Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.     

Valence orbital response to methylation of uracil

Orbital signatures of the methyl group in thymine are identified using information from both coordinate and momentum spaces, in comparison with RNA base uracil. The B3LYP/aug‐cc‐pVTZ//B3LYP/TZVP calculations show that the orbitals of methyl group may be identified as 9a′, 15a′, 2a″, and 25a′, respectively. Generally, large changes in orbital energies directly lead to large changes in orbital momentum distributions and orbital wavefunctions despite strong pyrimidine ring buffer (exceptions of 19a′ and 21a′ of thymine). A general conclusion about the chemical bindings of pyrimidine, cytosine, thymine, and uracil is obtained for the first time. © 2013 Wiley Periodicals, Inc.     

Assisted intramolecular proton transfer in (uracil)2Ca2+ complexes

The structure and relative stability of the complexes between uracil dimers and Ca²⁺, as well as the proton transfer (PT) processes within these dimers, have been investigated by the density functional theory methods. Although in uracil dimers PT occurs as an almost synchronous double PT processes that connect the diketo dimer with a keto-enol dimer, the process within the most stable (uracil)₂Ca²⁺ complexes is much more complicated, and the product of the reaction looks like the result of an intramolecular PT from one of the NH groups of one monomer to one of the carbonyl groups of the same monomer. An analysis of the force profile along the reaction coordinate shows that the intimate mechanism implies three elementary steps, two intermolecular PTs, and an in-plane displacement of one monomer with respect to the other. The result of this so-called assisted intramolecular proton transfer is the formation of a dimer in which only one monomer is a keto-enol derivative, the other monomer being apparently unchanged, although it suffers significant structural rearrangements along the reaction coordinate. Quite importantly, this dimer is significantly stabilized upon Ca²⁺ association; therefore, while the most stable uracil dimers correspond systematically to associations involving only the diketo forms, in (uracil)₂Ca²⁺ complexes the most stable structures correspond to those in which one of the monomers is a keto-enol uracil isomer.     

Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations

Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters. Copyright © 2009 John Wiley & Sons, Ltd.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

Quantum-chemical study on uracil and thymine nitrosonium complexes

Quantum-chemical calculations at the RI-MP2/L1 level of theory showed that the most energetically favorable complexes of uracil and thymine with nitrosonium cation are those of n-type with NO⁺ coordination at the nitrogen or oxygen atom. A correlation was found between the experimental and calculated affinities of the dioxo tautomer of thymine for nitrosonium ion ( $ A_{NO^ + } $ ). A linear relation was revealed between $ A_{NO^ + } $ values for structurally similar tautomers of uracil and thymine.     

Application of chromium‐doped fullerene as a carrier for thymine and uracil nucleotides: Comprehensive density functional theory calculations

The interactions of the nucleobases thymine (C₅H₆N₂O₂) and uracil (C₄H₄N₂O₂) with Cr‐doped C₂₀ fullerene (C₁₉Cr) are investigated by performing density functional theory calculations. The adsorption of these nucleobases on C₁₉Cr leads to two distinct geometries (P1 and P2) differing in the orientation of the nucleobases. The interaction of the nucleobases with the C₁₉Cr nanocluster is highly exothermic, revealing that they are chemically adsorbed on C₁₉Cr. The results show that the binding energy of the thymine–C₁₉Cr complex is slightly higher than that of the uracil–C₁₉Cr complex. In addition, the P2 geometry is more stable compared to P1 due to the higher binding energy in the former configuration. However, based on the results of natural bond orbital and frontier molecular orbitals analyses, the C₁₉Cr nanocage has higher reactivity with the nucleobases in P1 geometry in comparison with P2 due to the larger charge transfer and orbital hybridization in the former geometry. Moreover, the band gap of the C₁₉Cr nanocage decreases after interaction with the nucleobases, and interestingly the impact is more pronounced for P1 geometry, confirming the higher sensitivity of C₁₉Cr to the nucleobases in P1 geometry. Our findings reveal the promising potential of C₁₉Cr as an organometallic carrier for nucleobases thymine and uracil.     

Mono- and binuclear complexes involving [Pd(N,N-dimethylethylenediamine)(H2O)2]2+, 4,4′-bipiperidine and DNA constituents

The Pd(dmen)Cl₂, where dmen?=?N,N-dimethethylenediamine, was synthesized and characterized by elemental analysis and spectroscopy. The complex-formation equilibria in the reaction of [Pd(dmen)(H₂O)₂]²⁺ with 4,4′-bipiperidine (Bip) and DNA constituents were investigated at 25°C and 0.1?mol?L^?1 ionic strength. The results show the formation of [(H₂O)(dmen)Pd(Bip)Pd(dmen)(H₂O)]⁴⁺. Inosine, uracil, and thymine interact with the previously mentioned complex by the substitution of two-coordinated water molecules. The formation constants of all possible mono- and binuclear complexes were determined and their speciation diagrams were evaluated.     

Insight into the Mechanism of the Initial Reaction of an OH Radical with DNA/RNA Nucleobases: A Computational Investigation of Radiation Damage

Earlier theoretical investigations of the mechanism of radiation damage to DNA/RNA nucleobases have claimed OH radical addition as the dominating pathway based solely on energetics. In this study we supplement calculations of energies with the kinetics of all possible reactions with the OH radical through hydrogen abstraction and OH radical addition onto carbon sites, using DFT at the ωB97X‐D/6‐311++G(2df,2pd) level with the Eckart tunneling correction. The overall rate constants for the reaction with adenine, guanine, thymine, and uracil are found to be 2.17×10^?12, 5.64×10^?11, 2.01×10^?11, and 5.03×10^?12 cm³ molecules^?1 s^?1, respectively, which agree exceptionally well with experimental values. We conclude that abstraction of the amine group hydrogen atoms competes with addition onto C₈ as the most important reaction pathway for the purine nucleobases, while for the pyrimidine nucleobases addition onto C₅ and C₆ competes with the abstraction of H₁. Thymine shows favourability against abstraction of methyl hydrogens as the dominating pathway based on rate constants. These mechanistic conclusions are partly explained by an analysis of the electrostatic potential together with HOMO and LUMO orbitals of the nucleobases.     

Gas‐phase hydration of Mg2+ complexes with deprotonated uracil,thymine, uridine,and thymidine

The gas‐phase hydration of Mg²⁺ complexes with deprotonated uracil ( U ), thymine ( T ), uridine ( U _r , uracil riboside), and thymidine ( T _dr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2 U ‐H+Mg]⁺) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3 U _r ‐H+Mg]⁺). The efficiency of gas‐phase hydration of the ions [2 U ‐H+Mg]⁺ and [2 T ‐H+Mg]⁺ was similar. However, the efficiency of gas‐phase hydration of the ion [ U + U _r ‐H+Mg]⁺ was much higher than that of gas‐phase hydration of the ion [ T + T _dr ‐H+Mg]⁺. On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [ T + T _dr ‐H+Mg]⁺, we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [ U + U _r ‐H+Mg]⁺, the position of the sugar moiety does not affect water attachment.     

Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density‐functional calculations. The total interaction energy ΔE^T of the C_4h‐symmetric guanine quartet consisting of Hoogsteen‐type base pairs with two hydrogen bonds between two neighbor bases is −66.07 kcal/mol at the highest level. The uracil quartet with C6 H6O4 interactions between the individual bases has only a small interaction energy of −20.92 kcal mol⁻¹, and the interaction energy of −24.63 kcal/mol for the alternative structure with N3 H3O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25% to all interaction energies. Complexes of metal ions with G‐quartets can be classified into different structure types. The one with Ca²⁺ in the central cavity adopts a C_4h‐symmetric structure with coplanar bases, whereas the energies of the planar and nonplanar Na⁺ complexes are almost identical. The small ions Li⁺, Be²⁺, Cu⁺, and Zn²⁺ prefer a nonplanar S₄‐symmetric structure. The lack of coplanarity prevents probably a stacking of these base quartets. The central cavity is too small for K⁺ ions and, therefore, this ion favors in contrast to all other investigated ions a C₄‐symmetric complex, which is 4.73 kcal/mol more stable than the C_4h‐symmetric one. The distance 1.665 Å between K⁺ and the root‐mean‐square plane of the guanine bases is approximately half of the distance between two stacked G‐quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen‐bonded biological systems. Compared with the before‐mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U‐quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C HO contacts in the uracil quartet. In the G‐quartet, the MMFF94 hydrogen bond distances N2 H22N7 are shorter than the DFT distances, whereas the N1 H1O6 distances are longer. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 109–124, 2001     

Speciation studies of mono- and binuclear Pd(II) complexes involving mixed nitrogen–sulfur donor ligand and 4,4′-bipiperidine as a linker

Pd(MME)Cl₂ complex, where MME = methionine methyl ester, was synthesized and characterized by elemental analysis and spectroscopic techniques. [Pd(MME)(H₂O)₂]²⁺ interacts with some DNA constituents giving 1 : 1 and 1 : 2 complexes. The binuclear complexes having 4,4′-bipiperidine as a linker and involving [Pd(MME)(H₂O)₂]²⁺ and DNA constituents were investigated. The results show formation of [(H₂O)(MME)Pd(Bip)Pd(MME)(H₂O)]⁴⁺. Inosine, uracil, and thymine interact with the previously mentioned complex by substitution of the two coordinated water molecules. Formation constants of all possible mono- and binuclear complexes were determined and their speciation diagrams were evaluated.     

A novel and specific fluorescence reaction for uracil

Facile and specific methods to quantify a nucleobase in biological samples are of great importance for diagnosing disorders in nucleic acid metabolism. In the present study, a novel fluorogenic reaction specific for uracil has been developed. The reaction was carried out in an alkaline medium containing benzamidoxime and K₃[Fe(CN)₆] which were heated for 2.0 min. Under the optimum reaction conditions, strong fluorescence was produced only from uracil, not from other many biogenic compounds tested such as cytosine, thymine, adenine, guanine, nucleobases, nucleosides, nucleotides, amino acids, saccharides, creatine, creatinine and urea. The sensitivity of this method was compared with a known fluorogenic reaction using phenacylbromide which does not react with uracil but reacts with cytosine, adenine and their analogues. The proposed uracil-specific reaction showed approximately 400-fold higher sensitivity than the phenacylbromide reaction. The lower detection limit of uracil by the present method was 100 pmol mL⁻¹, and a good linearity of the calibration curve was obtained up to 100 nmol mL⁻¹ uracil. Due to its high sensitivity and specificity, the quantitative determination of uracil was possible by the proposed fluorimetric method.     

Decameric uracil complexes around Li+

Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li⁺ ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U₁₀Li⁺ is formed, which was referred to as an indication for so‐called ‘magic number’ cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas‐phase structure which is compatible with all experimental findings. Copyright © 2010 John Wiley & Sons, Ltd.     

Novel Ionophores for Barium‐Selective Electrodes: Synthesis and Analytical Characterization

A novel way of synthesis is developed for the Ba²⁺ selective neutral Ionophore 2a : 2,2′‐[1,2‐phenylenebis(oxyethane‐2,1‐diyloxy)]bis(N‐benzyl‐N‐phenylacetamide) and its methyl ( 2b ), buthyl ( 2c ), and hexyl ( 2d ) derivatives. Ba²⁺ selective electrodes based on Ionophores 2a – d are compared with those with commonly used Ionophore 1 : N,N,N′,N′‐tetracyclohexyl‐oxybis(o‐phenyleneoxy) diacetamide. It is shown that Ionophores 2a – d , particularly 2b , are superior for measurements of Ba²⁺ in the presence of Ca²⁺, and in acidic solutions. Segmented sandwich membrane studies suggest formation of complexes IL₂²⁺ for Ba²⁺, Ca²⁺ and Mg²⁺ ions with Ionophore 2b , while H⁺ ions apparently form complexes H₂L²⁺. The values of the complex formation constants are consistent with the selectivity coefficients.     

Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.     

ESI‐MS studies of the non‐covalent interactions between biologically important metal ions and N‐sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non‐covalent interaction of two biologically active ligands, N‐1 ‐ (p‐toluenesulfonyl)cytosine, 1‐TsC, 1 and N‐1 ‐ methanesulfonylcytosine, 1‐MsC, 2 and their Cu(II) complexes Cu(1‐TsC‐N3)₂Cl₂, 3 and Cu(1‐MsC‐N3)₂Cl₂ and 4 with biologically important cations: Na⁺, K⁺, Ca²⁺, Mg²⁺ and Zn²⁺. The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1–4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.     

Regioselective synthesis of 1-allyl- and 1-arylmethyl uracil and thymine derivatives

2,4-Bis(trimethylsiloxy) pyrimidines 1 with allyl halides and arylmethyl halides in 1,2-dichloroethane in the presence of I₂ regioselectively provide 1-allyl-/1-arylmethyl-uracil and thymine derivatives. The secondary aryl alkyl and diaryl methyl halides with 1 provide chiral 1-arylalkyl/1-(diarylmethyl) uracil/thymine derivatives. The procedure has been extended to the synthesis of fluorescent uracil/thymine derivatives.     

Potentiometric and Speciation Studies on the Complex Formation Reactions of [Pd(2-methylaminomethyl)-pyridine)(H<Subscript>2</Subscript>O)<Subscript>2</Subscript>]<Superscript>2+</Superscript> with Some Bio-active Ligands and Displacement Reaction of Coordinated Inosine

The stoichiometry and stability constants of the complexes formed between [Pd(MAMP)(H₂O)₂]²⁺ and various biologically relevant ligands containing different functional groups were investigated. The ligands used are amino acids, peptides and DNA constituents. The results show the formation of 1:1 complexes with amino acids and peptides and the corresponding deprotonated amide species. Structural effects of peptides on amide deprotonation were investigated. The purine and pyrimidine bases uracil, uridine, cytosine, inosine, inosine 5′-monophosphate (5′-IMP) and thymine form 1:1 and 1:2 complexes. The concentration distribution of the various complex species was calculated as a function of pH. The effect of chloride ion concentration on the formation constant of CBDCA with Pd(MAMP)²⁺ was also reported. The results show ring opening of CBDCA and monodentate complexation of the DNA constituent with the formation of [Pd(MAMP)(CBDCA-O)DNA], where (CBDCA-O) represents cyclobutane dicarboxylate coordinated by one carboxylate oxygen. The equilibrium constant of the displacement reaction of coordinated inosine, as a typical DNA constituent, by SMC and/or methionine was calculated. The results are expected to contribute to the chemistry of antitumor agents. The calculated parameters of the optimized complexes support the measured formation constants.