Quantifying the relative contribution of hydrogen bonding and hydrophobic environments, and coordinating groups, in the zinc(II)-water acidity by synthetic modelling chemistry

Ligands derived from the tripodal N4 ligand tris(pyridylmethyl)amine ((pyCH2)3N, tpa) of general formula (6-RNHpyCH2)nN(CH2py)(3-n)(R = H, n= 1-3 L(1-3); R = neopentyl, n= 1-3 L'(1-3)) were used to elucidate and quantify the magnitude of the effects exerted by hydrogen bonding and hydrophobic environments in the zinc-water acidity of their complexes. The pKa of the zinc-bound water molecule of [(L(1-3))Zn(OH2)]2+ and [(L'(1-3))Zn(OH2)]2+ 1'-3' was determined by potentiometric pH titrations in water (1-3) or water-ethanol (1:1) (1'-3'). The zinc(II) water acidity gradually increases as the number of -NH2 hydrogen bonding groups adjacent to the water molecule increases. Thus, the zinc-bound water of [(L3)Zn(OH2)]2+ and [(tpa)Zn(OH2)]2+ deprotonate with pKa values of 6.0 and 8.0, respectively. The pKa of the water molecule, however, is only raised from 8.0 in [(tpa)Zn(OH2)]2+ to 9.1 in [(bpg)Zn(OH2)]+ (bpa =(pyCH2)2N(CH2COO-)). Moreover, the acidity of the zinc-bound water of several of the five-coordinate zinc(II) complexes with the hydrogen bonding groups is greater than that of four-coordinate [((12)aneN3)Zn(OH2)]2+ (pKa = 7.0). This result shows that the magnitude of the effect exerted by the hydrogen bonding groups can be larger than that induced by changing one neutral by one anionic ligand, and/or even by changing the coordination number of the zinc(II) centre. The X-ray structure of [(L'2)Zn(OH)]ClO4 2' and [(L'3)Zn(OH)]ClO4.CH3CN 3'.CH3CN is reported, and show the neopentylamino groups forming N-H...O hydrogen bonds with the zinc-bound hydroxide. Although, which have hydrogen bonding and hydrophobic groups, have a zinc-bound water more acidic than [(tpa)Zn(OH2)]2+, their pKa is not always lower than that of 1-3. This result suggests that a hydrogen bonding microenvironment may be more effective than a hydrophobic one to increase the zinc-water acidity.     

Crystallographic evidence for intermolecular hydrogen bonding between aryl groups and OH groups in silanols

In crystals of the silanols (Me₃Si)₃CSiPh(X)OH (X  I or OMe) there is intermolecular π ⋯ HO bonding between a phenyl group in one molecule and an OH group in another, and there are probably intramolecular π ⋯ HO interactions in two silanols previously reported to show no hydrogen bonding. It is suggested that similar interactions should exist for OH groups attached to other metals or metalloids.     

LZnX complexes of tripodal ligands with intramolecular RN-H hydrogen bonding groups: structural implications of a hydrogen bonding cavity, and of X/R in the hydrogen bonding geometry/strength

Tripodal ligands N(CH2Py)3-n(CH2Py-6-NHR)n(R=H, n=1-3 L1-3, n=0 tpa; R=CH2tBu, n=1-3 L'1-3) are used to investigate the effect of different hydrogen bonding microenvironments on structural features of their LZnX complexes (X=Cl-, NO3-, OH-). The X-ray structures of [(L2)Zn(Cl)](BPh4)2.0.5(H2O.CH3CN), [(L3)Zn(Cl)](BPh4)3.CH3CN, [(L'1)Zn(Cl)](BPh4) 1', [(L'2)Zn(Cl)](BPh4)2'.CH3OH, and [(L'3)Zn(Cl)](BPh4)3' have been determined and exhibit trigonal bipyramidal geometries with intramolecular (internal) N-HCl-Zn hydrogen bonds. The structure of [(L'2)Zn(ONO2)]NO3 4'.H2O with two internal N-HO-Zn hydrogen bonds has also been determined. The axial Zn-Cl distance lengthens from 2.275 A in [(tpa)Zn(Cl)](BPh4) to 2.280-2.347 A in 1-3, 1'-3'. Notably, the average Zn-N(py) distance is also progressively lengthened from 2.069 A in [(tpa)Zn(Cl)](BPh4) to 2.159 and 2.182 A in the triply hydrogen bonding cavity of 3 and 3', respectively. Lengthening of the Zn-Cl and Zn-N(py) bonds is accompanied by a progressive shortening of the trans Zn-N bond from 2.271 A in [(tpa)Zn(Cl)](BPh4) to 2.115 A in 3 (2.113 A in 3'). As a result of the triply hydrogen bonding microenvironment the Zn-Cl and Zn-N(py) distances of 3 are at the upper end of the range observed for axial Zn-Cl bonds, whereas the axial Zn-N distance is one of shortest among N4 ligands that induce a trigonal bipyramidal geometry. Despite the rigidity of these tripodal ligands, the geometry of the intramolecular RN-HX-Zn hydrogen bonds (X=Cl-, OH-, NO3-) is strongly dependent on the nature of X, however, on average, similar for R=H, CH2tBu.     

Concerning the acidity and hydrogen bonding of hydroxyphenanthroperylene quinones like fringelite D,hypericin, and stentorin

Summary The strongly enhanced acidity of the bay hydroxyl group as compared to the respectiveperi hydroxyl groups of fringelite D, hypericin, and stentorin could be rationalized on the basis of a vinylogous carboxylic acid and was nicely corroborated by semiempirical calculations of the AM1 type. Experimental data obtained from several independent experimental methods, like polarized absorption spectroscopy, hole burning, and isotope effects, as well as from semiempirical AM1 and 6–31G levelab initio calculations conclusively pointed to dissymmetrical hydrogen bonding systems in both theperi andbay regions of the correspondingbay phenolate ions.

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Zu Acidität und Wasserstoffbrückenbindung von Hydroxyphenanthroperylenchinonen wie Fringelit D, Hypericin und Stentorin

Zusammenfassung Die stark erhöhte Acidität der bay-Hydroxylgruppen gegenüber jener derperi-Hydroxylgruppen von Fringelit D, Hypericin und Stentorin läßt sich auf der Basis einer vinylogen Carbonsäure verstehen und wurde auch durch semiempirische Rechnungen vom AM1-Typ erhärtet. Daten aus unabhängigen Experimenten wie Polarisationsspektroskopie, Lochbrennen und Isotopeneffekte sowie semiempirische AM1- undab initio-Rechnungen auf 6–31G Niveau belegen ein unsymmetrisches Wasserstoffbrückenbindungssystem sowohl für denperi-als auch denbay-Bereich der entsprechendenbay-Phenolationen.

     

Effects of hydrogen bonding on the acidity of adenine, guanine, and their 8-oxo derivatives

Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.     

Phosphorus-based functional groups as hydrogen bonding templates for rotaxane formation

We report on the use of the hydrogen bond acceptor properties of some phosphorus-containing functional groups for the assembly of a series of [2]rotaxanes. Phosphinamides, and the homologous thio- and selenophosphinamides, act as hydrogen bond acceptors that, in conjunction with an appropriately positioned amide group on the thread, direct the assembly of amide-based macrocycles around the axle to form rotaxanes in up to 60% yields. Employing solely phosphorus-based functional groups as the hydrogen bond accepting groups on the thread, a bis(phosphinamide) template and a phosphine oxide-phosphinamide template afforded the corresponding rotaxanes in 18 and 15% yields, respectively. X-ray crystallography of the rotaxanes shows the presence of up to four intercomponent hydrogen bonds between the amide groups of the macrocycle and various hydrogen bond accepting groups on the thread, including rare examples of amide-to-phosphinamide, -thiophosphinamide, and -selenophosphinamide groups. With a phosphine oxide-phosphinamide thread, the solid-state structure of the rotaxane is remarkable, featuring no direct intercomponent hydrogen bonds but rather a hydrogen bond network involving water molecules that bridge the H-bonding groups of the macrocycle and thread through bifurcated hydrogen bonds. The incorporation of phosphorus-based functional groups into rotaxanes may prove useful for the development of molecular shuttles in which the macrocycle can be used to hinder or expose binding ligating sites for metal-based catalysts.     

On the acidity of hydrogen fluoride

An explanation is proposed for the rapid increase in acidity in progressing from dilute solutions of HF in H₂O to solutions of greater concentration ($\text{ca.}$ 10M). Anhydrous HF has been shown to be more acidic than generally believed and to require very small adventitious concentrations of F^? to become quite basic. Oxidation of I₂ is used to demonstrate the dependence of the nature of species in HF solution on the acidity or basicity of the medium.     

Extensive hydrogen and halogen bonding,and absence of intramolecular hydrogen bonding between alcohol and nitro groups in a series of endo‐nitronorbornanol compounds

The influence of the substituent at the C2 position on the hydrogen‐bonding patterns is compared for a series of five related compounds, namely (±)‐3‐exo,6‐exo‐dibromo‐5‐endo‐hydroxy‐3‐endo‐nitrobicyclo[2.2.1]heptane‐2‐exo‐carbonitrile, C₈H₈Br₂N₂O₃, (II), (±)‐3‐exo,6‐exo‐dibromo‐6‐endo‐nitro‐5‐exo‐phenylbicyclo[2.2.1]heptan‐2‐endo‐ol, C₁₃H₁₃Br₂NO₃, (III), (±)‐methyl 3‐exo,6‐exo‐dibromo‐5‐endo‐hydroxy‐3‐endo‐nitrobicyclo[2.2.1]heptane‐2‐exo‐carboxylate, C₉H₁₁Br₂NO₅, (IV), (±)‐methyl 3‐exo,6‐exo‐dibromo‐7‐diphenylmethylidene‐5‐endo‐hydroxy‐3‐endo‐nitrobicyclo[2.2.1]heptane‐2‐exo‐carboxylate, C₂₂H₁₉Br₂NO₅, (V), and (±)‐methyl 3‐exo,6‐exo‐dibromo‐5‐endo‐hydroxy‐3‐endo‐nitro‐7‐oxabicyclo[2.2.1]heptane‐2‐exo‐carboxylate, C₈H₉Br₂NO₆, (VI). The hydrogen‐bonding motif in all five compounds is a chain, formed by O—H...O hydrogen bonds in (III), (IV), (V) and (VI), and by O—H...N hydrogen bonds in (II). All compounds except (III) contain a number of Br...Br and Br...O halogen bonds that connect the chains to each other to form two‐dimensional sheets or three‐dimensional networks. None of the compounds features intramolecular hydrogen bonding between the alcohol and nitro functional groups, as was found in the related compound (±)‐methyl 3‐exo,6‐exo‐dichloro‐5‐endo‐hydroxy‐3‐endo‐nitrobicyclo[2.2.1]heptane‐2‐exo‐carboxylate, (I) [Boeyens, Denner & Michael (1984b). J. Chem. Soc. Perkin Trans. 2, pp. 767–770]. The crystal structure of (V) exhibits whole‐molecule disorder.     

Lifetime regulation of the charge-separated state in DNA by modulating the oxidation potential of guanine in DNA through hydrogen bonding

A series of naphthalimide (NI)- and 5-bromocytosine ((br)C)-modified oligodeoxynucleotides (ODNs) were prepared, and their lifetimes of the charge-separated states during the photosensitized one-electron oxidation of DNA were measured. Various lifetimes of the charge-separated states were observed depending on the sequence and the incorporation sites of (br)C, and the oxidation potential of G in the (br)C:G base-pair relative to that of G in the C:G base-pair and in the GGG sequence was determined by comparing the lifetimes of the charge-separated states. The change in the cytosine C5 hydrogen to bromine resulted in a 24 mV increase in the oxidation potential of G in the (br)C:G base-pair as compared to that of G in the C:G base-pair, the value of which is comparable to a 58 mV decrease in the oxidation potential of G in the GGG sequence. These results clearly demonstrate that hole transfer in DNA can be controlled through hydrogen bonding by introducing a substituent on the cytosine.     

An investigation of the role of the disparate redox states of the tetrathiafulvalene unit in modulating hydrogen bonding interactions in solution

We have investigated the electrochemically controlled hydrogen bonding interactions between tetrathiafulvalene host 3 and guests 4 or 5. Stabilisation of the 3⁺ state is dependent upon the nature of the guest species, whereas both guests prevent precipitation of the electrochemically generated 3²⁺ species at the working electrode via hydrogen bonded molecular recognition processes.     

The conformational composition of 3-buten-1-ol, the importance of intramolecular hydrogen bonding

The conformations of 3-buten-1-ol (1), and its model compounds cis-6-methyl-3-cyclohexen-1-ol (6), 3-cyclopenten-1-ol (7) and epicholesterol (9) have been investigated by FT-IR and ¹H NMR spectroscopy. The energies and geometries of 1, 6 and 7 were also investigated by molecular mechanics, semiempirical molecular orbital and ab initio calculations, while 9 was investigated by molecular mechanics only. The objective of the work was to study the conformational composition and importance of intramolecular OH…π hydrogen bonding for this composition in 1. Only two conformers of 1 have a geometrical possibility for intramolecular hydrogen bonding: Conformers 12 and 13 (Fig. 1). Compounds 6 and 7 were used as models for Conformer 12, while 9 was used as a model for Conformer 13. The investigations showed that Conformer 13 is the only hydrogen-bonded conformer, and that Conformer 12 is not intramolecularly hydrogen bonded. Conformer 13 was the most populated conformer, while Conformer 12 was hardly populated. The combination of experimental and theoretical data, and the use of model compounds was found necessary to obtain this conclusion.     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

Asymmetric hydrogenation of alkenes lacking coordinating groups

Asymmetric hydrogenation of olefins is one of the most important reactions for the synthesis of optically active compounds, especially in industry. Chiral iridium catalysts based on P,N ligands have strongly expanded their application range. In contrast to rhodium and ruthenium diphosphine complexes they do not require the presence of a coordinating group near the C=C bond and, therefore, allow highly enantioselective hydrogenations of largely unfunctionalized alkenes.     

含有配位基团的芳基汞化合物的金属转移反应

本文综述了含有配位基团芳基汞化合物与过渡金属和非过渡金属之间的金属转移反应。讨论了底物中的配位基团对于某些金属转移产物形成的影响.     

Chemical bonding in the hydrogen molecule

The chemical bond in the hydrogen molecule is examined using the electron density and the generalized overlap amplitudes. Logarithmic derivatives of the electron density provide a clear picture of its behavior in the bonding region as well as in the outer region. The GOA expansion of the density is used to examine the dependence of the rate of decay of the density on the GOA ionization potentials. The increase in the electron density at the nuclei and in the bonding region coincides with the higher ionization potential of H₂ over the H atom. The density in the bonding region along the internuclear axis does not decay exponentially, but its shape is very nearly an inverted Gaussian. © 1996 John Wiley & Sons, Inc.     

Vibrations and hydrogen bonding in porphycene

Combined use of IR, Raman, neutron scattering and fluorescence measurements for porphycene isolated in helium nanodroplets, supersonic jet and cryogenic matrices, as well as for solid and liquid solutions, resulted in the assignments of almost all of 108 fundamental vibrations. The puzzling feature of porphycene is the apparent lack of the N-H stretching band in the IR spectrum, predicted to be the strongest of all bands by standard harmonic calculations. Theoretical modeling of the IR spectra, based on ab initio molecular dynamics simulations, reveals that the N-H stretching mode should appear as an extremely broad band in the 2250-3000 cm(-1) region. Coupling of the N-H stretching vibration to other modes is discussed in the context of multidimensional character of intramolecular double hydrogen transfer in porphycene. The analysis can be generalized to other strongly hydrogen-bonded systems.     

Ansa-metallocenes with B---N and B---P linkages: the importance of N---HF---C hydrogen bonding in pentafluorophenyl boron compounds

The reaction of Cp′(Cp^B)ZrCl₂ [Cp^B=η⁵-C₅H₄B(C₆F₅)₂] with LiNHCMe₃ gave Cp′(Cp^B)(μ-NHCMe₃)ZrCl, with a constrained-geometry type Cp---B---N chelate ligand. The ¹⁹F-NMR spectrum of the zirconium complexes, as well as that of the titanium analogue, reveals C---FH---N hydrogen bonding to one of the ortho-F atoms of a C₆F₅ ring, strong enough to persist in solution at room temperature. The reaction of Cp′(Cp^B)TiCl₂ with LiPPh₂ affords the Cp---B---P chelate complex Cp′(Cp^B)(μ-PPh₂)TiCl, the first example of a crystallographically characterised Ti(IV) phosphido compound. A ¹⁹F-NMR study of a number of adducts of B(C₆F₅)₃ with prim- and sec-amines demonstrates the importance of intramolecular hydrogen bonding to C₆F₅ in this class of compounds, while there are no such interactions in B(C₆F₅)₃(PHR₂) (R=Cy, Ph). The crystal structures of Cp′(Cp^B)(μ-PPh₂)TiCl, B(C₆F₅)₃(NHMe₂) and B(C₆F₅)₃(PHCy₂) are reported.     

Diffusion controlled hydrogen atom abstraction from tertiary amines by the benzyloxyl radical. The importance of C-H/N hydrogen bonding

The rate constants for H-atom abstraction (k(H)) from 1,4-cyclohexadiene (CHD), triethylamine (TEA), triisobutylamine (TIBA), and DABCO by the cumyloxyl (CumO(?)) and benzyloxyl (BnO(?)) radicals were measured. Comparable k(H) values for the two radicals were obtained in their reactions with CHD and TIBA whereas large increases in k(H) for TEA and DABCO were found on going from CumO(?) to BnO(?). These differences are attributed to the rate-determining formation of BnO(?) C-H/amine N lone-pair H-bonded complexes.     

An NMR investigation of the importance of intramolecular hydrogen bonding in determining the conformational equilibrium of ethylene glycol in solution

Although conformational analysis by NMR of ethylene glycol indicates generally strong preferences for the gauche conformation in solvents ranging from water to chloroform, the bulk of the NMR evidence indicates that intramolecular hydrogen bonding between the hydroxyl groups is unlikely to be a significant factor in determining that preference, except possibly in fairly non-polar solvents. The 'gauche effect' is clearly very important, especially in aqueous solution.     

Contrast effect of hydrogen bonding on the acceptor and donor OH groups of intramolecularly hydrogen-bonded OH pairs in diols

We studied the influence of hydrogen bonding on the fundamental and overtone bands of the OH-stretching vibration of each OH group in the intramolecularly hydrogen-bonded OH(I)::OH(II) pair in 1,2-, 1,3- and 1,4-diols. The hydrogen bonding between the two OH groups significantly increases in strength from the five-membered ring of a 1,2-diol to the seven-membered ring of a 1,4-diol. Although the hydrogen bonding does not affect the vibrational property of the OH(II) (or acceptor), it significantly influences the OH(I) (or donor). As the hydrogen bonding becomes stronger from a 1,2- to a 1,4-diol, the fundamental band of the OH-stretching shifts downwards by from about 50 to 140 cm(-1), and the overtone band markedly decreases in intensity, although the effect on the intensity and bandwidth of the fundamental band varies among 1,2-, 1,3- and 1,4-diols. The quantum-mechanically calculated normal frequencies of the acceptor and donor OH groups in the hydrogen-bonded ring are in good agreement with the observed frequencies. The calculated interatomic distance between the O of an acceptor OH and the H of a donor OH is the shortest for a 1,4-diol, which is consistent with the largest frequency shift caused by the hydrogen bonding.