Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, π-stacking and solvent effects

Our dispersion-corrected DFT computations reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide.     

Infrared study of hydrogen bonds involving 2,2′-bipyridine and 2,2′-bipyrimidine. Influence of equivalent nitrogen atoms on the hydrogen bond strength

Hydrogen bonding between proton donors (phenols and water) and 2,2′-bipyridine (BPR) or 2,2′-bipyrimidine (BPM) has been investigated by infrared and FT-infrared techniques. The thermodynamic parameters (K, - ΔH, - ΔS°) and the frequency shifts of the ν_OH stretching vibrations have been determined in carbon tetrachloride solution. The spectroscopic results suggest that the complexes formed between phenols covering a large pK_a range (10.3–3.50) and BPR or BPM are of the normal OH⋯N type. The thermodynamic and spectroscopic properties of the BPR and BPM complexes are compared with those previously reported for the interaction between the same proton donors and the model molecules pyridine and pyrimidine. The BPR and pyridine complexes belong to the same series. The behaviours of BPM and pyrimidine are in complete contrast, the thermodynamic parameters and the related proton affinity being much higher for BPM than for pyrimidine. The results are probably ascribable to the presence of two equivalent neighbouring nitrogen atoms, the approach of a hydroxylic proton donor being greatly favoured in this electron-rich region. This effect does not exist in BPR, owing to its transoid configuration in solvents of weak polarity.     

NMR study of 1-aryl-1,2-dicarba-closo-dodecaboranes: intramolecular C-H?O hydrogen bonding in solution

Dicarba-closo-dodecaborane(12) (carborane) has recently received much attention as a building block for supramolecular assemblies and bioactive compounds. Among carborane isomers, 1,2-dicarba-closo-dodecaborane(12) (o-carborane) has unique chemical properties, including the ability of the o-carborane C-H hydrogens to form hydrogen bonds. To evaluate intramolecular hydrogen bond formation between the o-carborane C-H hydrogen and various hydrogen bond acceptors in solution, we have designed and synthesized 1-aryl-o-carboranes 2. Intramolecular hydrogen bonding ability was evaluated by means of ¹H NMR measurement of the o-carborane C-H hydrogen signal of 2. The 1-(2-methoxyphenyl)-o-carborane derivative 2m appeared to form an intramolecular hydrogen bond between o-carborane C-H hydrogen and the oxygen atom acting as a hydrogen bonding acceptor. In this study, we present evidence for hydrogen bond formation in solution between the o-carborane C-H and hydrogen bond acceptors positioned with appropriate geometry.     

How computational methods and relativistic effects influence the study of chemical reactions involving Ru‐NO complexes?

Two treatments of relativistic effects, namely effective core potentials (ECP) and all‐electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2‐TZVP calculations. Specifically, the reaction energies of reduction ( A ‐ F ), isomerization ( G‐I ), and Cl⁻ negative trans influence in relation to NH₃ ( J ‐ L ) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A ‐ L . From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC‐wPBE, and CCSD(T) (reference method). For reactions A ‐ I , B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J ‐ L . © 2017 Wiley Periodicals, Inc.     

Intramolecular hydrogen bonds C-H?N in bisheterocyclic compounds according to 1H and 13C NMR data

Data of ¹H and ¹³C NMR spectra show that in 2,2??-bipyridyl, 1-vinyl-2(2??-pyridyl)benzimidazole, 1-vinyl-3-vinylsulfanyl-5-(2-furyl)-1,2,4-triazole, and 1-vinyl-5-vinylsulfanyl-3-(2-furyl)-5-vinylthio-1,2,4-triazole exists a weak intramolecular hydrogen bond between the heterocyclic fragments. It causes a downfield shift of the bridging proton signal in the ¹H NMR spectrum by 0.6?C0.7 ppm and an increase in the corresponding direct coupling constant ¹³C-¹H by 1.5?C2.0 Hz. These variations in the spectral parameters can be efficiently used in the conformational analysis for establishing with the use of NMR method which conformers are predominantly populated in the heterocyclic compounds.     

Uncommon hydrogen bonds between a non-classical ethyl cation and π hydrocarbons: a preliminary study

This study undertakes a theoretical investigation into uncommon hydrogen bonds between the ethyl cation (C₂H₅ ⁺) and π hydrocarbons. Firstly, it considers the hyperconjugation effect of the ethyl cation, in which the non-localized hydrogen (H⁺) is taken to be a pseudoatom bound to the carbons of the methyl groups. The goal of the research is to use this electronic phenomenon to gain a better understanding of the (H⁺···π) and (H⁺···p-π) hydrogen bonds, which are considered uncommon because they are formed through the interaction of the H⁺ of the ethyl cation with the π bonds of the acetylene (C₂H₂) and ethene (C₂H₄), as well as with the pseudo-π bond of the cyclopropane (C₃H₆). In view of this, B3LYP/6-311++G(d,p) calculations were used to determine the geometries of the C₂H₅ ⁺···C₂H₂, C₂H₅ ⁺···C₂H₄, and C₂H₅ ⁺···C₃H₆ hydrogen-bonded complexes. Deformations of the bond lengths and bond angles of these systems were analyzed geometrically. Examination of the stretch frequencies and absorption intensities of the (H⁺···π) and (H⁺···p-π) hydrogen bonds has revealed red-shifts in π and p-π bonds. After structural modeling and vibrational characterization, analysis of the charge transfer following the ChelpG approach and subsequently quantification of the hydrogen bond energies (basis sets superpostition error and zero point vibrational energies being considered) were used to predict the strength of the (H⁺···π) and (H⁺···p-π) hydrogen bonds. In addition, the molecular topography was estimated using the quantum theory of atoms in molecules (QTAIM). QTAIM was chosen because of a desire to understand the (H⁺···π) and (H⁺···p-π) hydrogen bonds chemically on the basis of the quantity of charge density and interpretation of Laplacian fields. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hydrocarbons as proton donors in C–H⋯N and C–H⋯S hydrogen bonds

C–H?N and C–H?S hydrogen bonds were analyzed in complexes where acetylene, ethylene, methane and their derivatives are proton donors while ammonia and hydrogen sulfide are proton acceptors. Ab initio calculations were performed to analyze those interactions; MP2 method was applied and the following basis sets were used: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. The results showed that hydrogen bonds for complexes with ammonia are systematically stronger than such interactions in complexes with hydrogen sulfide. If the fluorine substituted hydrocarbons are considered then F-substituents enhance the strength of hydrogen bonding. For a few complexes, mainly those where carbon atom in proton donating C–H bond possesses sp³ hybridization, the blue-shifting hydrogen bonds were detected. Additionally, Quantum Theory of ‘Atoms in Molecules’ and Natural Bond Orbitals method were applied to analyze H-bond interactions.     

BN-Substituted fullerenes C60−2x (BN) x : a computational 11B and 15N NMR study

Density functional theory has been used to investigate the ¹⁵N and ¹¹B NMR parameters of heterofullerenes C_60?2x (BN) _x (x = 1, 2, 3, 6, 9, 12, 15, 18, 21, and 24). Geometry structures of all the BN-substituted fullerenes have been optimized at the B3LYP/6-31+G* level of theory. Afterward, ¹¹B and ¹⁵N chemical shielding isotropy and anisotropy (CSI, CSA) parameters have been calculated at the same level. The obtained results illustrate the electrostatic environment divisions of the nuclei into few layers, which have been then confirmed by calculating natural charges at B and N sites. A good correlation has been seen between the layers of CSI and CSA values and three local structures around boron and nitrogen atoms. The effects of curvature of fullerene structure on chemical shielding (CS) parameters of heterofullerenes have also been investigated by computing CS tensors for curved and relaxed structures of a set of small fragments separated from the heterofullerenes, suggesting high sensitivity of CS parameters to the curvature of fullerene structure.     

C(Ar)-H···O hydrogen bonds in substituted isobenzofuranone derivatives: geometric, topological, and NMR characterization

Substituted isobenzofuranone derivatives 1a-3a and bindone 4 are characterized by the presence of an intramolecular C(Ar)-H···O hydrogen bond in the crystal (X-ray), solution ((1)H NMR and specific and nonspecific IEF-PCM solvation model combined with MP2 and B3LYP methods), and gas (MP2 and B3LYP) phases. According to geometric and AIM criteria, the C(Ar)-H···O interaction weakens in 1a-3a (independent of substituent nature) and in 4 with the change in media in the following order: gas phase > CHCl(3) solution > DMSO solution > crystal. The maximum value of hydrogen bond energy is 4.6 kcal/mol for 1a-3a and 5.6 kcal/mol for 4. Both in crystals and in solutions, hydrogen bond strength increases in the order 1a < 2a < 3a with the rising electronegativity of the ring substituents (H < OMe < Cl). The best method for calculating (1)H NMR chemical shifts (δ(calcd) - δ(expl) < 0.7 ppm) of hydrogen bonded and nonbonded protons in 1a-3a and 1b-3b (isomers without hydrogen bonds) is the GIAO method at the B3LYP level with the 6-31G** and 6-311G** basis sets. For the C-H moiety involved in the hydrogen bond, the increase of the spin-spin coupling constant (1)J((13)C-(1)H) by about 7.5 Hz is in good agreement with calculations for C-H bond shortening and for blue shifts of C-H stretching vibrations (by 55-75 cm(-1)).     

Influence of OH⋯N and NH⋯O inter- and intramolecular hydrogen bonds in the conformational equilibrium of some 1,3-disubstituted cyclohexanes through NMR spectroscopy and theoretical calculations

The analysis of concentration effects in the (1)H NMR data of cis-3-aminocyclohexanol (ACOL) showed that its diequatorial conformer changes from 60% at 0.01 mol L(-1) to 70% at 0.40 mol L(-1) in acetone-d(6). A similar increase was also observed for the diequatorial conformer of cis-3-N-methylaminocyclohexanol (MCOL), from 32% (CDCl(3) 0.01 mol L(-1)) to 55% (CDCl(3) 0.40 mol L(-1)). The increase in solvent basicity leads to a large stabilization effect for the diequatorial conformer of both compounds too. For ACOL, it changes from 47% (ΔG(eqeq-axax)=0.06 kcal mol(-1)) in CCl(4) to 93% (ΔG(eqeq-axax)=-1.53 kcal mol(-1)) in DMSO, while for MCOL it goes from 7% (ΔG(eqeq-axax)=1.54 kcal mol(-1)) in CCl(4) to 82% (ΔG(eqeq-axax)=-0.88 kcal mol(-1)) in pyridine-d(6). These results indicate that the intramolecular hydrogen bonds (IAHB) OH?N and NH?O stabilize the diaxial conformers of these compounds in a non-polar solvent. For cis-3-amino-1-methoxycyclohexane (ACNE) and cis-3-N-methylamino-1-methoxy-cyclohexane (MCNE) no changes were observed in equilibrium with the variation of solvent polarity. These results indicate for the first time that the IAHB NH?O is not strong enough to stabilize the diaxial conformer of these compounds and that the conformation equilibria of the cis isomers of compounds ACOL and MCOL are influenced only by the IAHB OH?N. Moreover, the presence of a secondary amino group (93% of diaxial conformer in CCl(4)) leads to an IAHB OH?N stronger than in primary and tertiary amino-derivatives (53 and 54% of diaxial conformer, respectively) for 1,3-disubstituted cyclohexanes. Values obtained from the theoretical data through the B3LYP functional are in agreement with the experimental results and indicate that the IAHB strength that influences the conformational equilibrium of these compounds is the IAHB OH?N. Thus, the IAHB NH?O do not stabilize the diaxial conformer of the cis isomer of compounds ACNE and MCNE showing that the diequatorial conformer will always be more stable than the diaxial conformer, independent of concentration or solvent.     

Nature and strength of C-H···O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H···O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of α-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H···O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H···O interactions in the crystal packing of formyl compounds.     

Experimental and computational studies of molecules with close,non-bonded hydrogen–hydrogen contacts: common computational methods grossly overestimate some ‘through-space’ NMR scalar coupling constants

The NMR spin–spin scalar coupling constants (J_HH's) of closely contacting, but non-bonded hydrogen atoms in a series of highly strained molecules (including a new in,in-cyclophane made specifically for this study) have been examined both experimentally and computationally. The experimental J_HH's are invariably quite small (0.1–0.6 Hz), but common DFT methods with modest basis sets nearly always overestimate these values, by factors of 10–30, and even with quite large basis sets (up to cc-pVQZ) the J_HH's of two of the molecules are overestimated by a factor of 10 or more. Possible reasons for these discrepancies are discussed.     

Mononuclear zinc(II) and mercury(II) complexes of Schiff bases derived from pyrrolealdehyde and cysteamine containing intramolecular NH?S hydrogen bonds

Two neutral group 12 metal complexes, bis(pyrrol-2-ylmethyleneaminoethylthio)zinc(II) (1) and bis(pyrrol-2-ylmethyleneaminoethylthio)mercury(II) (2), with the (N_imine)₂S₂ coordination mode were synthesized by using metal-templated Schiff base condensation, and their molecular structures were determined by X-ray diffraction analysis. Complex 1 exhibits a distorted tetrahedral geometry around the metal, whereas the metal center has a bisphenoidal configuration in complex 2. Both mononuclear complexes possess intramolecular NH?S hydrogen bonds, as evidenced by IR, ¹H NMR and X-ray crystallography. The hydrogen-bond donor (H-N_pyrrole) and acceptor (S atom) are coming from different ligands within a single molecule. Complex 2 represents the first example of a mercury complex in the N₂S₂ coordination mode with intramolecular NH?S hydrogen-bond interactions. An investigation of the effects of the NH?S hydrogen bonding on the stability of 1 and 2, using an N-methyl pyrrolyl analogue, demonstrated that the N-H hydrogen-bond donor from the pyrrolyl moiety probably played a role in the stability of 1, but not 2.     

Energetic effects between halogen bonds and anion-π or lone pair-π interactions: a theoretical study

Energetic effects between halogen bonds and anion-π or lone pair-π interactions have been investigated by means of ab initio MP2 calculations. 1,4-diiodo-perfluorobenzene, a very effective building block for crystal engineering based on halogen bonding, is selected in this work both as electron-deficient π aromatic ring and as halogen bond donor. Additive and diminutive effects are observed when halogen bonds and anion-π/lone pair-π interactions coexist in the same complex, which can be ascribed to the same direction of charge transfer for the two interactions. These effects have been analyzed in detail by the structural, energetic, and AIM properties of the complexes. Finally, experimental evidence of the combination of the interactions has been obtained from the Cambridge Structural Database.     

The open-close mechanism of M2 channel protein in influenza A virus:A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41

The M2 protein from influenza A virus is a tetrameric ion channel. It was reported that the permeation of the ion channel is correlated with the hydrogen bond network among His37 residues and the cation-π interactions between His37 and Trp41. In the present study,the hydrogen bonding network of 4-methyl-imidazoles was built to mimic the hydrogen bonds between His37 residues,and the cation-π interactions between 4-methyl-imidazolium and indole systems were selected to represent the interac-tions between His37 and Trp41. Then,quantum chemistry calculations at the MP2/6-311G level were carried out to explore the properties of the hydrogen bonds and the cation-π interactions. The calcula-tion results indicate that the binding strength of the N-H···N hydrogen bond between imidazole rings is up to -6.22 kcal·mol-1,and the binding strength of the strongest cation-π interaction is up to -18.8 kcal·mol-1(T-shaped interaction) or -12.3 kcal·mol-1(parallel stacking interaction). Thus,the calcu-lated binding energies indicate that it is possible to control the permeation of the M2 ion channel through the hydrogen bond network and the cation-π interactions by altering the pH values.     

The system of hydrogen bonds in Ba2Re6Te8(CN)6·12H2O: Simulation and NMR study

The crystal hydrate Ba₂Re₆Te₈(CN)₆· 12H₂O whose structural fragments are the cluster onions [Ba₂Re₆Te₈(CN)₆]^4? is studied by¹H NMR. In the triclinic cell (space group P-1), the barium atoms coordinated by six water molecules are united into the dimers [Ba· 5H₂O] ₂ ⁴⁺ by two bridging H₂O molecules; the water molecules lying outside the coordination sphere of Ba are located in the structure channels running along the [001] direction. Diffusion of H₂O molecules was found in the range of temperatures 100?C below the temperature of intense dehydration of the crystal. The structure of the water lattice of the compound is modeled by calculating Coulomb interactions between hydrogen and surrounding atoms and analyzing the NMR spectra recorded under translational diffusion conditions for H₂O. Half of the protons in H₂O molecules are involved in the formation of hydrogen bonds whose lengths lie within 2.78–2.86 å (O-H…O) and 2.92-3.13 å (O-H…N). The water lattice structure is preserved up to ≈100?C. The water subsystem is radically rearranged upon subsequent heating followed by partial dehydration of the crystal.     

Comparative estimation of the energies of intramolecular C-H…O,N-H…O,and O-H…O hydrogen bonds according to the QTAIM analysis and NMR spectroscopy data

The energies of intramolecular C-H…O, N-H…O, and O-H…O hydrogen bonds in model compounds are empirically estimated based on the values of the hydrogen bond induced weak-field shift of the bridging hydrogen atom signal in the ¹H NMR spectrum. It is supported by a theoretical estimation of these energies based on the electron density value at the hydrogen bond critical point calculated within the QTAIM method. Good agreement between the empirical and theoretical estimates is found, which gives evidence of their reliability. It is shown that from the standpoint of their strength the intramolecular N-H…O and O-H…O hydrogen bonds can be classified as moderate whereas the intramolecular C-H…O hydrogen bonds must be classified as very weak interactions similar in their energy significance to van der Waals interactions.     

Vibrational dynamics and hydrogen bond properties of β-CD nanosponges: an FTIR-ATR, Raman and solid-state NMR spectroscopic study

Cyclodextrin nanosponges (CDNS) are cross-linked polymers with remarkable inclusion/release properties. CDNS show swelling capability and a hydrophilicity/hydrophobicity balance that can be dramatically modified by the type and quantity of cross-linking agents. Here, we focus our attention on samples of β-cyclodextrin nanosponges (β-CDNS) obtained by reacting β-cyclodextrin (β-CD) with the cross-linking agent carbonyldiimidazole at different β-CD:cross-linking agent molar ratio. The vibrational properties of CDNS thus synthesized have been investigated by Fourier transform infrared spectroscopy in attenuated total reflectance geometry and Raman spectroscopy in the dry state at room temperature. The quantitative analysis of the O–H stretching region (3,000–3,800 cm^?1) allowed us to obtain structural information on the role played by primary and secondary OH groups in the hydrogen bond network of the polymer. Also, the contribution of interstitial and intracavity crystallization water molecules is reported. Solid-state NMR spectroscopy is used to study the molecular mobility of the polymer by measuring the ¹H spin–lattice relaxation time in the rotating frame (T_1ρ). The T_1ρ values obtained for the polymer β-CDNS are compared with free β-CD. The observed relaxation parameters point out that the ester formation occurs mainly at the primary OH groups of CDs, also supporting the interpretation of vibrational spectra.