Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH₃, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 977–988, 1998     

Development of One-Step Non-Solvent Extraction and Sensitive UHPLC-MS/MS Method for Assessment of N-(n-Butyl) Thiophosphoric Triamide (NBPT) and N-(n-Butyl) Phosphoric Triamide (NBPTo) in Milk

N-(n-butyl) thiophosphoric triamide (NBPT) is a urease inhibitor utilised in urea-based fertilizers. In Ireland, fertilizer treated with NBPT is applied to pasture to mitigate both ammonia and nitrous oxide emissions, but concerns arise as to the potential for residues in milk products. A quick ultrafiltration extraction and ultra-high performance liquid chromatography coupled with mass spectrometry triple quadrupole (UHPLC-MS/MS) quantitation method was developed and validated in this study. The method was applied in the analysis of samples collected from a field study investigating potential transfer of NBPT residues into milk. NBPT and NBPTo residues, were extracted from fortified milk samples and analysed on a UHPLC-MS/MS with recoveries ranging from 74 to 114%. Validation of the UHPLC-MS/MS method at low (0.0020 mg kg⁻¹) and high (0.0250 mg kg⁻¹) concentration levels in line with SANTE/12682/2019 showed overall trueness in the range of 99 to 104% and precision between 1 and 10%, RSD for both compounds. The limit of quantitation (LOQ) was 0.0020 mg kg⁻¹ and other tested parameters (linearity, sensitivity, specificity, matrix effect, robustness, etc.) satisfied acceptance criteria. Stability assessment using spiked samples revealed the compounds were stable in raw and pasteurised milk for 4 weeks at –80 °C storage temperature. Maintaining samples at pH 8.5–9.0 further improved stability. Analysis of 516 milk samples from the field study found that NBPT and NBPTo concentrations were below the LOQ of 0.0020 mg kg⁻¹, thus suggesting very low risk of residues occurring in the milk. The method developed is quick, robust, and sensitive. The method is deemed fit-for-purpose for the simultaneous determination of NBPT and NBPTo in milk.     

Molecular Gallium Arsenide Phosphide Clusters Prepared from AsP3, P4, and [{GaC(SiMe3)3}4]

Treatment of AsP₃ with 0.75 equivalents of [{GaC(SiMe₃)₃}₄] resulted in selective insertion of three equivalents of {GaC(SiMe₃)₃} into the three As? P bonds to give [As{GaC(SiMe₃)₃}₃P₃] ( 1 ‐As) with an intact cyclo‐P₃ ring. This yellow compound has been characterized by NMR spectroscopy, combustion analysis, single‐crystal X‐ray diffraction, UV/Vis spectroscopy, Raman spectroscopy, and cyclic voltammetry (THF, 0.2 M [TBA][B(C₆F₅)₄]; TBA=tetrabutyl ammonium). Computational models of 1 ‐As and the isomeric [P{GaC(SiMe₃)₃}₃AsP₂] ( 1 ‐P) have been investigated as well, revealing several interesting electronic features of these cage molecules. Following from the cyclic voltammetry studies of 1 ‐As that highlight an irreversible two‐electron reduction at ?2.2 V versus Fc/Fc⁺, treatment with one equivalent of [Mg(C₁₄H₁₀)(thf)₃] resulted in two‐electron reduction to provide [As{GaC(SiMe₃)₃}₃P₃Mg(thf)₃] ( 2 ), in which the Mg²⁺ ion has inserted into one of the P? P bonds of the cyclo‐P₃ ring. It was also found that treatment of AsP₃ or P₄ with one equivalent of [{GaC(SiMe₃)₃}₄] resulted in formation of the quadruple insertion products [As{GaC(SiMe₃)₃}₄P₃] ( 3 ) and [P{GaC(SiMe₃)₃}₄P₃] ( 4 ), respectively.     

A cycle for organic nitrile synthesis via dinitrogen cleavage

In the presence of NaH, the reaction between N2 and Mo(N[t-Bu]Ar)3 (Ar = 3,5-C6H3Me2) proceeds at room temperature to afford NMo(N[t-Bu]Ar)3 (95%). Lewis acidic silyl triflates (Me3SiOTf + pyridine or (i-Pr)3SiOTf) mediate a reaction between acid chlorides and NMo(N[t-Bu]Ar)3 to yield acyl imidos [RC(O)NMo(N[t-Bu]Ar)3][OTf] (R = Me, 92%; Ph, 75%; t-Bu, 64%). The reduction of [RC(O)NMo(N[t-Bu]Ar)3][OTf] by magnesium anthracene followed by treatment with Me3SiOTf affords molybdenum ketimides, R(Me3SiO)CNMo(N[t-Bu]Ar)3 (R = Me, 82%; Ph, 77%; t-Bu, 46%). Exposing R(Me3SiO)CNMo(N[t-Bu]Ar)3 to SnCl2 or ZnCl2 produces ClMo(N[t-Bu]Ar)3 (71-93% for SnCl2) and RCN (97-99%). Magnesium metal reduces ClMo(N[t-Bu]Ar)3 to Mo(N[t-Bu]Ar)3 (74%), completing a synthetic cycle. New strategies for the functionalization of sterically hindered nitrides and nitrile extrusion from d2 ketimides are presented in the context of a new route for derivatizing N2.     

A diamagnetic dititanium(III) paddlewheel complex with no direct metal-metal bond

Reaction of Ti[N(But)Ar]3 (Ar = 3,5-C6H3Me2 or Ar' = C6H5) with CO2 at -40 degrees C produces diamagmetic Ti(III) paddlewheel complexes with long Ti-Ti separations (>3.4 Angstrom), thus excluding direct Ti-Ti bonding. 1H NMR spectroscopy shows that the compounds are diamagnetic in solution in the temperature range of -65 to +70 degrees C. In the solid state, the diamagnetism was found to persist between 2 and 300 K. Calculations at the density functional theory level suggest that the diamagnetism results from antiferromagnetic coupling by superexchange through the ligand pi system.     

Computation of three-dimensional Brinkman flows using regularized methods

The Brinkman equations of fluid motion are a model of flows in a porous medium. We develop the exact solution of the Brinkman equations for three-dimensional incompressible flow driven by regularized forces. Two different approaches to the regularization are discussed and compared on test problems. The regularized Brinkman model is also applied to the unsteady Stokes equation for oscillatory flows since the latter leads to the Brinkman equations with complex permeability parameter. We provide validation studies of the method based on the flow and drag of a solid sphere translating in a Brinkman medium and the flow inside a cylindrical channel of circular cross-section. We present a numerical example of a swimming organism in a Brinkman flow which shows that the maximum swimming speed is obtained with a small but non-zero value of the porosity. We also demonstrate that unsteady Stokes flows with oscillatory forcing fall within the same framework and are computed with the same method by applying it to the motion of the oscillating feeding appendage of a copepod.     

Longevity bond premiums: The extreme value approach and risk cubic pricing

The purpose of this study is to analyze the securitization of longevity risk with an emphasis on longevity risk modeling and longevity bond premium pricing. Various longevity derivatives have been proposed, and the capital market has experienced one unsuccessful attempt by the European Investment Bank (EIB) in 2004. After carefully analyzing the pros and cons of previous securitizations, we present our proposed longevity bonds, whose payoffs are structured as a series of put option spreads. We utilize a random walk model with drift to fit small variations of mortality improvements and employ extreme value theory to model rare longevity events. Our method is a new approach in longevity risk securitization, which has the advantage of both capturing mortality improvements within sample and extrapolating rare, out-of- sample longevity events. We demonstrate that the risk cubic model developed for pricing catastrophe bonds can be applied to mortality and longevity bond pricing and use the model to calculate risk premiums for longevity bonds.     

A niobaziridine hydride system for white phosphorus or dinitrogen activation and N- or P-atom transfer

This short review describes a breakthrough embodied by the synthesis of a niobaziridine hydride complex. This reactive entity reacts directly with white phosphorus to provide a bridging diphosphorus diniobium complex that upon reduction splits to afford a terminal niobium phosphide anion, isolated as its sodium salt. Reactions of the latter with acid chlorides constitute a new synthesis of phosphaalkynes, while treatment with chlorodiorganophosphanes leads to complexed 1,1-diorganophosphanylphosphinidene systems. Additionally, reactions of the sodium salt of the niobium phosphide anion with divalent main group element salts (E = Ge, Sn, or Pb) provide complexed triatomic EP2 triangles. Dinitrogen cleavage was realized via reduction of a heterodinuclear niobium/molybdenum dinitrogen complex, and this provided an entry to a nitrogen-15 labeled terminal nitride anion of niobium as its sodium salt. In a fashion analogous to the aforementioned phosphaalkyne synthesis, acid chlorides are transformed upon reaction with the niobium nitride anion into corresponding nitrogen-15 labeled organic nitriles. Complete synthetic cycles are achieved in both the phosphaalkyne and the organic nitrile syntheses, as the oxoniobium(v) byproduct can be recycled in high yield to the title niobaziridine hydride complex.