Syntheses and Comparative Base Hydrolysis Reactions of Chlorocobalt(III) Complexes of Pendant-Arm Macrocyclic Polyamines and Polyamino Acids

1997 ◽  
Vol 50 (9) ◽  
pp. 883 ◽  
Author(s):  
Yakup Baran ◽  
Trevor W. Hambley ◽  
Geoffrey A. Lawrance ◽  
Eric N. Wilkes
Keyword(s):  
Water Molecule ◽  
Activation Enthalpy ◽  
Base Hydrolysis ◽  
Secondary Amines ◽  
Methyl Groups ◽  
Monoclinic Space Group ◽  
Carboxylate Group ◽  
Hydrolysis Kinetics ◽  
Pendant Arm ◽  
Macrocyclic Polyamines

Chlorocobalt(III) complexes of the pendant-arm macrocycles 1,4,8,12-tetraazacyclopentadecane-10-carboxylate (2) and 1,5,9,13-tetraazabicyclo[11.2.2]heptadecane-7-carboxylate (4) have been prepared to complement the known complexes of 10-methyl-1,4,8,12-tetraazacyclopentadecan-10-amine (1) and 7-methyl-1,5,9,13-tetraazabicyclo[11.2.2]heptadecan-7-amine (3). The pairs (1),(3) and (2),(4) differ in replacement of pendant amine and methyl groups in the former pair by a pendant carboxylate group and hydrogen in the latter pair. The macromonocyclic ligands (1) and (2) form cis-chlorocobalt(III) complexes whereas the macrobicyclic ligands (3) and (4) (which contain an additional –CH2–CH2– ‘strap’ linking two amines) form trans-chlorocobalt(III) complexes, defined in terms of location of the pendant donor and the chloride donor. Chloride base hydrolysis kinetics varies with ligand {cis-[Co(1)Cl]2+, kOH 6700 dm3 mol-1 s-1 ; cis-[Co(2)Cl] +, kOH 1800 dm3 mol-1 s-1;trans-[Co(3)Cl]2+, kOH 3450 dm3 mol-1 s-1; trans-[Co(4)Cl]+, kOH 2250 dm3 mol-1 s-1 at 25°C}. Variations in rate constant are tied mainly to variations in activation enthalpy. Chloride hydrolyses occur with retention of configuration, but slow following isomerization can lead to products such as trans-[Co(2)(OH2)] (ClO4)2.2H2O, which crystallizes in the monoclinic space group P21/c, a 9·581(2), b 16·214(2), c 14·350(2) Å and β 94·66(1)°. The pendant carboxylate group and two adjacent secondary amines necessarily occupy an octahedral face, with the water molecule bound trans to the pendant carboxylate. The four Co–N distances range from 1·981(2) to 2·22(3) Å, and along with carboxylate Co–O (1·882(3) Å) and water Co-O (1·934(2) Å) distances are similar to usual distances in cobalt(III) complexes.

Synthesis and Complexation of a Chiral Sexidentate Pendant-Arm Macropolycyclic Polyamino Acid

2002 ◽  
Vol 55 (10) ◽  
pp. 667 ◽  
Author(s):  
G. Wei ◽  
T. W. Hambley ◽  
G. A. Lawrance ◽  
M. Maeder
Keyword(s):  
Carboxylic Acid ◽  
Metal Ions ◽  
Secondary Amines ◽  
Distorted Octahedral Geometry ◽  
Monoclinic Space Group ◽  
Basic Solution ◽  
Polyamino Acid ◽  
Pendant Arm ◽  
Distorted Octahedral ◽  
Acyclic Complex

The reaction of the acyclic complex ion (methyl (SS,SS)-3-[(2�-aminocyclohexyl)amino]-2-[(2�-aminocyclohexyl)-aminomethyl]propionate)copper(II) with formaldehyde and nitroethane in basic solution yields the pendant-arm macrocyclic complex (SS,SS)-(methyl-15-methyl-15-nitro-2,6,13,17-tetraazatricyclo[16.4.0.07,12]docosane-4-carboxylate)copper(ii) ion. Reduction with zinc in hydrochloric acid yields the hydrochloride salt of the pendant-arm macrocycle (SS,SS)-15-amino-15-methyl-2,6,13,17-tetraazatricyclo[16.4.0.07,12]docosane-4-carboxylic acid (1), separated into and isolated as the major trans (1a) and minor cis (1b) isomers. Co-ordination of (1) to several metal ions [CoIII, CrIII, NiII, ZnII, CuII] and comparison with a previously reported analogue without the cyclohexane rings, trans-13-amino-13-methyl-1,4,8,11-tetraazacyclotetradecane-6-carboxylic acid (2a) salt, is described. The [Ni{(1a) – H+}](ClO4) crystallizes in the monoclinic space group P21, a 9.710(2), b 14.442(1), c 10.317(2) Å, β 96.02(2)°. The nickel displays a distorted octahedral geometry, with all four secondary amines coordinated (Ni–N range 2.044(7)–2.063(6) Å), in addition to pendant primary amine (Ni–N, 2.109(6) Å) and carboxylate (Ni–O, 2.100(6) Å) groups. Protonation constants for the trans (1a) and cis (1b) isomers and stability constants of these isomers with the labile metal ions ZnII, CdII, HgII, PbII, MnII, and CoII were determined by potentiometric titrations. The log K values for 1 : 1 complexes show small variations between geometric isomers.

Quinquedentate Coordination of 10-Methyl-1,4,8,12-tetraazacyclopentadecan-10-amine (L) to Rhodium(III). Crystal Structure of cis-[Rh(L)Cl][ClO4]2.H2O And Comparative Activation Volumes for Base Hydrolysis of [M(L)Cl]2+ (M = Rh, Co, Cr)

1992 ◽  
Vol 45 (2) ◽  
pp. 351 ◽  
Author(s):  
GA Lawrance ◽  
M Martinez ◽  
BW Skelton ◽  
R Vaneldik ◽  
AH White
Keyword(s):  
Primary Amine ◽  
Metal Ion ◽  
Exchange Chromatography ◽  
Hot Water ◽  
Base Hydrolysis ◽  
Secondary Amines ◽  
Orthorhombic Space Group ◽  
Pendant Arm ◽  
Base Mechanism ◽  
Hydrolysis Of

The pendant-arm macrocycle 10-methyl-1,4,8,12-tetraazacyclopentadecan-10-amine (1) reacts slowly in hot water with rhodium(III) chloride to yield, following cation-exchange chromatography, exclusively cis -[ Rh (l) Cl ]2+. The cis -complex was crystallized readily as a perchlorate monohydrate salt, in the orthorhombic space group Pn21a, a 16.854(3), b 13.341(3), c 9.985(1) � , Z = 4, isomorphous with its cobalt(III) counterpart; a single-crystal X-ray structure determination was refined to R 0.027 for 1626 'observed' reflections. The pendant primary arnine and two adjacent secondary amines necessarily occupy an octahedral face, with the chloro ligand cis to the primary amine, and secondary amines adopt R,R,S,S stereochemistries. The Rh -N distances [2.056(6) � (pendant primary amine), average 2.08 � (secondary amines)], are at the short end of the range for Rh-N bonds. The Rh-Cl distance is 2.347(2) �. Activation volumes for chloride base hydrolysis were determined for cis -[ Rh (l) Cl ]2+as +19.5( � 1.2), for cis -[Co(l) Cl ]2+ as +27.1(�0.4), and for trans-[Cr(l) Cl ]2+ as +31.1( �0.1) cm3 mol-l, and are consistent with a conjugate base mechanism in each case; variations with metal ion are discussed.

Structural characterization and theoretical calculations of the monohydrate of the 1:2 cocrystal salt formed from acriflavine and 3,5-dinitrobenzoic acid

2021 ◽  
Vol 77 (2) ◽  
pp. 116-122
Author(s):  
Maria Marczak ◽  
Kinga Biereg ◽  
Beata Zadykowicz ◽  
Artur Sikorski
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Intermolecular Interactions ◽  
Structural Characterization ◽  
Theoretical Calculations ◽  
Lattice Energy ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Porous Organic Framework ◽  
Organic Framework

The synthesis and structural characterization of the monohydrated 1:2 cocrystal salt of acriflavine with 3,5-dinitrobenzoic acid [systematic name: 3,6-diamino-10-methylacridin-10-ium 3,5-dinitrobenzoate–3,5-dinitrobenzoic acid–water (1/1/1), C14H14N3 +·C7H3N2O6 −·C7H4N2O6·H2O] are reported. Single-crystal X-ray diffraction measurements show that the title solvated monohydrate salt crystalizes in the monoclinic space group P21 with one acriflavine cation, a 3,5-dinitrobenzoate anion, a 3,5-dinitrobenzoic acid molecule and a water molecule in the asymmetric unit. The neutral and anionic forms of 3,5-dinitrobenzoic acid are linked via O—H...O hydrogen bonds to form a monoanionic dimer. Neighbouring monoanionic dimers of 3,5-dinitrobenzoic acid are linked by nitro–nitro N—O...N and nitro–acid N—O...π intermolecular interactions to produce a porous organic framework. The acriflavine cations are linked with carboxylic acid molecules directly via amine–carboxy N—H...O, amine–nitro N—H...O and acriflavine–carboxy C—H...O hydrogen bonds, and carboxy–acriflavine C—O...π, nitro–acriflavine N—O...π and acriflavine–nitro π–π interactions, or through the water molecule by amino–water N—H...O and water–carboxy O—H...O hydrogen bonds, and are located in the voids of the porous organic framework. The intermolecular interactions were studied using the CrystalExplorer program to provide information about the interaction energies and the dispersion, electrostatic, polarization and repulsion contributions to the lattice energy.

Combining CDIF and PDF information in problem solving: Crystal structure of a corrosion deposit, hexaaquairon(II) trifluoromethanesulfonate

1999 ◽  
Vol 14 (3) ◽  
pp. 166-170
Author(s):  
J. A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Problem Solving ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Powder Diffraction ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
Crystal Data ◽  
Major Phase ◽  
Corrosion Deposit

The title compound was identified as the major phase in a corrosion deposit by indexing its powder pattern, and locating an isostructural vanadium(II) compound in the NIST Crystal Data Identification File. The identity of the compound was confirmed by a Rietveld refinement. Hexaaquairon(II) trifluoromethanesulfonate crystallizes in the monoclinic space group C2/m, with a=18.6415(14), b=6.9291(5), c=6.5938(5) Å, β=104.742(6)°, V=823.68(10) Å3, and Z=2. The structure consists of alternating layers of octahedral hexaaquairon(II) cations and triflate anions. The cations and anions are linked into layers parallel to the bc plane by hydrogen bonds. Each water molecule donates two protons to sulfonate oxygens, and each sulfonate oxygen acts as an acceptor of two protons. A reference powder diffraction pattern is reported.

Intermediate Products of the Reaction of (4,4,9,9-Tetramethyl-5,8-diazadodecane-2,11-dione dihydrazone)nickel(II) With Butane-2,3-dione; the Structure of cis-Aqua(3,4,7,9,9,14,14,16-octamethyl-1,2,5,6,10,13-hexaazacyclohexadeca-1(16),4,6-tien-3-Ol)nickel(II) Perchlorate Trihydrate

1994 ◽  
Vol 47 (10) ◽  
pp. 1885 ◽  
Author(s):  
NF Curtis ◽  
AR Davis ◽  
FWB Einstein
Keyword(s):  
Water Molecule ◽  
Hydroxy Group ◽  
Secondary Amine ◽  
Macrocyclic Ligand ◽  
Equilibrium Mixture ◽  
Monoclinic Space Group ◽  
Amine Nitrogen ◽  
Space Group ◽  
X Ray ◽  
Intermediate Products

Intermediate products have been isolated from the reaction of (4,4,9,9-tetramethyl-5,8-diazadodecane-2,11-dione dihydrazone )nickel(II) perchlorate with butane-2,3-dione which finally yields the macrocyclic product (3,4,7,9,9,14,14,16-octamethyl-1,2,5,6,10,13-hexaazacyclohexa-deca-2,4,6,16-tetraene)nickel(II) perchlorate , [Ni( omht )] (ClO4)2. An initial violet product is assigned a structure with the macrocyclic ligand 3-acetyl-3,6,8,8,13,13,15-heptamethyl-1,2,4,5,9,12-hexaazacyclopentadeca-5,15-diene. In water this converts into an equilibrium mixture of the tautomeric cations blue cis-aqua(3,4,7,9,9,14,14,16-octamethyl-1,2,5,6,10,13-hexaazacyclohexadeca-1(16),4,6-trien-3-ol)nickel(II), cis-[Ni(L2)(H2O)]2+, and orange (3,6,8,- 8,13,13-hexamethyl-4,5,9,12-tetraazahexadeca-3,5-diene-2,15-dione 15-hydrazone)nickel(II), [Ni(L3)]2+. The rates at 25°C of the forward and reverse reactions of this tautomerism, and of the slower conversion of the equilibrium mixture to [Ni( omht )](ClO4)2, are reported. The structure of cis -[Ni(L2)(H2O)](ClO4)2.3H2O has been determined by X-ray diffractometry (monoclinic, space group P21/n, a 9.694(8), b 19.218(14), c 16.652(9) Ǻ, β 94.88(1)°, R 0.079 for 3254 reflections). This has NiII in octahedral coordination by secondary amine nitrogen atoms 10 and 13, hydrazone nitrogen atoms 1 and 6, and the carbinolamine oxygen substituent at position 3 of the pentadentate macrocyclic ligand L2, with a water molecule coordinated cis to the hydroxy group. Compounds of the tautomeric cations [Ni(L2)]2+ and [Ni(L3)]2+ with coordinated thiocyanate, azide, nitrite, oxalate and acetate are described.

scholarly journals The transition state for peptide bond formation reveals the ribosome as a water trap

2010 ◽  
Vol 107 (5) ◽  
pp. 1888-1893 ◽  
Author(s):  
Göran Wallin ◽  
Johan Åqvist
Keyword(s):  
Water Molecule ◽  
Transition State ◽  
Activation Enthalpy ◽  
Molecular Model ◽  
Isotope Effects ◽  
Bond Formation ◽  
Transition States ◽  
Peptide Bond ◽  
Hydroxyl Group ◽  
Peptide Bond Formation

Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered “double proton shuttle” mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.

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