Design of amino acid sulfonamides as transition-state analogue inhibitors of arginase

Arginase is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine plus urea. Chiral L-amino acids bearing sulfonamide side chains have been synthesized in which the tetrahedral sulfonamide groups are designed to target bridging coordination interactions with the binuclear manganese cluster in the arginase active site. Syntheses of the amino acid sulfonamides have been accomplished by the amination of sulfonyl halide derivatives of (S)-(tert-butoxy)-[(tert-butoxycarbonyl)amino]oxoalkanoic acids. Amino acid sulfonamides with side chains comparable in length to that of L-arginine exhibit inhibition in the micromolar range, and the X-ray crystal structure of arginase I complexed with one of these inhibitors, S-(2-sulfonamidoethyl)-L-cysteine, has been determined at 2.8 A resolution. In the enzyme-inhibitor complex, the sulfonamide group displaces the metal-bridging hydroxide ion of the native enzyme and bridges the binuclear manganese cluster with an ionized NH(-) group. The binding mode of the sulfonamide inhibitor may mimic the binding of the tetrahedral intermediate and its flanking transition states in catalysis. It is notable that the ionized sulfonamide group is an excellent bridging ligand in this enzyme-inhibitor complex; accordingly, the sulfonamide functionality can be considered in the design of inhibitors targeting other binuclear metalloenzymes.     

Ureases: quantum chemical calculations on cluster models

Herein, we present results from a computational study of dinickel complexes that are relevant to the catalytic hydrolysis of urea exerted by the urease enzymes. The B3LYP density functional is used to characterize the equilibrium geometry, electronic and magnetic properties, and energies for a series of realistic complexes modeling the active site of ureases. The analysis of the theoretical results gives new insight into the structure, substrate binding, and catalytic mechanism. The water bridge between the two Ni(II) ions observed in the crystallographic structures of the ureases was assigned to a hydroxide bridge in agreement with the observed small antiferromagnetic coupling. Both monodentate and bidentate urea-bound complexes, in which urea had favorable orientations for catalysis, were characterized. Finally, two reaction mechanisms were investigated starting from the monodentate and bidentate urea-bound complexes, respectively. Both a Ni1...Ni2 bridging hydroxide and a Ni2-bound water molecule play crucial roles in the two mechanisms.     

Synthesis and characterization of the tetranuclear iron(III) complex of a new asymmetric multidentate ligand. A structural model for purple acid phosphatases

The ligand, 2-((2-hydroxy-5-methyl-3-((pyridin-2-ylmethylamino)methyl)benzyl)(2-hydroxybenzyl)amino)acetic acid (H(3)HPBA), which contains a donor atom set that mimics that of the active site of purple acid phosphatase is described. Reaction of H(3)HPBA with iron(III) or iron(II) salts results in formation of the tetranuclear complex, [Fe(4)(HPBA)(2)(OAc)(2)(mu-O)(mu-OH)(OH(2))(2)]ClO(4) x 5H(2)O. X-Ray structural analysis reveals the cation consists of four iron(III) ions, two HPBA(3-) ligands, two bridging acetate ligands, a bridging oxide ion and a bridging hydroxide ion. Each binucleating HPBA(3-) ligand coordinates two structurally distinct hexacoordinate iron(III) ions. The two metal ions coordinated to a HPBA(3-) ligand are linked to the two iron(III) metal ions of a second, similar binuclear unit by intramolecular oxide and hydroxide bridging moieties to form a tetramer. The complex has been further characterised by elemental analysis, mass spectrometry, UV-vis and MCD spectroscopy, X-ray crystallography, magnetic susceptibility measurements and variable-temperature M?ssbauer spectroscopy.     

Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

catena‐Poly­[[bis­(thio­cyanato‐κN)cadmium(II)]‐di‐μ‐thio­urea‐κ4S:S]

The Cd^II ion in the title complex, [Cd(SCN)₂{SC(NH₂)₂}₂]_∞, is situated at a centre of symmetry, and is bound to two N atoms belonging to thio­cyanate groups and to four S atoms of bridging thio­urea ligands. The structure consists of infinite chains of slightly distorted edge‐shared Cd‐centred octahedra. The bridging S atoms of two thio­urea ligands comprise the common edge. Some thermal properties are described.     

镉(Ⅱ)与对乙酰氨基苯甲酸、4，4′-联吡啶配位聚合物的合成、晶体结构及荧光性质

The complex {[Cd₂(C₉H₈O₃N)₂(CH₃COO)₂(4,4′-bipy)₂]·(4,4′-bipy)·(H₂O)₄}_n with 4-acetamidobenzoic acid and 4,4′-bipyridine has been synthesized with liquid diffusion method and characterized. It crystallizes in the monoclinic space group C2/c. The crystal structure shows that two neighboring cadmium(Ⅱ) ions are linked together by two bridging acetic acid radicals, forming a binuclear structure. Adjacent binnuclear structure is linked together by two bridging 4,4′-bipy molecules and the complex molecule forms an one-dimensional double-chain structure. The luminescent properties of the complex were studied. CCDC: 734878.     

Determination of hexamethylene tetramine in the process solution of sol-gel method for nuclear fuel fabrication

Hexamethylene tetramine (HMTA) was determined in the presence of large quantities of urea, formaldehyde and ammonium hydroxide by potentiometric titration with perchloric acid solution using an autotitrator coupled to a personal computer. This analysis is required for the process control of the sol-gel method in the production of ceramic metal oxide (e.g., oxides and mixed oxides of Th, U and Pu) microspheres using the internal gelation route. Feed solution used for preparation of microspheres contains large quantities of urea. The washings of gel microspheres produced after the internal geletion process contain urea, formaldehyde, urea-formaldehyde complex and ammonium hydroxide. The presence of these constituents in the feed solution and washings seriously interfere in the commonly used methods for the determination of HMTA. Using this method the relative standard deviation was found to be 0.27% in eleven determinations of a typical feed solution (3.0M HMTA) when the aliquots contained 75 to 125 mg of HMTA. Time required for each titration was 5–7 minutes. Feed and effluent solutions of sol-gel process were analysed.     

Dissociation rates of urea in the presence of NiOOH catalyst: a DFT analysis

Single molecule reactions have been studied between nickel oxyhydroxide, urea, and the hydroxide ion to understand the process of urea dissociation into ammonia, isocyanic acid, cyanate ion, carbon dioxide, and nitrogen. In the absence of hydroxide ions, nickel oxyhydroxide will catalyze urea to form ammonia and isocyanic acid with the rate-limiting step being the formation of ammonia with a rate constant of 1.5 × 10?? s?1. In the presence of hydroxide, the evolution of ammonia was also the rate-limiting step with a rate constant of 1.4 × 10?2? s?1. In addition, desorption of the cyanate ion presented an energy barrier of 6190 kJ mol?1 suggesting that the cyanate ion cannot be separated from NiOOH unless further reactions occurred. Finally, elementary dissociation reactions with hydroxide ions deprotonating urea to produce nitrogen and carbon dioxide were analyzed. These elementary reactions were investigated along three paths differing in the order that protons were removed and the nitrogen atoms were rotated. The rate-limiting step was found to be the removal of carbon dioxide with a rate constant of 4.3 × 10??? s?1. Therefore, the catalyst could be deactivated by the surface blockage caused by carbon dioxide adsorption.     

Urea decomposition facilitated by a urease model complex: a theoretical investigation

Density functional theory calculations were used to examine the role of the urease model complex [Ni2(bdptz)(micro-OH)(micro-H2O)(H2O)2](OTs)3(bdptz=1,4-bis(2,2'-dipyridylmethyl)-phthalazine; OTs=tosylate) in the degradation of urea. An elimination mechanism that converts urea to ammonium cyanate was investigated in detail. The lowest energy pathway involves urea coordination through the oxygen atom to a Ni center followed by protonation of a urea NH2 group by the bridging water ligand. Subsequent rotation of the protonated urea, followed by deprotonation of the NH2 by a bridging OH ligand generates the bound, disproportionated urea substrate, HNCONH3, from which ammonium cyanate was produced.     

Electro-nuclear double resonance spectroscopic evidence for a hydroxo-bridge nucleophile involved in catalysis by a dinuclear hydrolase

Despite the current availability of several crystal structures of purple acid phosphatases, to date there is no direct evidence for solvent-derived ligands occupying terminal positions in the active enzyme. This is of central importance, because catalysis has been shown to proceed through the direct attack on a metal-bound phosphate ester by a metal-activated solvent-derived moiety, which has been proposed to be either (i) a hydroxide ligand terminally bound to the ferric center or (ii) a bridging hydroxide. In this work we use (2)H Q-band (35 GHz) pulsed electron-nuclear double resonance (ENDOR) spectroscopy to identify solvent molecules coordinated to the active mixed-valence (Fe(3+)Fe(2+)) form of the dimetal center of uteroferrin (Uf), as well as to its complexes with the anions MoO(4), AsO(4), and PO(4). The solvent-derived coordination of the dinuclear center of Uf as deduced from ENDOR data includes a bridging hydroxide and a terminal water/hydroxide bound to Fe(2+) but no terminal water/hydroxide bound to Fe(3+). The terminal water is lost upon anion binding while the hydroxyl bridge remains. These results are not compatible with a hydrolysis mechanism involving a terminal Fe(3+)-bound nucleophile, but they are consistent with a mechanism that relies on the bridging hydroxide as the nucleophile.     

The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme

Urease, the most efficient enzyme known, contains an essential dinuclear Ni^II cluster in the active site. It catalyzes the hydrolysis of urea, inducing a rapid pH increase that has negative effects on human health and agriculture. Thus, the control of urease activity is of utmost importance in medical, pharmaceutical, and agro‐environmental applications. All known urease inhibitors are either toxic or inefficient. The development of new and efficient chemicals able to inhibit urease relies on the knowledge of all steps of the catalytic mechanism. The short (microseconds) lifetime of the urease–urea complex has hampered the determination of its structure. The present study uses fluoride to substitute the hydroxide acting as the co‐substrate in the reaction, preventing the occurrence of the catalytic steps that follow substrate binding. The 1.42 Å crystal structure of the urease–urea complex, reported here, resolves the enduring debate on the mechanism of this metalloenzyme.     

First computational evidence for a catalytic bridging hydroxide ion in a phosphodiesterase active site.

Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulates the intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding the structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it is uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand is theoretically determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.     

A rapid spectrophotometric method for determination of fluoride in silicates with the zirconyl-xylenol orange complex

A critical study has been made of the effect of acid concentration and of polymerized and depolymerized zirconyl ions on the formation of ZrO-XO complexes and their stabilities. At an optimum acidity of 0.5-0.6M hydrochloric acid, most of the common cations occurring in silicates do not interfere. Maximum colour development is almost instantaneous for the depolymerized ZrO-XO complex, but takes a few hours for the polymerized complex; the colour is stable for several hours. The absorbance is highest for the depolymerized ZrO-XO complex and decreases with an increase in polymerization of the zirconyl ions. Dissolved oxides of nitrogen affect the stability of the ZrO-XO complex but can be eliminated with urea. A simple, rapid and sensitive spectrophotometric method has been worked out for use of this complex in determination of fluoride in silicates, without separation, after fusion of the sample with sodium hydroxide at 450-550 degrees.     

Reactivity of mu-hydroxodizinc(II) centers in enzymatic catalysis through model studies

The stable dinuclear complex [Zn2(BPAM)(mu-OH)(mu-O2PPh2)](ClO4)2, where BPAN = 2,7-bis[2-(2-pyridylethyl)-aminomethyl]-1,8-naphthyridine, was chosen as a model to investigate the reactivity of (mu-hydroxo)dizinc(II) centers in metallohydrolases. Two reactions, the hydrolysis of phosphodiesters and the hydrolysis of beta-lactams, were studied. These two processes are catalyzed in vivo by zinc(II)-containing enzymes: P1 nucleases and beta-lactamases, respectively. The former catalyzes the hydrolysis of single-stranded DNA and RNA. beta-Lactamases, expressed in many types of pathogenic bacteria, are responsible for the hydrolytic degradation of beta-lactam antibiotic drugs. In the first step of phosphodiester hydrolysis promoted by the dinuclear model complex, the substrate replaces the bridging diphenylphosphinate. The bridging hydroxide serves as a general base to deprotonate water, which acts as a nucleophile in the ensuing hydrolysis. The dinuclear model complex is only 1.8 times more reactive in hydrolyzing phosphodiesters than a mononuclear analogue, Zn(bpta)(OTf)2, where bpta = N,N-bis(2-pyridylmethyl)-tert-butylamine. Hydrolysis of nitrocefin, a beta-lactam antibiotic analogue, catalyzed by [Zn2(BPAN)(mu-OH)(mu-O2PPh2)](ClO4)2 involves monodentate coordination of the substrate via its carboxylate group, followed by nucleophilic attack of the zinc(II)-bound terminal hydroxide at the beta-lactam carbonyl carbon atom. Collapse of the tetrahedral intermediate results in product formation. Mononuclear complexes Zn(cyclen)-(NO3)2 and Zn(bpta)(NO3)2, where cyclen = 1,4,7,10-tetraazacyclododecane, are as reactive in the beta-lactam hydrolysis as the dinuclear complex. Kinetic and mechanistic studies of the phosphodiester and beta-lactam hydrolyses indicate that the bridging hydroxide in [Zn2(BPAN)(mu-OH)(mu-O2PPh2)](ClO4)2 is not very reactive, despite its low pKa value. This low reactivity presumably arises from the two factors. First, the briding hydroxide and coordinated substrate in [Zn2(BPAN)(mu-OH)(substrate)]2+ are not aligned properly to favor nucleophilic attack. Second, the nucleophilicity of the bridging hydroxide is diminished because it is simultaneously bound to the two zinc(II) ions.     

A Novel Two‐Dimensional Cadmium Polymeric Aminonaphthalene Sulfonate and its Application in the Synthesis of CdS Materials

A new mixed‐ligand complex, [CdL(bipy)(CH₃OH)(NO₃)]_n ( 1 ), (HL = 4‐amino‐1‐naphthalene sulfonic acid and bipy = 4,4′‐bipyridine) could be achieved by combining d¹⁰ Cd²⁺ to HL and bridging ligand 4,4′‐bipy. The structure is characterized by X‐ray single‐crystal diffraction. 4‐amino‐1‐naphthalene sulfonate and 4,4′‐bipyridine act as bridging ligands, linking two adjacent Cd^II atom to form a two‐dimensional coordination polymer, respectively. N‐H···O hydrogen‐bonding interaction between these networks to form the face‐to‐face three‐dimensional architecture. By carrying out the reaction of polymeric cadmium naphthalene sulfonate with Na₂S in the presence of sodium hydroxide, scalelike CdS materials have been obtained. The structure has been characterized by scanning electron microscopy and powder X‐ray diffraction.     

苎麻叶中绿原酸的分光光度法测定

探讨了采用分光光度法测定苎麻叶中绿原酸的含量的方法。12.5%的醋酸用量为0.1mL,7%尿素2.0mL,0.5%亚硝酸钠0.25mL,3min后加入5%氢氧化钠0.5mL,绿原酸与试剂形成鲜红色络合物,通过在510nm处测定溶液的吸光度确定绿原酸的含量。绿原酸浓度在0.01~0.12g/L范围内与吸光度值有良好的线性关系,回收率为95%~107%,相对标准偏差(RSD)为2.4%。该方法简便、快速。     

Formation and stability of mononuclear and dinuclear Eu(III) complexes and their catalytic reactivity toward cleavage of an RNA analog

The complex between Eu(III) and 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid (L4) was characterized by pH potentiometric titration and 1H NMR spectroscopy. The conversion of the monomer to a dimeric complex is observed as the pH is increased from 7 to 10 in a reaction that releases one mol/HO- per dimer formed. The dimeric complex undergoes a further ionization with a pKa of 10.7. Kinetic parameters are reported for the cleavage of the simple phosphodiester 2-hydroxypropyl-4-nitrophenyl phosphate catalyzed by both the monomeric and the dimeric Eu(III) complexes. These data show that the monomer and dimer stabilize their bound reaction transition states with similar free energies of 7.1 and 7.6 kcal/mol, respectively. Clearly, a bridging hydroxide is not an optimal linker to promote cooperative catalysis between Eu(III) centers in macrocycles with multiple polyaminocarboxylate pendent groups.     

Structure-based analysis and optimization of a highly enantioselective catalyst for the strecker reaction

A mechanistic investigation of the asymmetric Strecker reaction catalyzed by a metal-free Schiff base catalyst was conducted. The active site of the catalyst, the relevant stereoisomer of the imine substrate, and the solution structure of the imine-catalyst complex were elucidated using a series of kinetics, structure-activity, and NMR experiments. An unusual bridging interaction between the imine and the urea hydrogens of the catalyst was identified and supported by computation. Rational optimization of catalyst structure based on the mechanistic insight led to an improved catalyst for the asymmetric Strecker reaction.     

Correlation of structure and function in oligonuclear zinc(II) model phosphatases

A series of pyrazolate-based dizinc(II) complexes has been synthesized and investigated as functional models for phosphoesterases, focusing on correlations between hydrolytic activity and molecular parameters of the bimetallic core. The Zn...Zn distance, the (bridging or nonbridging) position of the Zn-bound hydroxide nucleophile, and individual metal ion coordination numbers are controlled by the topology of the compartmental ligand scaffold. Species distributions of the various dizinc complexes in solution have been determined potentiometrically, and structures in the solid state have been elucidated by X-ray crystallography. The hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) promoted by the dinuclear phosphoesterase model complexes has been investigated in DMSO/buffered water (1:1) at 50 degrees C as a function of complex concentration, substrate concentration, and pH. Coordination of the phosphodiester has been followed by ESI mass spectrometry, and bidentate binding could be verified crystallographically in two cases. Drastic differences in hydrolytic activity are observed and can be attributed to molecular properties. A significant decrease of the pK(a) of zinc-bound water is observed if the resulting hydroxide is involved in a strongly hydrogen-bonded intramolecular O(2)H(3) bridge, which can be even more pronounced than for a bridging hydroxide. Irrespective of the pK(a) of the Zn-bound water, a hydroxide in a bridging position evidently is a relatively poor nucleophile, while a nonbridging hydroxide position is more favorable for hydrolytic activity. Additionally, the metal array has to provide a sufficient number of coordination sites for activating both the substrate and the nucleophile, where phosphate diesters such as BNPP preferentially bind in a bidentate fashion, requiring a third site for water binding. Product inhibition of the active site by the liberated (p-nitrophenyl)phosphate is observed, and the product-inhibited complex could be characterized crystallographically. In that complex, the phosphate monoester is found to cap a rectangular array of four zinc ions composed of two bimetallic entities.     

Syntheses and structures of ytterbium(II) hydride and hydroxide complexes: similarities and differences with their calcium analogues

The Yb(II) hydride complex (DIPP-nacnac)YbH x THF (3-Yb, DIPP-nacnac = CH{(CMe)(2,6-iPr(2)C(6)H(3)N)}(2)) was prepared by a mild metathesis reaction of (DIPP-nacnac)Yb[N(SiMe(3))(2)].THF with PhSiH(3). 3-Yb crystallizes as a dimer with bridging hydride ions, and its geometry is similar to that of the analogue calcium hydride complex (3-Ca). 3-Yb is well soluble in benzene and remarkably stable in solution at room temperature. Ligand exchange to the homoleptic Yb(II) complexes takes place at higher temperatures (3-Yb is less stable than the analogue 3-Ca). The soluble hydride complexes 3-Ca and 3-Yb are catalysts for the hydrosilylation of 1,1-diphenylethylene, but differences in the product distributions are observed. Slow hydrolysis of (DIPP-nacnac)Yb[N(SiMe(3))(2)].THF gave reduction of water and unidentified Yb(III) complexes. Fast hydrolysis at low temperature, however, resulted in the first Yb(II) hydroxide complex, (DIPP-nacnac)Yb(OH) x THF (4-Yb, 20% yield), which is a dimer with bridging hydroxide ions in the solid state. The crystal structure is isomorphous to that of the calcium analogue 4-Ca. 4-Yb is well soluble in benzene and considerably more stable against ligand exchange and formation of homoleptic species than 3-Yb.