Interactions Between Amino Groups in DNA. An Ab Initio Study and a Comparison with Empirical Potentials

Abstract

An ab initio quantum chemical analysis of the close amino group contacts, existing in many DNA crystal structures, is presented. The calculations are made at the Hartree-Fock (HF) level with medium 6–31G* and 6–31 G(NH₂*) basis sets as well as with inclusion of correlation energy using the second order Møller-Plesset theory (MP2) with the 6–31G* basis set. We demonstrate that the model system (methylamine dimer, cytosine dimer) amino groups are forced to adopt significantly non-planar geometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyze the amino group contacts occurring in the DNA double helices. We propose that the mutual amino group interactions contribute to the conformational variability of the CpG and ApT B-DNA steps.     

Theoretical Investigation of the Molecular Structure of the πκ DNA Base Pair

Abstract

The structure of the nonclassical πκ base pair (7–methyl-oxoformycin … 2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6–31G* and 6–31G** basis sets. The πκ base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al. Nature 343, 33(1990)). By the HF/6- 31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the κ-base amino groups. The rings of both the π and κ molecules remain nearly planar. This nonplanar structure of the πκ base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6- 31G* level gas-phase interaction energy of πκ (—13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (—13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6–31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol.     

UV Photoelectron Spectroscopy and Ab Initio Characterization of Valence Orbital Structures and Conformations of Neutral Phosphate Esters

Abstract

The Hel UV photoelectron spectrum of trimethyl phosphate (TMP) has been measured and interpreted with the aid of SCF molecular orbital calculations carried out with STO-3G, STO-3G* and 4–31G basis functions. The photoelectron spectrum of TMP is more accurately reproduced by results from 4–31G calculations than by results from STO-3G or STO-3G* calculations. However, all three basis sets yield results which predict the same assignment of the photoelectron spectrum. Results at the 4–31G level indicate that whether calculations are based on crystallographic bond angles and bond lengths or on STO-3G optimized geometries has little effect on the energetic ordering of the upper occupied orbitals. The energetic ordering of orbitals is also found to be only weakly dependent upon the torsional angle φ, describing rotation of ester groups about P-O bonds and upon the torsional angle ψ, describing rotation of methyl groups about C-O bonds. For trimethyl phosphate, with C₃ symmetry, the vertical ionization potentials of the upper occupied orbitals are 10.81 eV (8e), 11.4 eV (9a), 11.93 eV (7e), 12.6–12.9 eV (8a and 6e), 14.4 eV (7a) and 15.0–16.0 eV(5e and 6a). Calculations at the 4–31G level indicate that many of the highest occupied orbitals in neutral dimethyl phosphate and methyl phosphate have energies and electron distributions similar to orbitals in TMP.

For TMP, a search for optimized values of φ and ψ has been carried out at the STO-3G* level. In agreement with previous NMR studies and with classical potential calculations, the STO- 3G* results indicate that both the gauche φ= 53.1 °) and anticlinal (φ = 141.9°) conformations are thermally accessible. Also in agreement with the classical potential calculations, the STO-3G* results predict that in the all gauche conformation energy is minimized when the methyl groups assume a staggered geometry (ψ= 60° to 80°) and that an energy maximum occurs for an eclipsed geometry (ψ = 0° to 20°). A study of the dependence of optimized values of O-P-O ester bond angles on the torsional angles, φ, was carried out at the STO-3G, STO-3G* and 4–31G levels. The results demonstrate that for C₃ symmetry, the coupling of O-P-O angles to φ is influenced by repulsive steric interactions.     

Structures of Oligonucleotides Containing 5-(methoxymethyl)-2′-deoxyuridine Determined by NMR Spectroscopy

Abstract

Base pairing of 5-(methoxymethyl)-2′-deoxyuridine (MMdU) opposite either adenine or guanine in a seven base pair oligonucleotide duplex has been studied by NMR spectroscopy. When paired with A, we observe that the MMdU. Abase pair adopts Watson-Crick geometry. The methoxymethyl substituent is not held in a fixed conformation and may rotate around the C5-CH₂ and CH₂?O bonds. Examination of the potential energy as a function of rotation around these bonds indicates the presence of four low energy conformations. No hydrogen bonding is indicated for the methoxymethyl substituent, and the four potential minima result from reduced steric clash. For the MMdU. G base pair, the two bases adopt a wobble geometry which does not change with increasing solvent pH. Similarly, we find four low energy conformations for the methoxymethyl substituent in the major groove of the DNA helix.     

Reaction Mechanism for the Diastereocontrolled Synthesis of Phosphorothioate DNA by the Oxazaphospholidine Approach

Abstract

Reaction mechanisms for the diastereoselective synthesis of deoxyribonucleoside 3′-cyclic phosphoramidites as well as dinucleoside phosphite intermediates by the oxazaphospholidine approach were analyzed by means of ab initio molecular orbital calculations at the HF/6-31G* level. These reactions are essential for the diastereoselective synthesis of phsophorothioate DNA.     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

Five novel palladium(II) complexes of 8-hydroxyquinoline and amino acids with hydrophobic side chains: synthesis,characterization, cytotoxicity,DNA- and BSA-interaction studies

Abstract

The side effects and resistance of metal-based anticancer drugs prompted us to synthesis a novel series of five Pd(II) complexes of the type [Pd(8-QO)(AA)]; where 8-QO?=?anion of 8-hydroxyquinoline and AA?=?anions of amino acids having nonpolar aliphatic side chain such as glycine (–H), alanine (–CH₃), valine (–CH(CH₃)₂), leucine (–CH₂–CH(CH₃)₂) and isoleucine (–CH(CH₃)CH₂–CH₃). The complexes have been characterized with the help of FT-IR, UV–Vis, one and two-dimensional ¹H-NMR, elemental analysis and conductivity measurements. On the basis of these characterization data, a four coordinated square planar geometry for all of these complexes have been proposed. The compounds were screened for their in vitro activities against human cancer cell line, MOLT-4 and their 50% inhibition concentration were ascertained by means of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Since four out of the five newly synthesized compounds were found to be more active than the standard anticancer drug, cisplatin, their detailed interaction with calf thymus DNA (as a target) and bovine serum albumin (BSA) (as a carrier) were also carried out by utilizing absorption spectra, fluorescence spectra and ethidium bromide displacement studies. In these experiments, several binding and thermodynamic parameters were also calculated. These results suggested that hydrogen binding and van der Waals forces play a major role in the interaction between metal complexes with CT-DNA and BSA.

Communicated by Ramaswamy H. Sarma     

Ab initio computational insight into the ion-pair SN2 reaction of lithium isothiocyanate and methyl fluoride in the gas phase and in acetone solution

The ion-pair S_N2 reaction LiNCS + CH₃F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction pathways in the title reaction are proposed. The inversion mechanism through a six-membered-ring transition-state structure is the most favorable. Methyl thiocyanate should form preferentially in the gas phase and the more stable methyl isothiocyanate will be the main product in CH₃COCH₃. The retardation of the reaction in CH₃COCH₃ solution was attributed to the differences in the solvation free energies in the separated reactants and transition structures. All of the theoretical results are consistent with the experiment.     

Computational Study of the Sulfonylated Amino Acid Hydroxamates Binding to the Zinc Ion within the Active Site of Carbonic Anhydrase

Abstract

The B3LYP/6–311+G(d,p) method and three ONIOM extrapolation methods ONI-OM (B3LYP/6–311+G(d,p): AM1); ONIOM(B3LYP/6–311+G(d,p): MNDO); ONIOM (B3LYP/6–311+G(d,p): HF/3-21G(d)) were used to characterize the complexes of Zn²⁺ cation with anionic sulfonylated amino acid hydroxamates (RSO₂NH-AA-CON(-)OH), possessing an unsubstituted RSO₂NH—amino acyl moiety. According to the R moiety we distinguish between pentafluorophenyl and 4-methoxyphenyl derivates. The amino acid hydroxamates included in the study were the Gly, Ala, and Leu derivates. Of the inhibitors investigated, the weakest zinc affinity exhibits the pentafluorophenyl derivate with Gly amino acid and the strongest affinity the 4-methoxyphenyl derivate with Leu amino acid. The inhibitors form bidentate coordination bonds with the zinc cation by means of the sulfonyl oxygen and the ionized hydroxamate nitrogen atoms, respectively. The zinc affinities computed using the B3LYP/6–311 +G(d,p)//HF/6–31 +G(d,p) method are in very good agreement with the full density functional theory (DFT) B3LYP/6–311+G(d,p)//B3LYP/6- 311+G(d,p) method and this method can be adopted to model larger complexes of inhibitors with the active site of carbonic anhydrase.     

The Hydronium Tetrafluoroborate Dimer in Nonpolar Media and its Proton NMR Spectrum

Hydronium tetrafluoroborate ion pairs, H₃O⁺·BF₄ ^- have been shown computationally to be unstable toward decomposition, in the absence of solvation or electrostatic interactions existing in crystals. As the proton NMR spectrum of a hydronium salt with the octanesulfonate-antimony pentachloride complex anion was reported in freon solution, we investigated the hypothesis that larger ionic clusters were present in the nonpolar solvent. It was found that the dimer (H₃O⁺·BF₄ ^-)₂ was stable at the MP2/6-31G* level. GIAO-B3LYP chemical shift calculations with the same basis set and also with the 6-31G**, 6-31++G**, 6-311++G**, dzvp, tzp, tz2p, and qz2p basis sets conducted on the hydronium fluoroborate dimer reproduce the main features of the experimental spectrum: the existence of two signals with a two-to-one intensity ratio and the more intense resonance at higher frequency (more deshielded). The alternative structures, of hydronium tetrafluoroborate ion pairs with one and with two hydrogen bonds between anion and cation, give calculated chemical shifts which are farther from the experimental values.     

Theoretical ab Initio Study of the Effects of Methylation on Structure and Stability of G:C Watson-Crick Base Pair

Abstract

Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6–31G(d) basis set was used. The single-point calculations have been performed at the MP2/6–31G(d,p), MP2/6–31₊₊G(d,p), and MP2/6–311₊₊G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.     

Post Hartree-Fock Studies of the Canonical Watson-Crick DNA Base Pairs: Molecular Structure and the Nature of Stability

Abstract

Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6–31G(d) and 6- 31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases.     

An Improved Method for the Preparation of Methyl dichlorophosphite. A Key Reagent In the Phosphite Method of Oligonucleotide Synthesis

Abstract

The reaction between phosphorus trichloride (PCl₃) and trimethyl phosphite (CH₃O)3^p, has been examined by ³¹Pnmr, in order to achieve a simple and efficient procedure for the formation of methyl dichlorophosphite (CH₃OPCl₂), which is a key intermediate in the synthesis of oligonucleotides. The yield of the reaction was also studied on a preparative scale and it was found that the optimal condition is obtained when the reactants molar ratio is 1:1.     

Methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate:A combined experimental and theoretical investigation

The title compound, methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate (C₂₅H₂₀O₇), was prepared and characterized by IR and single-crystal X-ray diffraction (XRD). The compound crystallizes in the triclinic space group P ?1 with a?=?8.9554(9) Å, b?=?10.0018(10) Å, c?=?12.7454(13) Å, α?=?67.678(7)°, β?=?89.359(8)° and γ?=?88.961(8)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in the ground state have been calculated using semiempirical AM1 and PM3 methods, as well as Hartree-Fock (HF) and density functional (B3LYP) levels of theory with 6–31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were performed by the B3LYP/6–31G(d) method.     

Application of ab initio molecular-orbital calculations to the structural moieties of carbohydrates. Part VI

Ab initio RHF/4–31G molecular-orbital calculations have been conducted on methoxymethyl formate and methoxymethyl acetate as models for examining the anomeric effect and stereochemistry of 1-O-acetylglycopyranoses. The results indicate that, as with the methyl glycopyranosides, the α-⁴C₁(D) configurations are more stable than the β-⁴C₁(D), except that the energy difference is more dependent on the disposition about the glycosidic bond. The lowest-energy conformations occur with glycosidic torsion-angles of ?  180°, where the anomeric energy is about 4 kcal/mol. There is a secondary energy-minimum at ?  90°, for which the anomeric energy is less, about 2 kcal/mol. This orientation corresponds to the conformation most commonly observed in the crystal structures of peracetylated glycopyranoses. Small differences in the CO single-bond lengths, which are observed experimentally in both the α and β anomers, are reproduced by the theoretical calculations.     

Conformation and tautomerizm of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule. An ab initio study

The protomeric tautomerizm and conformation of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule were investigated, and its three neutral tautomers (B₁,B₂,B₃) and their rotamers (C₁,C₂,C₃) were considered. Full geometry optimizations were carried out at the HF/6-31G* and B3LYP/6-31G* levels in gas phase and in water. The tautomerization processes in water (ɛ = 78.54) were studied by using self-consistent reaction field theory. The calculation showed that the boat conformation is dominant for the seven-membered diazepine ring in all of the structures, even with different double bond positions. The calculated relative free energies (ΔG) showed that the tautomer C₁ was the most stable structure, and its conformer B₁ was the second most stable in the gas phase and in water. Figure 2-Methyl-4-pyridin-2′-yl-1,5-benzodiazepine     

Theoretical mechanistic study of the reaction of the methylidyne radical with methylacetylene

A detailed doublet potential energy surface for the reaction of CH with CH₃CCH is investigated at the B3LYP/6-311G(d,p) and G3B3 (single-point) levels. Various possible reaction pathways are probed. It is shown that the reaction is initiated by the addition of CH to the terminal C atom of CH₃CCH, forming CH₃CCHCH 1 (1a,1b). Starting from 1 (1a,1b), the most feasible pathway is the ring closure of 1a to CH₃–cCCHCH 2 followed by dissociation to P ₃ (CH₃–cCCCH+H), or a 2,3 H shift in 1a to form CH₃CHCCH 3 followed by C–H bond cleavage to form P ₅ (CH₂CHCCH+H), or a 1,2 H-shift in 1 (1a, 1b) to form CH₃CCCH₂ 4 followed by C–H bond fission to form P ₆ (CH₂CCCH₂+H). Much less competitively, 1 (1a,1b) can undergo 3,4 H shift to form CH₂CHCHCH 5. Subsequently, 5 can undergo either C–H bond cleavage to form P ₅ (CH₂CHCCH+H) or C–C bond cleavage to generate P ₇ (C₂H₂+C₂H₃). Our calculated results may represent the first mechanistic study of the CH + CH₃CCH reaction, and may thus lead to a deeper understanding of the title reaction.     

Simulation and optical spectroscopy of a DC discharge in a CH<Subscript>4</Subscript>/H<Subscript>2</Subscript>/N<Subscript>2</Subscript> mixture during deposition of nanostructured carbon films

Two-dimensional numerical simulations of a dc discharge in a CH₄/H₂/N₂ mixture in the regime of deposition of nanostructured carbon films are carried out with account of the cathode electron beam effects. The distributions of the gas temperature and species number densities are calculated, and the main plasmachemical kinetic processes governing the distribution of methyl radicals above the substrate are analyzed. It is shown that the number density of methyl radicals above the substrate is several orders of magnitude higher than the number densities of other hydrocarbon radicals, which indicates that the former play a dominant role in the growth of nanostructured carbon films. The model is verified by comparing the measured optical emission profiles of the H(n ≡ 3), C ₂ ^* , CH*, and CN* species and the calculated number densities of excited species, as well as the measured and calculated values of the discharge voltage and heat fluxes onto the electrodes and reactor walls. The key role of ion–electron recombination and dissociative excitation of H₂, C₂H₂, CH₄, and HCN molecules in the generation of emitting species (first of all, in the cold regions adjacent to the electrodes) is revealed.     

Biochemistry of Methanogenesis

Abstract

Methane is a product of the energy-yielding pathways of the largest and most phylogenetically diverse group in the Archaea. These organisms have evolved three pathways that entail a novel and remarkable biochemistry. All of the pathways have in common a reduction of the methyl group of methyl-coenzyme M (CH₃-S-CoM) to CH₄. Seminal studies on the CO₂-reduction pathway have revealed new cofactors and enzymes that catalyze the reduction of CO₂ to the methyl level (CH₃-S-CoM) with electrons from H₂ or formate. Most of the methane produced in nature originates from the methyl group of acetate. CO dehydrogenase is a key enzyme catalyzing the decarbonylation of acetyl-CoA; the resulting methyl group is transferred to CH₃-S-CoM, followed by reduction to methane using electrons derived from oxidation of the carbonyl group to CO₂ by the CO dehydrogenase. Some organisms transfer the methyl group of methanol and methylamines to CH₃-S-CoM; electrons for reduction of CH₃-S-CoM to CH₄ are provided by the oxidation of methyl groups to CO₂.     

An experimental and theoretical approach to the molecular structure of 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione

The title compound, 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione (C₂₄H₂₂N₂O₂S), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?19.7799(13) Å, b?=?6.7473(4) Å, c?=?15.7259(9) Å and β?=?103.416(5)°. In addition, the molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values of the title compound in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets, and compared with the experimental data. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 5°. Besides, molecular electrostatic potential, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were investigated by theoretical calculations.