The agonistic binding site at the histamine H2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven α-helical transmembrane domain

Summary In the first part (pp. 461–478 in this issue) of this study regarding the histamine H₂ receptor agonistic binding site, the best possible interactions of histamine with an -helical oligopeptide, mimicking a part of the fifth transmembrane -helical domain (TM5) of the histamine H₂ receptor, were considered. It was established that histamine can only bind via two H-bonds with a pure -helical TM5, when the binding site consists of Tyr¹⁸²/Asp¹⁸⁶ and not of the Asp¹⁸⁶/Thr¹⁹⁰ couple. In this second part, two particular three-dimensional models of G-protein-coupled receptors previously reported in the literature are compared in relation to agonist binding at the histamine H₂ receptor. The differences between these two receptor models are discussed in relation to the general benefits and limitations of such receptor models. Also the pros and cons of simplifying receptor models to a relatively easy-to-deal-with oligopeptide for mimicking agonistic binding to an agonistic binding site are addressed. Within complete receptor models, the simultaneous interaction of histamine with both TM3 and TM5 can be analysed. The earlier suggested three-point interaction of histamine with the histamine H₂ receptor can be explored. Our results demonstrate that a three-point interaction cannot be established for the Asp⁹⁸/Asp¹⁸⁶/Thr¹⁹⁰ binding site in either of the investigated receptor models, whereas histamine can form three H-bonds in case the agonistic binding site is constituted by the Asp⁹⁸/Tyr¹⁸²/Asp¹⁸⁶ triplet. Furthermore this latter triplet is seen to be able to accommodate a series of substituted histamine analogues with known histamine H₂ agonistic activity as well.     

Effect of Ethylene Glycol on the Molecular Organization of H2O in Comparison with Methanol and Glycerol: A Calorimetric Study

Excess partial molar enthalpies of ethylene glycol, H ^E _EG, in binary ethylene glycol–H₂O, and those of 1-propanol, H ^E _IP, in ternary 1-propanol–ethylene glycol (or methanol)–H₂O were determined at 25°C. From these data, the solute–solute interaction functions, H ^E _EG–EG = N(H ^E _EG/n _EG) and H ^E _1P–1P = N(H ^E _1P/n _1P), were calculated by graphical differentiation without resorting to curve fitting. Using these, together with the partial molar volume data, the effect of ethylene glycol on the molecular organization of H₂O was investigated in comparison with methanol and glycerol. We found that there are three concentration regions, in each of which the mixing scheme is qualitatively different from the other regions. Mixing scheme III operative in the solute-rich region is such that the solute molecules are in a similar situation as in the pure state, most likely in clusters of its own kind. Mixing scheme II, in the intermediate region, consists of two kinds of clusters each rich in solute and in H₂O, respectively. Thus, the bond percolation nature of the hydrogen bond network of liquid H₂O is lost. Mixing scheme I is a progressive modification of liquid H₂O by the solute, but the basic characteristics of liquid H₂O are still retained. In particular, the bond percolation of the hydrogen bond network is still intact. Similar to glycerol, ethylene glycol participates in the hydrogen bond network of H₂O via-OH groups, and reduces the global average of the hydrogen bond probability and the fluctuations inherent in liquid H₂O. In contrast to glycerol, there is also a sign of a weak hydrophobic effect caused by ethylene glycol. However, how these hydrophobic and hydrophilic effects of ethylene glycol work together in modifying the molecular organization of H₂O in mixing scheme I is yet to be elucidated.     

Discovery of Potential,Dual-Active Histamine H3 Receptor Ligands with Combined Antioxidant Properties

In an attempt to find new dual acting histamine H₃ receptor (H₃R) ligands, we designed a series of compounds, structurally based on previously described in our group, a highly active and selective human histamine H₃ receptor (hH₃R) ligand KSK63. As a result, 15 obtained compounds show moderate hH₃R affinity, the best being the compound 17 (hH₃R K_i = 518 nM). Docking to the histamine H₃R homology model revealed two possible binding modes, with key interactions retained in both cases. In an attempt to find possible dual acting ligands, selected compounds were tested for antioxidant properties. Compound 16 (hH₃R K_i = 592 nM) showed the strongest antioxidant properties at the concentration of 10⁻⁴ mol/L. It significantly reduced the amount of free radicals presenting 50–60% of ascorbic acid activity in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, as well as showed antioxidative properties in the ferric reducing antioxidant power (FRAP) assay. Despite the yet unknown antioxidation mechanism and moderate hH₃R affinity, 16 (QD13) constitutes a starting point for the search of potential dual acting H₃R ligands-promising tools for the treatment of neurological disorders associated with increased neuronal oxidative stress.     

Tunable Diode Laser Absorption Studies of Hydrocarbons in RF Plasmas Containing Hexamethyldisiloxane

Tunable infrared diode laser absorption spectroscopy has been used to detect the methyl radical and three stable molecules, CH₄, C₂H₂ and C₂H₆, in radio frequency plasmas (f=13.56 MHz) containing hexamethyldisiloxane (HMDSO). The methyl radical concentration and the concentration of the stable hydrocarbons, produced in the plasma, have been measured in pure HMDSO discharges and with admixtures of Ar, while discharge power (P=20–200 W), total gas pressure (p=0.08–0.6 mbar), gas mixture and total gas flow rate (=1–10 sccm) were varied. The methyl radical concentration was found to be in the range of 10¹³ molecules cm^-3, while methane and ethane are the dominant hydrocarbons with concentrations of 10¹⁴–10¹⁵ mol cm^-3. Conversion rates to the measured stable hydrocarbons (RC(C_xH_y): 2×10¹²–2×10¹⁶ molecules J^-1 s^-1) could be estimated in dependence on power, flow, mixture and pressure. Under the used experimental conditions a maximum deposition rate of polymer layers of about 400 nm min^-1 has been found.     

Synthesis of 1-fluoroindan-1-carboxylic acid (FICA) and its properties as a chiral derivatizing agent

1-Fluoroindan-1-carboxylic acid (FICA) (1) was designed and synthesized as its methyl ester (FICA Me ester) (4) in order to develop an efficient chiral derivatizing agent (CDA) which excels α-methoxy-α-(trifluoromethyl)phenylacetic acid (MTPA) in capability. FICA Me ester (4) was prepared by fluorination of methyl 1-hydroxyindan-1-carboxylate (3) with (diethylamino)sulfur trifluoride (DAST) and derived to the esters of racemic secondary alcohols by ester exchange reaction. The resulting Δδ_F value was large in the case of 2-butyl ester of FICA (5a), whereas not detectable in the case of the corresponding MTPA ester (6a). The magnitude of the Δδ_H values was similar to that of MTPA esters. The diastereomers of (R)-(−)-8-phenylmenthyl ester of FICA (5i) was separated and their ¹H NMR analyses revealed that the concept of the modified Mosher's method was successfully applied to 5i.     

Effect of ionic interactions on the oxidation of Fe(II) with H2O2 in aqueous solutions

The oxidation of Fe(II) with H₂O₂ has been measured in NaCl and NaClO₄ solutions as a function of pH, temperature T (K) and ionic strength (M, mol-L^–1). The rate constants, k (M^–1-sec^–1), d[Fe(II)]/DT=-k[Fe(II)][₂O₂]at pH=6.5 have been fitted to equations of the formlog k = log k₀+ AI ^1/2+BI+CI ^1/2/T Where log k₀=15.53-3425/T in water; A=–2.3, –1.35; B=0.334, 0.180; and C=391, 235, respectively, for NaCl (=0.09) and NaClO₄ ( =0.08). Measurements made in NaCl solutions with added anions yield rates in the order B(OH) ₄ ^– >HCO ₃ ^– >ClO ₄ ^– >Cl^–>NO ₃ ^– >SO ₄ ^2– and are attributed to the relative strength of the interactions of Fe²⁺ or FeOH⁺ with these anions. The FeB(OH) ₄ ⁺ species is more reactive while the FeCO ₃ ⁰ , FeCl⁺, FeNO ₃ ⁺ and FeSO ₄ ⁰ species are less reactive than the FeOH⁺ ion pair. The general trend is similar to our earlier studies of the oxidation of Fe(II) with O₂ except for B(OH) ₄ ^– . The effect of pH on the logk was found to be a quadratic function of the concentration of H⁺ or OH^– from pH=4 to 8. These results have been attributed to the different rate constants for Fe²⁺ (k₀) and FeOH⁺ (k₁) which are related to the measured k by, k=k_0Fe + k_1FeOH, where _i is the molar fraction of species i. The rates increase due to the greater reactivity of FeOH⁺ compared to Fe²⁺. k₀ is independent of composition and ionic strength but k₁ is a function of ionic strength and composition due to the interactions of FeOH⁺ with various anions.     

Synthesis and crystal structure of four Pd(II) complexes containing nido or closo carborane diphosphine ligands

Three Pd(II) complexes [Pd₂(μ-Cl)₂{7,8-(PPh₂)₂-7,8-C₂B₉H₁₀}₂] · 0.25CH₂Cl₂ (1), [Pd{7,8-(PPh₂)₂-7,8-C₂B₉H₁₀}₂] · 4CHCl₃ (2) and [PdCl₂(1,2-(PPh₂)₂-1,2-C₂B₁₀H₁₀)] (3) have been synthesized by the reactions of 1,2-(PPh₂)₂-1,2-C₂B₁₀H₁₀ with PdCl₂ in acetonitrile, cyanophenyl and dichloromethane, respectively. A fourth complex, [PdI₂(1,2-(PPh₂)₂-1,2-C₂B₁₀H₁₀)] (4), was obtained by a ligand exchange reaction through the substitution of the Cl⁻ of complex 3 with I⁻. All four complexes have been characterized by elemental analysis, FT-IR, ¹H and ¹³C NMR spectroscopy and X-ray structure determination. Single crystal X-ray determination showed that the carborane cage, nido for 1, 2 and closo for 3, 4, was coordinated bidentately to the Pd atom through the two P atoms, and the geometry at the Pd atom was square-planar in all the complexes.     

A pseudopotential study of the hydrogen bond in H2O·H2S,H2S·H2S and H2O·H2Se systems

Intermolecular potential energy curves for the hydrogen bonded systems H₂O·H₂S, H₂O·H₂Se and H₂S·H₂S were calculated with nonempirical pseudopotentials using optimized-in-molecules basis sets augmented by polarization functions. The H₂O·H₂O interaction energy curve has been also considered as a test case. The present results for H₂O·H₂S and H₂S·H₂S indicate much weaker intermolecular interactions than those found in previous ab initio calculations. The H₂O·H₂Se interaction was found to be quite similar to H₂O·H₂S.This work was partly supported by the Polish Academy of Sciences within the Project PAN-09, 7.1.1.1On leave from Quantum Chemistry Laboratory, Dept. of Chemistry, University of Warsaw, Pasteura 1, 02-093. Warsaw, Poland     

Catalytic hydrogenation of CO and CN bonds via heterolysis of H2 mediated by metal-sulfur bonds of rhodium and iridium thiolate complexes

Coordinatively unsaturated rhodium and iridium complexes having a bulky thiolate, [Cp∗M(PMe₃)(SDmp)](BAr^F₄) (1a: M = Rh; 1b: M = Ir; Dmp = 2,6-(mesityl)₂C₆H₃, Ar^F = 3,5-(CF₃)₂C₆H₃), catalyzed the hydrogenation of benzaldehyde, N-benzylideneaniline, and cyclohexanone, under 1 atm of H₂ at low temperatures. In these catalytic reactions, the M-H/S-H complexes [Cp∗M(PMe₃)(H)(HSDmp)](BAr^F₄) (2a: M = Rh; 2b: M = Ir) generated via H₂ heterolysis by 1a or 1b were suggested to transfer both M-H hydride and S-H proton to substrates. The catalytic reactions were terminated by the dissociation of H-SDmp from the metal centers of 2a and 2b that occurs at ambient temperature under H₂ atmosphere.     

Aromatic stability energy studies on five-membered heterocyclic C4H4M (M = O, S, Se, Te, NH, PH, AsH and SbH): DFT calculations

Energetic, geometric and magnetic criteria were applied to examine the stability and/or aromatic character for the cyclic molecules C ₄ H ₄ M (M = O, S, Se, Te, NH, PH, AsH and SbH) at B3LYP/6-311++G^** and MP2/6-311++G^** levels of theory. The isodesmic reactions and nuclear independent chemical shifts (NICS) calculations were utilized to examine the molecules for energetic and magnetic criteria, respectively. The isodesmic reaction energies reveal that thiophene (C ₄ H ₄ S, ?23.269 kcal/mol) and pyrrole (C ₄ H ₄ NH, ?20.804 kcal/mol) have the greatest aromatic stabilization energies and tellurophene (C ₄ H ₄ Te, ?15.114 kcal/mol) and stibole (C ₄ H ₄ SbH, ?1.169 kcal/mol) have the lowest aromatic stabilization energies in their corresponding groups at MP2/6-311++G^**. The NICS calculations confirmed the results obtained through isodesmic reaction energies.     

Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin

A computational model of the transmembrane domain of the human 5-HT₄ receptor complexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp^3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser^5.43; (iii) the hydrogen bond between the ether oxygen and Asn^6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the electrons of Phe^6.51; and (v) the - aromatic-aromatic interaction between the indole ring and Phe^6.52.This computational model offers structural indications about the role of Asp^3.32, Ser^5.43, Phe^6.51, Phe^6.52, and Asn^6.55 in the experimental binding affinities. Asp^3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe^6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe^6.52Val mutant the indole ring of the ligand replaces the interaction with Phe^6.52 by a similarly intense interaction with Tyr^5.38, with no significant effect in the binding of GR113808. The mutation of Asn^6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn^6.55 to Cys^5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SHO and NHO hydrogen bonds.Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.     

Crystal structures of Co3(SeO3)3·H2O and Ni3(SeO3)3·H2O,two new isotypic compounds

Summary The crystal structures of the new, hydrothermally synthesized, isotypic compounds Co₃(SeO₃)₃·H₂O and Ni₃(SeO₃)₃·H₂O were determined by direct and Fourier methods and refined toR _w=0.023, 0.032 using single crystal X-ray data up to sin/=0.81 Å^–1 [space group P ,a=8.102 (2), 7.986 (3) Å;b=8.219 (2), 8.133 (3) Å;c=8.572 (2), 8.422 (3) Å, =69.15 (1), 69.50 (1)°; =62.88 (1), 62.50 (1)°; =67.23 (1), 67.64 (1)°;Z=2]. The structures are built up from [Me ₅(SeO₃)₆·2H₂O]^2– sheets containing three crystallographically different types of octahedrally coordinatedMe ²⁺ and trigonal pyramidal coordinated Se⁴⁺ atoms, respectively. These sheets are linked only by a fourth type ofMe ^2+[6] atom. All coordination polyhedra deviate significantly from their ideal shapes, bond lengths within the extremly distortedMe(4)O₆ polyhedra range from 1.983 (2) Å to 2.403 (2) Å in Co₃(SeO₃)₃·H₂O and from 1.987 (4) Å to 2.301 (3) Å in the Ni compound, O-Se-O bond angles were found between 92.8 (2)° and 104.9 (1)°. Hydrogen bond lengths are 2.802 (3)Å and 2.600 (4)Å in the Co compound, and 2.762 (6) Å and 2.561 (6) Å in Ni₃(SeO₃)₃·H₂O. The latter is one of the shortest known hydrogen bonds donated by a water molecule.

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Die Kristallstrukturen von Co₃(SeO₃)₃·H₂O und Ni₃(SeO₃)₃·H₂O, zwei neue isotype Verbindungen

Zusammenfassung Die Kristallstrukturen der neuen, hydrothermal synthetisierten, isotypen Verbindungen Co₃(SeO₃)₃·H₂O und Ni₃(SeO₃)₃·H₂O wurden mit direkten und Fourier-Methoden bestimmt und unter Verwendung von Einkristallröntgendaten bis sin/=0.81 Å^–1 aufR _w-Werte von 0.023, 0.032 verfeinert [Raumgruppe P ,a=8.102 (2), 7.986 (3) Å;b=8.219 (2), 8.133 (3) Å;c=8.572 (2), 8.422 (3) Å, =69.15 (1), 69.50 (1)°; =62.88 (1), 62.50 (1)°; =67.23 (1), 67.64 (1)°;Z=2]. Die Strukturen werden von [Me ₅(SeO₃)₆·2H₂O]^2– Schichten aufgebaut, die je drei kristallographisch unterschiedliche Arten von oktaedrisch koordiniertenMe ²⁺ und trigonal pyramidal koordinierten Se⁴⁺ Atomen enthalten. Diese Schichten sind nur durch eine vierte Art vonMe ^2+[6] Atomen verknüpft. Alle Koordinationspolyeder weichen deutlich von ihren Idealformen ab, Bindungslängen in den extrem verzerrtenMe(4)O₆ Polyedern variieren zwischen 1.983 (2) Å und 2.403 (2) Å in Co₃(SeO₃)₃·H₂O und zwischen 1.987 (4) Å und 2.301 (3) Å in der Ni-Verbindung, O-Se-O-Bindungswinkel liegen zwischen 92.8 (2)° und 104.9 (1)°. Wasserstoffbrückenlängen sind 2.802 (3) Å und 2.600 (4) Å in der Co-Verbindung, und 2.762 (6) Å und 2.561 (6) Å in Ni₃(SeO₃)₃·H₂O. Letztere ist eine der kürzesten bekannten Wasserstoffbrücken eines Wassermoleküls.

     

An aqueous thermodynamic model for Ca2+−SO 3 2− ion interactions and the solubility product of crystalline CaSO3·1/2H2O

The solubility of CaSO₃·1/2H₂O(c) was studied under alkaline conditions (pH>8.2), in deaerated and deoxygenated Na₂SO₃ solutions ranging in concentration from 0.0002 to 0.4M and in CaCl₂ solutions ranging in concentration from 0.0002 to 0.01M, for equilibration periods ranging from 1 to 7 days. Equilibrium was approached from both the over- and the under-saturation directions. In all cases, equilibrium was reached in <1 days. The aqueous Ca²⁺–SO ₃ ^2– ion interactions can be satisfactorily modeled using either ion-association or ion-interaction aqueous thermodynamic models. In the ion-association model, the log K°=2.62±0.07 for Ca²⁺+SO ₃ ^2– CaSO ₃ ⁰ . In the Pitzer ion-interaction model, the binary parameters (⁰) and (¹) for Ca²⁺–SO ₄ ^2– were used, and the value of (²) was determined from the experimental data. As expected given the strong association constant, the value of (⁰) was quite small (about –134). We feel a combination of the two models is most useful. The logarithm of the thermodynamic equilibrium constant (K°) of the CaSO₃·1/2H₂O(c) solubility reaction (CaSO₃·1/2H₂O(c)Ca²⁺+SO ₃ ²⁺ +0.5H₂O) was found to be –6.64±0.07.     

Valence-bond studies of AH2 molecules

Minimal Slater basis set calculations are reported for H₂S. The calculations used both natural and hybrid atomic orbitals. The calculations were performed at H-S-H bond angles of 90 °, 92.2 ° and 95 °. The results are compared with similar calculations on H₂O and with calculations using the molecular orbital approximation. The only definite trend found in going from H₂O to H₂S is that the importance of the SH⁺H^– structure decreases. Changes in the relative importance of covalent and ionic structures depend upon which measure of importance is used. Calculations using a set of orthogonal hybrid orbitals again find the hybrid orbitals exhibiting non-perfect following behaviour with the hybrids remaining at about the equilibrium bond angle. Localized molecular orbitals were found to move in the opposite direction to the change in the H-S-H bond angle.     

Topological complexity of potential surfaces and application to C2H2 molecule

Summary In this work, we search for the simplest complete surfaces of systems with three and four atoms, i.e. the minimal sets of critical points with their index, which are topologically consistent in the whole configuration space. Then we show the smallest change in the A₂B₂ system by requiring at least one stable acetylene configuration and one stable vinylidene configuration, like on the C₂H₂ surface. Finally, we give complete sets of minima, saddle points and maxima obtained for C₂H₂ with analytical potentials proposed in the literature and with a semi-empirical method at the CAS-CI level.     

H6P2W18O62-18H2O,a Green and Reusable Catalyst for the Three-Component,One-Pot Synthesis of 4,6-Diarylpyrimidin-2(1H)-ones Under Solvent-Free Conditions

Three-component, one-pot synthesis of 4,6-diarylpyrimidin-2(1H)-ones and 9-phenyl-8-oxa-10,12-diaza-tricyclo[7.3.1.0^2,7]trideca-2(7),3,5-trien-11-one by condensing acetophenone derivatives, aldehydes, and urea in the presence of trimethylsilyl chloride using a catalytic amount of H₆P₂W₁₈O₆₂-18H₂O under solvent-free conditions is reported.     

Infrared spectra (700–200 cm−1) and6Li/7Li and H2O/D2O isotope effects for four isotopically substituted lithium formate monohydrates

The infrared spectra, in the 700–200 cm^–1 region, have been reported for⁶LiHCO₂ · H₂O,⁶LiHCO₂ · D₂O,⁷LiHCO₂ · H₂O and⁷LiHCO₂ · D₂O and the observed fundamental bands have been discussed taking into account the⁶Li/⁷Li and H₂O/D₂O isotope wavenumber shifts on the fundamental vibrations.

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Infrarotspektren (700–200 cm^–1) und⁶Li/⁷Li- und H₂O/D₂O-Isotopeneffekte für vier isotopensubstituierte Lithiumformat-monohydrate

Zusammenfassung Die Infrarotspektren in der Region von 700–200 cm^–1 werden für⁶LiHCO₂ · H₂O,⁶LiHCO₂ · D₂O,⁷LiHCO₂ · H₂O und⁷LiHCO₂ · D₂O angegeben und die beobachteten Grundschwingungen zusammen mit den isotopischen Verschiebungen der Wellenzahlen diskutiert.