MP2 study on the hydrogen-bonding interaction between O 4-methylthymine and DNA bases: A,C, G,and T

The O ⁴-methylthymine (m⁴T) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen-bonding base pairs involving m⁴T bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error, using the full Boys–Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: m⁴T:G > m⁴T:A > m⁴T:C > m⁴T:T.     

MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A,C, G,T

The 5-hydroxymethyl-uracil (HmU) is a product of oxidative attack on the methyl group of thymine in DNA. In this work, we present the hydrogen bonding complexes formation involving HmU bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: HmU:A > HmU:G > HmU:C > HmU:T.     

MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A,C, G,T

The 5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen bonding base pairs involving 5-OH-5-Me-dHyd bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-OH-5-Me-dHyd:G>5-OH-5-Me-dHyd:A>5-OH-5-Me -dHyd:C~5-OH-5-Me-dHyd:T.     

MP2 study on the hydrogen-bonding interaction between 5-fluorouracil and DNA bases: A,C,G,T

The 5-fluorouracil is a pyrimidine analog effective in the treatment of cancer. In this work, we present the hydrogen-bonding base pairs involving 5-FU bound to the four bases in DNA: adenine, cytosine, guanine, and thymine. Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error, using the full Boys-Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-FU:A > 5-FU:G > 5-FU:T > 5-FU:C.     

DFT and MP2 investigations on the hydrogen bonding interaction between 5,6-dihydrothymine and dna bases: A, C, G, T

5,6-Dihydrothymine (DHT) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this work, we present the hydrogen bonding base pairs involving 5,6-dihydrothymine bound to four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations are performed for the studied complexes by the B3LYP method. Interaction energies are corrected for the basis set superposition error, using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs are characterized using NBO and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: DHT:G ～ DHT:A > DHT:C > DHT:T.     

The effect of oxidation on the stability of G:C base pair: a MP2 study

The base-pairing energies of eleven oxidized G:C base pairs were characterized by Møller–Plesset perturbation theory. The analysis was focused on the base pairs consisting of guanine and one of the following cytosine derivatives: G:C1 (5-hydroxycytosine); G:C2 (5-hydroxyuracil); G:C3 (5,6-dihydroxy-cytosine); G:C4 (5,6-dihydroxy-uracil); G:C5 (cytosine glycol);G:C6 (isodialuric acid); G:C7 (uracil glycol), and the base pairs between cytosine and one of the following guanine derivatives: G8:C (8-oxo-guanine); G9:C (6-enol-8-keto-guanine); G10:C (xantho-sine); and G11:C (8-hydroxy-guanine). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. The results obtained show that the interaction energies of the base pairs decrease in the following order: G8:C > G:C5 ~ G:C1 > G:C3 ~ G:C ~ G11:C > G:C2 > G:C4 > G:C7 > G:C6 > G10:C > G9:C.     

MP2 study on the hydrogen-bonding interactions between 4-thiouracil and four RNA bases

The 4-thiouracil (s⁴U) is a sulphur-containing analog of uracil, a natural component of RNA. In this work, we present the interaction energies of complexes formation involving s⁴U bound to the four bases in RNA: adenine (A), uracil (U), guanine (G), and cytosine (C). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. We find that the order of stability for the base pairs is s⁴U: G > s⁴U: A > s⁴U: U ~ s⁴U: C.     

Inclusion complexes of 5-flucytosine with β-cyclodextrin and hydroxypropyl-β-cyclodextrin: characterization in aqueous solution and in solid state

Complexation between 5-flucytosine (5-FC), a cytosine analogue with in vitro antifungal and antiyeast activity, and β-cyclodextrins (β-cyclodextrin and hydroxypropyl-β-cyclodextrin) was studied in solution and in solid states. Complexation in solution was evaluated using solubility studies, UV–vis and ¹H-NMR. In the solid state, differential scanning calorimetry (DSC), scanning electron microscopy (SEM), FT-IR and X-ray diffraction studies were used. UV–vis, FT-IR and ¹H-NMR spectroscopy studies showed that the complex formed occurs by complexation of piridinique base analogue into inner cavity. DSC studies showed the existence of a complex of 5-FC with β-CDs. X-ray studies confirmed the DSC results of the complex existence. Solubility studies showed that the complexed drug is forty times more soluble than free 5-FC, indicating the obtained systems as future, promising drug carriers.     

A Comparative Study of Hydrogen Bonding Using Density Functional Theory

The hydrogen‐bond energies of water dimer and water‐formaldehyde complexes have been studied using density functional theory (DFT). Basis sets up to aug‐cc‐pVXZ (X=D, T, Q) were used. It was found that counterpoise corrected binding energies using the aug‐cc‐pVDZ basis set are very close to those predicted with the aug‐cc‐pVQZ set. Comparative studies using various DFT functionals on these two systems show that results from B3LYP, mPW1PW91 and PW91PW91 functionals are in better agreements with those predicted using high‐level ab initio methods. These functionals were applied to the study of hydrogen bonding between guanine (G) and cytosine (C), and between adenine (A) and thy mine (T) base pairs. With the aug‐cc‐pVDZ basis set, the predicted binding energies of base pairs are in good agreement with the most elaborate ab initio results.     

Prototropic changes in cationic base-pair adducts. II. Guanine methylation

AM 1 calculations have been used to study the effects of CH attachment on the structures, energies, and, in some cases, proton transfer reactions of guanine cytosine base pairs. Methylation of both the guanine 3- and O⁶-positions is predicted to lead to chemically significant concentrations of intermediate base pairs arising from proton transfer from the guanine 1- to the cytosine 3-position. The possible biological implications of such intermediates in nucleic acids is discussed in relation to the formation of either doubly abasic sites or abasic sites opposite potentially miscoding DNA lesions. © 1992 John Wiley & Sons, Inc.     

Prevalence of Genetically Modified Rice, Maize, and Soy in Saudi Food Products

Qualitative and quantitative DNA-based methods were applied to detect genetically modified foods in samples from markets in the Kingdom of Saudi Arabia. Two hundred samples were collected from Al-Qassim, Riyadh, and Mahdina in 2009 and 2010. GMOScreen 35S and NOS test kits for the detection of genetically modified organism varieties in samples were used. The positive results obtained from GMOScreen 35S and NOS were identified using specific primer pairs. The results indicated that all rice samples gave negative results for the presence of 35S and NOS terminator. About 26 % of samples containing soybean were positive for 35S and NOS terminator and 44 % of samples containing maize were positive for the presence of 35S and/or NOS terminator. The results showed that 20.4 % of samples was positive for maize line Bt176, 8.8 % was positive for maize line Bt11, 8.8 % was positive for maize line T25, 5.9 % was positive for maize line MON 810, and 5.9 % was positive for StarLink maize. Twelve samples were shown to contain <3 % of genetically modified (GM) soy and 6 samples >10 % of GM soy. Four samples containing GM maize were shown to contain >5 % of GM maize MON 810. Four samples containing GM maize were shown to contain >1 % of StarLink maize. Establishing strong regulations and certified laboratories to monitor GM foods or crops in Saudi market is recommended.     

Theoretical studies of the structures and properties of (Br<Subscript>2</Subscript>InN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–6) clusters

In an attempt to find single-source precursors, a series of small clusters of inorganic azides of indium (Br₂InN₃) _n (n = 1–6) were studied using the dispersion correction density functional theory (wB97XD). The obtained (Br₂InN₃) _n (n = 2–6) clusters have the core structures of 2n-membered ring with alternating indium and α-nitrogen atoms. The influences of cluster size (oligomerization degree n) on the structures, energies, IR spectra, and thermodynamic properties of clusters were discussed. The computed binding energies indicate the stability: 3A > 3B, 4B > 4C > 4A > 4D, 5E > 5D > 5B = 5C > 5A and 6I > 6C > 6D > 6G ≥ 6H > 6F > 6E > 6B > 6A. It is also found that (Br₂InN₃)₂ and (Br₂InN₃)₄ clusters possess higher stability than their neighbor sizes judged by the calculated second-order difference of energies (Δ₂ E). Meanwhile, thermodynamic properties for (Br₂InN₃) _n (n = 1–6) clusters increase with the increasing temperature and oligomerization degree n, and the oligomerizations are thermodynamically favorable at temperatures up to 800 K.     

Synthesis of nucleobase-calix[4]arenes via click chemistry and evaluation of their complexation with alkali metal ions and molecular assembly

In this study, calix[4]arene derivatives (11–14) bearing a single nucleobase (adenine, thymine, cytosine or guanine) were synthesised via click chemistry. The complexation ability of the synthesised derivatives with alkali metal ions was measured using MALDI-TOF mass spectrometry, and their molecular assembly in CDCl₃ was determined using ¹H NMR. Calix[4]arene derivatives (11–14) formed 1:1 complexes with all alkali metal ions and the rank order for the complexation selectivity was Rb⁺ > Cs⁺ > K⁺ ? Na⁺ > Li⁺. The attachment of nucleobase at the upper rim of calix[4]arene had little effect on its complexation selectivity for alkali metal ions. Thymine-, adenine- and guanine-calix[4]arenes formed self-assembled structures in CDCl₃ via base–base interactions. In addition, adenine-calix[4]arene (11) bound to thymine-calix[4]arene (12) to form a discrete species via Hoogsteen hydrogen bonding.     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil. We have calculated the interaction energy of base-pair formation involving 5-formyluracil bound to the natural DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T), and discuss the effects of the 5-formyl group with respect to similar base-pairs containing uracil, 5-hydroxyuracil, thymine (5-methyluracil), and 5-hydroxycytosine. The interaction geometries and energies were calculated four ways: (a) using density functional theory (DFT) without basis set super-position error (BSSE) corrections, (b) using DFT with BSSE correction of geometries and energies, (c) using M?ller-Plesset second order perturbation theory (MP2) without BSSE correction, and (d) using MP2 with BSSE geometry and energy correction. All calculations used the 6-311G(d,p) basis set. Notably, we find that the A:5-formyluracil base-pair is more stable than the precursor A:T base-pair. The relative order of base-pair stabilities is A:5-Fo-U > G:5-Fo-U > C:5-Fo-U > T:5-Fo-U.     

Selective complexation of alkali metal ions and nanotubular cyclopeptides: a DFT study

A density functional theory based on interaction of alkali metal cations (Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺) with cyclic peptides constructed from 3 or 4 alanine molecule (CyAla3 and CyAla4), has been investigated using mixed basis set (C, H, O, Li⁺, Na⁺ and K⁺ using 6-31+G(d), and the heavier cations: Rb⁺ and Cs⁺ using LANL2DZ). The minimum energy structures, binding energies, and various thermodynamic parameters of free ligands and their metal cations complexes have been determined with B3LYP and CAM-B3LYP functionals. The order of interaction energies were found to be Li⁺ > K⁺ > Na⁺ > Rb⁺ > Cs⁺ and Li⁺ > Na⁺ > K⁺ ? Rb⁺ > Cs⁺, calculated at CAM-B3LYP level for the M/CyAla3 and M/CyAla4 complexes, respectively. Their selectivity trend shows that the highest cation selectivity for Li⁺ over other alkali metal ions has been achieved on the basis of thermodynamic analysis. The main types of driving force host–guest interactions are investigated, the electron-donating O offers lone pair electrons to the contacting LP* of alkali metal cations.     

Molecular dynamics simulation studies of the ε-CL-20/HMX co-crystal-based PBXs with HTPB

Molecular dynamics simulations were carried out to explore a ε-CL-20/HMX (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexazaisowurtzitane/1,3,5,7-tetranitro-1,3,5,7- tetrazacyclooctane) co-crystal-based polymer-bonded explosive (PBX) with HTPB (hydroxyl-terminated polybutadiene). The binding energies, pair correlation functions, and mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that the order of the binding energies per unit surface between the crystalline surface and HTPB is (0 1 0) > (1 0 0) > (0 0 1). The pair correlation function revealed that the H···O and H···N H-bonds exist on the interfaces between the crystalline surfaces and HTPB, and the number of H???O hydrogen bonds (H-bonds) atom pairs is ten times more than that of H???N H-bonds. Additionally, the calculated mechanical data indicated that the stiffness of the co-crystal/HTPB PBX is weaker and its ductility is better than those of the co-crystal.     

Potentiometric Studies on Complexation of Cu(II) Ion with Methyl/Nitro-Substituted 1,10-Phenanthrolines and Selected Amino Acids

Protonation constants of methyl/nitro substituted 1,10-phenanthrolines {(m/n-sphen): 4-methyl-phenanthroline (4-mphen), 5-methyl-1,10-phenanthroline (5-mphen), 4,7-dimethyl-1,10-phenanthroline (dmphen), 3,4,7,8-tetramethyl-1,10-phenanthroline (tmphen) and 5-nitro-1,10-phenanthroline (5-nphen)] and the amino acids (aa) l-tyrosine (tyr) and glycine (gly), and their corresponding binary and ternary stability constants with Cu(II), were determined in aqueous 0.1 mol·L^?1 KCl ionic media at 298.15 K. The protonation constants of the ligands and the stability constants of the binary and ternary complexes of Cu(II) with the ligands were calculated from the potentiometric data using the “BEST” software package. The species distribution diagrams were obtained using the “SPE” software package under the experimental conditions described. The order of stability of the ternary complexes in terms of the primary ligands is [Cu(tmphen)(aa)]⁺ > [Cu(dmphen)(aa)]⁺ > [Cu(4-mphen)(aa)]⁺ > [Cu(5-mphen)(aa)]⁺ > [Cu(5-nphen)(aa)]⁺. The stability constants of the ternary complexes decrease in the following order: [Cu(m/n-sphen)(gly)]⁺ > [Cu(m/n-sphen)(tyr)]⁺, which is identical to the sequence found for the binary complexes of Cu(II) with gly and tyr.     

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.