Comparison of the acid-base properties of ribose and 2'-deoxyribose nucleotides

The extent to which the replacement of a ribose unit by a 2'-deoxyribose unit influences the acid-base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5'-di- and 5'-triphosphates of 2'-deoxyguanosine [i.e., of H(2)(dGDP)(-) and H(2)(dGTP)(2-)] as well as of the 5'-mono-, 5'-di-, and 5'-triphosphates of 2'-deoxyadenosine [i.e., of H(2)(dAMP)(+/-), H(2)(dADP)(-), and H(2)(dATP)(2-)]. These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2'-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2'-OH group is dependent on the number of 5'-phosphate groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is most significantly enhanced (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or N1H(+) sites is less pronounced but clearly present. In addition, (1)H NMR chemical shift change studies in dependence on pD in D(2)O have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. Overall, our results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact basis for the calculation, determination, and understanding of perturbed pK(a) values in DNAzymes and ribozymes, as needed for the delineation of acid-base mechanisms in catalysis.     

Understanding the reactivity and basicity of zeolites: a periodic DFT study of the disproportionation of N(2)O(4) on alkali-cation-exchanged zeolite Y

The disproportionation of N(2)O(4) into NO(3)(-) and NO(+) on Y zeolites has been studied through periodic DFT calculations to unravel 1) the role of metal cations and the framework oxygen atoms and 2) the relationship between the NO(+) stretching frequency and the basicity of zeolites. We have considered three situations: adsorption on site II cations with and without a cation at site III and adsorption on a site III cation. We observed that cations at sites II and III cooperate to stabilize N(2)O(4) and that the presence of a cation at site III is necessary to allow the disproportionation reaction. The strength of the stabilization is due to the number of stabilizing interactions increasing with the size of the cation and to the Lewis acidity of the alkali cations, which increases as the size of the cations decreases. In the product, NO(3)(-) interacts mainly with the cations and NO(+) with the basic oxygen atoms of the tetrahedral aluminium through its nitrogen atom. As the cation size increases, the NO(3)(-)...cation interaction increases. As a result, the negative charge of the framework is less well screened by the larger cations and the interaction between NO(+) and the basic oxygen atoms becomes stronger. NO(+) appears to be a good probe of zeolite basicity, in agreement with experimental observations.     

Computed CH Acidity of Biaryl Compounds and Their Deprotonative Metalation by Using a Mixed Lithium/Zinc‐TMP Base

With the aim of synthesizing biaryl compounds, several aromatic iodides were prepared by the deprotonative metalation of methoxybenzenes, 3‐substituted naphthalenes, isoquinoline, and methoxypyridines by using a mixed lithium/zinc‐TMP (TMP=2,2,6,6‐tetramethylpiperidino) base and subsequent iodolysis. The halides thus obtained, as well as commercial compounds, were cross‐coupled under palladium catalysis (e.g., Suzuki coupling with 2,4‐dimethoxy‐5‐pyrimidylboronic acid) to afford various representative biaryl compounds. Deprotometalation of the latter compounds was performed by using the lithium/zinc‐TMP base and evaluated by subsequent iodolysis. The outcome of these reactions has been discussed in light of the CH acidities of these substrates, as determined in THF solution by using the DFT B3LYP method. Except for in the presence of decidedly lower pK_a values, the regioselectivities of the deprotometalation reactions tend to be governed by nearby coordinating atoms rather than by site acidities. In particular, azine and diazine nitrogen atoms have been shown to be efficient in inducing the reactions with the lithium/zinc‐TMP base at adjacent sites (e.g., by using 1‐(2‐methoxyphenyl)isoquinoline, 4‐(2,5‐dimethoxyphenyl)‐3‐methoxypyridine, or 5‐(2,5‐dimethoxyphenyl)‐2,4‐dimethoxypyrimidine as the substrate), a behavior that has already been observed upon treatment with lithium amides under kinetic conditions. Finally, the iodinated biaryl derivatives were involved in palladium‐catalyzed reactions.     

Gas-phase protonation and deprotonation of acrylonitrile derivatives N[triple chemical bond]C--CH==CH--X (X=CH(3), NH(2), PH(2), SiH(3))

A combined experimental and theoretical study on the gas-phase basicity and acidity of a series of cyanovinyl derivatives is presented. The gas-phase basicities and acidities of (N[triple chemical bond]C--CH==CH--X, X=CH(3), NH(2)) were obtained by means of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry techniques. The corresponding calculated values were obtained at the G3B3 level of theory. The effects of exchanging CH(3) for SiH(3), and NH(2) for PH(2), were analyzed at the same level of theory. For the neutral molecules, the Z isomer is always the dominant species under standard gas-phase conditions at 298 K. The loss of the proton from the substituent X was found systematically to be much more favorable than deprotonation of the HC==CH linking group. The corresponding isomeric E ion is much more stable than the Z ion, so that only the former should be found in the gas phase. The most significant structural changes upon deprotonation occur for the methyl and amino derivatives because, in both cases, deprotonation of X leads to a significant charge delocalization in the corresponding anion. Protonation takes place systematically at the cyano group, whereby the isomeric E ion is again more stable than the Z ion. Push-pull effects explain the preference of aminoacrylonitrile to be protonated at the cyano group, which also explains the high basicity of this derivative relative to other members of the analyzed series that present rather similar gas-phase basicities, GB approximately 780 kJ mol(-1), indicating that the different nature of the substituents has only a weak effect on the intrinsic basicity of the cyano group. The cyanovinyl derivatives have a significantly stronger gas-phase acidity than that of the corresponding vinyl compounds CH(2)==CH--X. This acidity-strengthening effect of the cyano group is attributed to the greater stabilization of the anion with respect to the corresponding neutral compound.     

Acid-base properties of xanthosine 5'-monophosphate (XMP) and of some related nucleobase derivatives in aqueous solution: micro acidity constant evaluations of the (N1)H versus the (N3)H deprotonation ambiguity

The first acidity constant of fully protonated xanthosine 5'-monophosphate, that is, of H3(XMP)+, was estimated by means of a micro acidity constant scheme and the following three deprotonations of the H2(XMP)+/- (pKa=0.97), H(XMP)- (5.30), and XMP2- (6.45) species were determined by potentiometric pH titrations; further deprotonation of (XMP-H)3- is possible only with pKa>12. The most important results are that the xanthine residue is deprotonated before the P(O)2(OH)- group loses its final proton; that is, twofold negatively charged XMP carries one negative charge in the pyrimidine ring and one at the phosphate group. Micro acidity constant evaluations reveal that this latter mentioned species occurs with a formation degree of 88 %, whereas its tautomer with a neutral xanthine moiety and a PO3(2-) group is formed only to 12 %; this distinguishes XMP from its related nucleoside 5'-monophosphates, like guanosine 5'-monophosphate. At the physiological pH of about 7.5 mainly (XMP-H)3- exists. The question, which of the purine sites, (N1)H or (N3)H, is deprotonated in this species cannot be answered unequivocally, though it appears that the (N3)H site is more acidic. By application of several methylated xanthine species intrinsic micro acidity constants are calculated and it is shown that, for example, for 7-methylxanthine the N1-deprotonated tautomer occurs with a formation degree of about 5 %; a small but significant amount that, as is discussed, may possibly be enhanced by metal ion coordination to N7, which is known to occur preferably to this site.     

Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective

The one‐step tautomerization processes of uracil and its radical cation and radical anion have been investigated in the light of the reaction force and reaction electronic flux (REF) formalisms. The relative energies of the different tautomers as well as the corresponding tautomerization barriers have been obtained through the use of the G4 high‐level ab initio method and by means of B3LYP/6‐311+G(3df,2p)//B3LYP/6‐311+G(d, p) calculations. Systematically, the enol radical cations are more stable in relative terms than the neutral, due to the higher ionization energy of the diketo forms with respect to the enolic ones. Conversely, the enol radical anions, with the only exception of the 2‐keto‐N1 anion, are found to be less stable than the neutral. The effects of the ionization are also sizable on the tautomerization barriers although this effect also depends on the particular tautomerization process. The reaction force analysis shows that all reactions are mainly activated through structural rearrangements that initiate the electronic activity. This electronic activity is monitored along the reaction coordinate through the REF that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer. © 2015 Wiley Periodicals, Inc.     

Distinct Hydroxy‐Radical‐Induced Damage of 3′‐Uridine Monophosphate in RNA: A Theoretical Study

Cutting ties : Strand scission and base release in hydroxy‐radical adducts of 3′‐uridine monophosphate (UMP) have been explored by using density functional theory. The presence of the ribose 2′‐OH group and the resultant formation of low‐barrier hydrogen bonds with oxygen atoms of the 3′‐phosphate linkage are highly important for hydrogen transfer and the subsequent bond‐breakage reactions (see picture).

     

Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation

We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases.     

Protonation of glycine and alanine: proton affinities, intrinsic basicities and proton transfer path

Proton affinities and intrinsic basicities for nitrogen and oxygen protonation in the gas phase of the amino acids glycine and alanine were calculated using density functional theory (DFT) and ab initio methods at different levels of theory from Hartree-Fock (HF) to G2 approximations. All methods gave good agreement for proton affinities for nitrogen protonation for both amino acids. However, dramatic differences were found between DFT, MP4//MP2, and G2 results on one hand, and MP4//HF results on the other to the calculation of structural and energetic characteristics of oxygen protonation in glycine and alanine. An investigation into the source of these differences revealed that electron correlation effects are chiefly responsible for the differences in calculated oxygen proton affinities between the various methods. It has been found that proton transfer between nitrogen and oxygen protonation sites in both amino acids occurs without a transfer path barrier when correlated methods were used to calculate the path energetics.     

Hydroxyl radical reactions with adenine: reactant complexes, transition states, and product complexes

In order to address problems such as aging, cell death, and cancer, it is important to understand the mechanisms behind reactions causing DNA damage. One specific reaction implicated in DNA oxidative damage is hydroxyl free-radical attack on adenine (A) and other nucleic acid bases. The adenine reaction has been studied experimentally, but there are few theoretical results. In the present study, adenine dehydrogenation at various sites, and the potential-energy surfaces for these reactions, are investigated theoretically. Four reactant complexes [A···OH]* have been found, with binding energies relative to A+OH* of 32.8, 11.4, 10.7, and 10.1 kcal mol(-1). These four reactant complexes lead to six transition states, which in turn lie +4.3, -5.4, (-3.7 and +0.8), and (-2.3 and +0.8) kcal mol(-1) below A+OH*, respectively. Thus the lowest lying [A···OH]* complex faces the highest local barrier to formation of the product (A-H)*+H(2)O. Between the transition states and the products lie six product complexes. Adopting the same order as the reactant complexes, the product complexes [(A-H)···H(2)O]* lie at -10.9, -22.4, (-24.2 and -18.7), and (-20.5 and -17.5) kcal mol(-1), respectively, again relative to separated A+OH*. All six A+OH* → (A-H)*+H(2)O pathways are exothermic, by -0.3, -14.7, (-17.4 and -7.8), and (-13.7 and -7.8) kcal mol(-1), respectively. The transition state for dehydrogenation at N(6) lies at the lowest energy (-5.4 kcal mol(-1) relative to A+OH*), and thus reaction is likely to occur at this site. This theoretical prediction dovetails with the observed high reactivity of OH radicals with the NH(2) group of aromatic amines. However, the high barrier (37.1 kcal mol(-1)) for reaction at the C(8) site makes C(8) dehydrogenation unlikely. This last result is consistent with experimental observation of the imidazole ring opening upon OH radical addition to C(8). In addition, TD-DFT computed electronic transitions of the N(6) product around 420 nm confirm that this is the most likely site for hydrogen abstraction by hydroxyl radical.     

Understanding the nature of the molecular mechanisms associated with the competitive Lewis acid catalyzed [4+2] and [4+3] cycloadditions between arylidenoxazolone systems and cyclopentadiene: a DFT analysis

The molecular mechanisms of the reactions between aryliden-5(4H)-oxazolone 1, and cyclopentadiene (Cp), in presence of Lewis acid (LA) catalyst to obtain the corresponding [4+2] and [4+3] cycloadducts are examined through density functional theory (DFT) calculations at the B3LYP/6-31G* level. The activation effect of LA catalyst can be reached by two ways, that is, interaction of LA either with carbonyl or carboxyl oxygen atoms of 1 to render [4+2] or [4+3] cycloadducts. The endo and exo [4+2] cycloadducts are formed through a highly asynchronous concerted mechanism associated to a Michael-type addition of Cp to the beta-conjugated position of alpha,beta-unsaturated carbonyl framework of 1. Coordination of LA catalyst to the carboxyl oxygen yields a highly functionalized compound, 3, through a domino reaction. For this process, the first reaction is a stepwise [4+3] cycloaddition which is initiated by a Friedel-Crafts-type addition of the electrophilically activated carbonyl group of 1 to Cp and subsequent cyclization of the corresponding zwitterionic intermediate to yield the corresponding [4+3] cycloadduct. The next rearrangement is the nucleophilic trapping of this cycloadduct by a second molecule of Cp to yield the final adduct 3. A new reaction pathway for the [4+3] cycloadditions emerges from the present study.     

Contrast of Bonding and Characters for C6, B3N3, C6H6 and B3N3H6 Molecules

Through integrative consideration of NICS, MO, MOC and NBO, we precisely investigated delocalization and bonding characters of C₆, C₆H₆, B₃N₃ and B₃N₃H₆ molecules. Firstly, we originally discovered and testified that C₆ cluster was sp² hybridization. Negative NICS values in 0 and 1 Å indicated that C₆ had δ and Π aromaticity. Secondly, B₃N₃ with sp² hybridization had obvious δ aromaticity. Finally, WBI values approved that there were delocalization in C₆, C₆H₆ and B₃N₃ molecules, but B₃N₃H₆ structure did not have delocalization with the WBI 1.0. Moreover, total WBI values of carbon, boron and nitrogen atoms were four, three and three, respectively. Namely, the electrons of B₃N₃H₆ and B₃N₃ were localized in nitrogen atoms and they did not form delocalized bonding. In a word, bonding characters of carbon, boron and nitrogen atoms were dissimilar although the molecules composed of carbon, boron and nitrogen were regarded as isoelectronic structures.     

Prototropic tautomers of 5‐methylcytosine and enthalpy changes of their protonation,deprotonation, and deamination: Hybrid density functional B3LYP study

Molecular and thermodynamic properties such as geometric parameters, dipole moments, vibrational frequencies, the first ionization potentials, relative tautomerization energies, and tautomeric equilibrium constants of all prototropic tautomers of 5‐methylcytosine have been studied at the hybrid density functional level B3LYP/6‐31+G(d,p). The methylation on the C5 atom does not lead to significant geometric deformation of the pyrimidine structures of the corresponding tautomers of cytosine, which maintains the similar stability order. The tautomeric species 2‐oxo‐4‐amino [T(0)], 2‐hydroxy‐4‐amino [T(1‐2s) and T(1‐2t)], and trans‐2‐oxo‐4‐imino [T(3‐4t)] are predominated in the gas phase. The zwitterionic conformers of tautomerism [T(1‐4)] and protonation [P(4), P(1‐2s‐4), P(1‐2t‐4), and P(1‐3‐4)] are investigated for the first time due to their close relationship with deamination during genetic repair. Enthalpy changes (Δ_rH) of protonation, deprotonation, and deamination are calculated for these tautomeric species at room temperature; it is noted that the relative enthalpies [δ(ΔH)] of the tautomers are rationalized well in terms of a second‐order polynomial of the sum of the mean Δ_rH values of protonation and deprotonation processes. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Protolytic Equilibrium of the Isomeric Phenyl-1,2,4-triazines

The protonation constants for the first and second stages (pK_BH+, pK_BH2+) of a series of 1,2,4-triazines with a phenyl substituent at various positions in the ring were determined in aqueous solution by a spectrophotometric method. The values of the basicity constants characterizing the first protonation of the heterocycles investigated was in the range of acidity of the medium of pH 3.5 to H ₀ -2, and the second from H ₀ -7.3 to H ₀ -8.7. The position of the phenyl substituent proved to have a significant effect on the size of pK_BH+. According to the results of ab initio calculations using HF/6-31G** for the heterocycles investigated the 1H⁺ form is thermodynamically most stable among the monocations, with the exception of 6-phenyl-1,2,4-triazine for which the existence of the monocation in the 1H⁺ and 2H⁺ forms are equally probable. In the case of the dications of all the triazines the 2,4-H,H²⁺ tautomer is the most preferred. The aromaticity of the 1,2,4-triazine ring is changed insignificantly on mono- and diprotonation.     

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen,oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.     

Probing the basicity of regular and defect sites of alkaline earth metal oxide surfaces by BF3 adsorption: a theoretical analysis.

The basicity of regular and low-coordinate (LC) sites (steps, edges and corners) at the surface of alkaline earths with NaCl structure (MgO, CaO, SrO, and BaO) has been investigated by using BF3 as a probe molecule. B-O and B-F distances; O-B-F bond angles; B-F asymmetric stretching frequencies; O, B and F 1s core-level binding energies; and the interaction energy of adsorbed BF3 were determined by means of DFT calculations on cluster models. These adsorption properties were compared with those of complexes of BF3 with molecules with various basicities (water, ammonia, phosphine, etc.). We show that many properties of adsorbed BF3, and in particular the experimentally accessible shifts in vibrational frequency, in B and F 1s core levels, and in BF3 desorption temperature, exhibit a linear correlation with the surface basicity as measured by the vertical ionization potential of the oxide anions. On the other hand, shifts of the O 1s core level binding energy do not provide a simple way to detect surface basicity. On a given oxide surface, the differing basicities of various sites result in measurable differences in adsorption properties. This suggests the potential use of BF3 as a probe molecule for titrating LC sites on the surface of ionic oxides.     

Spin–Spin Artificial DNA Intercalated with Silver Cations: Theoretical Prediction

The indirect nuclear spin–spin coupling constants of Ag⁺ cation intercalated between imidazole rings in DNA chains are calculated by means of DFT with relativistic effects taken into account by the use of the zeroth‐order regular approximation Hamiltonian (DFT‐ZORA). The calculations model how the ¹J(¹⁵N,¹⁰⁹Ag) coupling constant is affected by different types of geometry deformations and by the presence of water, which is simulated by means of the polarizable continuum model and explicitly present water molecules. Calculations for systems containing two and three imidazole pairs are also carried out to model the influence of stacking interactions. The computed ¹J(¹⁵N,¹⁰⁹Ag) spin–spin coupling constant is in the range of 85–105 Hz (depending on the computational model) and is in good agreement with the experimental value (ca. 92 Hz). This coupling constant is very little affected by the presence of solvent, stacking interactions, and geometry deformations. Such behavior is explained by visualization of the coupling path by means of coupling energy density (CED). Bigger models allow the coupling constant between two adjacent silver ions to be computed, and give a value of approximately 1 Hz, which is probably too small to be of practical interest. The ²J(¹⁵N,¹⁵N) value is calculated to be about 2.5 Hz, and is therefore of measurable magnitude.