The binding of human carbonic anhydrase II by functionalized folded polypeptide receptors

Several receptors for human carbonic anhydrase II (HCAII) have been prepared by covalently attaching benzenesulfonamide carboxylates via aliphatic aminocarboxylic acid spacers of variable length to the side chain of a lysine residue in a designed 42 residue helix-loop-helix motif. The sulfonamide group binds to the active site zinc ion of human carbonic anhydrase II located in a 15 A deep cleft. The dissociation constants of the receptor-HCAII complexes were found to be in the range from low micromolar to better than 20 nM, with the lowest affinities found for spacers with less than five methylene groups and the highest affinity found for the spacer with seven methylene groups. The results suggest that the binding is a cooperative event in which both the sulfonamide residue and the helix-loop-helix motif contribute to the overall affinity.     

Theoretical study of the human DNA repair protein HOGG1 activity

We have examined the role of the catalytic lysine (Lys 249) in breaking the glycosidic bond of 8-oxoguanine in the enzyme human 8-oxoguanine DNA glycosylase. Until quite recently it has been assumed that this lysine acts as a nucleophile in an S(N)2 type of reaction after being activated through a donation of a proton to a strictly conserved aspartate, also located in the active site. However, evidence from crystallographic, as well as biochemical studies, questions this assumption mainly because the lysine is not ideally positioned for such an attack. In addition, the catalytic activity is preserved even after that aspartate is mutated to a residue not accepting protons, but still keeping the interactions in the active site. In this study, we have investigated several different reaction mechanisms to discover plausible ways where the lysine could assist in breaking the glycosidic bond. We use hybrid density functional theory to characterize both associative and dissociative pathways. We find that the smallest energetical barrier involves an S(N)1 type of mechanism where the lysine electrostatically stabilizes the dissociating base and then donates a proton with a very small barrier and then finally attacks the sugar ring to create the covalently bound protein-DNA intermediate complex. The S(N)2 mechanism also has a lower barrier than the "spontaneous" bond breaking but considerably above that of the S(N)1 reaction. However, in current conditions, the reactants placed in a conformation posed for an S(N)2 reaction is substantially more stable than if posed for the S(N)1 reaction, indicating that the active site has to bind stronger to the latter in order to achieve a full catalytic effect. An analysis of the polarization of the transition states shows that the polarization is largest for the S(N)1 reaction, indicating that this path will gain most by being placed in a prepolarized active site. These findings give further support to the hypothesis that a dissociative mechanism may be the preferred mode of action for this type of enzymes.     

Mono- und dicarbenkomplexe durch reaktion von pentacarbonyleisen mit einigen dialkylamiden des zwei- und vierwertigen zinns

The dialkylamides of tin react with ironpentacarbonyl to form carbene complexes. With Me₂Sn(NMe₂)₂ and Sn(NMe₂)₄ yellow dicarbene complexes are formed by addition of two Sn---N bonds to adjacent carbonyl groups. The two carbenoid systems on the central atom are parts of a chelate ligand connected by an ---O---Sn---O--- bridge. Using [Sn(NMe₂)₂]₂, a red monomeric compound (CO)₃Fe(CONMe₂)₂Sn containing the same cyclic structural unit can be isolated. The free activation enthalpy of rotation about the C(carbene)---N bond in the tin (IV) dicarbene complexes was found to be 16.5 kcal mol^-1.     

The coordination chemistry of "[BP3]NiX" platforms: targeting low-valent nickel sources as promising candidates to L3Ni=E and L3Ni(triple bond)E linkages

A series of divalent, monovalent, and zerovalent nickel complexes supported by the electron-releasing, monoanionic tris(phosphino)borate ligands [PhBP3] and [PhBPiPr3] ([PhBP3] = [PhB(CH2PPh2)3]-, [PhBPiPr3] = [PhB(CH2PiPr2)3]-) have been synthesized to explore fundamental aspects of their coordination chemistry. The pseudotetrahedral, divalent halide complexes [PhBP3]NiCl (1), [PhBP3]NiI (2), and [PhBPiPr3]NiCl (3) were prepared by the metalation of [PhBP3]Tl or [PhBPiPr3]Tl with (Ph3P)2NiCl2, NiI2, and (DME)NiCl2 (DME = 1,2-dimethoxyethane), respectively. Complex 1 is a versatile precursor to a series of complexes accessible via substitution reactions including [PhBP3]Ni(N3) (4), [PhBP3]Ni(OSiPh3) (5), [PhBP3]Ni(O-p-tBu-Ph) (6), and [PhBP3]Ni(S-p-tBu-Ph) (7). Complexes 2-5 and 7 have been characterized by X-ray diffraction (XRD) and are pseudotetrahedral monomers in the solid state. Complex 1 reacts readily with oxygen to form the four-electron-oxidation product, [[PhB(CH2POPh2)2(CH2PPh2)]NiCl] (8A or 8B), which features a solid-state structure that is dependent on its method of crystallization. Chemical reduction of 1 using Na/Hg or other potential 1-electron reductants generates a product that arises from partial ligand degradation, [PhBP3]Ni(eta2-CH2PPh2) (9). The more sterically hindered chloride 3 reacts with Li(dbabh) (Hdbabh = 2,3:5,6-dibenzo-7-azabicyclo[2.2.1]hepta-2,5-diene) to provide the three-coordinate complex [kappa2-PhBPiPr3]Ni(dbabh) (11), also characterized by XRD. Chemical reduction of complex 1 in the presence of L-type donors produces the tetrahedral Ni(I) complexes [PhBP3]Ni(PPh3) (12) and [PhBP3]Ni(CNtBu) (13). Reduction of 3 following the addition of PMe3 or tert-butyl isocyanide affords the Ni(I) complexes [PhBPiPr3]Ni(PMe3) (14) and [PhBPiPr3]Ni(CNtBu) (15), respectively. The reactivity of these [PhBP3]NiIL and [PhBPiPr3]NiIL complexes with respect to oxidative group transfer reactions from organic azides and diazoalkanes is discussed. The zerovalent nitrosyl complex [PhBP3]Ni(NO) (16) is prepared by the reaction of 1 with excess NO or by treating 12 with stoichiometric NO. The anionic Ni(0) complexes [[kappa2-PhBP3]Ni(CO)2][nBu4N] (17) and [[kappa2-PhBPiPr3]Ni(CO)2][ASN] (18) (ASN = 5-azoniaspiro[4.4]nonane) have been prepared by reacting [PhBP3]Tl or [PhBPiPr3]Tl with (Ph3P)2Ni(CO)2 in the presence of R4NBr. The photolysis of 17 appears to generate a new species consistent with a zerovalent monocarbonyl complex which we tentatively assign as [[PhBP3]Ni(CO)][nBu4N], although complete characterization of this complex has been difficult. Finally, theoretical DFT calculations are presented for the hypothetical low spin complexes [PhBP3]Ni(NtBu), [PhBPiPr3]Ni(NtBu), [PhBPiPr3]Ni(NMe), and [PhBPiPr3]Ni(N) to consider what role electronic structure factors might play with respect to the relative stability of these species.     

Ligand-field excited states of metal hexacarbonyls

Over 35 years ago, the low-lying bands in the absorption spectra of metal hexacarbonyls were assigned to ligand-field (LF) excitations. Recent time-dependent density functional theory (TDDFT) calculations on M(CO)6 (M = Cr, Mo, W) are not in accord with this interpretation. Here we extend TDDFT calculations to the isoelectronic series V(CO)6-, Cr(CO)6, and Mn(CO)6+. By analyzing the trends in the energies of the various electronic excitations, we are able to fully assign the spectra of the complexes. In particular, we demonstrate that the LF excitation 1A1g -->1T1g is observed at 4.12 eV in the Mn(CO)6+ spectrum, but all LF features in the spectra of V(CO)6- and Cr(CO)6 are obscured by intense metal-to-ligand charge-transfer absorptions. Our results suggest that use of B3LYP as the exchange-correlation functional and inclusion of solvation effects through a continuum solvation model lead to the most accurate calculated transition energies.     

Prediction of adsorption behavior of activated carbons

A study was made of the effect of temperature on predictive equations recently developed and applied to gas adsorption by beds of activated and impregnated carbons. Adsorption parameters, obtained for the adsorbate DMMP on small gram quantities of impregnated carbon at 25°C and applied to carbon bed breakthru times, were analyzed for changes resulting from direct temperature effects on gas diffusion, adsorption—desorption equilibria, volume expansion, relative pressure, and adsorbate—adsorbent interactions. Modifications in the adsorption parameters, calculated for bed temperatures ranging between 40.3 and 46.7°C, were used in the kinetic equations to predict breakthru times for M10 gas filters, each containing 13,847 g of carbon. The predicted values compared very well with those experimentally determined, the mean deviation in breakthru time being 5.82%, without regard to sign. A general analysis of a 10°C rise in temperature, from 25 to 35°C, for the M10 gas filter under the test conditions used, showed that the breakthru time would be lowered 20.0 min, 87% of this lowering due to a reduced adsorption rate constant, 9% due to a reduced adsorption capacity, and 4% due to volume expansion effects on concentration and flowrate.     

NMR study of deuterium molybdenum bronze

The deuterium NMR lineshape and spin—lattice relaxation time, T₁, have been measured in deuterium molybdenum bronze, D_1.6MoO₃, over the temperature range 166–400 K. The ²D quadrupole coupling constant is 21 kHz at room temperature. The temperature dependence of the ²D T₁ has been interpreted in terms of two independent motional processes for deuterium. The data suggest that one of the processes corresponds to diffusion of the ²D nuclei whereas the other may arise from a 180° flipping of the OD₂ moieties. This specific interpretation agrees with the results obtained for proton T₁ and proton lineshape data reported earlier.     

Pyrosequencing trade mark technology at elevated temperature

To date, the Pyrosequencing trade mark technology has been performed at 28 degrees C due to the low thermostability of the firefly luciferase. In this study, firefly luciferase was stabilized in the presence of glycine betaine, allowing DNA sequencing at 37 degrees C. By increasing the temperature to 37 degrees C, false signals due to primer-dimers and loop-structures were decreased significantly. In addition, a combination of (i) replacing the natural dGTP with 7'deaza-dGTP in the polymerase chain reaction (PCR), (ii) 1.6 M glycine betaine, and (iii) an increase of the temperature to 37 degrees C enabled us to sequence a DNA template with the initial sequence 3'-ATGGCCCGGGGGGGAGCTCCA em leader 5'. Furthermore, we describe a method to analyze if a primer forms a primer-dimer with extendable 3'-ends.     

Considering Fe(II/IV) redox processes as mechanistically relevant to the catalytic hydrogenation of olefins by [PhBP iPr 3]Fe-H x species

Several coordinatively unsaturated pseudotetrahedral iron(II) precursors, [PhBP(iPr)(3)]Fe-R ([PhBP(iPr)(3)] = [PhB(CH(2)P(i)Pr(2))(3)](-); R = Me (2), R = CH(2)Ph (3), R = CH(2)CMe(3) (4)) have been prepared from [PhBP(iPr)(3)]FeCl (1) that serve as precatalysts for the room-temperature hydrogenation of unsaturated hydrocarbons (e.g., ethylene, styrene, 2-pentyne) under atmospheric H(2) pressure. The solid-state crystal structures of 2 and 3 are presented. To gain mechanistic insight into the nature of these hydrogenation reactions, a number of [PhBP(iPr)(3)]-supported iron hydrides were prepared and studied. Room-temperature hydrogenation of alkyls 2-4 in the presence of a trapping phosphine ligand affords the iron(IV) trihydride species [PhBP(iPr)(3)]Fe(H)(3)(PR(3)) (PR(3) = PMe(3) (5); PR(3) = PEt(3) (6); PR(3) = PMePh(2) (7)). These spectroscopically well-defined trihydrides undergo hydrogen loss to varying degrees in solution, and for the case of 7, this process leads to the structurally identified Fe(II) hydride product [PhBP(iPr)(3)]Fe(H)(PMePh(2)) (9). Attempts to prepare 9 by addition of LiEt(3)BH to 1 instead lead to the Fe(I) reduction product [PhBP(iPr)(3)]Fe(PMePh(2)) (10). The independent preparations of the Fe(II) monohydride complex [PhBP(iPr)(3)]Fe(II)(H)(PMe(3)) (11) and the Fe(I) phosphine adduct [PhBP(iPr)(3)]Fe(PMe(3)) (8) are described. The solid-state crystal structures of trihydride 5, monohydride 11, and 8 are compared and demonstrate relatively little structural reorganization with respect to the P(3)Fe-P' core motif as a function of the iron center's formal oxidation state. Although paramagnetic 11 (S = 1) is quantitatively converted to the diamagnetic trihydride 5 under H(2), the Fe(I) complex 8 (S = (3)/(2)) is inert toward atmospheric H(2). Complex 10 is likewise inert toward H(2). Trihydrides 5 and 6 also serve as hydrogenation precatalysts, albeit at slower rates than that for the benzyl complex 3 because of a rate-contributing phosphine dependence. That these hydrogenations appear to proceed via well-defined olefin insertion steps into an Fe-H linkage is indicated by the reaction between trihydride 5 and ethylene, which cleanly produces the ethyl complex [PhBP(iPr)(3)]Fe(CH(2)CH(3)) (13) and an equivalent of ethane. Mechanistic issues concerning the overall reaction are described.     

Iron(II) and copper(I) coordination polymers: electrochromic materials with and without chiroptical properties

The electrochemical and optical properties of films prepared from two different Fe(II) coordination polymers (TPT[Fe(II)TPT](n)(PF(6))(2)(n) (TPT = terpyridine-phenyl-terpyridine) and CTPCT[Fe(II)CTPCT](n)(PF(6))(2)(n) (CTPCT = chiral terpyridine-phenyl-chiral terpyridine)) and a coordination polymer based on Cu(I) metal centers (PDP[Cu(I)PDP](n)(BF(4))(n)) (PDP = phenanthroline-dodecane-phenanthroline) have been studied. The oxidation of a PDP[Cu(I)PDP](n)(BF(4))(n) film coated on an indium-tin oxide (ITO) electrode by stepping the potential from 0.0 to +1.4 V vs Ag/AgCl led not only to the complete bleaching of the absorption in the visible region of the spectrum within 5 min but also to a redox-induced dissociation and dissolution of the polymer. The reverse reaction of binding and reassembling the polymer at the electrode surface, upon stepping the potential back to 0.0 V, occurred with a rate which was at least 1 order of a magnitude slower. In contrast, the bis(2,2':6',2' '-terpyridine)iron(II)-based redox polymers TPT[Fe(II)TPT](n)(PF(6))(2)(n) and CTPCT[Fe(II)CTPCT](n)(PF(6))(2)(n), during similar spectroelectrochemical experiments, not only exhibited a dramatically enhanced switching rate but also displayed symmetric switching kinetics. The films did not show signs of deterioration over 150 switching cycles. Additionally, in an effort to assemble an electrochromic device with chiroptical properties, the electrochromism of films generated from the enantiomerically pure CTPCT[Fe(II)CTPCT](n)(PF(6))(2)(n) polymer was studied through circular dichroism.