Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester

The hydrolysis of methyl 8-dimethylamino-1-naphthyl phosphate 4 and its reactions with a representative range of nucleophiles are catalyzed by the dimethylammonium group at acidic pH with rate accelerations of the order of 106. The reaction persists up to pH 7 because the strong intramolecular hydrogen bond, which is the key to efficient general acid catalysis, is present also in the reactant. The sensitivity to the basicity of the nucleophile (Br?nsted beta(nuc) = 0.29) lies between values measured previously for mono- and triesters. The comparisons suggest that general acid catalyzed reactions of phosphate mono- or diesters with strongly basic oxyanion nucleophiles (like those derived from a serine oxygen or a bound water molecule in an enzyme active site) will be fastest when their negative charges are neutralized by protonation. Reactions with NH2OH and its N-methylated derivatives show an apparent alpha-effect, but NH2OMe reacts no faster than a primary amine of similar basicity. It is suggested that the reaction involving NH2OH as an oxygen nucleophile proceeds through the pre-equilibrium formation of the tautomer H3N+-O- as the active nucleophile: ab initio calculations support this idea.     

Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases--a comparative molecular dynamics study

We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O???N)) ≤ 2.6 A?), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects.     

Fluorescence sensing of anions based on inhibition of excited-state intramolecular proton transfer

Condensation of 2-(2'-aminophenyl)benzoxazole with p-toluenesulfonyl chloride and phenyl isocyanate yields two new anion sensors (TABO and PUBO), which can undergo excited-state intramolecular proton transfer (ESIPT) upon excitation. For the acid receptor TABO, the ESIPT process can be readily disturbed by basic anions such as F-, CH3COO-, and H2PO4- by deprotonating the sulfonamide unit, whereas in the case of PUBO, a good hydrogen-bonding donor, the ESIPT process is inhibited either by the fluoride-induced deprotonation of the urea unit or by the formation of a strong CH3COO--urea intermolecular hydrogen bond complex, and these two types of inhibition mechanisms consequently result in different ratiometric responses. But other anions with less hydrogen-bonding acceptor abilities cannot inhibit the ESIPT. Interestingly, the different inhibition abilities of F-, CH3COO-, and H2PO4- produce different spectral behaviors in PUBO, so this new sensor successfully distinguishes the subtle difference in these three anionic substrates of similar basicity and surface charge density.     

Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 < or = pH < or = 8.6. This degradation is been attributed to (i) nucleophilic substitution of the imidazolide and (ii) catalysis of the P-N bond hydrolysis by phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).     

Phosphate activation in the ground state of purine nucleoside phosphorylase

Phosphate and ribose 1-phosphate (R1P) bound to human purine nucleoside phosphorylase (PNP) have been studied by FTIR spectroscopy for comparison with phosphate bound with a transition state analogue. Bound phosphate is dianionic but exists in two distinct binding modes with similar binding affinities. The phosphate of bound R1P is also dianionic. Bound R1P slowly hydrolyzes to ribose and phosphate even in the absence of nucleobase. The C-OP bond is cleaved in bound R1P, the same as in the PNP-catalyzed reaction. Free R1P undergoes both C-OP and CO-P solvolysis. A hydrogen bond to one P-O group is stronger than those to the other two P-O groups in both the PNP.R1P complex and in one form of the PNP.PO4 complex. The average hydrogen bond strength to the PO bonds in the PNP.R1P complex is less than that in water but stronger than that in the PNP.PO4 complex. Hydrolysis of bound R1P may be initiated by distortion of the phosphate moiety in bound R1P. The unfavorable interactions on the phosphate moiety of bound R1P are relieved by dissociation of R1P from PNP or by hydrolysis to ribose and phosphate. The two forms of bound phosphate in the PNP.PO4 complex are interpreted to be phosphate positioned as the product in the nucleoside synthesis direction and as the reactant in the phosphorolysis reaction; their interconversion can occur by the transfer of a proton from one PO bond to another. The electronic structure of phosphate bound with a transition state analogue differs substantially from that in the Michaelis complexes.     

Theoretical study of thiolysis in penicillins and cephalosporines

Semiempirical calculations were used to conduct a comprehensive study of the thiolysis of the fundamental core of penicillins and cephalosporins. The significance of the intramolecular protonation of the β‐lactam nitrogen in the formation and cleavage of the tetrahedral intermediate ( T in Scheme 1 ) was examined in two thiols bearing substituents of different basicity in β with respect to the thiol group in the attacking nucleophile, namely 2‐mercaptoethanol ( 6 ) and 2‐mercaptoethylamine ( 7 ). Based on the results, the rate‐determining step in the reaction of penicillins is the cleavage of the tetrahedral intermediate, consistent with an intramolecular acid catalysis process in their thiolysis by 2‐mercaptoethylamine. On the other hand, the rate‐determining step in the reaction of cephalosporins, which possess an appropriate leaving group at position 3', is the formation of the tetrahedral intermediate, so the desolvation energy of the nucleophile is a major contributor to the overall energy of the process. This differential behavior between the two types of β‐lactam bicycles arises from the presence of the acetate group at 3' and the delocalization of π electrons over the N₅–C₄–C₃ system in cephalosporins; this favors the formation of a thiolate with the 5‐ethoxymethylene‐1,3‐thiazine group in the cleavage of the tetrahedral intermediate, which is stabilized by an intramolecular hydrogen bond between N₅ and the alcohol or amine group in β of the attacking thiol. The theoretical results are consistent with previous experimental data showing that, unlike penicillins, cephalosporins undergo no intramolecular acid catalysis in their thiolysis. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 434–443, 2005     

A charge transfer-type fluorescent molecular sensor that "lights up" in the visible upon hydrogen bond-assisted complexation of anions

A charge transfer-type fluorescent molecular sensor consisting of a bisamidopyridine receptor and two styryl base chromophores shows H(2)PO(4)(-) and acetate-enhanced fluorescence due to the conversion of weak intramolecular hydrogen bonds into strong ones in the host-guest ensemble.     

Brønsted basicities of diamines in the gas phase, acetonitrile, and tetrahydrofuran

A comprehensive basicity study of alpha,omega-alkanediamines and related bases has been carried out. Basicities in acetonitrile (AN, pK(a) values), tetrahydrofuran (THF, pK(alpha) values), and gas phase (GP, GB values), were measured for 16, 14, and 9 diamine bases and for several related monoamines. In addition the gas-phase basicities and equilibrium geometries were computed for 19 diamino bases and several related monoamines at the DFT B3LYP 6-311+G** level. The effects of the different factors (intrinsic basicity of the amino groups, formation of intramolecular hydrogen bonds, and molecular strain) determining the diamine basicities were estimated by using the method of isodesmic reactions. The results are discussed in terms of molecular structure and solvation effects. The GP basicity is determined by the molecular size and polarizability, the extent of alkylation, and the energy effect of intramolecular hydrogen bond formation in the protonated base. The basicity trends in the solvents differ very much from those in GP: 1) The solvents severely compress the basicity range of the bases studied (3.5 times for the 1,3-propanediamine family in AN, and 7 times in THF), and 2) while stepwise alkylation of the basicity center leads to a steady basicity increase in the gas phase, the picture is complex in the solvents. Significant differences are also evident between THF and AN. The high hydrogen bond acceptor strength of THF leads to this solvent favoring the bases with "naked" protonation centers. In particular, the basicity order of N-methylated 1,3-propanediamines is practically inverse to that in the gas phase. The picture in AN is intermediate between that of GP and THF.     

Fluoride-selective colorimetric sensor based on thiourea binding site and anthraquinone reporter

A structurally simple colorimetric sensor, N-4-nitrobenzene-N'-1'-anthraquinone-thiourea (1), for anions was synthesized and characterized by (1)H NMR, ESI mass and IR methods. In acetonitrile, the addition of F(-) changed 1 solution from colorless to yellow. In the presence of other anions such as CH(3)CO(2)(-), H(2)PO(4)(-), HSO(4)(-) and Cl(-), however, the absorption spectrum of 1 was slightly red shifted with no obvious color changes observed. The association constants of anionic complexes followed the order of F(-)>CH(3)CO(2)(-)>H(2)PO(4)(-)>HSO(4)(-)>Cl(-)>Br(-), which was different from the order of anion basicity. AM1 calculation results indicated that the most stable configuration of 1 existed in the Z-E-conformation with a six-membered ring via intramolecular hydrogen bond. This made thiourea moiety of 1 in an unfavorable conformation to bond with oxygen-anionic substrates such as CH(3)CO(2)(-) and H(2)PO(4)(-), thus leading to a high selectivity and sensitivity for the detection of F(-).     

1,8-bis(dimethylethyleneguanidino)naphthalene: tailoring the basicity of bisguanidine "proton sponges" by experiment and theory

1,8-bis(dimethylethyleneguanidino)naphthalene (DMEGN), the second example of a peralkyl guanidine "proton sponge" based on the 1,8-naphthalene backbone, was prepared and fully characterized. The crystal structure analysis of monoprotonated DMEGN reveals an unsymmetrical intramolecular hydrogen bridge. A decrease in the basicity with respect to the noncyclic parent 1,8-bis(tetramethylguanidino)naphthalene was found. Nevertheless, a new proton sponge provides a new crossbar in the ladder of highly basic neutral organic compounds. A detailed theoretical study of DMEGN and related cyclic guanidines explains this surprising experimental result. Homodesmotic reactions reveal that the intramolecular hydrogen bond contributes effectively 10 kcal/mol to proton affinity of DMEGN.     

How Strong is Hydrogen Bonding to Amide Nitrogen?

The protonation of the carboxamide nitrogen atom is an essential part of in vivo and in vitro processes (cis-trans isomerization, amides hydrolysis etc). This phenomenon is well studied in geometrically strongly distorted amides, although there is little data concerning the protonation of undistorted amides. In the latter case, the participation of amide nitrogen in hydrogen bonding (which can be regarded as the incipient state of a proton transfer process) is less well-studied. Thus, it would be a worthy goal to investigate the enthalpy of this interaction. We prepared and investigated a set of peri-substituted naphthalenes containing the protonated dimethylamino group next to the amide nitrogen atom (“amide proton sponges”), which could serve as models for the study of an intramolecular hydrogen bond with the amide nitrogen atom. X-Ray analysis, NMR spectra, basicity values as well as quantum chemical calculations revealed the existence of a hydrogen bond with the amide nitrogen, that should be attributed to the borderline between moderate and weak intramolecular hydrogen bonds (2–7 kcal ⋅ mol⁻¹).     

Hydrogen-bonding cooperativity: using an intramolecular hydrogen bond to design a carbohydrate derivative with a cooperative hydrogen-bond donor centre

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.     

Isolation and characterization of a neutral imino-semiquinone radical

The neutral imino-semiquinone, 4,6-di-tert-butyl-2-tert-butylimino-semiquinone (isqH.), can be prepared by a conproportionation of the parent aminophenol and iminoquinone compounds. The neutral radical species has been characterized in the solid state by X-ray diffraction and in solution by EPR and UV-vis absorption spectroscopy. The stability of the open-shell radical is derived from the basicity of the tert-butylimino group and the intramolecular hydrogen bond.     

Light-Modulated Self-Blockage of a Urea Binding Site in a Stiff-Stilbene Based Anion Receptor

Anion binding to a receptor based on stiff-stilbene, which is equipped with a urea hydrogen bond donating group and a phosphate or phosphinate hydrogen bond accepting group, can be controlled by light. In one photoaddressable state (E isomer) the urea binding site is available for binding, while in the other (Z isomer) it is blocked because of an intramolecular interaction with its hydrogen bond accepting motif. This intramolecular interaction is supported by DFT calculations and ¹H NMR titrations reveal a significantly lower anion binding strength for the state in which anion binding is blocked. Furthermore, the molecular switching process has been studied in detail by UV/Vis and NMR spectroscopy. The presented approach opens up new opportunities toward the development of photoresponsive anion receptors.     

Activating water: important effects of non-leaving groups on the hydrolysis of phosphate triesters

The high rate of spontaneous hydrolysis of tris-2-pyridyl phosphate (TPP) is explained by the activating effects of the non-leaving ("spectator") groups on P-OAr cleavage, and not by intramolecular catalysis. Previous work on phosphate-transfer reactions has concentrated on the contributions to reactivity of the nucleophile and the leaving group, but our results make clear that the effects of the non-leaving groups on phosphorus can be equally significant. Rate measurements for three series of phosphate triesters showed that sensitivities to the non-leaving groups are substantial for spontaneous hydrolysis reactions, although significantly smaller for reactions with good nucleophiles. There are clear differences between triaryl and dialkyl aryl triesters in sensitivities to leaving and non-leaving groups with the more reactive triaryl systems showing lower values for both β(LG) and β(NLG). Intramolecular catalysis of the hydrolysis of TPP by the neighbouring pyridine nitrogens is insignificant, primarily because of their low basicity.     

Conformational switching between carboxylic acid and carboxylate anion states by NH-O hydrogen bonding

Biologically important Ca-proteins and Ca-biominerals as metal-polymer complexes are often regulated by the complexation and demetalation with the biopolymers. Metal-oxygen bond is supported by NH···O hydrogen bonds between coordinating oxyanion and neighboring amide NH and by the successive hydrogen bonding networks. Carboxylate anion under hydrophobic conditions has a high basicity that leads to a covalent Ca-O bond character that is significantly affected by the NH···O hydrogen bond. The hydrogen bonds in Asp-containing tripeptide fragments in Ca-proteins presumably control coordination/dissociation of metal-oxygen bonds. Our systematic studies of carboxylate, sulfonate and phosphate Ca(II) complexes demonstrate a relationship between the basicity of oxyanion in carboxylate and hydrogen bonds as cooperating with the oligopeptide conformation in Asp-containing Ca(II) complexes. Hydrogen bonds between carboxylate oxyanion and amide NH, controlled by a conformational switching of oligopeptide fragments, seem to be one of essential factors for the regulatory formation of Ca-proteins and nano-architectures in connection with the interface structure of inorganic and organic phases in biominerals.     

Synthesis and structure of 5,7-Di(<Emphasis Type="Italic">tert</Emphasis>-butyl)-2-(8-methanesulfonyloxyquinolin-2-yl)-1,3-tropolone

5,7-Di(tert-butyl)-2-(8-methanesulfonyloxyquinolin-2-yl)-1,3-tropolone whose structure was established by X-ray diffraction analysis and confirmed by ¹H and ¹³C NMR, IR spectroscopy, and mass spectrometry, was obtained by the reaction of 2-methyl-8-methanesulfonyloxyquinoline with 3,5-di(tert-butyl)-1,2-benzoquinone. According to X-ray diffraction study, this sulfonyloxyquinolinotropolone exists in the NH tautomeric form with methanesulfonyloxy group in the exo position to the tropolone ring and the sixmembered chelate ring produced by the quinoline and tropolone moieties stabilized by strong intramolecular hydrogen bond. The strong intramolecular hydrogen bond between the phenolic oxygen atom and the six-membered chelate ring provides supplementary contribution to the stabilization of the NH tautomeric form.     

FT-IR and FT-Raman study of hydrogen bonding in p-alkylcalix[8]arenes

The FTIR and FT Raman spectra of p-alkylcalix[8]arenes (alkyl = tert-butyl, isononyl) were recorded. Analysis of IR spectra showed that the cyclic cooperative intramolecular hydrogen bond is realized in calix[8]arene. It was found that the strength of the cyclic cooperative intramolecular hydrogen bond in the series of alkyl derivatives of calix[8]arenes depends very little on the replacement of the p-tert-butyl groups by the more bulky isononyl group. From our data follows that the orientation of aromatic fragments in calixarene molecules depends on the type of alkyl substituent.An analysis of the changes in the IR spectra with heating and dissolution shows that the conformation of the “pleated-loop” is retained in p-tert-butylcalix[8]arene. It turned out that the intramolecular hydrogen bond is a “probe” of the conformation of calixarene molecules and IR spectroscopy is a unique method that allows one to follow the slightest nuances of changes in the H-bound system of these supermolecules.     

The shape of beta-alanine

The combination of Fourier transform microwave spectroscopy in a pulsed supersonic jet with laser ablation has made beta-alanine amenable to a structural study in the gas phase. Two new conformers of beta-alanine have been identified together with the two previously observed by McGlone and Godfrey [J. Am. Chem. Soc. 1995, 117, 1043]. The comparison between the experimental rotational and 14N nuclear quadrupole coupling constants and those calculated ab initio provide a definitive test for molecular structures and confirm unambiguously the identification of all conformers. For the two most abundant conformers, an intramolecular hydrogen bond between the amino group and carbonyl oxygen (N-H...O=C) is established, and the COOH adopts a cis-COOH configuration. The next conformer in order of abundance presents an O-H...N intramolecular hydrogen bond with a trans configuration for the COOH group. The high sensitivity of the experiment has allowed us to detect for the first time a conformer uniquely stabilized by an n-pi* hyperconjugative interaction between the nucleophile N: of the amino group and the pi* orbital at the carbonyl group. Partial conformational relaxation has been observed in the supersonic expansion.     

Tailoring the key in a molecular lock-and-key model system: the propylene oxide...2-fluoroethanol complex

The conformational isomerism of the propylene oxide (PO)...2-fluoroethanol (FE) complex has been investigated using molecular beam Fourier-transform microwave spectroscopy complemented with high level ab initio calculations. Rotational transitions of three different binary conformers have been observed experimentally. On the basis of the agreement of the experimental and calculated rotational constants, they could be identified as the three most stable structures, anti G-g+, anti G+g-, and syn G+g-. All the observed structures exhibit a primary O-H...O hydrogen bond, an intramolecular O-H...F hydrogen bond and two secondary intermolecular C-H...F contacts. The two anti conformers, with FE and the PO methyl group on the opposite sides of the oxirane ring, show higher abundances than the syn conformer. In all three observed conformers, FE remains approximately in its favorable compact gauche conformation. The monofluorination of the molecular lock-and-key model system PO...ethanol increases not only the number of possible binary conformers, but also the discrimination energy among them. The superior discrimination ability of FE as compared to ethanol classifies it as a tailored key to the PO lock.