Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors

Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute ?9.8 kcal/mol to the free energy of binding, with a 10⁸-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is ?11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO^?₂ group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.     

Die thermische Umlagerung von 2-(Buta-1′,3′-dienyl)-phenolen in 2-Alkyl-2H-chromene; Beispiele für aromatische [1,7a]- und [1,5s]sigmatropische Wasserstoffverschiebungen

2-(1′-cis,3′-cis-)- and 2-(1′-cis,3′-trans-Penta-1′,3′-dienyl)-phenol (cis, cis- 4 and cis, trans- 4 , cf. scheme 1) rearrange thermally at 85–110° via [1,7 a] hydrogen shifts to yield the o-quinomethide 2 (R ? CH₃) which rapidly cyclises to give 2-ethyl-2H-chromene ( 7 ). The trans formation of cis, cis- and cis, trans- 4 into 7 is accompanied by a thermal cis, trans isomerisation of the 3′ double bond in 4. The isomerisation indicates that [1,7 a] hydrogen shifts in 2 compete with the electrocyclic ring closure of 2 . The isomeric phenols, trans, trans- and trans, cis- 4 , are stable at 85–110° but at 190° rearrange also to form 7 . This rearrangement is induced by a thermal cis, trans isomerisation of the 1′ double bond which occurs via [1, 5s] hydrogen shifts. Deuterium labelling experiments show that the chromene 7 is in equilibrium with the o-quinomethide 2 (R ? CH₃), at 210°. Thus, when 2-benzyl-2H-chromene ( 9 ) or 2-(1′-trans,3′-trans,-4′-phenyl-buta1′,3′-dienyl)-phenol (trans, trans- 6 ) is heated in diglyme solution at >200°, an equilibrium mixture of both compounds (～ 55% 9 and 45% 6 ) is obtained.     

A new ℋ -space formalism

The equations governing geometrical objects in ? space are written in terms of operators adapted to families of left shear-freeσ ⁰= 0) cross sections of complexified null infinity (C I ⁺). The concept of ?-conformai weight (HCW) is introduced, and a derivative operatorI _a ^′ , which is closely connected with the covariant derivative but which (unlike the covariant derivative) maps objects having well-defined HCW to other such objects, is defined. A function ?, derived from the Gaussian curvature of left shear-free slicings ofC I ⁺ and having a well-defined HCW, is shown to contain all the curvature information for ? space.     

A tensiometric study of diamond (111) and (110) faces

Tensiometric contact angle measurements of diamond surfaces in both the air:water and octane:water systems reveal moderate hydrophobicity, as might be expected of a surface with a minority of oxygen-containing groups. High-temperature reaction with oxygen or hydrogen leads to large changes in the contact angles. Spectroscopic methods show a “one-third” coverage by oxygen. The response to pH and adsorption of ferric ion suggests that the oxygen is present as an hydroxyl group. Steric resistance to higher oxide coverage, because of the small lattice constant of the crystal, may be an explanation for the natural hydrophobicity of the diamond surface.     

The formation of polymerizable tubules

We have been investigating the crystallization behavior of the phospholipid amphiphile, 1,2 bis (10, 12-tricosadiynol)-sn-glycero-3-phosphocholine, DC_8,9PC, which forms both vesicles and hollow tubules as well as Langmuir Blodgett monolayers and multilayers. This material has polymerizable diacetylene groups in equivalent positions on the two hydrocarbon tails. The direct crystallization from solution of this amphiphile has been studied using different solvent mixtures and temperatures. The Langmuir Blodgett technique was also used to compress and orient the tubules.     

Selectivity in microemulsion electrokinetic chromatography

Microemulsion electrokinetic chromatography (MEEKC) is a most promising separation technique providing good selectivity and high separation efficiency of anionic, cationic as well as neutral solutes. In MEEKC lipophilic organic solvents dispersed as tiny droplets in an aqueous buffer by the use of surfactants provide a pseudo-stationary phase to which the solutes may have an affinity either to the surface or they may even partition into the droplets. When the droplets are charged, typically negatively, they will migrate opposite to the electroosmotic flow and hence separation of neutral solutes may take place. In the present paper focus has been set on how to change selectivity in MEEKC. Changes in the nature of surfactant as well as in pH have been shown to be powerful tools in changing the selectivity. The type of lipophilic organic phase is of less importance for the separation of fairly lipophilic solutes. Also changes in the temperature surrounding the capillary may alter the selectivity.     

The determination of trace amounts of tin by flow-injection hydride generation atomic-absorption spectrometry with on-line ion-exchange separation and preconcentration

A hydride generation atomic-absorption spectrometric (AAS) method with flow-injection (FI), aimed at developing a practical routine assay for the determination of tin in food digests, is described. In order to modify the sample matrix and to achieve optimized and reproducible conditions for the hydride generation reaction, the analyte is initially converted into its chlorostannate-complex thereby allowing it to be separated and preconcentrated on-line on an incorporated micro-column packed with a strongly basic anion exchanger and subsequently to be eluted by diluted nitric acid under strictly controlled conditions. Optimum acidic conditions for the FI hydride generation AAS system was found to be 0.01-0.05M nitric acid. At a consumption of 2.7-ml sample volume, aspirated by time-based injection, the procedure resulted in an enrichment factor of 3.5 and yielded a detection limit of 0.08 microg/l. (3sigma) at a sampling frequency of 72/hr. The precision was 2.5% rsd at the 10 microg/l. level. Potential interferents, such as Ni(II), Co(II), Zn(II) and Fe(III) could, at a Sn level of 10 microg/l., be tolerated at an excess of 1000 times without impairing the assay, while a 100-1000-fold excess of Cu(II) decreased the signal by 10-15%. Recoveries in the range 94-102% were obtained for canned food sample digests spiked with 10 microg/l. Sn.     

Design of pure heterodinuclear lanthanoid cryptate complexes

Heterolanthanide complexes are difficult to synthesize owing to the similar chemistry of the lanthanide ions. Consequently, very few purely heterolanthanide complexes have been synthesized. This is despite the fact that such complexes hold interesting optical and magnetic properties. To fine-tune these properties, it is important that one can choose complexes with any given combination of lanthanides. Herein we report a synthetic procedure which yields pure heterodinuclear lanthanide cryptates LnLn*LX₃ (X = NO₃⁻ or OTf⁻) based on the cryptand H₃L = N[(CH₂)₂N CH–R–CH N–(CH₂)₂]₃N (R = m-C₆H₂OH-2-Me-5). In the synthesis the choice of counter ion and solvent proves crucial in controlling the Ln–Ln* composition. Choosing the optimal solvent and counter ion afford pure heterodinuclear complexes with any given combination of Gd(iii)–Lu(iii) including Y(iii). To demonstrate the versatility of the synthesis all dinuclear combinations of Y(iii), Gd(iii), Yb(iii) and Lu(iii) were synthesized resulting in 10 novel complexes of the form LnLn*L(OTf)₃ with LnLn* = YbGd 1, YbY 2, YbLu 3, YbYb 4, LuGd 5, LuY 6, LuLu 7, YGd 8, YY 9 and GdGd 10. Through the use of ¹H, ¹³C NMR and mass spectrometry the heterodinuclear nature of YbGd, YbY, YbLu, LuGd, LuY and YGd was confirmed. Crystal structures of LnLn*L(NO₃)₃ reveal short Ln–Ln distances of ∼3.5 Å. Using SQUID magnetometry the exchange coupling between the lanthanide ions was found to be anti-ferromagnetic for GdGd and YbYb while ferromagnetic for YbGd.

We present a synthetic strategy to prepare the first heterodinuclear lanthanide(iii) cryptate complexes. The cryptate design ensures that the complexes are stable in solution for days. The exchange coupling in YbYb, GdGd and YbGd is investigated.     

Formation of Heptaleno[1,2-c]furans and Heptaleno[1,2-c]furanones

The dehydrogenation reaction of the heptalene-4,5-dimethanols 4a and 4d , which do not undergo the double-bond-shift (DBS) process at ambient temperature, with basic MnO₂ in CH₂Cl₂ at room temperature, leads to the formation of the corresponding heptaleno[1,2-c]furans 6a and 6d , respectively, as well as to the corresponding heptaleno[1,2-c]furan-3-ones 7a and 7d , respectively (cf. Scheme 2 and 8). The formation of both product types necessarily involves a DBS process (cf. Scheme 7). The dehydrogenation reaction of the DBS isomer of 4a , i.e., 5a , with MnO₂ in CH₂Cl₂ at room temperature results, in addition to 6a and 7a , in the formation of the heptaleno[1,2-c]-furan-1-one 8a and, in small amounts, of the heptalene-4,5-dicarbaldehyde 9a (cf. Scheme 3). The benzo[a]heptalene-6,7-dimethanol 4c with a fixed position of the C?C bonds of the heptalene skeleton, on dehydrogenation with MnO₂ in CH₂Cl₂, gives only the corresponding furanone 11b (Scheme 4). By [²H₂]-labelling of the methanol function at C(7), it could be shown that the furanone formation takes place at the stage of the corresponding lactol [3-²H₂]- 15b (cf. Scheme 6). Heptalene-1,2-dimethanols 4c and 4e , which are, at room temperature, in thermal equilibrium with their corresponding DBS forms 5c and 5e , respectively, are dehydrogenated by MnO₂ in CH₂Cl₂ to give the corresponding heptaleno[1,2-c]furans 6c and 6e as well as the heptaleno[1,2-c]furan-3-ones 7c and 7e and, again, in small amounts, the heptaleno[1,2-c]furan-1-ones 8c and 8e , respectively (cf. Scheme 8). Therefore, it seems that the heptalene-1,2-dimethanols are responsible for the formation of the furan-1-ones (cf. Scheme 7). The methylenation of the furan-3-ones 7a and 7e with Tebbe's reagent leads to the formation of the 3-methyl-substituted heptaleno[1,2-c]furans 23a and 23e , respectively (cf. Scheme 9). The heptaleno[1,2-c]furans 6a, 6d , and 23a can be resolved into their antipodes on a Chiralcel OD column. The (P)-configuration is assigned to the heptaleno[1,2-c]furans showing a negative Cotton effect at ca. 320 nm in the CD spectrum in hexane (cf. Figs. 3–5 as well as Table 7). The (P)-configuration of (–)- 6a is correlated with the established (P)-configuration of the dimethanol (–)- 5a via dehydrogenation with MnO₂. The degree of twisting of the heptalene skeleton of 6 and 23 is determined by the Me-substitution pattern (cf. Table 9). The larger the heptalene gauche torsion angles are, the more hypsochromically shifted is the heptalene absorption band above 300 nm (cf. Table 7 and 8, as well as Figs. 6–9).     

Thermal Reaction of Azulene and Some of Its Symmetrically Substituted Methyl Derivatives with Dimethyl Acetylenedicarboxylate

It is shown that azulene ( 1 ) and dimethyl acetylenedicarboxylate (ADM) in a fourfold molar excess react at 200° in decalin to yield, beside the known heptalene- ( 5 ) and azulene-1,2-dicarboxylates ( 6 ), in an amount of 1.6% tetramethyl (1RS,2RS,5SR,8RS)-tetracyclo[6.2.2.2^2,50^1,5]tetradeca-3,6,9,11,13-pentaene-3,4,9,10-tetracarboxylate(‘anti’-7) as a result of a SHOMO (azulene)/LUMO(ADM)-controlled addition of ADM to the seven-membered ring of 1 followed by a Diels-Alder reaction of the so formed tricyclic intermediate 16 (cf. Scheme 3) with a second molecule of ADM. The structure of ‘anti’-7 was confirmed by an X-ray diffraction analysis. Similarly, the thermal reaction of 5,7-dimehtylazulene ( 3 ) with excess ADM in decalin at 120° led to the formation of ca. 1% of ‘anti’- 12 , the 7,12-dimethyl derivative of‘anti’-7, beside of the corresponding heptalene- 10 and azulene-1,2-dicaboxylated (cf Scheme 2). The introduction of Me groups at C(1)and C(3)of azulene ( 1 ) and its 5,7-dimethyl derivative 3 strongly enhance the thermal formation of the corresponding tetracyclic compound. Thus, 1,3-dimethylazulene ( 2 ) in the presence of a sevenfold molar excess of ADM at 200° yielded 20% of ‘anti’- 9 beside an equal amount of dimethyl 3-mehtylazulene-1,2-dicarboxylate ( 8 ;cf. Scheme 1), and 1,3,5,7-tetramethylazulene ( 4 ) with a fourfold molar excess of ADM AT 200° gave a yield of 37% of‘anti’- 15 beside small amount of the corresponding heptalene- 13 and azulene-1,2-dicarboxylates 14 (cf.Scheme 2).