy of OH?N were calculated. The calculated results show that pure NMP solvent does not weaken the hydrogen bond of OH?N in coal. However, trace amounts of NMP and CS₂/NMP (1:1 by volume) have a strong capacity to weaken the hydrogen bond of OH?N in coal. The H2–N3 distances are elongated from 1.87 Å to 3.80 Å and 3.44 Å, the bond orders of H2–N3 all disappear, and the corresponding hydrogen bond energies of OH?N in coal decrease from 45.72 kJ mol^?1 to 7.06 and 11.24 kJ mol^?1, respectively. These results show that CS₂ added to pure NMP solvent plays an important role in releasing the original capacity of NMP to weaken the hydrogen bond of OH?N in coal, in agreement with experimental observations.     

Electronic structure and polarizabilities of some heterocycles: I. Hydroxypyrazoles and related systems

The (hyper)polarizabilities of different tautomer forms of hydroxypyrazoles and pyrazolones have been calculated by the finite-field procedure in the MNDO approximation and the sum of states formalism in the PPP approximation, with all singly- and doubly-excited electronic configurations in the CI method. It was shown that while in the ground electronic state the values of the (hyper) polarizabilities are not essentially different, in the first excited singlet Franck-Condon state an increase of the molecular polarizabilities of some tautomers is observed. This increase is attributed to a specific change in the electronic structure of the excited state, demonstrated by the localization of the electronic transition in the different pyrazolone tautomers. The electron-donor capabilities of phenyl-substituted hydroxypyrazoles and pyrazolones are discussed.     

Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Extensive DFT and ab initio calculations were performed to characterize the conformational space of pamidronate, a typical pharmaceutical for bone diseases. Mono-, di- and tri-protic states of molecule, relevant for physiological pH range, were investigated for both canonical and zwitterionic tautomers. Semiempirical PM6 method were used for prescreening of the single bond rotamers followed by geometry optimizations at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. For numerous identified low energy conformers the final electronic energies were determined at the MP2/6-311++G(2df,2p) level and corrected for thermal effects at B3LYP level. Solvation effects were also considered via the COSMO and C-PCM implicit models. Reasonable agreement was found between bond lengths and angle values in comparison with X-ray crystal structures. Relative equilibrium populations of different conformers were determined from molecular partition functions and the role of electronic, vibrational and rotational degrees of freedom on the stability of conformers were analyzed. For no level of theory is a zwitterionic structure stable in the gas-phase while solvation makes them available depending on the protonation state. Geometrically identified intramolecular hydrogen bonds were analyzed by QTAIM approach. All conformers exhibit strong inter-phosphonate hydrogen bonds and in most of them the alkyl-amine side chain is folded on the P-C-P backbone for further hydrogen bond formation.

Mycorrhizal mediation of plant N acquisition and residue decomposition: Impact of mineral N inputs

Mycorrhizas are ubiquitous plant–fungus mutualists in terrestrial ecosystems and play important roles in plant resource capture and nutrient cycling. Sporadic evidence suggests that anthropogenic nitrogen (N) input may impact the development and the functioning of arbuscular mycorrhizal (AM) fungi, potentially altering host plant growth and soil carbon (C) dynamics. In this study, we examined how mineral N inputs affected mycorrhizal mediation of plant N acquisition and residue decomposition in a microcosm system. Each microcosm unit was separated into HOST and TEST compartments by a replaceable mesh screen that either prevented or allowed AM fungal hyphae but not plant roots to grow into the TEST compartments. Wild oat (Avena fatua L.) was planted in the HOST compartments that had been inoculated with either a single species of AM fungus, Glomus etunicatum, or a mixture of AM fungi including G. etunicatum. Mycorrhizal contributions to plant N acquisition and residue decomposition were directly assessed by introducing a mineral ¹⁵N tracer and ¹³C‐rich residues of a C₄ plant to the TEST compartments. Results from ¹⁵N tracer measurements showed that AM fungal hyphae directly transported N from the TEST soil to the host plant. Compared with the control with no penetration of AM fungal hyphae, AM hyphal penetration led to a 125% increase in biomass ¹⁵N of host plants and a 20% reduction in extractable inorganic N in the TEST soil. Mineral N inputs to the HOST compartments (equivalent to 5.0 g N m^?2 yr^?1) increased oat biomass and total root length colonized by mycorrhizal fungi by 189% and 285%, respectively, as compared with the no‐N control. Mineral N inputs to the HOST plants also reduced extractable inorganic N and particulate residue C proportion by 58% and 12%, respectively, in the corresponding TEST soils as compared to the no‐N control, by stimulating AM fungal growth and activities. The species mixture of mycorrhizal fungi was more effective in facilitating N transport and residue decomposition than the single AM species. These findings indicate that low‐level mineral N inputs may significantly enhance nutrient cycling and plant resource capture in terrestrial ecosystems via stimulation of root growth, mycorrhizal functioning, and residue decomposition. The long‐term effects of these observed alterations on soil C dynamics remain to be investigated.     

Excited-state relaxation paths of oxo/hydroxy and N9H/N7H tautomers of guanine: a CC2 theoretical study

We performed a theoretical investigation, at the CC2/aug-cc-pVDZ level, of the ring-deformation mechanisms of four guanine tautomers (oxo, hydroxy, N9H, and N7H). The study showed that the optimized conical intersections S₀/S₁ are accessible through the ¹ππ* excited states of tautomers. The optimized conical intersections S₀/S₁, which show deformation at the pyrimidine ring, have high energies. This means that the relaxations of the ¹ππ* excited states via internal conversion are disfavored. For two tautomers we found crossing points ¹ππ*/¹πσ* of the excited-state reaction paths, revealing the possibility of a population of the ¹πσ* excited state by the ¹ππ* excited state.

Effect of protonation of nucleic acid bases on the energy of formation of the Watson-Crick pairs

Neutral and protonated nucleic bases and their complexes were calculated using a modified MNDO method. On the basis of the obtained proton affinities we conclude that proton transfer from positively charged amino acid residues to nucleic bases is quite possible. The protonation influence upon the structure and the energy of complementary base pairs was studied. The protonation of guanine is shown to stabilize the GC complex, but the protonation of cytosine destabilizes it. The energy of the AU pair increases upon protonation of adenine due to ion--dipole interactions. The protonation of uracil leads to a proton transfer between the bases and to the stabilization of the AU pair.     

Quantum chemical study of the structure and properties of citrinin

Detailed structures and electronic properties of three tautomeric forms of the toxin citrinin were investigated using several quantum calculation methods. Energetic preference of the predominant p- and o-quinone methide tautomeric forms is dependent on the method of calculation. A previously unstudied carboxylic acid enol tautomer was calculated to be surprisingly stable in vacuo, being within 2.5 kcal mol^? 1 at the B3LYP/6-311++G(2d,2p) level of theory. Despite differences in bond nature and connectivity of tautomers, the natural bond orbital analysis revealed that tautomeric forms share similar natural charges and natural electron configurations. Calculated bond lengths corresponded with experimentally observed values and assignments for the calculated infrared vibrational frequencies are reported.     

Aminequinone-hydroxylquinoneimine tautomeric equilibrium revisited: molecular modeling study of the tautomeric equilibrium and substituent effects in 4-(4-R-phenylamino)naphthalene-1,2-diones

Semi-empirical (AM1 and PM3) and DFT (B3LYP/6-31G(d)) calculations were employed to study the tautomeric equilibrium between the aminequinone A and hydroxylquinoneimine B forms of 4-(4-R-phenylamino)naphthalene-1,2-diones. Substituent effects on the tautomeric equilibrium as well as on geometric and electronic parameters were also determined. In the gas phase the hydroxylquinoneimine B form is the most stable, whereas in water the aminequinone A form becomes more stable. The substituents do not modify the relative energies of the two tautomers. These results are in accordance with experimental data reported in the literature.     

Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM)

Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6?311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6?311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.     

Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods

Glucosamine synthase (E.C. 2.6.1.16) is a promising target in antifungal drug design. It has been reported that its potent inhibitor, N³-(4-methoxyfu-maroyl)-L-2,3-diaminopropanoic acid (FMDP), inactivates the enzyme by the Michael addition of the S-H group to the FMDP molecule followed by cyclisation reactions. In this study we have investigated, by means of semiempirical MNDO, PM3 and molecular mechanics methods, the energetics and kinetic possibility of the formation of various stereoisomers of the products of cyclisation of the Michael addition products detected experimentally. It was found that the substituted 1,4-thiazin-3-one can be formed in one step under alkaline conditions; the stereoisomers of this compound predicted to be the most stable on the basis of theoretical calculations are also the dominant ones in reality.Abbreviations FMDP N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid - MNDO Modified Neglect of Diatomic Overlap - AM1 Advanced Method 1 - PM3 (full abbreviation: MNDOPM3) Modified Neglect of Diatomic Overlap, Parametrised Method 3 Correspondence to: A. Liwo     

Nonorthogonal tight-binding model with H–C–N–O parameterisation

A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info.     

Infrared investigation of poly-L-histidine structure dependent on protonation

Poly-L -histidine (PLH) films at different degrees of protonation were produced mid subjected to infrared spectroscopic investigation (range 4000-650 cm^?1). In addition, the N-deuterated film spectra were plotted. The amide II and III bands show that the peptide group is present in the trans form. The amide I and II bands show that at 0% and 50% protonation the PLH occurs as an α-helix and at 100% protonation as a random coil with some ranges in β structure. At 0% and 50% protonation, no hydration water is bound to the backbone. At 0% protonation all NH groups are linked to each other or to water molecules via hydrogen bonds. At 50% protonation NH⁺?N bonds form between the imidazole rings. These protons are present in continuous energy level distribution. Such bonds with tunneling protons are extremely polarizable and between these bonds may act proton dispersion forces. The Cl^? ions are bonded to the NH groups of the imidazole groups. The hydration water is bonded to the Cl^?? ions and to the NH groups. At 100% protonation, hydration water is bonded also to the CO groups of the backbone. The NH groups of the backbone, like those of the rings, endeavor especially in the dry state to bond to the Cl^? ions. This leads to a strong steric constraint of the random coil.     

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.