Inclusion complexes phenanthrene-β-cyclodextrin and their interactions with aliphatic amines

In the present work the formation constant of phenanthrene- β-cyclodextrin (Ph-β-CD) complexes in water and in H₂O-DMSO(Dimethyl sulfoxide)20 % were calculated. Interactions between the complexes and two aliphatic amines: diethylamine (DEA) and triethylamine (TEA) were also studied. The characteristies of the amine, in relation to the solvent used, were seen to be very important.     

Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.     

Theoretical analysis based on X-H bonding strength and electronic properties in red- and blue-shifting hydrogen-bonded X-H···π complexes

A theoretical study based on the X-H bond strength of the proton donor fragment and its concomitant classical red-shifting or improper blue-shifting of the pure stretching frequency, in weakly hydrogen-bonded X-H···π complexes, is presented. In this sense, the dissociation energy differences, defined as, ΔD(e) = D(e)(X-H)[complex] - D(e)(X-H) [isolated], showed to be linearly connected with the change in stretching frequencies, Δν = ν(X-H)[complex] - ν(X-H)[isolated], of red- and blue-shifting H-bonds. This relationship allows us to define a threshold for the type of the stretching shift of the X-H bond: ΔD(e)(X-H) > 50.3 kcal mol(-1) leads to blue-shifting whereas ΔD(e)(X-H) < 50.3 kcal mol(-1) leads to red-shifting behavior. Complementarily, natural bond orbital analysis along the X-H stretching coordinate and electric dipole polarizability was performed to investigate the factors involved in red- or blue-shifting hydrogen-bonded complexes. It has been found that a high tendency to deplete the electronic population on the H atom upon X-H stretching is exhibited in blue-shifting H-bonded complexes. On the other hand, these types of complexes present a compact electronic redistribution in agreement with polarizability values. This study has been carried out taking as models the following systems: chloroform-benzene (Cl(3)C-H···C(6)H(6)), fluoroform-benzene (F(3)C-H···C(6)H(6)), chloroform-fluorobenzene, as blue-shifting hydrogen-bonded complexes and cyanide acid-benzene (NC-H···C(6)H(6)), bromide and chloride acids-benzene ((Br)Cl-H···C(6)H(6)) and acetylene-benzene (C(2)H(2)···C(6)H(6)) as red-shifting complexes.     

QTAIM and ETS-NOCV analyses of intramolecular CH···HC interactions in metal complexes

The topological analysis, based on the quantum theory of atoms in molecules (QTAIM) of Bader and the ETS-NOCV charge and energy decomposition method have been used to characterize coordination bonds, chelating rings, and additional intramolecular interactions in the ZnNTA and ZnNTPA complexes in solvent. The QTAIM and ETS-NOCV studies have conclusively demonstrated that the H-clashes (they are observed only in the ZnNTPA complex and classically are interpreted as steric hindrance destabilizing a complex) are characterized by (i) the electron flow channel between the H-atoms involved, as discovered by the ETS-NOCV analysis (on average, ΔE(orb) = -1.35 kcal mol(-1)) and (ii) QTAIM-defined a bond path that indicates the presence of a preferred quantum-mechanical exchange channel, hence, they should be seen as H-H intramolecular bonding interactions. The main reason for the formation of a weaker ZnNTPA complex was attributed to the strain energy (from both QTAIM and ETS-NOCV techniques) and the larger Pauli repulsion contribution found from the ETS-NOCV analysis. An excellent agreement between physical properties controlling the stability of the two complexes was found from the two techniques, QTAIM and ETS-NOCV.     

New trends in the chemistry of α-fluorinated ethers, thioethers, amines and phosphines

Fluorine, the most electronegative element plays nowadays a key role in pharmaceutical, agrochemical and material sciences. About 20% of all pharmaceuticals and about 30% of agrochemicals under development or recently introduced on the market contain fluorine. However, when one examines the relevant structures more closely, one quickly recognizes a structural monotony. The same fluorine bearing aromatic or heterocyclic “cores” appear over and over again. The search for novel molecules having “emergent” fluorinated groups and the development of an efficient access toward them is a challenging task for industrial as well as academic laboratories. For example, the trifluoromethoxy group finds increased utility as a substituent in bioactives, but it is still perhaps the least well understood fluorine substituent in currency. The present review will give an updated overview on the synthesis of α-fluorinated ethers, thioethers, amines and phosphines.     

Intramolecular OH···π interactions in alkenols and alkynols

The vibrational overtone spectra of propargyl alcohol (prop-2-yn-1-ol, PA), allyl alcohol (prop-2-en-1-ol, AA), propargyl carbinol (but-3-yn-1-ol, PC) and allyl carbinol (but-3-en-1-ol, AC) were recorded with intracavity laser photoacoustic spectroscopy (ICL-PAS) in the Δv(OH) = 3, 4 and 5 regions for propargyl alcohol and allyl alcohol and in the Δv(OH) = 4 and 5 regions for propargyl carbinol and allyl carbinol. Local mode anharmonic oscillator calculations were performed with explicitly correlated coupled cluster methods to guide spectral assignment. Atoms in molecules (AIM) and non-covalent interactions (NCI) calculations were carried out to analyze the interactions between the OH-group and the π-electrons of the carbon-carbon multiple bonds. We ascertain the effect of the carbon chain length and saturation on the conformation and spectroscopy of the four alcohols in relation to intramolecular hydrogen bonding interactions.     

Some group VB chloride complexes with thiourea and N,N′-diethyl-dithiooxamide

The following complexes of thiourea(tu) and N,N′-diethyl-dithioxamide (Et₂DH₂) with phosphorous (III), arsenic(III), antimony(III) and bismuth(III) have been prepared and characterises: PCl₃(tu) (DMF)₂; AsCl₃(tu)₃(DMSO)₃: MCl₃(tu)₃ (M = As, Bi); SbCl₃(tu)₂(DMF) and SbCl₃(Et₂DH₂)_1.5 (C₂H₄Cl₂). IR and NMR (¹H, ¹³C and ³¹P) spectral data provides evidence for ligand attachment exclusively by sulphur coordination in all complexes excepting PCl₃(tu) (DMF)₂. For the latter additional metal-nitrogen bonding is proposed.     

Intramolecular NH···Pt interactions of platinum(II) diimine complexes with phenyl ligands

Pt(pipNC)(2)(phen) [pipNC(-) = 1-(piperidylmethyl)phenyl anion; phen = 1,10-phenanthroline] was prepared by the reaction of cis-Pt(pipNC)(2) with phen. Crystallographic and (1)H NMR data establish that the phen ligand is bidentate, whereas each piperidyl ligand is monodentate and bonded to the platinum at the ortho position of the phenyl group. Acidic conditions allowed for isolation of the salts of diprotonated Pt(pipNHC)(2)(diimine)(2+) adducts (diimine = phen, 2,2'-bipyridine, or 5,5'-ditrifluoromethyl-2,2'-bipyridine). Crystallographic and spectroscopic data for the diprotonated complexes are consistent with H···Pt interactions (2.32-2.51 ?) involving the piperidinium groups, suggesting that the metal center behaves as a Br?nsted base. Metal-to-ligand (diimine) charge-transfer states of Pt(pipNHC)(2)(phen)(2+) in solution are strongly destabilized (>2500 cm(-1)) relative to Pt(pipNC)(2)(phen), in keeping with the notion that NH···Pt interactions effectively reduce the electron density at the metal center. Though N···Pt interactions in Pt(pipNC)(2)(phen) appear to be weaker than those found for outer-sphere two-electron reagents, such as Pt(pip(2)NCN)(tpy)(+) [pip(2)NCN(-) = 1,3-bis(piperidylmethylphenyl anion; tpy = 2,2':6',2'-terpyridine], each of the Pt(pipNC)(2)(diimine) complexes undergoes diimine ligand dissociation to give back cis-Pt(pipNC)(2) and free diimine ligand. Electrochemical measurements on the deprotonated complexes suggest that the piperidyl groups help to stabilize higher oxidation states of the metal center, whereas protonation of the piperidyl groups has a destabilizing influence.     

Simultaneous interactions of pyridine with substituted benzene ring and H–F in X-ben⊥pyr···H–F complexes: a cooperative study

The cooperative effects between T-shape stacking and hydrogen bond interactions in X-ben⊥pyr···H–F complexes were investigated in this work. The results indicate that the electron-withdrawing/donating substituents decrease/increase the magnitude of the binding energies compared to the unsubstituted X-ben⊥pyr···H–F (X = H) complex. The cooperative effects have been studied while using the atoms in molecules (AIM) and natural bond orbital (NBO) methods, allowing us to evaluate the interplay between T-shape stacking and hydrogen bond interactions. There are good relationships among binding energies, Hammett constants, geometrical parameters, and the results of AIM and NBO analysis in X-ben⊥pyr···H–F complexes.     

Comparison of P···D (D = P,N) with other noncovalent bonds in molecular aggregates

All the minima on the potential energy surfaces of homotrimers and tetramers of PH(3) are identified and analyzed as to the source of their stability. The same is done with mixed trimers in which one PH(3) molecule is replaced by either NH(3) or PFH(2). The primary noncovalent attraction in all global minima is the BP···D (D = N,P) bond which is characterized by the transfer of charge from a lone pair of the donor D to a σ? B-P antibond of the partner molecule which is turned away from D, the same force earlier identified in the pertinent dimers. Examination of secondary minima reveals the presence of other weaker forces, some of which do not occur within the dimers. Examples of the latter include PH···P, NH···P, and PH···F H-bonds, and "reverse" H-bonds in which the source of the electron density is the smaller tail lobe of the donor lone pair. The global minima are cyclic structures in all cases, and exhibit some cooperativity, albeit to a small degree. The energy spacing of the oligomers is much smaller than that in the corresponding strongly H-bonded complexes such as the water trimer.     

A new noncovalent force: comparison of P···N interaction with hydrogen and halogen bonds

When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(?) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(?) orbital that is closest to the P. In contrast to halogen bonds, there is no requirement of a σ-hole of positive electrostatic potential on the P atom, nor is it necessary for the two interacting atoms to be of differing potential. In fact, the two atoms can be identical, as the global minimum of the PH(3) homodimer has the same structure, characterized by a P···P attraction. Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction.     

Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Intramolecular C—F→Ln dative interactions in lanthanide complexes with fluorinated ligands

Complexes reported in the literature and potentially capable of intramolecular C—F→Ln interactions were analyzed. It was proposed to use the ToposPro software for structural and topological analysis to search for intramolecular C—F→Ln interactions. The shortest detected Ln···F contact amounted to 2.374 Å, while the longest weak non-valence contact was 4.060 Å. For all lanthanide complexes with Ln···F distances shorter than 3.447 Å, only strong intramolecular (valence) interactions between these atoms were observed. These interactions can affect the physicochemical properties of complexes and they are to be taken into account in determination of the coordination environment of lanthanide atoms.     

Evidence for cation-π interactions in calixcrown·KPic complexes from X-ray crystal structure analysis and energy calculations

Abstract

The crystal and molecular structures of the 1,3-diisopropoxy-p-tertbutyl calix[4]arene crown-5 fixed in the partial cone conformation and that of its potassium picrate salt have been determined by single crystal X-ray diffraction studies. Energy calculations have been performed to gain more insight on the stabilizing cation…ligand interactions. The calculation of the total potential energy indicates that the contribution which comes from the electrostatic polarization induced by the electric field of the cation on the rotated nucleus gives a net stabilizing contribution of almost 6 kcal/mol. A comparison between the molecular geometry of some partial cone 1,3-disubstituted-p-tertbutylcalix[4]arene derivatives is reported and discussed in view of the preorganization principle.     

Solid and liquid phase equilibria and solid-hydrate formation in binary mixtures of water with amines

Solid and liquid phase diagrams have been constructed for {water+triethylamine,or+N,N-dimethylformamide(DMF) or+N,N-dimethlacetamide (DMA)} Solid-hydrates form with the empirical formulae N(C2H5)3 3H2O,DMF 3H2O,DMF 2H2O,DMA 3H2O and (DMA)2 3H2O.All are congruently melting except the first which melts incongruently.The solid-hydrate formation is attributed to hydrogen bond.The results are compared with the references     

Mutual enhancing effects of the σ-hole interactions and halogen/hydrogen-bonded interactions in the iodine-ylide containing complexes

The region of positive electrostatic potentials (σ-hole) has been found along the extension of the C–I bond in the iodine-ylide CH₂IH, which suggests that the iodine-ylide could interact with nucleophiles to form weak, directional noncovalent interactions. MP2 calculations confirmed that the I···N σ-hole interaction exists in the CH₂IH···NCX (X = H, F, Cl, Br, I) bimolecular complexes. The NCCl···CH₂IH···NCX (X = H, F, Cl, Br, I) termolecular complexes were constructed to investigate the weakly bonded σ-hole interactions to be strengthened by Cl···C halogen bond. And then, the NCY···CH₂IH···NCCl (Y = H, F, Cl, Br, I) termolecular complexes were designed to investigate the enhancing effects of the I···N σ-hole interaction on the Y···C halogen/hydrogen-bonded interactions. Accompany with the mutual enhancing processes of the σ-hole interactions and halogen/hydrogen-bonded interactions in the iodine-ylide containing termolecular complexes, both the I···N σ-hole interactions and Y···C halogen/hydrogen-bonded interactions become more polarizable.