Hypothetical Complex Research Articles

Endohedral analogs of ferrocene: ab initio theoretical predictions

The problem of the existence of endohedral analogs of ferrocene is discussed. It is shown that radical CorH 5 , where Cor is corannulene C 20H 10 and five atoms H are added to the α-positions relative to the five-membered cycle ( pent*) of Cor, can form stable polyhedral dimer D 2 h -C 40H 30 (D). The ground state of D is triplet. The energy of dimerization of CorH 5 is equal to 175 kcal mol −1. The geometric and electronic structure of hypothetical endohedral complex D 5 d -2η 5-Fe@D ( 1) and its isomer D 5 d -2η 5-Fe(CorH 5) 2 ( 1b), which is a sandwich complex, are simulated by the ab initio MO LCAO SCF method (HF/3-21G). It is found that the energy of 1 is less than the energy of 1b by 171 kcal mol −1. The energies of the Fe pent* bond in complexes 1 (115 kcal mol −1) and 1b (111 kcal mol −1) are close to those of the FeCp bond in bis(cyclopentadienyl)iron FeCp 2 (110 kcal mol −1). Complex 1 and also complex D 5 d -2η 5-Fe@C 40H 10 ( 2), carbon skeletons of which have an analogous structure to 1 and with ten H added to the α-positions relative to polar pentagons ( pent*), can be considered as endohedral analogs of ferrocene. Atom Fe in these complexes interacts with atoms of both polar pentagons. The binding energy of the atom Fe with the polyhedral fragment C 40H 10 of 2 is a bit less than in 1 (on 6 kcal mol −1).

Hodge Numbers of a Hypothetical Complex Structure on the Six Sphere

We prove that the terms Erp,q(S6) in the Frolicher spectral sequence associated to any hypothetical complex structure on S6 would satisfy Serre duality. It is also shown that the vanishing of the Dolbeault cohomology group H1,1(S6) ensures the existence of a holomorphic 2-form on S6 living even in E22,0(S6), which in particular implies the nondegeneration of Frolicher's sequence at the second level.

Prediction of the Bond Lengths, Vibrational Frequencies, and Bond Dissociation Energy of Octahedral Seaborgium Hexacarbonyl, Sg(CO)6

The recent syntheses of several new elements (including the recent reports of elements 116 and 118), coupled with the controversy surrounding the naming of elements 104--109, have stimulated a great interest in the chemistry of the transactinide elements. This contribution addresses hypothetical hexacarbonyl complex of seaborgium (Sg, element 106), which is predicted to be a 6d-block transition element with six valence electrons, analogous to Cr, Mo, and W. The authors have previously predicted that, if it were to exist, Sg(CO){sub 6} would exhibit metal-carbonyl bonding that is very similar to that in Cr(CO){sub 6}, Mo(CO){sub 6}, and W(CO){sub 6}, and quite unlike that of the unknown valence isoelectronic actinide complex U(CO){sub 6}. This finding is in accord with the scant experimental data available for Sg. The relativistic DV-X{alpha} method used in the earlier paper facilitated the analysis of the molecular orbitals of Sg(CO){sub 6}, but did not allow for the calculation of total-energy properties, such as bond lengths and vibrational frequencies. Here the authors will use the superior methodology they have applied to other transactinide molecules to compare the bond lengths, vibrational frequencies, and CO dissociation energy of hypothetical Sg(CO){sub 6} to those of Mo(CO){sub 6} and W(CO){sub 6}.

The presumed potassium carrier Trk2p in Saccharomyces cerevisiae determines an H +-dependent, K +-independent current

Ionic currents related to the major potassium uptake systems in Saccharomyces cerevisiae were examined by whole cell patch-clamping, under K + replete conditions. Those currents have the following properties. They (1) are inward under all conditions investigated, (2) arise instantaneously with appropriate voltage steps, (3) depend solely upon the moderate affinity transporter Trk2p, not upon the high affinity transporter Trk1p. They (4) appear to be independent of the extracellular K + concentration, (5) are also independent of extracellular Ca 2+, Mg 2+ and Cl − but (6) are strongly dependent on extracellular pH, being large at low pH (up to several hundred pA at −200 mV and pH 4) and near zero at high pH (above 7.5). They (7) increase in proportion to log[H +] o, rather than directly in proportion to the proton concentration and (8) behave kinetically as if each transporter cycle moved one proton plus one (high pH) or two (low pH) other ions, as yet unidentified. In view of background knowledge on K + transport related to Trk2p, the new results suggest that the K + status of yeast cells modulates both the kinetics of Trk2p-mediated transport and the identity of ions involved. That modulation could act either on the Trk2 protein itself or on interactions of Trk2 with other proteins in a hypothetical transporter complex. Structural considerations suggest a strong analogy to the KtrAB system in Vibrio alginolyticus and/or the TrkH system in Escherichia coli.

The synergetic effect of catalytic systems in 2,4-tolylene diisocyanate reactions with macrodiols—I. A reaction model with catalysts molar ratio 1:1

A critical opinion of the in former papers applied model of 2,4-tolylene diisocyanate reactions with macrodiols catalyzed by catalytic systems: tri(tributyltin)isocyanate+triethylenediamine, di(tributyltin)carbodiimide+triethylenediamine and tin(II) chloride (SnCl 2)+triethylenediamine is expressed. A new model for the reactions considering the synergetic effect observed in real reaction systems is proposed. Test results of the model for catalytic system creating hypothetical complex (during selforganization processes) in molar ratio of two catalysts, di(tributyltin)carbo-diimide and triethylenediamine as 1:1, are presented. The good optimization of this system is then stated.

Interaction site for soluble cytochromes on the tetraheme cytochrome subunit bound to the bacterial photosynthetic reaction center mapped by site-directed mutagenesis.

The crystallographic structure of the Blastochloris (formerly called Rhodopseudomonas) viridis tetraheme cytochrome subunit bound to the photosynthetic reaction center (RC) suggests that all four hemes are located close enough to the surface of the protein to accept electrons from soluble cytochrome c2. To identify experimentally the site of this reaction we prepared site-directed mutants of Rubrivivax gelatinosus RCs with surface charge substitutions in the bound cytochrome subunit and studied the kinetics of their reduction by soluble cytochromes (mitochondrial horse cytochrome c, Blc. viridis cytochrome c2, and Rvi. gelatinosus cytochrome c8). In comparison with the wild-type, the mutants E79K (glutamate-79 substituted by lysine), E93K (glutamate-93 substituted by lysine), and E85K (glutamate-85 substituted by lysine) located near the solvent-exposed edge of low-potential heme 1, the fourth heme from the special pair of bacteriochlorophyll, exhibited decreased second-order rate constants for the reaction between the tetraheme subunit and the soluble cytochromes. Double charge substitutions in this region: E79K/E85K (glutamate-79 and -85 both replaced by lysine) and E93K/E85K (glutamate-93 and -85 both replaced by lysine) appeared to show an additive inhibitory effect. Mutations in other charged regions did not alter the kinetics of electron transfer between bound and soluble cytochromes. In light of the available structural information on Blc. viridis RC, these results indicate that the cluster of acidic residues immediately surrounding the distal heme 1 of the RC-bound tetraheme subunit forms an electrostatically favorable binding site for soluble cytochromes. Thus, all four hemes in the subunit seem to be directly involved in the electron transfer toward the photo-oxidized special pair of bacteriochlorophyll. On the basis of these findings, a model is proposed for the hypothetical cytochrome c2-RC transient complex for Blc. viridis.

The amino acid sequences of isoforms of the bromelain inhibitor from pineapple stem.

Eight bromelain inhibitor (BI) isoform fractions were isolated from pineapple stem, and then submitted to conventional amino acid sequencing after performic acid oxidation and subsequent separation of the resulting light and heavy chains. The results revealed that all fractions exhibited microheterogeneity, containing at least two major components, but that all the isoinhibitors have a common double-chain structure (Mr = ca. 5,700-5,900) with five disulfide bonds and similar amino acid sequences. Notably, Fraction BI-VIII exhibited less than 40% of the specific inhibitory activity toward stem bromelain as compared with the other inhibitor fractions. This fraction was a mixture of two isoforms, BI-VIII(1) and BI-VIII(2), the latter lacking the arginine or glutamine residue at the COOH-terminus of the light chain. Furthermore, the oxidized light chain of BI-III, used as a representative normal isoinhibitor, was found to exhibit significant inhibitory activity, whereas the oxidized light chain of BI-VIII(2) lacking the COOH-terminal Arg or Gln showed only very low inhibitory activity. Therefore, the major bromelain-inhibitory site was indicated to be the COOH-terminal residue, Arg or Gln, of the light chain. This is consistent with the three-dimensional structure model constructed by computer modeling for the hypothetical complex between BI-VI and papain, a close homolog of bromelain.

Molecular modeling studies of the DNA-topoisomerase I ternary cleavable complex with camptothecin.

The present studies provide a three-dimensional model for the postulated ternary cleavable complex of topoisomerase I (top1), DNA, and camptothecin (CPT). Molecular simulations were done using the AMBER force field. The results suggest that a ternary cleavable complex might be stabilized by several hydrogen bonds in the binding site. In this proposed "drug-stacking" model, CPT is pseudointercalated in the top1-linked DNA cleavage site and interacts with the protein near its catalytic tyrosine through hydrogen bonding and stacking. The structural model is consistent with the following experimental observations: (i) the N3 position of the 5' terminal purine of the cleaved DNA strand is readily alkylated by 7-chloromethyl 10,11-methylenedioxy CPT; (ii) CPT generally tolerates substituents at positions 7, 9, and 10 but is inactivated by additions at position 12; (iii) 10,11-methylenedioxy (MDO) CPT is much more potent than 10,11-dimethoxy (DMO) CPT; (iv) the lactone portion of CPT is essential for top1 inhibitory activity; (v) 20S derivatives of CPT are much more potent than the 20R analogues; (vi) a catalytic tyrosine hydroxyl in top1 covalently links to the 3' terminal base, T, of the cleaved DNA strand; and (vii) top1 mutation Asn722Ser leads to CPT resistance. A total of 18 camptothecin derivatives with different DNA cleavage potencies were docked into the hypothetical cleavable complex binding site to test and refine the model. These studies provide insight into a possible mechanism of top1 inhibition by CPT derivatives and suggest rational approaches for the design of new CPT derivatives.

Adsorption of Trivalent Cations on Silica

Gadolinium and yttrium show very similar adsorption behaviors on silica. For the both trivalent cations, the adsorption isotherms are insensitive to the ionic strength. The slope of the log–log adsorption isotherms at a constant pH is considerably lower than 1, except for the range of very low equilibrium concentrations. This behavior can be explained without invoking surface heterogeneity considering the presence of a small concentration of anions, An2–, as an impurity. A hypothetical ternary complex SiOGdAn is very strong and this leads to enhanced uptake at low initial concentrations. When [Gd3+] ⪢ [An2–], only a small fraction of Gd can be adsorbed as SiOGdAn and the percentage of uptake is low.

Specifically Targeted Modification of Human Aldose Reductase by Physiological Disulfides

Aldose reductase is inactivated by physiological disulfides such as GSSG and cystine. To study the mechanism of disulfide-induced enzyme inactivation, we examined the rate and extent of enzyme inactivation using wild-type human aldose reductase and mutants containing cysteine-to-serine substitutions at positions 80 (C80S), 298 (C298S), and 303 (C303S). The wild-type, C80S, and C303S enzymes lost >80% activity following incubation with GSSG, whereas the C298S mutant was not affected. Loss of activity correlated with enzyme thiolation. The binary enzyme-NADP+ complex was less susceptible to enzyme thiolation than the apoenzyme. These results suggest that thiolation of human aldose reductase occurs predominantly at Cys-298. Energy minimization of a hypothetical enzyme complex modified by glutathione at Cys-298 revealed that the glycyl carboxylate of glutathione may participate in a charged interaction with His-110 in a manner strikingly similar to that involving the carboxylate group of the potent aldose reductase inhibitor Zopolrestat. In contrast to what was observed with GSSG and cystine, cystamine inactivated the wild-type enzyme as well as all three cysteine mutants. This suggests that cystamine-induced inactivation of aldose reductase does not involve modification of cysteines exclusively at position 80, 298, or 303.

Alkaline earth and uranyl cation complexes of a calix[4]arene-tetraamide: MD and FEP simulations in aqueous and acetonitrile solutions and X-ray structure of its Sr(Picrate)2 complex

We report the X-ray structure of the L·Sr(Picrate)2(L =tert-butyl-calix [4] arene-tetrakis(diethylamide) and MD simulations on the L·M2+ complexes in vacuo, in water and in acetonitrile solutions (M2+= Mg 2+, Ca2+, Sr2+, Ba2+), with a comparison of ‘converging’ Lc and ‘diverging’ LD conformers, In the simulated and solid-state structures of the L·Sr2+ complex, the cation is completely encapsulated within the polar pseudo-cavity of L, without coordination to its counterion in the crystal, or to solvent molecules in solution. Computations show that the L·M2+ complexes are of converging type in water and in acetonitrile. This contrasts with the L·M+ alkali cation complexes, which display conformational flexibility in solution. Subtle structural changes from Mg2+ to Ba2+ are compared in the gas phase and in solution. In the L·UO22+ hypothetical complex, simulated for comparison, the UO22 + cation is calculated to be less bound by L than the alkaline earth cations. The solvent content of the cone is shown to depend on the size of the complexed cation and modulated by the top–bottom mechanical coupling in the calixarene. Based on free energy perturbation calculations, we calculate a binding sequence of alkaline earth cations (Ca2+ > Sr2+ > Ba2+ > Mg2+) in agreement with experiment.

Molecular interplay of murein synthases and murein hydrolases in Escherichia coli.

Affinity chromatography using different lytic transglycosylases as a specific ligand revealed an interaction of both murein hydrolases and murein synthases. This interaction is taken as evidence for the assemblage into a multienzyme complex that could function as a murein replicase precisely copying the given three-dimensional structure of the murein sacculus. The sacculus of the mother cell would function as a template, which is identically replicated by copying the lengths of the existing glycan strands and the pattern of crosslinkages. A hypothetical enzyme complex specifically involved in cell division and a complex specifically involved in cell elongation are presented. It is postulated that PBPs 1a and/or 1b are present in both complexes, whereas the presence of PBP2 or PBP3 defines the specificity of the murein-synthesizing machinery as being involved in either cell elongation or septation. Moreover, the proposed "holoenzyme" suprastructure could explain why the specific inhibition of PBPs 1a/1b results in bacteriolysis and why inhibition of PBP2 and PBP3 causes the well-known morphological alterations, spherical growth, and filamentation, respectively.

Kinetic testing of a hypothetical complex between flavocytochrome b2 and cytochrome c

Kinetic testing of a hypothetical complex between flavocytochrome b2 and cytochrome c

Fractional composition of fly ash from the first unit of the Berezovskaya GRES-1 State regional power plant

The problem of the existence of endohedral analogs of ferrocene is discussed. It is shown that radical CorH5, where Cor is corannulene C20H10 and five atoms H are added to the α-positions relative to the five-membered cycle (pent*) of Cor, can form stable polyhedral dimer D2h-C40H30 (D). The ground state of D is triplet. The energy of dimerization of CorH5 is equal to 175 kcal mol−1. The geometric and electronic structure of hypothetical endohedral complex D5d-2η5[email protected] (1) and its isomer D5d-2η5-Fe(CorH5)2 (1b), which is a sandwich complex, are simulated by the ab initio MO LCAO SCF method (HF/3-21G). It is found that the energy of 1 is less than the energy of 1b by 171 kcal mol−1. The energies of the Fepent* bond in complexes 1 (115 kcal mol−1) and 1b (111 kcal mol−1) are close to those of the FeCp bond in bis(cyclopentadienyl)iron FeCp2 (110 kcal mol−1). Complex 1 and also complex D5d-2η5[email protected]40H10 (2), carbon skeletons of which have an analogous structure to 1 and with ten H added to the α-positions relative to polar pentagons (pent*), can be considered as endohedral analogs of ferrocene. Atom Fe in these complexes interacts with atoms of both polar pentagons. The binding energy of the atom Fe with the polyhedral fragment C40H10 of 2 is a bit less than in 1 (on 6 kcal mol−1).

Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies.

Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain operating between substrate electron donors and respiratory electron acceptors, in sulfate-reducing bacteria (Desulfovibrio species). The nature and properties of the complex formed between these proteins are revealed by 1H-NMR and molecular modeling approaches. Our previous study with the Desulfovibrio vulgaris proteins [Moura, I., Moura, J.J. G., Santos, M.H., & Xavier, A. V. (1980) Cienc. Biol. (Portugal) 5, 195-197; Stewart, D.E. LeGall, J., Moura, I., Moura, J. J. G., Peck, H.D. Jr., Xavier, A. V., Weiner, P. K., & Wampler, J.E. (1988) Biochemistry 27, 2444-2450] indicated that the complex between cytochrome c3 and flavodoxin could be monitored by changes in the NMR signals of the heme methyl groups of the cytochrome and that the electrostatic surface charge (Coulomb's law) on the two proteins favored interaction between one unique heme of the cytochrome with flavodoxin. If the interaction is indeed driven by the electrostatic complementarity between the acidic flavodoxin and a unique positive region of the cytochrome c3, other homologous proteins from these two families of proteins might be expected to interact similarly. In this study, three homologous Desulfovibrio cytochromes c3 were used, which show a remarkable variation in their individual isoelectric points (ranging from 5.5 to 9.5). On the basis of data obtained from protein-protein titrations followed at specific proton NMR signals (i.e., heme methyl resonances), a binding model for this complex has been developed with evaluation of stoichiometry and binding constants. This binding model involves one site on the cytochromes c3 and two sites on the flavodoxin, with formation of a ternary complex at saturation. In order to understand the potential chemical form of the binding model, a structural model for the hypothetical ternary complex, formed between one molecule of Desulfovibrio salexigens flavodoxin and two molecules of cytochrome c3, is proposed. These molecular models of the complexes were constructed on the basis of complementarity of Coulombic electrostatic surface potentials, using the available X-ray structures of the isolated proteins and, when required, model structures (D. salexigens flavodoxin and Desulfovibrio desulfuricans ATCC 27774 cytochrome c3) predicted by homology modeling.

Mononuclear bis-aminocarbyne complexes of tungsten with Tp′ ligands; theory of metal-centred carbyne-carbyne coupling

An efficient procedure for the synthesis of mononuclear bis-aminocarbyne complexes of tungsten is reported starting from Tp′(CO) 2WCN (R)Et ( 1a: R  Me; 1b: R  Et) (Tp′= hydrido(3,5-dimethylpyrazol-1-yl)borate). In the first step oxidative decarbonylation of 1a and 1b with Br 2 occurs to afford the six-coordinate aminocarbyne complexes Tp′(Br) 2WCN(R)Et ( 2a, 2b) in high yield. Similarly, complexes 1a and 1b are converted by I 2 into the diiodo derivatives Tp′(I) 2WCN(R)Et ( 3a, 3b). Reductive dehalogenation of 3a and 3b by Na/Hg in the presence of EtNC gives the electron-rich mono-aminocarbyne complexes Tp′(EtNC) 2WCN(R)Et ( 4a, 4b), which are finally alkylated with [Et 3O]BF 4 at one isocyanide-nitrogen to yield the bis- aminocarbyne complexes {Tp′(EtNC)W[ ▪CN(R)Et][ ▪CNEt 2]}BF 4 ( 5a, 5b). Extended-Hückel calculations on the hypothetical 18e bis-carbyne complex [CpW(CO)(CH) 2] + predict a spontaneous rearrangement to the energetically favoured 16e acetylene complex [CPW(CO)(HCCH)] + and show, in full agreement with the experimental work, that introduction of amino-substituents on both carbyne-carbons stabilizes the bis-carbyne form relative to the alkyne isomer. The solid-state structure of 2b was determined by a single- crystal X-ray diffraction study revealing a distorted octahedral complex with a short WC carbyne bond. The short C carbyne N bond and the planar amino-nitrogen indicate a high degree of π-bonding between the carbyne-carbon and the amino-nitrogen.

A hypothetical complex between crystalline flavocytochrome b2 and Cytochrome c

Flavocytochrome b2 and cytochrome c are physiological electron transfer partners in yeast mitochondria. The formation of a stable complex between them has been demonstrated both in solution and in the crystalline state. On the basis of the three-dimensional structures, using molecular modeling and energy minimization, we have generated a hypothetical model for the interaction of these redox partners in the crystal lattice. General criteria such as good charge and surface complementarity, plausible orientation, and separation distance of the prosthetic groups, as well as more specific criteria such as the stoichiometry determined in the crystal, and the involvement of both domains and of more than one subunit of flavocytochrome b2 led us to discriminate between several possible interaction sites. In the hypothetical model we present, four cytochrome c molecules interact with a tetramer of flavocytochrome b2. The b2 and c hemes are coplanar, with an edge-to-edge distance of 14 A. The contact surface area is ca. 800 A2. Several electrostatic interactions involving the flavin and the heme domains of flavocytochrome b2 stabilize the binding of cytochrome c.

Opening of metal carbonyl cluster complexes by ligand addition. Synthesis and structural characterization of osmium cluster Os3(CO)11(.mu.-CNCF3)2, a stabilized derivative of the hypothetical complex Os3(CO)13

Opening of metal carbonyl cluster complexes by ligand addition. Synthesis and structural characterization of osmium cluster Os3(CO)11(.mu.-CNCF3)2, a stabilized derivative of the hypothetical complex Os3(CO)13

Annexin V membrane interaction: an electrostatic potential study

The possible role of electrostatic interactions for membrane binding and pore formation of annexin V has been analysed on the basis of a simple dielectric model. It is suggested that the binding of phospholipids to annexin V is regulated, at least initially, by the protein's electrostatic potential. The calculations show that a strong local gradient of the electrostatic potential exists at the membrane-protein interface and a membrane pore may be generated by electroporation. The observed specificity and regulation of ion conduction is suggested to reside in the protein part of the pore. On the basis of the three-dimensional structures of the protein and its hypothetical membrane complex, and electrophysiological measurements, a mechanical model of the transmembrane voltage regulation of the annexin's ion conduction properties is proposed.

Spin rovibronic symmetry in the formation of Van der Waals complexes

To include weak electron spin rovibronic and nuclear interaction other than electrostatic interaction we invoke the coupling of the spin rovibronic states of the molecular fragments as they form Van der Waals complexes. It is shown how concerted and cooperative rotation/vibration, etc. will preserve the relative geometry and potential for the complex. Stateto-state symmetry correlations, including the Fermion symmetry of protons are performed for the formation of a hypothetical dimer of C2h symmetry from a monomer ABH3 of C3v symmetry, and for the formation of a hypothetical complex of C3v symmetry from ABH3 coupled with C6H6 Cor C6F6) of D6h symmetry.