On the prebiotic selection of nucleotide anomers: A computational study

Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calculations. An interplay of kinetics and thermodynamics must have driven evolutionary selection of life's building blocks. In this work, based on quantum chemical calculations, we focus on the latter control as a tool for “natural selection”.

Multicomponent supramolecular assemblies of 1(2H)-Phthalazinone and Tetrafluoroterephthalic acid: Understanding the role of hydrogen bonding on the structure and properties using experimental and computational analyses

Two novel cocrystals were successfully constructed by 1(2H)-Phthalazinone (PHT) and Tetrafluoroterephthalic acid (TETA) based on O-H⋯O, N-H⋯O, C-H⋯O, C-H⋯F, N-H⋯N and C-H⋯N hydrogen bonding networks, and were well depicted by single crystal diffraction analysis. As predicted by electrostatic potential analysis, the stoichiometry of PHT to TETA is 2:1 and stabilized by O-H⋯O and N-H⋯O hydrogen bonds. The single crystal X-ray diffraction characterized that the two cocrystals were all made up by 2PHT-TETA motif in different ways. AIM analysis and Hirshfeld surfaces indicated the adjacent 2PHT-TETA units assemble through C-H⋯O, C-H⋯F and C-H⋯N hydrogen bonds, producing a 2D plane structure in cocrystal I. Meanwhile, the C-H⋯F, N-H⋯N and C-H⋯O hydrogen bonds between 2PHT-TETA units were the stabilizing factors in cocrystal II. Topological parameters such as ∇²ρ and H revealed the strength of hydrogen bonds were moderate in nature except O31⋯H32-O34 (1.704Å, -60.336kJmol^-1) in compound I. The hydrogen bonding interactions, cocrystal stability and electron donor-acceptor interactions were investigated using natural bonding orbital analysis. It showed that electron transfer of n(O) σ*(O-H) and n(O) σ*(N-H) between PHT and TETA influence the packing characteristics significantly. Structural changes accompanying cocrystal process have been rationalized through the IR spectrum along with the quantum chemical calculations. The frequency downshifts of CO, N-H and O-H stretching after cocrystallization have been attributed to hydrogen bonding interactions.

Anionic ribose related species explored through PES experiments, DFT calculations, and through comparison with anionic fructose species

Generation of (ribose-H)⁻ is dependent on deposition substrates, while generation of two types of (ribose-H₂O)⁻ isomers (open chain) is not.

Anionic fructose-related conformational and positional isomers assigned through PES experiments and DFT calculations

Fructose⁻ exists as an open chain structure with substrate dependent specific conformational isomers. (Fructose-H₂O)⁻ evidences two types of positional isomers.

Rotational spectroscopy of the atmospheric photo-oxidation product o-toluic acid and its monohydrate

o-Toluic acid, a photo-oxidation product in the atmosphere, and its monohydrate were characterized in the gas phase by pure rotational spectroscopy. High-resolution spectra were measured in the range of 5-14 Hz using a cavity-based molecular beam Fourier-transform microwave spectrometer. Possible conformers were identified computationally, at the MP2/6-311++G(2df,2pd) level of theory. For both species, one conformer was identified experimentally, and no methyl internal rotation splittings were observed, indicative of relatively high barriers to rotation. In the monomer, rocking of the carboxylic acid group is a large amplitude motion, characterized by a symmetrical double-well potential. This and other low-lying out-of-plane vibrations contribute to a significant (methyl top-corrected) inertial defect (-1.09 amu Å(2)). In the monohydrate, wagging of the free hydrogen atom of water is a second large amplitude motion, so the average structure is planar. As a result, no c-type transitions were observed. Water tunneling splittings were not observed, because the water rotation coordinate is characterized by an asymmetrical double-well potential. Since the minima are not degenerate, tunneling is precluded. Furthermore, a concerted tunneling path involving simultaneous rotation of the water moiety and rocking of the carboxylic acid group is precluded, because the hilltop along this coordinate is a virtual, rather than a real, saddle-point. Inter- and intramolecular non-covalent bonding is discussed in terms of the quantum theory of atoms in molecules. The percentage of o-toluic acid hydrated in the atmosphere is estimated to be about 0.1% using statistical thermodynamics.

Non-covalent intermolecular carbon-carbon interactions in polyynes

Polyynes, the smaller analogues of one dimensional infinite chain carbon allotrope carbyne, have been studied for the type and strength of the intermolecular interactions in their dimer and tetramer complexes using density functional theory. The nature of end group functionalities and the chain length of the polyynes are varied to assess their role in modulating the non-covalent interaction energy. As seen in molecular electrostatic potential analysis, all the polyyne complexes showed a multitude of non-covalent CC interactions, resulting from complementary electrostatic interactions between relatively electron rich formal triple bond region of one monomer and the electron deficient formal single bond region of the other monomer. This type of paired (C[triple bond, length as m-dash]C)(C-C) bonding interaction, also characterized using quantum theory of atoms-in-molecules, increases with increase in the monomer chain length leading to substantial increase in interaction energy (Eint); -1.07 kcal mol(-1) for the acetylene dimer to -45.83 kcal mol(-1) for the 50yne dimer. The magnitude of Eint increases with substitutions at end positions of the polyyne and this effect persists even up to 50 triple bonds, the largest chain length analyzed in this paper. The role of CC interactions in stabilizing the polyyne dimers is also shown by sliding one monomer in a dimer over the other, which resulted in multiple minima with a reduced number of CC interactions and lower values of Eint. Furthermore, strong cooperativity in the CC bond strength in tetramers is observed as the interaction energy per monomer (Em) of the polyyne is 2.5-2.8 times higher compared to that of the dimer in a test set of four tetramers. The huge gain in energy observed in large polyyene dimers and tetramers predicts the formation of polyyne bundles which may find use in the design of new functional molecular materials.

Intermolecular carbon-carbon, nitrogen-nitrogen and oxygen-oxygen non-covalent bonding in dipolar molecules

Clear evidence for the existence of intermolecular carbon-carbon (C···C), nitrogen-nitrogen (N···N) and oxygen-oxygen (O···O) interactions between atoms in similar chemical environments in homogeneous dimers of organic dipolar molecules has been obtained from molecular orbital (MO), natural bond orbital (NBO) and atoms-in-molecule (AIM) electron density analyses at the M06L/6-311++G(d,p) level of density functional theory (DFT). These X···X type interactions are mainly the result of local polarization effects, causing segregation of electron-rich and electron-deficient regions in the X atoms, leading to complementary electrostatic interactions. NBO analysis provides evidence of charge transfer between the two X atoms. Even in symmetrical molecules such as acetylene, induced dipoles in the dimer create C···C bonding interactions. The strength of this type of interaction increases with increase in the dipole moment of the molecule. Energy decomposition analysis (EDA) shows that the electrostatic component of the interaction energy (Eint) is very high, up to 95.86%. The C···C interactions between similar carbon atoms are located for several crystal structures obtained from the literature. In addition, MO, AIM and electrostatic potential analyses support interactions between similar oxygen (O···O) and nitrogen (N···N) atoms in a variety of molecular dimers. Good prediction of Eint is achieved in terms of the total gain in electron density at non-covalently interacting intermolecular bonds (∑ρ) and the monomer dipole moment (μ). A rigorously tested QSAR equation has been derived to predict Eint for all dimer systems: Eint (kcal mol(-1)) = -138.395∑ρ(au) - 0.551μ (Debye). This equation suggests that the polarization-induced bonding interaction between atoms in a similar chemical environment could well be a general chemical phenomenon. The results have been further validated by different density functional methods and also by G3MP2 method.

Conformational and H-bonding preferences for facile racemate crystallization of ribose

Recalcitrant crystallization and syrup formation are frequent features of natural sugars. This is the case of D-ribose, yielding low-quality crystals of mixed α- and β-pyranose anomers. However, large crystals of DL-ribose can be grown easily. The crystal structures of stable D-ribose forms I and II as well as DL-form II have been analyzed in terms of their compatibility with the molecular aggregation. The comparison of the potential energy of all conformers and their OH···O hydrogen-bonding patterns is consistent with the preferential racemate crystallization in terms of departures from the optimized isolated ribose molecule and its directional interactions. This analysis is aimed at rationalizing the interplay between the molecular structure and spontaneous crystallization of chiral compounds.

Guanidine complexes of platinum: a theoretical study

We have studied theoretically the complexes of model N-phenylguanidine/ium derivatives with PtCl3(-) and PtCl2 in different coordinating modes (mono- and bidentate) with different N atoms of the guanidine/ium moiety using the B3LYP/6-31+G** and LANL2DZ mixed basis set. This will aid the understanding of the complexation between platinum and the guanidine or guanidinium moiety in order to design dual anticancer agents that combine a guanidine-based DNA minor groove binder and a cisplatin-like moiety. Calculated interaction and relative energies, analysis of the electron density, and examination of the orbital interactions indicate that the most stable type of complex is that with a monodentate interaction between PtCl3(-) and guanidinium established through one of the NH2 groups. Next, we optimized the structure of three bis-guanidinium diaromatic systems developed in our group as DNA minor groove binders and their complexation with PtCl3(-), finding that the formation of Pt complexes of these minor groove binders is favorable and would produce stable monodentate coordinated systems.

Significant evidence of C⋯O and C⋯C long-range contacts in several heterodimeric complexes of CO with CH3–X, should one refer to them as carbon and dicarbon bonds!

An illustrated example of a ‘dicarbon bond’ formed between a pair of two carbon atoms of the OC⋯CH₃–Cl₃intermolecular complex, one corresponding to the methylated carbon in 1,1,1-trichloro-ethane (CH₃–Cl₃) and one to the carbon in the carbon dioxide (CO) molecule.