Magnetic properties of a manganese(II) trinuclear complex involving a tridentate Schiff-Base ligand

The Schiff condensation of 2-pyridinecarboxaldehyde N-oxide with 2-aminophenol gave a tridentate ligand, abbreviated as Hpoxap. This ligand bears the functionality of a terminating group in a trinuclear complex [Mn(poxap)Mn(ac)4Mn(poxap)], where ac- is the acetate bridge. The magnetic data were treated simultaneously during the fitting procedure with the spin Hamiltonian containing isotropic exchange, the zero-field splitting parameters, and the molecular-field correction and resulted in JMn-Mn/hc = -4.73 cm-1, gMn(t) = 1.96, DMn(t)/hc = -0.45 cm-1, and zj/hc = +0.45 cm-1 with ground state S = 5/2, where t = terminal atom. At low temperature, the features of a ferromagnetic correlation become evident.     

Reliability and uncertainty in the estimation of p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> by least squares nonlinear regression analysis of multiwavelength spectrophotometric pH titration data

When drugs are poorly soluble then, instead of the potentiometric determination of dissociation constants, pH-spectrophotometric titration can be used along with nonlinear regression of the absorbance response surface data. Generally, regression models are extremely useful for extracting the essential features from a multiwavelength set of data. Regression diagnostics represent procedures for examining the regression triplet (data, model, method) in order to check (a) the data quality for a proposed model; (b) the model quality for a given set of data; and (c) that all of the assumptions used for least squares hold. In the interactive, PC-assisted diagnosis of data, models and estimation methods, the examination of data quality involves the detection of influential points, outliers and high leverages, that cause many problems when regression fitting the absorbance response hyperplane. All graphically oriented techniques are suitable for the rapid estimation of influential points. The reliability of the dissociation constants for the acid drug silybin may be proven with goodness-of-fit tests of the multiwavelength spectrophotometric pH-titration data. The uncertainty in the measurement of the pK _a of a weak acid obtained by the least squares nonlinear regression analysis of absorption spectra is calculated. The procedure takes into account the drift in pH measurement, the drift in spectral measurement, and all of the drifts in analytical operations, as well as the relative importance of each source of uncertainty. The most important source of uncertainty in the experimental set-up for the example is the uncertainty in the pH measurement. The influences of various sources of uncertainty on the accuracy and precision are discussed using the example of the mixed dissociation constants of silybin, obtained using the SQUAD(84) and SPECFIT/32 regression programs.     

A novel microbial biosensor based on cells of <Emphasis Type="Italic">Gluconobacter oxydans</Emphasis> for the selective determination of 1,3-propanediol in the presence of glycerol and its application to bioprocess monitoring

Novel and selective microbial amperometric biosensors that use Gluconobacter oxydans cells to monitor the bacterial bioconversion of glycerol (Gly) to 1,3-propanediol (1,3-PD) are described. Two different mediators, ferricyanide and flexible polyvinylimidazole osmium functionalized polymer (Os-polymer), were employed to prepare two different microbial biosensors, both of which gave high detection performance. The good operational stabilities of both types of biosensor were underlined by the ability to detect 1,3-PD throughout 140 h of continuous operation. Both microbial biosensor systems showed excellent selectivity for 1,3-PD in the presence of a high excess of glycerol [selectivity ratios (1,3-PD/Gly) of 118 or 245 for the ferricyanide and Os-polymer systems, respectively]. Further, the robustness of each microbial biosensor was highlighted by the high reliability of 1,3-PD detection achieved (average RSD of standards <2%, and well below 4% for samples). The biosensor implementing the Os-polymer mediator exhibited high selectivity towards 1,3-PD detection and allowed moderate sample throughput (up to 12 h⁻¹) when integrated into a flow system. This system was used to monitor the concentration of 1,3-PD during a real bioprocess. Results from biosensor assays of 1,3-PD in bioprocess samples taken throughout the fermentation were in a very good agreement with results obtained from reference HPLC assays (R ² = 0.999).     

New strong organic acceptors by cycloaddition of TCNE and TCNQ to donor-substituted cyanoalkynes

Donor-substituted 1,1,2,4,4-pentacyanobuta-1,3-dienes and a cyclohexa-2,5-diene-1,4-diylidene-expanded derivative were prepared by a [2 + 2] cycloaddition of tetracyanoethene (TCNE) or 7,7,8,8-tetracyanoquinodimethane (TCNQ) to anilino-substituted cyanoalkynes, followed by retro-electrocyclisation; they feature intense bathochromically-shifted intramolecular charge-transfer bands and undergo their first one-electron reductions at potentials similar to those reported for TCNE and TCNQ.     

Conformational behavior of basic monomeric building units of glycosaminoglycans: isolated systems and solvent effect

Our work reports in detail the results of systematic large-scale theoretical investigations of the glycosaminoglycan building units 1-OMe DeltaIdoA-2SNa2 (1; 2H1 and 1H2 forms), 1-OMe GlcN-S6SNa2 (2), 1,4-DiOMe GlcNa (3), 1,4-DiOMe GlcN-S3S6SNa3 (4), 1,4-DiOMe IdoA-2SNa2 (5; 4C1, 1C4, and 2So conformations), and 1,4-DiOMe GlcN-S6SNa2 (6) at the BP86/TZ2P level of the density functional theory. The optimized geometries indicate that the most stable structure of these monomeric units in the neutral state is stabilized via "multifurcated" sodium bonds. The equilibrium structure of the biologically active anionic forms of the glycosaminoglycans studied changed considerably in a water solution. The computed interaction energies, DeltaE, of sodium coordinated systems 1-6 are negative and span a rather broad energy interval (from -130 to -590 kcal mol-1). Computations that include the effect of solvation indicated that in water the relative stability of Na+...ligand ionic bonds is considerably diminished. The computed interaction energy in water is small (from -20 to -53 kcal mol-1) and negative, that is, stabilizing.     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

Reaction of hydrogen atoms with propyne at high temperatures: an experimental and theoretical study

The kinetics of the reaction of hydrogen atoms with propyne (pC3H4) was experimentally studied in a shock tube at temperatures ranging from 1200 to 1400 K and pressures between 1.3 and 4.0 bar with Ar as the bath gas. The hydrogen atoms (initial mole fraction 0.5-2.0 ppm) were produced by pyrolysis of C2H5I and monitored by atomic resonance absorption spectrometry under pseudo-first-order conditions with respect to propyne (initial mole fraction 5-20 ppm). From the hydrogen atom time profiles, overall rate coefficients k(ov) identical with -([pC3H4][H])(-1) x d[H]/dt for the reaction H + pC3H4 --> products ( not equal H) were deduced; the following temperature dependence was obtained: kov = 1.2 x 10(-10) exp(-2270 K/T) cm(3) s(-1) with an estimated uncertainty of +/-20%. A pressure dependence was not observed. The results are analyzed in terms of statistical rate theory with molecular and transition state data from quantum chemical calculations. Geometries were optimized using density functional theory at the B3LYP/6-31G(d) level, and single-point energies were computed at the QCISD(T)/cc-pVTZ level of theory. It is confirmed that the reaction proceeds via an addition-elimination mechanism to yield C2H2 + CH3 and via a parallel direct abstraction to give C3H3 + H2. Furthermore, it is shown that a hydrogen atom catalyzed isomerization channel to allene (aC3H4), H + pC3H4 --> aC3H4 + H, is also important. Kinetic parameters to describe the channel branching of these reactions are deduced.     

Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms

A new first-order procedure for locating transition structures (TS) that employs hybrid quantum mechanical/molecular mechanical (QM/MM) potentials has been developed. This new technique (RPATh+RESD) combines the replica path method (RPATh) and standard reaction coordinate driving (RCD) techniques in an approach that both efficiently determines reaction barriers and successfully eliminates two key weaknesses of RCD calculations (i.e., hysteresis/discontinuities in the path and the sequential nature of the RCD procedure). In addition, we have extended CHARMM's QM/MM reaction pathway methods, the RPATh and nudged elastic band (NEB) methods, to incorporate SCC-DFTB wave functions. This newly added functionality has been applied to the chorismate mutase-catalyzed interconversion of chorismate to prephenate, which is a key step in the shikimate pathway of bacteria, fungi, and other higher plants. The RPATh+RESD barrier height (DeltaE=5.7 kcal/mol) is in good agreement with previous results from full-energy surface mapping studies (Zhang, X.; Zhang, X.; Bruice, T. C. Biochemistry 2005, 44, 10443-10448). Full reaction paths were independently mapped with RPATh and NEB methods and showed good agreement with the final transition state from the RPATh+RESD "gold standard" and previous high-level QM/MM transition states (Woodcock, H. L.; Hodoscek, M.; Gilbert, T. B.; Gill, P. M. W.; Schaefer, H. F.; Brooks, B. R. J. Comput. Chem. 2007, 28, 1485-1502). The SCC-DFTB TS geometry most closely approximates the MP2/6-31+G(d) QM/MM result. However, the barrier height is underestimated and possibly points to an area for improvement in SCC-DFTB parametrization. In addition, the steepest descents (SD) minimizer for the NEB method was modified to uncouple the in-path and off-path degrees of freedom during the minimization, which significantly improved performance. The convergence behavior of the RPATh and NEB was examined for SCC-DFTB wave functions, and it was determined that, in general, both methods converge at about the same rate, although the techniques used for convergence may be different. For instance, RPATh can effectively use the adopted basis Newton-Raphson (ABNR) minimizer, where NEB seems to require a combination of SD and ABNR.