Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength

Matsuda and coworkers demonstrated that imidazopyridopyrimidine nucelobases (N ^N , O ^O , N ^O , tO ^O , and O ^N ) can mimic Watson–Crick nucleobase in forming H-bonds in DNA double helix. In the present study, we address the question about the strengths of the H-bonds in imidazopyridopyrimidine base pairs compared to those in Watson–Crick ones by focusing particularly on the nature of these interactions. Optimized structures of imidazopyridopyrimidine, imidazopyridopyrimidine–Watson–Crick, and Watson–Crick base pairs are obtained at the DFTB3LYP/6-311++G (d,p). The nature and strength of the intramolecular H-bonds in these base pairs have been investigated based on natural bond orbital (NBO method) to consider the effect of charge transfer, “atoms-in-molecules” (AIM) topological parameters, and decomposition of the interaction energies using the energy decomposition analysis (EDA). These investigations imply that N ^N –O ^O and N ^O –O ^N can form base pairs with four H-bonds (most stable than those of Watson–Crick base pairs) when they incorporated into DNA double helix. Furthermore, it can be deduced that O ^N and N ^N nucleobases form energetically more favorable pairs with adenine and guanine than the normal Watson–Crick counter parts. These results can be helpful for the stabilization and regulation of a variety of new base-pairing motif of DNA structures.     

The damage of the Watson–Crick base pairs by nickel nanoparticles: A first-principles molecular dynamics study

The nickel nanoparticles are harmful atmospheric pollutants, and the damage caused by them in humans has become a topic of great relevance. In this study we investigate the interaction of the Ni₂ and Ni₃ clusters with the AT and GC Watson–Crick base pairs in an aqueous medium. Molecular dynamics in combination with density functional theory are employed. A novel method is implemented to create realistic thermodynamic conditions (NVT) in the simulations. The energies, the charges of the interacting compounds, the temperature changes, and the geometric rearrangements are reported. The results show the formation of stable organometallic compounds of the nickel nanoparticles with the DNA nucleic acid bases. In this respect, the biological processes where the DNA is implicated may be altered by the formation of such super-structures.     

Computational investigation of thermochemical properties of non-natural C-nucloebases: different hydrogen-bonding preferences for non-natural Watson–Crick base pairs

In the present density functional theory study, we have compared intrinsic properties of non-natural nucleobases (acA, acG, acC, and acT nucleobases) such as proton affinities, gas phase acidities, tautomerization, and hydrogen-bonding properties with those in normal Watson–Crick nucleobases (A, G, C, T nucleobases). The hydrogen-bonding interactions in non-natural and Watson–Crick base pairs were studied at B3LYP/6-311++G (d,p) level regarding their geometries, energies, and topological features of the electron density. The quantum theory of atoms-in-molecule (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in base pairs. The electron density ρ(r) as well as its Laplacian $ \nabla^{2} $ ρ(r) at the hydrogen bond critical point predicted by QTAIM is strongly correlated with hydrogen bond structural parameter and the second-order perturbation energies in NBO scheme. Our results show that most of hydrogen bonds in normal Watson–Crick and non-natural base pairs must be considered as electrostatic interactions. Results of calculations revealed that energetic values of hydrogen bonds in T–A base pair are more than those in ac T–ac A base pair, while values of hydrogen bonds in C–G base pair and ac C–ac G base pair are almost the same. These results confirmed stability order of stabilization energies of these base pairs.     

Substituent Effects on Hydrogen Bonding in Watson–Crick Base Pairs. A Theoretical Study

We have theoretically analyzed Watson–Crick AT and GC base pairs in which purine C8 and/or pyrimidine C6 positions carry a substituent X = H, F, Cl or Br, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P. The purpose is to study the effects on structure and hydrogen bond strength if X = H is substituted by a halogen atom. Furthermore, we wish to explore the relative importance of electrostatic attraction versus orbital interaction in the above multiply hydrogen-bonded systems, using a quantitative bond energy decomposition scheme. We find that replacing X = H by a halogen atom has relatively small yet characteristic effects on hydrogen bond lengths, strengths and bonding mechanism. In general, it reduces the hydrogen-bond-accepting- and increases the hydrogen-bond-donating capabilities of a DNA base. The orbital interaction component in these hydrogen bonds is found for all substituents (X = H, F, Cl, and Br) to contribute about 41% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining 59% of the attraction.     

The effect of CH<Subscript>3</Subscript>, F and NO<Subscript>2</Subscript> substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X–adenine–thymine (X–A–T), X–thymine–adenine (X–T–A), X–guanine–cytosine (X–G–C), and X–cytosine–guanine (X–C–G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6–311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO₂) increase the total binding energy (ΔE) of X–G–C derivatives and the electron donating (ED) substituent (CH₃) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH₃ in the 1 position and F in the 5 position, which in both cases the ΔE value decreases negligibly small. With minor exceptions (X=8–CH₃, 8–F, and 9–NO₂), both ED and EW substituents increase slightly the ΔE values of X–A–T derivatives. The individual HB energies (∆E _HBs) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO₂ substituted derivative in each case.     

Noncovalent assembly of ferrocene on modified gold surfaces mediated by uracil–adenine base pairs

Redox-active ferrocene was assembled on gold surfaces through the hydrogen bonding interactions between adenine-substituted ferrocene and a uracil-terminated organothiol monolayer. The surface coverage of ferrocene Γ could be varied from ca. 4 × 10^? 11 to 2.0 × 10^? 10 mol cm^? 2 by diluting the thiol-modified uracil derivative with inert 1-octanethiol. A decrease in the apparent electron transfer rate constant for ferrocene, k_app, from ca. 50 to 10 s^? 1 was observed upon increasing Γ.     

Effect of temperature on acid–base equilibria in separation techniques. A review

Studies on the theoretical principles of acid–base equilibria are reviewed and the influence of temperature on secondary chemical equilibria within the context of separation techniques, in water and also in aqueous-organic solvent mixtures, is discussed. In order to define the relationships between the retention in liquid chromatography or the migration velocity in capillary electrophoresis and temperature, the main properties of acid–base equilibria have to be taken into account for both, the analytes and the conjugate pairs chosen to control the solution pH. The focus of this review is based on liquid–liquid extraction (LLE), liquid chromatography (LC) and capillary electrophoresis (CE), with emphasis on the use of temperature as a useful variable to modify selectivity on a predictable basis. Simpli?ed models were evaluated to achieve practical optimizations involving pH and temperature (in LLE and CE) as well as solvent composition in reversed-phase LC.     

A resonance light scattering sensor based on methylene blue–sodium dodecyl benzene sulfonate for ultrasensitive detection of guanine base associated mutations

A resonance light scattering (RLS) sensor for guanine base associated mutations has been developed on the basis of the high selectivity of methylene blue (MB) for guanine bases in the presence of sodium dodecyl benzene sulfonate (SDBS). MB, when bound to SDBS, underwent a dramatic enhancement of its RLS intensity. However, the addition of double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) caused the strong RLS intensity of MB-SDBS to decrease, and the RLS intensity of MB-SDBS-ssDNA was much lower than that of MB-SDBS-dsDNA. Consequently, it can be concluded that the binding abilities of MB-SDBS with ssDNA and dsDNA were different. Besides, the experimental results showed that MB-SDBS could bind specifically to oligonucleotides rich in guanine bases. Short DNA targets with sequences related to β-thalassaemia, thrombophilia and psoriasis, all of which are guanine base relevant mutations, were synthesized. It was found that MB-SDBS could recognize the single-base mismatches in the mutational DNA, followed by different RLS signal changes between MB-SDBS-normal DNA systems and MB-SDBS-mutational DNA systems. The ultrasensitive sensor allows simple, rapid, sensitive and selective detection of guanine base associated mutations, indicating its potential application in the medical field.     

Influence of temperature on thermodynamic properties of acid–base liquid mixtures

Ultrasonic velocity, u density, ?? and viscosity, ?? of mixtures of N,N-dimethyl acetamide with equimolar mixture of ethanol?+?isopropyl alcohol/isobutyl alcohol/isoamyl alcohol, including those of pure liquids over the entire composition have been measured at T?=?308.15, 313.15, and 318.15?K. Using this data, various thermo-acoustic parameters such as deviations in ultrasonic velocity, ?u, isentropic compressibility, ?k _s , viscosity, ????, excess molar volume, $ V_{\text{m}}^{\text{E}} $ and excess Gibb??s free energy of activation for viscous flow, ??G ^*E have been calculated at different temperatures. The calculated deviation and excess functions have been fitted to the Redlich?CKister type polynomial equation. The influence of temperature on the observed negative and positive values of deviation and excess thermodynamic properties has been explained in terms of molecular interactions present in the investigated acid?Cbase liquid mixtures. The experimental data of ultrasonic velocity have been used to check the applicability of velocity models of Nomoto, Van Dael and Vangeel and Junjie and viscosity data have also been availed to test the applicability of standard viscosity models of Grunberg-Nissan, Hind-Mc Laughlin, and Katti-Chaudhary for all the systems investigated at various temperatures.     

Effects of precipitate agents on temperature-responsive sol–gel transitions of PLGA–PEG–PLGA copolymers in water

This paper reports the effects of precipitate agents used in the collection of block copolymers composed of poly(lactic acid-co-glycolic acid) (PLGA) and poly(ethylene glycol) (PEG) on their thermogelling aqueous behaviors. We synthesized PLGA–PEG–PLGA triblock copolymers with a relatively wide distribution of molecular weight (MW) and then separated the crude polymers via three different precipitate agents (diethyl ether, hexane, or methanol). The obtained products exhibited, however, significantly different macroscopic states in water: some were sols, some were precipitates, and some underwent sol–gel transition upon heating. We found that by using different precipitate agents, ingredients of different MW were collected from the synthesized polymers, which accounted for the different states of the separated products in water. Our study strengthens the importance of an appropriate precipitate agent and reveals the subtle balance of hydrophobicity and hydrophilicity in this sort of amphiphilic block copolymers.     

Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson–Crick Edge

DNA duplexes comprising 6-(1H-pyrazol-1-yl)-9H-purine (6PP), 1-deaza-6PP (^1D6PP), 7-deaza-6PP (^7D6PP) and 1,7-dideaza-6PP (^1,7D6PP) 2′-deoxyribonucleosides, respectively, were investigated towards their ability to form metal-mediated base pairs in the presence of Ag^I. In 6PP and ^7D6PP, the Ag^I ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in ^1D6PP and ^1,7D6PP, so that in ^1D6PP an Ag^I coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the Ag^I-binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of Ag^I, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1- or N7-coordination is preferred in purine-based metal-mediated base pairs.     

Effects of Various Dopants on Solitons in Polyacetylene

The effects of various dopants on solitons in polyacetylene were studied by using CNDO/2 level semiempirical quantum chemical method. The width of solitons is reduced when dopant is present, and the charge density wave(CDW) is further gathered on the carbon atom in soliton center. The effects of p-type of dopants are greater than those of n-type of ones. The charge transfer in doped polyacetylene can be achieved by the propagation of CDW along the chain. The conductivity of doped polyacetylene is proportional to the quantity of charge transfer between dopant and polyacetylene chain.     

Influence of acid–base properties of cobalt–molybdenum catalysts supported on magnesium orthophosphates in isomerization of 3,3-dimethylbut-1-ene

Synthesis and physico-chemical characterization of a pure magnesium phosphate (MgP) prepared by coprecipitation, and MgP modified by introduction of cobalt–molybdenum (4–12 wt.% of MoO₃ with the Co/Mo ratio fixed at 0.5) have been carried out. The structural properties of these catalysts were characterized by X-ray diffraction, their textural properties were determined by N₂ adsorption–desorption isotherms and the dispersion of cobalt–molybdenum was studied by XPS spectroscopy. Their acid properties have been investigated by in situ FT-IR spectroscopy of adsorbed molecules, often, 2,6-dimethylpyridine (pK_a = 6.7), pyridine (pK_a = 5.3). Co–Mo incorporation leads to a modification in the MgP acid–base properties, especially on the acid sites type and number. Thus, lower loading of cobalt–molybdenum species decreased the number of strong Lewis acid sites whereas higher loading increased it. It was found that Lewis acid sites on magnesium phosphates play an important role in the isomerization of 3,3-dimethylbut-1-ene.The 3,3-dimethylbut-1-ene (33DMB1) conversion increases with the reaction temperature from 493 to 653 K for MgP, but decreases after 573 K for MgP supported by Co–Mo. A linear relationship between both types of acid sites and conversion values was found. The deactivation of the catalysts appears at high reaction temperature (>573 K).     

DFT study of adenine–cytosine mismatch in quaternary systems involving DNA bases

Structural Chemistry - In the present work, the adenine–cytosine mismatch is theoretically investigated in quaternary systems involving DNA bases. The calculations, in gas phase, are...     

Enthalpic interaction coefficients of NaI–alkanediol pairs in methanol and in water

The dissolution enthalpies of NaI in the mixtures of methanol with 1,2-alkanediols (1,2-propanediol, 1,2-butanediol, 1,2-pentanediol) and with ??,??-alkanediols (1,3-propanediol, 1,4-butanediol, 1,5-pentanediol), as well NaI in the mixtures of water with 1,3-propanediol and 1,2-pentanediol, were determined at 298.15?K. The energetic effect of interactions between the investigated alkanediols and NaI in methanol and in water was calculated using the enthalpic pair interaction coefficients (h _xy ) model. These results along with the other data concerning the NaI?Cnon-electrolyte pairs taken from our earlier reports and from the literature were analyzed with respect to the effect of the non-electrolyte properties on the variations of the h _xy values. The group contributions illustrating the interactions of NaI with selected functional groups in non-electrolyte (alkanediol and alkanol) molecules, namely: CH₂ and OH groups were calculated and discussed.     

Effects of microhydration on the characteristics of cation–phenol complexes

The properties of complexes formed by phenol and K⁺, Na⁺, Li⁺ and Mg²⁺ in the presence of up to four water molecules have been studied by means of computational methods. The interaction becomes stronger as the size of the cation decreases, showing almost no preference between coordinating to the aromatic ring or to the hydroxyl oxygen. As water molecules are introduced, a variety of stable structures arise, where water molecules establish hydrogen bonds among themselves and with the hydroxyl group of phenol. For the most polarizing cations, the strong cation···water interaction gives most stable minima corresponding to arrangements with water molecules and phenol coordinated directly to the cation, with no significant hydrogen bonds among them. However, in Na⁺ complexes and especially in K⁺ ones, the interaction with the cation is weaker, so hydrogen bond formation starts to be competitive as more water molecules are included, the most stable minima corresponding to structures where not all water molecules or phenol are directly bound to the cation. This behavior is also reflected on the predicted vibrational spectra, which agree with those determined experimentally. Up to three water molecules, only for K⁺ and to a less extent Na⁺, stable minima are found showing red-shifted O–H stretching bands corresponding to water···water and water···phenol hydrogen bonds. With four water molecules, at least one water molecule is located in a second solvation shell, all cations exhibiting red-shifted bands.     

Characterization of adsorption processes in analytical liquid–solid chromatography

This review discusses nonlinear chromatographic methods of importance for proper characterization of the adsorption processes in analytical chromatographic systems, with focus on reversed-phase liquid chromatography. Linear methods such as the linear solvation energy relationship (LSER) method and the Snyder–Dolan hydrophobic-subtraction model will also be reviewed briefly. The nonlinear methods for adsorption isotherm determination and the tools for further treatment of the nonlinear adsorption data will be extensively treated in a way suitable for the general chromatographer. Applications of the various methods will be given and the outcome and conclusions will be discussed. Special emphasis will be placed on discussing the possibilities of combining linear and nonlinear methods in order to obtain a deeper and more complete investigation of the interactions in the actual phase system.     

Effects of nitren extraction on a dissolving pulp and influence on cellulose dissolution in NaOH–water

A commercial dissolving pulp was treated with aqueous solutions containing 3, 5 and 7 % of an organometalic complex (nitren) with the aim to selectively extract xylan and study its impact on the conventional physical–chemical properties of the pulp. The influence of these treatments on the pulp dissolution in a moderate solvent (8 % NaOH aqueous solution) was assessed by measuring the dissolution yields and the dissolution mechanisms. The results of this study show that nitren treatment has the effect of removing a large part of the xylan present in a dissolving pulp. It is also removing mannans and most important, it is influencing cellulose in two ways, (1) extracting it with more intensity when the nitren concentration increases, and (2) decreasing its mean molecular mass, also more evident with nitren concentration increase. The nitren extractions are favourable for the dissolution in cold NaOH–water, being more effective with higher concentrations. This chemical modification of the fiber surface leads to the disassembly of the primary wall. This allows an easier access of the NaOH reagent to regions not accessible on the initial fibres, which with the decrease of the cellulose molecular weight allows an easier dissolution and gives different dissolution mechanisms.     

5-Aza-7-deazaguanine–Isoguanine and Guanine–Isoguanine Base Pairs in Watson–Crick DNA: The Impact of Purine Tracts,Clickable Dendritic Side Chains,and Pyrene Adducts

The Watson–Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson–Crick and purine–purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2′-deoxyguanosine, its tripropargylamine derivative, and 2′-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine–purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine–isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine–isoguanine base pair. Spacious residues are well accommodated in the large groove of purine–purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.