Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory

Atomic charges for conformationally rich molecules obtained through a modified principal component regression

A modification of the principal component regression model is proposed for obtaining a fixed set of atomic charges (referred to as dipole-derived charges) optimized for reproducing the dipole moment of a conformationally rich molecule, i.e., a molecule with multiple local minima on the potential energy surface. The method does not require any adjustable parameters and requires the geometries of conformers, their dipole moments and atomic polar tensor (APT) charges as the only input data. The fixed atomic charges generated by the method not only reproduce the molecular dipole moment in all the conformers accurately, but are also numerically close to the APT charges, thereby ensuring accurate reproduction of the dipole moment variations caused by small geometrical distortions (e.g., by vibrations) of the conformers. The proposed method has been applied to canonical 2'-deoxyribonucleotides, the model DNA monomers, and the dipole-derived charges have been shown to outperform both the averaged APT and RESP charges in reproducing the dipole moments of large sets of conformers, thus demonstrating a potential usefulness of the dipole-derived charges as a 'reference point' for modeling polarization effects in conformationally rich molecules.

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.

C60-DOM interactions and effects on C60 apparent solubility: a molecular mechanics and density functional theory study

Dissolved organic matter (DOM) plays a critical role in the transport of carbon nano-particles (e.g. C(60)) in the aquatic environment. However, the mechanism for C(60)-DOM interactions and its environmental implications needs further investigations. In this study, the interaction of C(60) with relevant reference compounds of DOM (DOM(R)) is computationally simulated by molecular mechanics and density functional theory (DFT). All the C(60)-DOM(R) complexes are firstly optimized by classical annealing, and then DFT using the Dmol(3) code. The adsorption energies of C(60) on DOM(R) were computed. The computed electrostatic potential indicates that DOM(R) are electron acceptors in the C(60)-DOM(R) complexes, and the thermodynamic calculations indicate that electrostatic interaction is the dominant driving force for the C(60)-gallic acid complexation process in water. The presence of DOM(R) increases the apparent water solubility of C(60). It is also observed that the C(60) apparent water solubility decrease with the increase of the energy gaps of frontier molecular orbitals (E(LUMO)-E(HOMO)) for each C(60)-DOM(R) complex. These findings indicate that computational simulation is an important tool for predicting the behavior and fate of carbon nano-particles in the aquatic environment.

Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations

Trans Hoogsteen/sugar edge (H/SE) RNA base pairs form one of the six families of RNA base pairs that utilize the 2'-hydroxyl group of ribose for base pairing and play key roles in stabilizing folded RNA molecules. Here, we provide a detailed quantum chemical characterization of intrinsic structures and interaction energies of this base pair family, along with the evaluation of solvent screening effects by a continuum solvent approach. We report DFT-optimized geometries and MP2 interaction energies for all 10 crystallographically identified members of the family, for a representative set of them, using complete basis set extrapolation. For 6 of the 10 base pairs, we had to apply geometric constraints to keep the geometries relevant to RNA. We confirm that the remaining, hitherto undetected, possible members of this family do not have appropriate steric features required to establish stable base pairing in the trans H/SE fashion. The interaction patterns in the trans H/SE family are highly diverse, with gas-phase interaction energies in the range from -1 to -17 kcal/mol. Except for the C/rC and G/rG trans H/SE base pairs, the interaction energy is roughly evenly distributed between the HF and correlation components. Thus, in the trans H/SE base pairs, the relative importance of electron correlation is noticeably smaller than in the cis WC/SE or cis and trans SE/SE base pairs, but still larger than in canonical base pairs. The trans H/SE A/rG base pair is the intrinsically most stable member of this family. This base pair is also known as the sheared AG base pair and belongs to the most prominent set of RNA base pairs utilized in molecular building blocks of functional RNAs. For all trans H/SE base pairs that we identified, in addition to conventional base pairing, viable alternative structures were stabilized by amino-acceptor interactions. In the QM calculations, these amino-acceptor complexes appear to be equally as stable as those with common H-bonds, and more importantly, the switch to amino-acceptor interaction does not require any significant geometrical rearrangement of the base pairs. Such interactions are worthy of further investigations, as X-ray crystallography cannot unambiguously distinguish between conventional and amino-acceptor interactions involving the 2'-hydroxyl group, formation of such interactions is usually not considered, and molecular modeling force fields do not include such interactions properly as a result of neglect of aminogroup pyramidalization.

Review of the establishment of nitro group charge method and its applications

On the basis of our previous work, a new approach, nitro group charge method (NGCM) is established and applied to understand, evaluate and predict the properties of nitro compounds or explosives, including molecular stability, impact sensitivity and nitrating reaction. At first, the more negative nitro charges (QNitro) correspond to the more stable nitro compounds. Secondly, for all nitro explosives in which the RNitro bond is the weakest, QNitro can be regarded as a structural parameter to assess and predict the impact sensitivity. The more negative QNitro means the higher H50. Thirdly, the conditions, the velocities and the products' occurrence ratios of some nitrating reactions can be approximately evaluated and compared using NGCM: the more negative QNitro corresponds to the easier and the faster reaction, and the higher occurrence ratio. Meanwhile, this idea of using charges on common atoms or groups to investigate related properties can be generalized to some other systems such as azide explosives.

A New Method to Evaluate the Stability of the Covalent Compound: By the Charges on the Common Atom or Group

A new method of comparing and analyzing the electrostatic potential (ESP) charges of the common atom or group to evaluate and compare the stabilities of covalent compounds was introduced. That is, covalent compounds will become more stable when the electron acceptors accept adequate electrons and possess adequate negative charges, and the electron donors donate adequate electrons and possess adequate positive charges accordingly. All calculations were performed by density functional theory (DFT) and the general gradient approximation (GGA) method with the Beck-LYP hybrid functional and the DNP basis set in Acceryls' code Dmol3. Calculation results verified the method considering the molecular structure is well applied in the covalent molecule systems of hydrides, oxides, alkyl radicals, and nitro compounds. Furthermore, the method has good operability, for the charges can be easily obtained by simple calculation.

AT Base Pair Anions versus (9-Methyl-A)(1-Methyl-T) Base Pair Anions

The anionic base pairs of adenine and thymine, (AT)(-), and 9-methyladenine and 1-methylthymine, (MAMT)(-), have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)(-) found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)(-) was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)(-) and a resulting (MAMT)(-) configuration that was either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)(-) occurred at a completely different electron binding energy than had (AT)(-). Moreover, the VDE value of (MAMT)(-) was in agreement with that predicted by theory. The configuration of (MAMT)(-) and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced DNA alterations, BFPT in the WC/HS configurations of (AT)(-) is not feasible.

Network visualization system for computational chemistry

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.

Molecular recognition of modified adenine nucleotides by the P2Y(1)-receptor. 2. A computational approach

The molecular recognition of C2- or C8-substituted ATP derivatives by the P2Y(1)-receptor (P2Y(1)-R) is analyzed using ab initio quantum mechanical calculations. Parameters that may determine ligand specificity toward P2Y(1)-R were examined on reduced models and correlated with the biochemical data for the parent compounds. These include tautomerism and protonation energy in the gas and aqueous phases, as well as molecular electrostatic potential (MEP) and dipole moment vector. The calculated electronic parameters cannot explain the inactivity of the C8-substituted ATP derivatives, nor the difference in activity among the C2-substituted ATP analogues. These results indicate that neither tautomerism nor changes in the electronic distribution of the adenine ring play a major role in determining binding specificity of adenine nucleotides to the receptor. It is suggested that the higher potency of the C2-substituted ATP derivatives, compared to ATP, might be due to interaction between the C2 side chain heteroatom and the receptor. Furthermore, the interaction of the C2 alkyl side chain with a hydrophobic pocket at the receptor binding site is suggested. In addition, NMR data in the companion paper indicate that the inactivity of the C8-substituted ATP analogues may be due to steric and conformational, rather than electronic, effects.