Computational analysis of ligand recognition mechanisms by prostaglandin E2 (subtype 2) and D2 receptors

The eight members of the prostanoid receptor family belong to the class A G protein-coupled receptors. We investigated the evolutionary relationship of the eight members by a molecular phylogenetic analysis and found that prostaglandin E₂ receptor subtype 2 (EP₂) and prostaglandin D₂ receptor (DP) were closely related. The structures of the ligands for the two receptors are similar to each other but are distinguished by the exchanged locations of the carbonyl oxygen and the hydroxy group in the cyclopentane ring. The ligand recognition mechanisms of the receptors were examined by an integrated approach using several computational methods, such as amino acid sequence comparison, homology modeling, docking simulation, and molecular dynamics simulation. The results revealed the similar location of the ligand between the two receptors. The common carboxy group of the ligands interacts with the Arg residue on the seventh transmembrane (TM) helix, which is invariant among the prostanoid receptors. EP₂ uses a Ser on TM1 to recognize the carbonyl oxygen in the cyclopentane ring of the ligand. The Ser is specifically conserved within EP₂. On the other hand, DP uses a Lys on TM2 to recognize the hydroxy group of the ?? chain of the ligand. The Lys is also specifically conserved within DP. The interaction network between the D(E)RY motif and TM6 was found in EP₂. However, DP lacked this network, due to the mutation in the D(E)RY motif. Based on these observations and the previously published mutational studies on the motif, the possibility of another activation mechanism that does not involve the interaction between the D(E)RY motif and TM6 will be discussed.     

(E)-[4,4,4-Trifluor-1-(trifluormethyl)-1,3-bis(trimethylsiloxy)-2-butenyl]diphenylphosphin als Ligand

The Ligand (E)-[4,4,4-Trifluoro-1-(trifluoromethyl)-1,3-bis(trimethylsiloxy)-2-butenyl]di-phenylphosphine The tertiary phosphine (E)-Ph₂PC(OSiMe₃)(CF₃)CH = C(OSiMe₃)CF₃ (L), 1 and the carbonyl Fe₂(CO)₉ react to give (OC)₄FeL, 2. Bis( 1,1,1,5,5,5-hexafluoropentane-2,4-dionato)palladium(II) and 1 furnish the diphenylphosphido group bridged palladium(II) complex 3 crystallizing from chloroform triclinic in the space group P1 with a = 12.600(3), b = 13.298(3), c = 13.975(3) Å, α = 93.27(2), β = 111.67(2), γ = 106.71(2)° The elementary cell contains Z = 2 formular units and two molecules CHCl₃ with two independent molecules 3 each showing an inversion centre. The planar [PdP], four membered ring system and the planar chelate units, exhibit a torsional angle of 6.75°     

Highly stereoselective synthesis of (2E,4E)-dienamides and (2E,4E)-dienoates via a double elimination reaction

Highly stereoselective synthesis of (2E,4E)-dienamides and (2E,4E)-dienoates was achieved through a double elimination reaction of β-acetoxy sulfones.     

One-Pot synthesis of (2E)- and (2E, 4E)- unsaturated carboxylic acid amides via organotellurium reagents

Di-n-butyl telluride, 2-bromoacetylisobutylamide (or 2-bromoacetylpiperidide) react directly with saturated or α,β-unsaturated aldehydes at room temperature in the presence of potassium carbonate(s) to afford (2E)-, or (2E, 4E)-unsaturated carboxylic acid amides, respectively, in excellent yields with high E stereoselectivity.     

Rate coefficients for the reaction of OH with (E)-2-pentenal, (E)-2-hexenal, and (E)-2-heptenal

Rate coefficients for the gas-phase reaction of the OH radical with (E)-2-pentenal (CH(3)CH(2)CH[double bond]CHCHO), (E)-2-hexenal (CH(3)(CH(2))(2)CH[double bond]CHCHO), and (E)-2-heptenal (CH(3)(CH(2))(3)CH[double bond]CHCHO), a series of unsaturated aldehydes, over the temperature range 244-374 K at pressures between 23 and 150 Torr (He, N(2)) are reported. Rate coefficients were measured under pseudo-first-order conditions in OH with OH radicals produced via pulsed laser photolysis of HNO(3) or H(2)O(2) at 248 nm and detected by pulsed laser-induced fluorescence. The rate coefficients were independent of pressure and the room temperature rate coefficients and Arrhenius expressions obtained are (cm(3) molecule(-1) s(-1) units): k(1)(297 K)=(4.3 +/- 0.6)x 10(-11), k(1)(T)=(7.9 +/- 1.2)x 10(-12) exp[(510 +/- 20)/T]; k(2)(297 K)=(4.4 +/- 0.5)x 10(-11), k(2)(T)=(7.5 +/- 1.1)x 10(-12) exp[(520 +/- 30)/T]; and k(3)(297 K)=(4.4 +/- 0.7)x 10(-11), k(3)(T)=(9.7 +/- 1.5)x 10(-12) exp[(450 +/- 20)/T] for (E)-2-pentenal, (E)-2-hexenal and (E)-2-heptenal, respectively. The quoted uncertainties are 2sigma(95% confidence level) and include estimated systematic errors. Rate coefficients are compared with previously published room temperature values and the discrepancies are discussed. The atmospheric degradation of unsaturated aldehydes is also discussed.     

E2(CN)2 (E = S, Se) and related compounds

A synthetic, spectroscopic, and theoretical study of Ex(CN)2 (E = S, Se; x = 1-3) is described. The X-ray structures of Se2(CN)2 and Se3(CN)2 have been determined. Se2(CN)2 crystallizes in a chiral space group with the CN groups approximately gauche.     

Synthesis of (E)-2-chlorovinyltellurium trichloride and (E,E)-bis(2-chlorovinyl) ditelluride

The reaction of tellurium tetrachloride with acetylene in CCl₄ at atmospheric pressure and ambient temperature affords earlier unknown (E)-2-chlorovinyltellurium trichloride in 30% yield, whose reduction with sodium bisulfite gives (E,E)-bis(2-chlorovinyl) ditelluride in 64% yield.     

Hydration changes of poly(2-(2-methoxyethoxy)ethyl methacrylate) during thermosensitive phase separation in water

Hydration changes of poly(2-(2-methoxyethoxy)ethyl methacrylate) (PMoEoEMa) during thermosensitive phase separation in water have been investigated by infrared spectroscopy. The C=O stretching band can be separated into three components assigned to non-hydrated carbonyl groups and singly and doubly hydrogen-bonded carbonyl groups (1728, 1709, and 1685 cm-1, respectively). Relatively large parts of the carbonyl groups (50% in 30 wt % solution) do not form hydrogen bonds even below the transition temperature (Tp) probably because they possess crowded positions near the backbone. The fraction of hydrogen-bonding carbonyl groups decreased during phase separation by approximately 0.2. Among five nu(C-H) bands, the highest- and the lowest-frequency bands (nu(C-H)A and nu(C-H)E) exhibited relatively large red shifts of 8 and 11 cm(-1), respectively. DFT calculations indicate that the formation of a H-bond between the ether oxygen and water leads to blue shifts of nu(C-H) of adjacent alkyl groups and has a larger effect than a direct H-bond to the alkyl groups, namely, C-H...O H-bonds. The fraction of hydrogen-bonding methoxy oxygens estimated from the position of the nu(C-H)A is 1 at Tp. This result indicates that the methoxy oxygens and the carbonyl are more favorably hydrated than the other at Tp, respectively.     

First row transition metal complexes of (E)-2-(2-(2-hydroxybenzylidene) hydrazinyl)-2-oxo-N-phenylacetamide complexes

Manganese(II), iron(II), cobalt(II), nickel(II), copper(II), and chromium(III) complexes of (E)-2-(2-(2-hydroxybenzylidene)hydrazinyl)-2-oxo-N-phenylacetamide were synthesized and characterized by elemental and thermal (TG and DTA) analyses, IR, UV-vis and (1)H NMR spectra as well as magnetic moment. Mononuclear complexes are obtained with 1:1 molar ratio except [Mn(HOS)(2)(H(2)O)(2)] and [Co(OS)(2)](H(2)O)(2) complexes which are obtained with 1:2 molar ratios. The IR spectra of ligand and metal complexes reveal various modes of chelation. The ligand behaves as a monobasic bidentate one and coordination occurs via the enolic oxygen atom and azomethine nitrogen atom. The ligand behaves also as a monobasic tridentate one and coordination occurs through the carbonyl oxygen atom, azomethine nitrogen atom and the hydroxyl oxygen. Moreover, the ligand behaves as a dibasic tridentate and coordination occurs via the enolic oxygen, azomethine nitrogen and the hydroxyl oxygen atoms. The electronic spectra and magnetic moment measurements reveal that all complexes possess octahedral geometry except the copper complexes possesses a square planar geometry. From the modeling studies, the bond length, bond angle, HOMO, LUMO and dipole moment had been calculated to confirm the geometry of the ligands and their investigated complexes. The thermal studies showed the type of water molecules involved in metal complexes as well as the thermal decomposition of some metal complexes. The protonation constant of the ligand and the stability constant of metal complexes were determined pH-metrically in 50% (v/v) dioxane-water mixture at 298 K and found to be consistent with Irving-Williams order. Moreover, the minimal inhibitory concentration (MIC) of these compounds against Staphylococcus aureus, Escherechia coli and Candida albicans were determined.     

Reactive E=C(p‐p)π‐Systems. 56 [1] Attempted Preparation of PhE=C(CF3)2 by Reactions of Hexafluoroacetone with PhE(SiMe3)2 (E = As,P)

The chance to prepare sterically and inductively stabilized arsa‐ and phosphaalkenes of the type PhE=C(CF₃)₂ (E = As, P) by reacting phenyl‐bis(trimethylsilyl)‐arsane ( 1 ) and ‐phosphane ( 5 ), respectively, with hexafluoroacetone (HFA) was investigated. The insertion of the carbonyl function in one of the Si–E bonds was found to occur at temperatures between ?78 and 20 °C. The elimination of hexamethyldisiloxane, which in case of acylamides and ketones spontaneously follows the insertion and in case of RE(SiMe₃)–CR′₂(OSiMe₃) at least can be initiated by solid sodium hydroxide as catalyst, turned out to be impossible for the primary products PhE(SiMe₃)–C(CF₃)₂‐OSiMe₃ [E = As ( 2 ), P ( 6 )]. 2 and 6 were characterized by analytical (C, H) and spectroscopic methods (IR, NMR, MS).     

Preparation and x-ray structures of alkali-metal derivatives of the ambidentate anions [tBuN(E)P(mu-NtBu)2P(E)NtBu]2- (E = S, Se) and [tBuN(Se)P(mu-NtBu)2PN(H)tBu)]-

The ambidentate dianions [(t)BuN(E)P(mu-N(t)Bu)(2)P(E)N(t)Bu](2)(-) (5a, E = S; 5b, E = Se) are obtained as their disodium and dipotassium salts by the reaction of cis-[(t)Bu(H)N(E)P(mu-N(t)Bu)(2)P(E)N(H)(t)Bu] (6a, E = S; 6b, E = Se), with 2 equiv of MN(SiMe(3))(2) (M = Na, K) in THF at 23 degrees C. The corresponding dilithium derivative is prepared by reacting 6a with 2 equiv of (t)BuLi in THF at reflux. The X-ray structures of five complexes of the type [(THF)(x)()M](2)[(t)BuN(E)P(mu-N(t)Bu)(2)P(E)N(t)Bu] (9, M = Li, E = S, x = 2; 11a/11b, M = Na, E = S/Se, x = 2; 12a, M = K, E = S, x = 1; 12b, M = K, E = Se, x = 1.5) have been determined. In the dilithiated derivative 9 the dianion 5a adopts a bis (N,S)-chelated bonding mode involving four-membered LiNPS rings whereas 11a,b and 12a,b display a preference for the formation of six-membered MNPNPN and MEPNPE rings, i.e., (N,N' and E,E')-chelation. The bis-solvated disodium complexes 11a,b and the dilithium complex 9 are monomeric, but the dipotassium complexes 12a,b form dimers with a central K(2)E(2) ring and associate further through weak K.E contacts to give an infinite polymeric network of 20-membered K(6)E(6)P(4)N(4) rings. The monoanions [(t)Bu(H)N(E)P(mu-N(t)Bu)(2)P(E)N(t)Bu)](-) (E = S, Se) were obtained as their lithium derivatives 8a and 8b by the reaction of 1 equiv of (n)BuLi with 6a and 6b, respectively. An X-ray structure of the TMEDA-solvated complex 8a and the (31)P NMR spectrum of 8b indicate a N,E coordination mode. The reaction of 6b with excess (t)BuLi in THF at reflux results in partial deselenation to give the monolithiated P(III)/P(V) complex [(THF)(2)Li[(t)BuN(Se)P(mu-N(t)Bu)(2)PN(H)(t)Bu]] 10, which adopts a (N,Se) bonding mode.     

Convenient one-pot synthesis of functionalized （E）-2-arylvinyl bromides from （E）-4-（2-bromovinyl）phenyl acetate

A convenient one-pot synthesis of functionalized (E)-2-arylvinyl bromides was achieved by microwave-induced deacetylation and subsequent acylation using dicyclohexyl carbodiimide (DCC) and dimethylamino-pyridine (DMAP) at room temperature from (E)-4-(2-bromovinyl)phenyl acetate.     

Bonding, structure, and energetics of gaseous E8(2+) and of solid E8(AsF6)2 (E = S, Se)

The attempt to prepare hitherto unknown homopolyatomic cations of sulfur by the reaction of elemental sulfur with blue S8(AsF6)2 in liquid SO2/SO2ClF, led to red (in transmitted light) crystals identified crystallographically as S8(AsF6)2. The X-ray structure of this salt was redetermined with improved resolution and corrected for librational motion: monoclinic, space group P2(1)/c (No. 14), Z = 8, a = 14.986(2) A, b = 13.396(2) A, c = 16.351(2) A, beta = 108.12(1) degrees. The gas phase structures of E8(2+) and neutral E8 (E = S, Se) were examined by ab initio methods (B3PW91, MPW1PW91) leading to delta fH theta[S8(2+), g] = 2151 kJ/mol and delta fH theta[Se8(2+), g] = 2071 kJ/mol. The observed solid state structures of S8(2+) and Se8(2+) with the unusually long transannular bonds of 2.8-2.9 A were reproduced computationally for the first time, and the E8(2+) dications were shown to be unstable toward all stoichiometrically possible dissociation products En+ and/or E4(2+) [n = 2-7, exothermic by 21-207 kJ/mol (E = S), 6-151 kJ/mol (E = Se)]. Lattice potential energies of the hexafluoroarsenate salts of the latter cations were estimated showing that S8(AsF6)2 [Se8(AsF6)2] is lattice stabilized in the solid state relative to the corresponding AsF6- salts of the stoichiometrically possible dissociation products by at least 116 [204] kJ/mol. The fluoride ion affinity of AsF5(g) was calculated to be 430.5 +/- 5.5 kJ/mol [average B3PW91 and MPW1PW91 with the 6-311 + G(3df) basis set]. The experimental and calculated FT-Raman spectra of E8(AsF6)2 are in good agreement and show the presence of a cross ring vibration with an experimental (calculated, scaled) stretching frequency of 282 (292) cm-1 for S8(2+) and 130 (133) cm-1 for Se8(2+). An atoms in molecules analysis (AIM) of E8(2+) (E = S, Se) gave eight bond critical points between ring atoms and a ninth transannular (E3-E7) bond critical point, as well as three ring and one cage critical points. The cage bonding was supported by a natural bond orbital (NBO) analysis which showed, in addition to the E8 sigma-bonded framework, weak pi bonding around the ring as well as numerous other weak interactions, the strongest of which is the weak transannular E3-E7 [2.86 A (S8(2+), 2.91 A (Se8(2+)] bond. The positive charge is delocalized over all atoms, decreasing the Coulombic repulsion between positively charged atoms relative to that in the less stable S8-like exo-exo E8(2+) isomer. The overall geometry was accounted for by the Wade-Mingos rules, further supporting the case for cage bonding. The bonding in Te8(2+) is similar, but with a stronger transannular E3-E7 (E = Te) bonding. The bonding in E8(2+) (E = S, Se, Te) can also be understood in terms of a sigma-bonded E8 framework with additional bonding and charge delocalization occurring by a combination of transannular n pi *-n pi * (n = 3, 4, 5), and np2-->n sigma * bonding. The classically bonded S8(2+) (Se8(2+) dication containing a short transannular S(+)-S+ (Se(+)-Se+) bond of 2.20 (2.57) A is 29 (6) kJ/mol higher in energy than the observed structure in which the positive charge is delocalized over all eight chalcogen atoms.     

Ni[(EPiPr2)2N]2 complexes: stereoisomers (E = Se) and square-planar coordination (E = Te)

The reaction of ((i)Pr 2PE) 2NM.TMEDA (M = Li, E = Se; M = Na, E = Te) with NiBr 2.DME in THF affords Ni[(SeP (i)Pr 2) 2N] 2 as either square-planar (green) or tetrahedral (red) stereoisomers, depending on the recrystallization solvent; the Te analogue is obtained as the square-planar complex Ni[(TeP (i)Pr 2) 2N] 2.     

Stereoselective synthesis of enantiomerically pure 1-(E)-alkenylsulfoximines

Optically active (E)-N-tosyl-S-(1-alkenyl)-S-phenylsulfoximines 4 are synthesized stereoselectively in a one pot sequence from readily available 1 via C-silylation, metallation and reaction of the corresponding lithiosulfoximine 3 with various carbonyl compounds. The El-MS spectra of the so prepared alkenylsulfoximines 4 show unexpected fragmentations, pointing to a new, unusual S-O-migration of the 1-alkenyl moiety.     

A facile and highly stereoselective synthesis of (2E)-, (2E,4E)-unsaturated amides and related natural products

A facile synthesis of (2E)-, (2E, 4E)-unsaturated amides was achieved via arsonium bromides with high stereoselectivity. Its application to the synthesis of related natural products 4 and 5 is also reported.     

Gas-phase rate coefficients for the reactions of nitrate radicals with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene at room temperature

Rate coefficients for reactions of nitrate radicals (NO3) with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene were determined to be (6.55 +/- 0.78)x 10(-13) cm3 molecule(-1) s(-1), (3.78 +/- 0.45)x 10(-13) cm3 molecule(-1) s(-1), (5.30 +/- 0.73)x 10(-13) cm(3) molecule(-1) s(-1), (3.83 +/- 0.47)x 10(-13) cm(3) molecule(-1) s(-1), (4.37 +/- 0.49)x 10(-13) cm(3) molecule(-1) s(-1), (3.61 +/- 0.40)x 10(-13) cm3 molecule(-1) s(-1) and (8.9 +/- 1.5)x 10(-12) cm3 molecule(-1) s(-1), respectively. We performed kinetic experiments at room temperature and atmospheric pressure using a relative-rate technique with GC-FID analysis. The experimental results demonstrate a surprisingly large cis-trans(Z-E) effect, particularly in the case of the pent-2-enes, where the ratio of rate coefficients is ca. 1.7. Rate coefficients are discussed in terms of electronic and steric influences, and our results give some insight into the effects of chain length and position of the double bond on the reaction of NO3 with unsaturated hydrocarbons. Atmospheric lifetimes were calculated with respect to important oxidants in the troposphere for the alkenes studied, and NO3-initiated oxidation is found to be the dominant degradation route for (Z)-pent-2-ene, (Z)-hex-3-ene and (E)-3-methylpent-2-ene.     

Reaction of Ni2Cp2(mu-CO)2 with the alkylgallium(I) and alkylindium(I) compounds E4[C(SiMe3)3]4 (E = Ga, In). Insertion of E-R groups into the Ni-Ni bond versus replacement of CO by the isolobal E-R ligands

The monomeric fragment In-C(SiMe3)3 was inserted into the Ni-Ni bond of Ni2Cp2(mu-CO)2 upon treatment of the carbonyl complex with the tetraindium(I) compound In4[C(SiMe3)3]4, 1, in a molar ratio of 4 to 1. The product (3) contains an indium atom coordinated to one alkyl substituent and two Ni(Cp)CO groups in a planar coordination sphere. Reaction of the starting compounds in a molar ratio of 2 to 1 led to the replacement of both CO ligands by two InR groups. A compound (4) was formed that is isostructural to the carbonyl nickel complex and has a Ni2 couple bridged by two InR ligands and two terminally coordinated cyclopentadienyl groups. The insertion product was not observed with the gallium derivative Ga4[C(SiMe3)3]4 (2); instead, a nickel gallium complex (5) analogous to 4 containing two bridging GaR ligands was isolated as the only product regardless of the ratio of the starting compounds. On the basis of quantum chemical calculations, we conclude that there is no evidence for an In-In or Ga-Ga bond in complexes 4 or 5, respectively. This, however, supports a butterfly geometry, which is isostructural to the starting carbonyl complex Ni2Cp2(mu-CO)2.     

(E)- and (Z)-1-benzenesulfonyl-4-trimethylsilyl-2-butenes as (E)-1-(1,3-butadienyl) synthons

(E)- and (Z)-1-benzenesulfonyl-4-trimethylsilyl-2-butenes (E/Z=9), prepared from 4-trimethylsilyl-1-buten-3-ol, $\text{n}$-butyllithium and benzenesulfenyl chloride and oxidation of the intermediate (E)- and (Z)-1-benzenesulfinyl-4-trimethylsilyl-2-butenes with hydrogen peroxide, react with $\text{n}$-butyllithium and then primary halides to give 4-benzenesulfonyl-1-trimethylsilyl-2-alkenes which are rapidly 1,4-debenzenesulfonyltrimethylsilated to (E)-1,3-alkadienes by tetra-$\text{n}$-butylammonium fluoride at O°C.     

The Jahn-Teller effect in CH(3)CN(+) (X(2)E) and CD(3)CN(+) (X(2)E) studied by zero kinetic energy photoelectron spectroscopy

The Jahn-Teller effect in CH(3)CN(+) (X(2)E) and CD(3)CN(+) (X(2)E) has been found experimentally by zero kinetic energy (ZEKE) photoelectron spectroscopy using coherent extreme ultraviolet (XUV) radiation. The vibronic bands of CH(3)CN(+) (X(2)E) and CD(3)CN(+) (X(2)E) at about 4500 cm(-1) above the ground states have been recorded. The spectra consist mainly of the Jahn-Teller active C-C[triple bond]N bending (v(8)), the CN stretching (v(2)), the CH(3) (CD(3)) deforming (v(6)), and the C-C stretching (v(4)) vibronic excitations. The Jahn-Teller active vibronic bands (v(8)) have been assigned with a harmonic model including linear and quadratic Jahn-Teller coupling terms, taking into account only the single mode vibronic excitation. The ionization potentials of CH(3)CN and CD(3)CN have also been determined, and their values are 12.2040(+/-0.001) and 12.2286(+/-0.001) eV, respectively.