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A detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses is reported. The rate of single-nucleotide incorporation for all four alpha-L-threofuranosyl nucleoside triphosphates (tNTPs) and beta-D-2'-deoxyribofuranosyl nucleoside triphosphates (dNTPs) from a DNA primer-template complex is examined.

A combination of density functional theory (DFT) and dielectric continuum solvation methods is used to study the possible hydrolysis pathways of mono-phosphate and tri-phosphate esters in gas phase and aqueous solution. Results indicate that for the mono-phosphate monoanion, the dissociative process is more favorable than the associative process, especially when an additional water molecule plays an active role in the dissociative process.

The chemical synthesis and stereochemical assignment of the tetrahedral intermediate of 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) defining the mechanism of this enzyme is described. A model substrate to evaluate condition that would effect debromination of a highly charged species and permit purification of an acid-labile product is presented.

Equilibrium and kinetic isotope effects were measured for several phosphorothioate esters of p-nitrophenol (pNPPT) and the results were compared with data from phosphate esters to study the comparative inherent chemistry of the two types of esters. Results of the study suggested that leading a group bond fission in the transition state of reactions of the monoester pNPPT was more advanced than for its phosphate counterpart pNNP, while alkaline hydrolysis of the phosphorothioate diester and triester somewhat less advanced bond fission than that of their phosphate ester counterparts.

Chemists are performing research on the hydrolysis of phosphate esters especially to the study of phosphoryl transfer reactions both in solution and those catalyzed by enzymes. The results of the theoretical calculations of (super 16)O/(super 18)O equilibrium isotope effects (EIEs) on deprotonation of phosphate and methyl phosphate monoanions as well as their deuterated counterparts are reported.

The studies revealed that squalene synthase (SQase) catalyzes two consecutive reactions in sterol biosynthesis. The first is the condensation of two molecules of famesyl diphosphate (FPP) to form acyclopropylcarbinyl intermediate, presqualene diphosphate (PSPP). It is concluded that the catalytic machinery of the enzyme can synthesize 1'-1 compounds typical of those seen in the sterol and carotenoid biosynthetic pathways, as well as the 1'-3 structures found in botryococcene.

The study revealed that squalene synthase (SQase) catalyzes the condensation of two molecules of farnesyl diphosphate (FPP) to form presqualene diphosphate (PSPP) and the subsequent rearrangement of NADPH-dependent reduction of PSPP to squalene (SQ). The study compared the SQase-catalyzed solvolysis of PSPP in the absence of NADPH(sub 3) to the reaction in the presence of NADPH(sub 3), and stated that it is apparent that the binding of the cofactor analogue substantially enhances the ability of SQase to control the regio-and stereochemistry of the rearrangements of PSPP.

A single-site organometallic mechanism was proposed for the oxidation of n-butane in VPO (vanadium phosphates) catalysts. The chelating configuration is maintained during the reaction until the formation of maleic anhydride.

Research is presented concerning the absolute and relative stereochemistry of the total synthesis of fostriecin (CI-920), a potent antitumor agent consisting of a phosphate monoester. The storage of fostriecin is discussed.

Issues concerning the investigation of a simple pathway to produce a number of open-framework metal phosphates using the reaction of a single amine phosphate are discussed. These phosphates exhibited a number of different structures including layered and three-dimensional and in particular linear chain structure made up of corner-shared four-membered rings.

Substrate-assisted general base catalysis of phosphoryl transfer has been evaluated for the hydrolysis of a phosphate monoester dianion in solution.

Research is presented describing the isolation of a family of salt-templated arsenates and phosphates, A2M3(X2O7)2.(salt). The MXO framework is not destroyed when the space-filling, charge-compensation alkali metal chloride salts are removed.

Research was conducted to examine the interactions of phosphate and pyrophosphate anions with polyammonium cations obtained from 14 polyamines in aqueous solution using potentiometric, microcalorimetric and NMR calculations in solution. Results provide insight into the interpretation of thermodynamic data for the formation of anion complexes since the formation of neutral complexes or hydrogen-bonded ion pairs from separated species is expected to be accompanied by quite different enthalpic and entropic contributions.

Research was conducted to examine a practical synthesis of O-glycosides using 2-(beta-D-glycosylocy)-3-methoxypyridine (MOP) donors. 1-phosphate esters of alpha-D-glucopyranose, alpha-D-galactopyranose and 2-azido-2-deoxy-alpha-D-galactopyranose were prepared without the need for protective groups since the reaction of MOP glycosides with phosphoric acid results in excellent stereoselectivity and the corresponding 1,2-cis-1-phosphates in good yield. Results demonstrate that MOP donors are versatile intermediates for the one-step stereocontrolled synthesis.

A chemical method of synthesis of oligodeoxynucleoside boranophosphates (BH3-ODNs) on a solid phase has been developed via an H-phosphonate chain elongation approach followed by boronation. The efficiency of the boronation procedure was found to be comparable to that of iodine oxidation to form phosphodiester oligodinucleosides. Studies of substrate properties showed that BH3-ODNs are readily 5'-phosphorylated by T4 polynucleotide kinase. The resulting BH3-ODNs can be easily handled, purified and analyzed by conventional HPLC and PAGE techniques.

The synthesis and characterization of pillared derivatives of gamma-zirconium phosphate, ZrP04[O2P(OH)2]1-x[O2-POH-(CH2)n-HOPO2]X/2.mH20 between the colloidal dispersions of exfoliated lamellae of gamma-ZrPO4[O2P(OH)2].2H2O and the 1,n-alkanedisphosphonic acid solutions were described. Soft topotactic reactions were found to be effective in preparing gamma-Zirconium phosphate derivatives. The gallery height of the derivatives ranged from 0.36 to 1.4 nm, while large lateral distances depended on the degree of pillaring.

A study was conducted to examine the reactivities of several phosphate diesters coordinated to a dinuclear Co(III) complex. Results indicated that the hydrolysis of the phosphate diesters are supported by an intramolecular oxide attack on the bridging phosphate. Findings also showed no significant proton transfer from the solvent to the leaving group in the rate-determining state.

Conformational studies were performed on the dimethyl phosphate anion, dimethyl phosphorothioate anion, dimethyl methylphosphonate and methyl ethylphosphonate anion in the gas phase and in aqueous solution. Results showed that the aqueous solvation effects have an important role in conformational stability and kinetics of conformationalf transitions of these esters. Also, the substitution of either O3' or O5' oxygen in the phosphodiester bonds enhances the local flexibility of the resulting DNA linkage.

A study was conducted to examine the photoionization of organic phosphates by 193 nm argon fluoride excimer laser. Solutions were daerated with argon or saturated with oxygen before being flowed through a Suprasil quartz cell supporting flow rates. Results indicated that the six-membered transition state supported hydrogen transfer at C4 to the phosphate group at C5 and C3. Findings also showed that the photolysis of phosphates resulted in the formation of oxygen-centered phosphate radicals.

A study was conducted to examine the ability of 5'-triphosphates to inhibit HIV reverse transcriptase (RT) to analyze the preference of 3'-azido-3'-deoxythimidine (AZT) for the extreme (sub 3)E conformation. Conformational preferences were corroborated by X-ray analysis. Results indicated that the inhibition of RT only occurred with the conformotionally locked (sub 2)E (N)-methano-carba-AZT 5'-triphosphate.

A study of the spatial distributions of five metal cations, Na+, Mg2+, K+, Ca2+ and Zn2+, and water around a negatively charged phosphate group shows that a significant fraction of metal cations and water is ordered and prefers to bind in sterically well-defined and distinct positions. Findings show that all these cations prefer asymmetric monodentate positions where they bind to only one of the two charged oxygens. A resemblance among the water distributions from the cations, except K+, is noted, but these are modified by the distribution of the accompanying metal.

The POF4- anion was identified. It was formed from N(CH3)4F and POF3 in CHF3 solution. Its geometry and spectroscopic properties were found similar with the isoelectronic SOF4 molecule. The anion was observed to be highly unstable and dismutates at -140 to -130 degrees to PO2F2- and PF6-. Theoretical calculations were made for better understanding of the fluxionality and dismutation of POF4-.

The new photoactivated protecting group, p-hydroxyphenacyl has been investigated as a phototrigger for the efficient, rapid release of inorganic phosphate and ATP. Irradiation of p-hydroxyphenacyl at wavelengths between 300-350 nm triggers the release of these bioactive phosphates. One of the structural features of the new a-keto phototrigger is the lack of chiral center but has a much improved aqueous buffer solubility compared to the desyl analogues. The disappearance and appearance quantum efficiencies were also measured.

Heavy-atom isotope effects were measured for the reactions of p-nitrophenyl phosphate (pNPP) in the stable Co complexes cis-(Co(en)2(OH)pNPP) (1), Co(NH3)5pNPP (2) and a Co(cyclen) complex of pNPP (4) which forms reversibly in solution. Complexes 1 and 2 undergo dissociation of pNPP in competition with nucleophilic attack to release p-nitrophenolate. The kinetic isotope effects on both processes were determined and theory and equations for measuring the isotope effects on both processes are shown.

The rate of bis(p-nitrophenyl) phosphate (BNPP) hydrolysis by the ammonium-functionalized copper(II) complex ((Ln)Cu(NO3)4.2(H2O)) where n = 1,2 where L = (6,6'-(Me2HNCH2C=C)2bpy)2+ (L1) or (6,6'-(Me3NCH2C=C)2bpy)2+ and bpy = 2,2'-bipyridine in ethanol-water solution was investigated. The results revealed (L1)Cu to be 1,000 times more reactive than (L2)Cu and 2,900 times more reactive than (bpy)Cu for the cleavage of the phosphodiester. These are possibly due to the hydrogen bonding of the coordinated phosphodiester with -NMe2H+ which electrostatically activates metal-hydroxide attack on BNPP.

The phosphate geometry was investigated in crystal environment by studying 178 crystal structures and in vacuo by ab initio computations of (di)hydrogen and dimethyl phosphates and a diphosphate model system, CH3OP(O2)O(CH2)3OP(O2)OCH3(diPh), at the MP2 and HF levels. Findings indicated that the internal phosphate geometry is sensitive to a counterion position as well as to values of the C-O-P-O(-C) torsion angles.

Electron spin resonance spectroscopy was employed to examine the physicochemical factors governing the generation of paramagnetic defect centers in aluminophosphate molecular sieves through dehydroxylation at 0.00010 Torr and 773 K. The molecular sieves ranged from small-pore to extra-large-pore systems. According to the results, the nature and amount of paramagnetic defect centers are influenced by their structure and preparation method.

Several nucleoside triphosphates (NTP) with deuterium labels on the 3', 4' and 5' carbons of ribose were synthesized using chemical and enzymatic methods. The chemical procedure entailed the conversion of glycerol-d8 into (D-d4-ribose). It was followed by four enzymatic reactions to transform ribose into adenosine triphospate, guanine triphosphate, CTP and UTP via purine salvage and pyrimidine biosynthetic routes.

The absolute configuration of natural protochlorophyllide a at C-13(sup 2) was derived based on the identical circular dichroism spectra between the protochlorophyllide a isolated from barley seedlings and protochlorophyll a synthesized by dehydrogenation. In addition, the steric requirements of two enzymes, chlorophyll synthase and dihydronicotinamide adenine dinucleotide phosphate-protochlorophyllide oxidoreductase, for chlorophyll biosynthesis was compared.

Previous studies have shown the ability of sapphyrins to serve as phosphate receptors via a unique approach to chelation. In this study, a model for the interaction of sapphyrins to nucleotides and nucleic acids in aqueous media is described. This interaction is carried out in three modes. The first involves the specific chelation of the oxyanion of a phosphorylated nucleotide or nucleic acid with the protonated core of sapphyrin via Coulombic interactions. The second mode involves a hydrophobic interaction between the sapphyrins and the nucleobases. The third involves the aggregation of a sapphyrin derivative on the surface of double-stranded, helical nucleic acids.

A unique approach to phosphate ion chelation based on the use of protonated sapphyrins, macromolecules that are also known as expanded porphyrins, is described. The study investigated three sapphyrin derivatives. The results showed that the diprotonated forms of sapphyrin are capable of forming stable complexes with phosphate-derived monoions. They are also capable of forming a 1:1 chelate complex in the solid state with either mono- or dibasic phosphoric acid. These results indicate that protonated sapphyrins are highly effective phosphate receptors.

A study has been conducted to describe the mechanisms involved in the hydration of the orthophosphate anion in the gas phase and its conversion to the metaphosphate ion using the Electrospray method. Mass spectrometry was also used to measure the ion concentration. Calculations suggest that conversion did not occur because the metaphosphate ion and its hydrates were not observed. The kinetic energy thresholds for collision-induced decomposition revealed a high activation energy barrier.

Molecular dynamics simulations were carried out to derive free energy profiles of the stacking conformation of all 16 ribodinucleoside monophosphates containing mixtures of adenine, cytosine, guanine and uracil bases in aqueous solution. The results, which were obtained via potential of mean force computations, underscored that the stacking-unstacking equilibrium of the unimolecular process is a function of the ribodinucleoside monophosphates' base sequence.

Mechanistic studies of the Cu(II) bipyridine system-mediated hydrolysis of phosphate triesters catalyzed by copper complexes indicate the ability of direction hydrogen bond-based molecular receptors to serve as the catalyst's substrate binder. Kinetic studies reveal the influence of pH and magnitude on the kinetic constants of this reaction, whose rate constant is high.

A multinuclear magnetic resonance spectroscopic study of La(NTA) (NTA: nitrilotriacetate) and La(EDTA) (EDTA: ethylenediaminetetraacetate)- catalyzed hydrolysis of trimetaphosphate (P3m) reveals a similarity in P-O bond activation of P3m and geometry of the complexes of the two catalysts. Tripolyphosphate (PPP), diphosphate (PP) and monophosphate (P) are the products of this hydrolysis. Conversion of PPP and PP to P occurs subsequently. Both P3m and P vie for complexation to La(III), which accounts for reaction inhibition at longer duration of hydrolysis. However, La(NTA) is the preferred catalyst, due to its efficiency of hydrolysis.

Oxygen-18 isotope effects are used to analyze the transition-state structures of phosphoryl transfer reactions of P-nitrophenyl phosphate in water, tert-butyl alcohol and alkaline phosphate catalyzed reactions. Similar transition-state structures are observed in water and tert-butyl alcohol. The bond order of P-O bond in nonbridged oxygen atom remains constant. Substrate binding and conformation change influence the kinetics of catalyzed reaction.

The synthesis of a water-soluble receptor, which bound to cyclic adenosine monophosphate, facilitated the study of molecular recognition on aqueous solutions. Hydrophobic interactions and a phosphate-guanidinium electrostatic interaction and Watson-Crick and Hoogsteen hydrogen-bonding were incorporated in the modular receptor. Such weak intermolecular interactions are responsible for molecular recognition phenomena.

The binding of 3'-uridine monophosphate to bovine pancreatic ribonuclease A for three protonation states of the enzyme-product complex is examined on the basis of stochastic boundary simulations. The function of specific residues is analyzed. In case where a phosphate dianion interacts with positively-charged His 12 and His 119, binding is maximal.

Theoretical analyses of the reaction of metaphosphate anion (PO3-) with one, two and three molecules of water involved 6-31+G geometry optimizations and HP4/6-31+G energy analyses. A planar six-membered cyclic hydrogen-bonded complex forms with PO3- from H2O. A second ring results with the addition of another H2O.

Ab initio quantum mechanical techniques are used to analyze the isomerization processes of PO3-.(H2O)n to H2PO4-.(H2O)n-1, where n = 1 to 3. Exothermicity, isomerization restriction height, structures of the intermediates and transition state products are predicted.

A study on the structural properties, relative energies and vibrational frequencies of the lipid models, dimethyl phosphate and methyl propyl phosphate anions is presented. Ab initio calculations are applied on the two lipid species to determine examine their energy surfaces and their desired molecular conformations. Results show that the gauche-gauche conformation is the most dominant structure of the dimethyl phosphate anion while the methyl propyl phosphate prefers the trans conformation as indicated by the CCOP torsional angle. Findings are compared with previous studies.

A study is done on the reactivities of ((cyclen)Co(OH2)2)3+ (1) and ((tetren)Co(OH2))3+ (2) for hydrolyzing dimethyl phosphate and its possible connection to the mechanistic role of metal ions in ribozymes. The results indicate the possibility of hydrolysis in 1 but not in 2, despite heating the reaction solution to 100 degrees centigrade for one month. The observed hydrolysis for 1 is explained by a mechanism which involves Lewis acid activation and metal hydroxide activation.

A study on the use of discrete monomeric metaphosphate anion as an intermediate in the hydrolysis of u-monothiopyrophosphate (MTP) is presented. A constant temperature of 25 degrees Centigrade in 10-mm nuclear magnetic resonance (NMR) tubes in a Bruker AM500 NMR spectrometer is used for all the experiments. The results are formulated based on a mechanism in which MTP is hydrolyzed into thiophosphate and discrete monomeric metaphosphate within a solvation sphere. The unique property of MTP as a phosphoryl group donor lies in the weakness of its P-S bonds compared to P-O or P-N bonds.

The source of the stability of compounds formed between divalent metal ions and dihydroxyacetone phosphate (DHAP2-) and glycerol 1-phosphate (G1P2-) is investigated. Results show that, for aqueous solutions and for water with 30% or 50% 1,4-dioxane, the stability of these compounds is determined by the metal ion affinity of the phosphate group. The carbonyl group of DHAP2- and the hydroxy group of G1P2- can contribute to complex formation to give seven-membered chelates.

The hydrolysis of bis(8-hydroxyquinoline) phosphate and bis(6-hydroxyquinoline) was undertaken at constant pH with or without certain metal ions as catalysts with the goal of synthesizing reagents capable of hydrolyzing DNA with sequence recognition. Results of the experiments show thatmetal ion catalysis is more effective for the hydrolysis reaction than specificacid catalysis. This indicates that the metal must react directly with the oxgen of the leaving group and that the proton is less active in this reaction.

Variable temperature 27Al and 31P magic-angle-spinning solid-state and 27Al quadrupole nutation NMR spectroscopy are applied to the study of hydrated aluminophosphate molecular sieve VPI-5. Within the temperature range of 343-353 degrees K, the structure of VPI-5 is converted to a higher framework symmetry, with two resonances detected for 31P and 27Al. Results also indicate the existence of two types of water molecules, including noncoordinated, more mobile and coordinated, less mobile molecules.

The hydrogen-bonded salts ((PhO)2PO2)(C3H3NHNMe), ((PhO)2PO2)(C3N2H5), (Cl3CP(OH)O2)(C3H3NHNMe).H2O, (Cl3CP(OH)O2)(C3N2H5).H2O and (PhP(OH)O2)(C3N2H5) were synthesized from the reaction of phosphorus acids with imidazole and 1-methylimidazole. The compounds were characterized by 1H NMR and infrared spectroscopy. The hydrogen bonding types and degrees were investigated for potential use in model studies of enzyme-substrate interactions.

A quadruply bonded dimolybdenum core was incorporated into layered vanadium and niobium phosphates via the redox intercalation of the dimolybdenum core following acetonitrile solvation and the ion-exchange reaction following NaBH4-reduction of the phosphate layer. The formed layers were studied using absorption spectroscopy, magnetic susceptibility and electron paramagnetic resonance measurements. The results indicated that antiferromagnetically coupled electrons comprised the layered structure resulting in weak exchange interaction coupling.

The selectivity and reaction rate for the beta- and gamma-cyclodextrin-initiated regioselective cleavage of adenosine 2',3'-cyclic phosphates are enhanced by cooperation with the alkali-metal halides NaCl, KCl, RbCl, CsCl, KBr and KF. The complex formation of the cyclodextrins with the cyclic phosphates lead to the differentiation of the reaction field for P-O(3') fission and that for P-O(2') fission. The regioselectivity by alpha-cyclodextrin is oriented toward the specificity of natural ribonuclease, while that for beta- and gamma-cyclodextrin is oriented in the opposite direction.

The molecule salicyloyl cyclic phosphate temporarily inhibits the class C beta-lactamase of Enterobacter cloacae P99, the class A TEM beta-lactamase, and also the DD-peptidase of Streptomyces R61. This was gleaned from an examination of the structure and properties of the molecule, wherein it was designed as a 'penicillin-like' inhibitor of beta-lactamases. The cyclic phosphate is the first member of a new class of molecules that can interact with beta-lactam recognizing enzymes to produce inert complexes.