Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations.

The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics.

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.

TAML activator/peroxide-catalyzed facile oxidative degradation of the persistent explosives trinitrotoluene and trinitrobenzene in micellar solutions.

TAML activators are well-known for their ability to activate hydrogen peroxide to oxidize persistent pollutants in water. The trinitroaromatic explosives, 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrobenzene (TNB), are often encountered together as persistent, toxic pollutants. Here we show that an aggressive TAML activator with peroxides boosts the effectiveness of the known surfactant/base promoted breakdown of TNT and transforms the surfactant induced nondestructive binding of base to TNB into an extensive multistep degradation process. Treatment of basic cationic surfactant solutions of either TNT or TNB with TAML/peroxide (hydrogen peroxide and tert-butylhydroperoxide, TBHP) gave complete pollutant removal for both in <1 h with >75% of the nitrogen and ≥20% of the carbon converted to nitrite/nitrate and formate, respectively. For TNT, the TAML advantage is to advance the process toward mineralization. Basic surfactant solutions of TNB gave the colored solutions typical of known Meisenheimer complexes which did not progress to degradation products over many hours. However with added TAML activator, the color was bleached quickly and the TNB starting compound was degraded extensively toward minerals within an hour. A slower surfactant-free TAML activator/peroxide process also degrades TNT/TNB effectively. Thus, TAML/peroxide amplification effectively advances TNT and TNB water treatment giving reason to explore the environmental applicability of the approach.

Catalase-peroxidase activity of iron(III)-TAML activators of hydrogen peroxide.

Exceptionally high peroxidase-like and catalase-like activities of iron(III)-TAML activators of H 2O 2 ( 1: Tetra-Amidato-Macrocyclic-Ligand Fe (III) complexes [ F e{1,2-X 2C 6H 2-4,5-( NCOCMe 2 NCO) 2CR 2}(OH 2)] (-)) are reported from pH 6-12.4 and 25-45 degrees C. Oxidation of the cyclometalated 2-phenylpyridine organometallic complex, [Ru (II)( o-C 6H 4py)(phen) 2]PF 6 ( 2) or "ruthenium dye", occurs via the equation [ Ru II ] + 1/2 H 2 O 2 + H +-->(Fe III - TAML) [ Ru III ] + H 2 O, following a simple rate law rate = k obs (per)[ 1][H 2O 2], that is, the rate is independent of the concentration of 2 at all pHs and temperatures studied. The kinetics of the catalase-like activity (H 2 O 2 -->(Fe III - TAML) H 2 O + 1/2 O 2) obeys a similar rate law: rate = k obs (cat)[ 1][H 2O 2]). The rate constants, k obs (per) and k obs (cat), are strongly and similarly pH dependent, with a maximum around pH 10. Both bell-shaped pH profiles are quantitatively accounted for in terms of a common mechanism based on the known speciation of 1 and H 2O 2 in this pH range. Complexes 1 exist as axial diaqua species [FeL(H 2O) 2] (-) ( 1 aqua) which are deprotonated to afford [FeL(OH)(H 2O)] (2-) ( 1 OH) at pH 9-10. The pathways 1 aqua + H 2O 2 ( k 1), 1 OH + H 2O 2 ( k 2), and 1 OH + HO 2 (-) ( k 4) afford one or more oxidized Fe-TAML species that further rapidly oxidize the dye (peroxidase-like activity) or a second H 2O 2 molecule (catalase-like activity). This mechanism is supported by the observations that (i) the catalase-like activity of 1 is controllably retarded by addition of reducing agents into solution and (ii) second order kinetics in H 2O 2 has been observed when the rate of O 2 evolution was monitored in the presence of added reducing agents. The performances of the 1 complexes in catalyzing H 2O 2 oxidations are shown to compare favorably with the peroxidases further establishing Fe (III)-TAML activators as miniaturized enzyme replicas with the potential to greatly expand the technological utility of hydrogen peroxide.

Density functional theory study of the structural, electronic, and magnetic properties of a mu-oxo bridged dinuclear Fe(IV) complex based on a tetra-amido macrocyclic ligand.

Recently, the synthesis, crystallographic structure, and Mossbauer characterization of the first example of an [(Fe(IV)TAML)2O](2-) (TAML = tetra-amido microcyclic ligand) complex were reported. Here, we elucidate the prominent structural, electronic, and magnetic properties of this complex on the basis of density functional theory (DFT) calculations. While the torsion between the molecular halves is caused by hydrogen bonding between the TAML moieties, the bending of the Fe-O-Fe unit is an intrinsic property of the bridge. The values for the (57)Fe isomer shift and quadrupole splitting obtained with DFT are in good agreement with experimental results and indicate that the irons have intermediate spin states (S1 = S2 = 1). The iron spins are coupled by strong antiferromagnetic exchange to yield a ground state with system spin S = 0. The Fe-O distances in the excited S > 0 states are significantly longer than in the ground state. Since the wave function of the ground state, in which the iron spins are antiferromagnetically coupled to give system spin S = 0, is a linear combination of Slater determinants that cannot be treated with existing DFT codes, the Fe-O distance for the S = 0 state has been estimated by extrapolation from the optimized geometries for the ferromagnetic state (S = 2) and the broken symmetry state to be 1.748 A, in good agreement with the crystallographic distance 1.728 A. To accommodate the spin-dependent reorganization energies, the conventional bilinear spin Hamiltonian has been extended with a biquadratic coupling term: H(ex) = c' + j0S1 x S2 + j1(S1 x S2)(2). A computational scheme is presented for estimating the exchange parameters, yielding the values j0 = 199 cm(-1) and j1 = -61 cm(-1) for [(Fe(IV)B*)2O](2-). Two mechanisms for biquadratic exchange are discussed.

Mechanistically inspired design of Fe(III)-TAML peroxide-activating catalysts.

Recent broad-ranging mechanistic studies of FeIII-TAML peroxide activators enable a strategy for designing catalysts with improved (i) hydrolytic and (ii) operational stabilities, (iii) faster activation of H2O2 and other peroxides, and (iv) a pH of highest activity closer to 7. Combining all items of insight leads to [Fe{1-NO2C6H3-3,4-(NCOCMe2NCO)2CF2}(OH2)]- (1a) which exhibits the most desirable technical performance in its class.

(TAML)FeIV O complex in aqueous solution: synthesis and spectroscopic and computational characterization.

Recently, we reported the characterization of the S = (1)/ 2 complex [Fe (V)(O)B*] (-), where B* belongs to a family of tetraamido macrocyclic ligands (TAMLs) whose iron complexes activate peroxides for environmentally useful applications. The corresponding one-electron reduced species, [Fe (IV)(O)B*] (2-) ( 2), has now been prepared in >95% yield in aqueous solution at pH > 12 by oxidation of [Fe (III)(H 2O)B*] (-) ( 1), with tert-butyl hydroperoxide. At room temperature, the monomeric species 2 is in a reversible, pH-dependent equilibrium with dimeric species [B*Fe (IV)-O-Fe (IV)B*] (2-) ( 3), with a p K a near 10. In zero field, the Mössbauer spectrum of 2 exhibits a quadrupole doublet with Delta E Q = 3.95(3) mm/s and delta = -0.19(2) mm/s, parameters consistent with a S = 1 Fe (IV) state. Studies in applied magnetic fields yielded the zero-field splitting parameter D = 24(3) cm (-1) together with the magnetic hyperfine tensor A/ g nbeta n = (-27, -27, +2) T. Fe K-edge EXAFS analysis of 2 shows a scatterer at 1.69 (2) A, a distance consistent with a Fe (IV)O bond. DFT calculations for [Fe (IV)(O)B*] (2-) reproduce the experimental data quite well. Further significant improvement was achieved by introducing hydrogen bonding of the axial oxygen with two solvent-water molecules. It is shown, using DFT, that the (57)Fe hyperfine parameters of complex 2 give evidence for strong electron donation from B* to iron.

Attaining control by design over the hydrolytic stability of Fe-TAML oxidation catalysts.

The iron(III) complexes of tetra amidato macrocyclic ligands (TAMLs) ([Fe{1-X1-2-X2C6H2-4,5-(NCOCMe2NCO)2CR2}(OH2)]- , 1: X1 = X2 = H, R2 = Me2 (a), R2 = (CH2)2 (b); X1 = X2 = Cl, R2 = F2 (c), etc.), which the proton is known to demetalate at pH < 3, are also subject to catalyzed demetalation by Brønsted acid buffer components at pH 4-9 such as H2PO4-, HSO3-, and CH3CO2H, HO2CCH2CO2-. Buffers based on pyridine (py) and tris(hydroxymethyl)aminomethane (TRIS) are catalytically inactive. Where reactions proceed, the products are demetalated TAMLs and iron species of variable composition. Pseudo-first-order rate constants for the demetalation (kobs) are linear functions of the acid concentrations, and the effective second-order rate constants k1,eff have a hyperbolic dependence on [H+] (k1,eff = a1[H+]/(b1+[H+]). The rate of demetalation of 1a in H2PO4-/HPO42- buffer is appreciable, but the kobs values for 1b and 1c are immeasurably low, showing that the rates are strongly affected by the CR2 or "tail" fragments, which are known to potently affect the TAML basicity. The reactivities of 1 depend insignificantly on the aromatic ring or "head" group of 1. The proposed mechanism involves precoordination of the acidic buffer species followed by hydrolysis. The demetalating abilities of buffer species depend on their structures and acidities. Thus, although pyridine-2-carboxylic (picolinic) acid catalyzes the demetalation, its 3- and 4-isomers (nicotinic and isonicotininc acids) are inactive. The difference is rationalized to result from the ability that only coordinated picolinic acid has to deliver a proton to an amidato nitrogen in an intramolecular manner. The reaction order in picolinic acid equals one for 1a and two for 1b. For 1b, "inactive" pyridine and nicotinic acid speed up the demetalation in the presence of picolinic acid, suggesting that the second order arises from the axial binding of two pyridine molecules, one of which must be picolinic acid. The binding of pyridine- and imidazole-type ligands was confirmed by UV/vis equilibrium measurements and X-ray crystallography. The implications of these mechanistic findings for designing superior Fe-TAML oxidation catalysts and catalyst formulations are discussed using the results of DFT calculations.

Chemical and spectroscopic evidence for an FeV-oxo complex.

Iron(V)-oxo species have been proposed as key reactive intermediates in the catalysis of oxygen-activating enzymes and synthetic catalysts. Here, we report the synthesis of [Fe(TAML)(O)]- in nearly quantitative yield, where TAML is a macrocyclic tetraamide ligand. Mass spectrometry, Mössbauer, electron paramagnetic resonance, and x-ray absorption spectroscopies, as well as reactivity studies and density functional theory calculations show that this long-lived (hours at -60 degrees C) intermediate is a spin S = 1/2 iron(V)-oxo complex. Iron-TAML systems have proven to be efficient catalysts in the decomposition of numerous pollutants by hydrogen peroxide, and the species we characterized is a likely reactive intermediate in these reactions.

Activity-stability parameterization of homogeneous green oxidation catalysts.

Small-molecule synthetic homogeneous-oxidation catalysts are normally poorly protected from self-destruction under operating conditions. Achieving design control over both activity and half-life is important not only in advancing the utility of oxidation catalysts, but also in minimizing hazards associated with their use and disposal. Iron(III)-TAML (tetraamido-macrocyclic ligand) oxidant catalysts rapidly activate H(2)O(2) for numerous significant processes, exhibiting high and differing activity and varying half-lives depending upon the TAML design. A general approach is presented that allows for the simultaneous determination of the second-order rate constant for the oxidation of a targeted substrate by the active catalyst (k(II)) and the rate constant for the intramolecular self-inactivation of the active catalyst (k(i)). The approach is valid if the formation of the active catalyst from its resting state and the primary oxidizing agent, measured by the second-order rate constant k(I), is fast and the catalyst concentration is very low, such that bimolecular inactivation pathways can be neglected. If the oxidation process is monitored spectrophotometrically and is set up to be incomplete, the kinetic trace can be analyzed by using the equation ln(lnA(t))/A(infnity)=ln(k(II)/k(i)[Fe(III)](tot)-k(i)t, from which k(II) and k(i) can be determined. Here, A(t) and A(infinity) are absorbances at time t and at the end of reaction (t=infinity), respectively, and [Fe(III)](tot) is the total catalyst concentration. Several tools were applied to examine the validity of the approach by using a variety of different Fe(III)-TAML catalysts, H(2)O(2) and tBuOOH as oxidizing agents, and the dyes safranine O and orange II as target substrates. Learning how catalyst activities (k(II)) and catalyst half-lives (k(i)) can be controlled by ligand design is an important step in creating green catalysts that will not persist in the environment after they have achieved their purpose.

Total degradation of fenitrothion and other organophosphorus pesticides by catalytic oxidation employing Fe-TAML peroxide activators.

A Fe-TAML/H2O2 catalytic oxidation process achieves facile in-solution total degradation of fenitrothion and two other organophosphorus (OP) pesticides. Degradation products have been identified and quantified providing evidence for oxidative hydrolysis, oxidative desulfuration, perhydrolysis, and deep oxidation. Degradation pathways can be selected by pH control to completely obviate all toxic residuals. Aquatic toxicity assays support the environmental compatibility of the degradation process.

High-valent iron complexes with tetraamido macrocyclic ligands: structures, Mössbauer spectroscopy, and DFT calculations.

Iron complexes of tetraamido macrocyclic ligands (TAML) are unique synthetic oxidation catalysts. In general, the central Fe(III) ion (S=3/2) is surrounded by four, almost planar, deprotonated amide-N sigma-donors although the full suite with new generation systems includes some substitution of amides with related donor functionalities. Oxidation under different conditions affords a variety of high-valent forms of iron-TAMLs. This review provides a summary and discussion of structural and spectroscopic features of complexes oxidized by one equivalent above the ferric state. These comprise Fe(IV)-TAML high spin (S=2) and intermediate spin (S=1) systems, wherein the oxidation equivalent can be taken from the metal (Fe(IV)) or the ligand (TAML radical-cation Fe(III)), and coupled spin (S=0) systems of mu-oxoiron(IV) dimers. The discussion is principally based on data obtained by X-ray crystallography, Mössbauer spectroscopy, and density functional theory calculations.