Hydrogen bonding in DNA base complexes.

Experimental intermolecular frequencies in the DNA base complexes 1-methylthymine (1-MT) and cytosine monohydrate (CMH) are analyzed in terms of simple analytic interatomic potentials. Calculations with two different values for the constants of the nonbonded interactions are considered, and the hydrogen bond potentials are determined for each of these models. The observed frequencies in 1-MT are reasonably well described, although corresponding potentials are very different in the two models. The observed frequencies in CMH are less well described, although corresponding hydrogen bond potentials are similar in the two models. Hydration interactions are found to be important in CMH and the role of the water molecule is discussed. Possible reasons for the shortcomings of this simple analysis are considered.     

Microsolvation of aminoethanol: a study using DFT combined with QTAIM

The microsolvation of aminoethanol (AE) with one, two, three or four water molecules was investigated using a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen-bonding characteristics of AE–(H₂O) _n (n = 1–4) complexes. The results showed that AE tends to break its intramolecular OH^AE···N^AE hydrogen bond (H-bond) upon microsolvation and form intermolecular H-bonds with water molecules, while complexes that retain the intramolecular OH^AE···N^AE H-bond show reduced stabilities. The intermolecular H-bond that forms between the nitrogen atom of AE and the hydroxyl of a water molecule is the strongest one for the most stable AE–(H₂O) _n (n = 1–4) complexes, and as n increases from 1 to 4 they grow stronger. The partial covalent character of this H-bond was confirmed by QTAIM analyses. Many-body interaction analysis showed that the relaxation energies and two- and three-body energies make significant contributions to the binding energies of the complexes.     

On bond-critical points in QTAIM and weak interactions

Bond critical points (BCPs) in the quantum theory of atoms in molecules (QTAIM) are shown to be a consequence of the molecular topology, symmetry, and the Poincaré-Hopf relationship, which defines the numbers of critical points of different types in a scalar field. BCPs can be induced by a polarizing field or by addition of a single non-bonded atom to a molecule. BCPs and their associated bond paths are therefore suggested not to be a suitable means of identifying chemical bonds, or even attractive intermolecular interactions.

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Graphical abstract Bond-critical points in QTAIM and weak interactions?

     

Photophysical properties, X-ray structures, electrochemistry, and DFT computational chemistry of osmium complexes

We report the synthesis of phosphorescent divalent osmium complexes of the form [Os(N-N)₂(L-L) or Os(L-L)₂(N-N)]²⁺ (PF₆)₂ where N-N is a derivative of 1,10-phenanthroline, and L-L is a diarsine or diphosphine ligand: 1,2-bis(dimethylphosphino)ethane, 1,2-bis(dicyclohexylphosphino)ethane, or 1,2-bis(dimethylarseno)benzene. X-ray structures have been determined, luminescent and electrochemical properties have been measured and DFT calculations have been performed on the complexes. The emission lifetime of complexes of structure Os(II)(L-L)₂(N-N) are longer than the those of Os(II)(N-N)₂(L-L). The DFT calculations show that there is significant mixing of the π−π^∗ into the dπ−π^∗ charge-transfer state for the complexes of the form Os(II)(L-L)₂(N-N) resulting in a longer lived excited state. Through DFT calculations we were able to conclude that the HOMO of the complexes is a d orbital on the osmium while the LUMO is the b₁(ψ) π^∗ system of the phenanthroline. However, we found that the HOMO did not have the correct symmetry to enable strong charge transfer to the phenanthroline to be observed, and the strong MLCT transition observed in the spectra is the metal d HOMO(−1) to the b1 π^∗ LUMO of the phenanthroline.     

New ruthenium(II) thiolato complexes: Synthesis, reactivity, spectral, structural and DFT studies

Ruthenium complexes [Ru(mpy)₂(DMSO)₂] (1) and [Ru(mbtz)₂(DMSO)₂] (2) containing 2-mercaptopyridine (mpy) and 2-mercaptobenzothiazole (mbtz) have been synthesized. Reactivity of 1 have been examined with 2,2′-bipyridine (bipy), 1,10-phenanthroline (phen), EPh₃ (E = P, As) and 1,2-bis(diphenylphosphino)-methane (dppm). It reacted with bipy or phen in DMF to afford [Ru(mpy)₂(bipy)] (3) and [Ru(mpy)₂(phen)] (4) while, its reaction with EPh₃ or dppm in common organic solvents failed to afford products containing EPh₃ or dppm. Complexes under investigation have been characterized by elemental analyses, spectral, electrochemical studies and structures of 1-4 have been determined crystallographically. Density functional theory calculations have been performed on 1-4 and the model complex [Ru(mpy)(PMe₃)₂] (5) using exchange correlation functionals BP86. Optimized bond length and angles are in good agreement with the structural data. The Ru-N and Ru-S bond distances in [Ru(mpy)₂]-moiety of 1 are relatively shorter than 5, indicating higher stability of 1 in comparison to 5. The WBI values of Ru-N1, Ru-N2, Ru-S1 and Ru-S2 bonds indicate Ru-mpy bonding trend as 3 > 4 > 1 > 5. There is an overall charge flow in the direction L → [Ru(mpy)₂] (L = DMSO, bipy, phen and PMe₃). Due to greater ionic character and Pauli repulsive interactions for Ru-PMe₃ bond in comparison to Ru-DMSO, the DMSO ligands in 1 may not be substituted by phosphine ligands experimentally.     

Hydrogen bonding patterns in pyrazole Pt(II- and IV) chloride complexes

The solid-state packing arrays of the platinum(II) trans- and cis-[PtCl₂(PzH)₂] (1 and 2) and platinum(IV) trans- and cis-[PtCl₄(PzH)₂] (3 and 4) complexes have been examined and the occurrence of N-H ? Cl hydrogen-bonding associations in those structures has been discussed. Although different packing motifs are observed, in all cases molecules are interacting mostly via NH ? Cl and CH ? Cl associations. The square planar 1 and 2 form stacked arrays of PtCl₂(PzH)₂, which are supported by NH ? Cl and CH ? Cl hydrogen bonding. The isomeric structure of the complexes and orientation of the PzH rings determine NH ? Cl bonding mode (intermolecular or intramolecular) and also the extent of the platinum-platinum interaction. The synthetic procedures for the preparation of 1-4 along with elemental and X-ray analyses, TG/DTA, FAB⁺-MS, IR, and ¹H and ¹³C{¹H} NMR data are also given in this article.     

Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Extensive DFT and ab initio calculations were performed to characterize the conformational space of pamidronate, a typical pharmaceutical for bone diseases. Mono-, di- and tri-protic states of molecule, relevant for physiological pH range, were investigated for both canonical and zwitterionic tautomers. Semiempirical PM6 method were used for prescreening of the single bond rotamers followed by geometry optimizations at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. For numerous identified low energy conformers the final electronic energies were determined at the MP2/6-311++G(2df,2p) level and corrected for thermal effects at B3LYP level. Solvation effects were also considered via the COSMO and C-PCM implicit models. Reasonable agreement was found between bond lengths and angle values in comparison with X-ray crystal structures. Relative equilibrium populations of different conformers were determined from molecular partition functions and the role of electronic, vibrational and rotational degrees of freedom on the stability of conformers were analyzed. For no level of theory is a zwitterionic structure stable in the gas-phase while solvation makes them available depending on the protonation state. Geometrically identified intramolecular hydrogen bonds were analyzed by QTAIM approach. All conformers exhibit strong inter-phosphonate hydrogen bonds and in most of them the alkyl-amine side chain is folded on the P-C-P backbone for further hydrogen bond formation.

Theoretical studies of structure, energetics and properties of Ca2+ complexes with alizarin glucoside

The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Density functional theory studies of interactions of polyphenol glycosides and Ca²⁺ were performed to determine preferred structures and the role of polyphenol and carbohydrate parts in the formation of complexes. The determination of these properties may be useful in designing new complexes, effectively interacting with calcium compounds. In the present study we try to define factors influencing interaction energies and stabilization. The determined structures were divided according to coordination numbers. Obtained data indicate that for stronger interactions complexes maximize the number of O-Ca²⁺ contacts.     

Hydrogen bonding in diruthenium(II,III) tetraacetate complexes with biologically relevant axial ligands

Three diadduct complexes of the mixed-valent form of diruthenium tetraacetate, [Ru₂(μ-O₂CCH₃)₄L₂](PF₆), where L are the biologically relevant ligands imidazole, 1, 7-azaindole, 2, and caffeine, 3, were synthesized and characterized by elemental analysis, IR and UV-Vis spectroscopy and X-ray crystallography. In order to further elucidate the potential interactions of these dimers with DNA, the nature of the ligand coordination and the secondary inter- and intramolecular hydrogen-bonding interactions in all three complexes were assessed. Complex 1 · CH₂Cl₂ shows, exclusively, intermolecular interactions with the counterion whereas complexes 2 · ClCH₂CH₂Cl and 3 · OC(CH₃)₂ · H₂O, in addition to extensive intermolecular interactions, show intramolecular hydrogen bonding from the axial ligand to the bridging acetate oxygens, locking the ligand mean planes in place between the bridging acetate mean planes. In addition, all three complexes display π-π stacking of axial ligand rings on adjacent diadduct units.     

Quadruplex DNA: sequence, topology and structure

G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.     

Drug-metal interactions: spectroscopic studies of copper hydantoin complexes.

The preparation and spectral properties of copper(II) complexes of two hydantoins are reported. Complexes of the general formula Cu(hyd)2(py)2, where hyd = phenytoin or nirvanol; and py = pyridine were prepared and characterized by infrared and ESR. Spectral data show that the copper atom is bound to the nitrogen atom of the hydantoin anion and to the nitrogen atom of the pyridine molecule to form 2:2:1 hydantoin:pyridine:copper complexes. The ESR data indicate that both complexes have tetragonal symmetry (g11 greater than g perpendicular greater than g e) with the unpaired electron in the d x2-y2 orbital.     

Hydrogen bonding interactions of polyamines with the 2'' OH of RNA.

Polyamines and other charged amines bind to RNA by hydrogen bonding to the 3' phosphate and to the 2' OH. This mode of binding suggests a mechanism by which DNA and RNA might be distinguished by enzymes.     

Hydrogen bonding in nucleosides and nucleotides

An analysis of the hydrogen bonding in 76 nucleoside and 11 nucleotide crystal structures shows that the hydrogen bond lengths fall into well-defined categories according to the nature of the donor or acceptor groups. The shortest bonds are those involving P---OH or O=P groups. For donor groups, the sequence in bond lengths is

P—OH<C—OH< N−H<O_w(H)—H<N(H)—H<C−H

There are ten examples of two centre

H—H…O

bonds, which are comparable in length with P---OH …O bonds. The acceptor seqeunce is

O=P<OH₂<OH₂<O=CO(H)C<N N(H₂)C<Cl^…<O<S=C

The number of three-centre bonds, about 24%, is comparable to that observed in the carbohydrates and the amino acids. Most hydrogen bonds are involved in short finite chains. Only in the nucleotides are cyclic hydrogen bonding schemes observed.     

DFT studies on the structural and vibrational properties of polyenes

Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C?=?C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae. BLYP/6-311++G** calculated ν(C?=?C) and ν(C–C) frequencies for all-trans and all-cis polyenes containing up to 14 carbon–carbon double bonds were used to estimate these values for very long chains. Correction of raw, unscaled vibrational data was performed by comparing theoretical and experimental wavenumbers for polyenes chains containing 3 to 12 conjugated C?=?C units with both ends substituted by tert-butyl groups. The corrected ν(C?=?C) and ν(C–C) wavenumbers for all-trans molecules were used to estimate the presence of 9 – 12 C?=?C units in all-trans polyene pigment in red coral.

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Graphical abstract Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C=C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae.

     

New insights into the stability of alkenes and alkynes, fluoro-substituted or not: a DFT, G4, QTAIM and GVB study

Many undergraduate organic chemistry books do not agree with the order of relative stability of alkenes towards hydrogenation reactions. Although they ascribe the stability of alkenes to the number and spatial position of the alkyl groups attached to the vinyl carbon atoms, results from the quantum theory of atoms in molecules indicate that the influence of an alkyl substituent on the stability of unsaturated hydrocarbons arises from the slight removal of electron density of the π bond, not from donation of their charge density to unsaturated carbon atoms as stated in many text books. There is an inverse relation between delocalization index—the number of shared electrons between two atoms, or Wiberg bond index of C=C bond—and the number of methyl groups attached to the vinyl carbon atoms. Electron withdrawing groups (EWGs) attached to unsaturated carbon atoms of alkenes and alkynes have two different behaviors: slight EWGs (alkyl groups) stabilize unsaturated carbon atoms while the strong EWG destabilizes the unsaturated carbon atoms. Generalized valence bond theory was also used to study the ambiguous behavior of fluorine substituents bonded to vinyl carbon atoms.