An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution

For the purpose to execute direct dynamics calculation in solution chemistry, we propose an optimum strategy for solution chemistry using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRP), i.e., the NDDO‐SSRP method. In this strategy, the empirical parameters of the semi‐empirical MO method were optimized individually for target molecule or ion by reference to the ab initio MO calculation data for many configurations on the potential energy surface near the reaction path. For demonstration, the NDDO‐SSRP method was applied to two molecules and two ions (OH^?, H₂O, NH₃, NH₄⁺) at their equilibrium states in aqueous solution, respectively. Accordingly, it was verified that both the potential energy surface and the charge distribution of these solutes in aqueous solution are dramatically improved to reproduce themselves accurately at ab initio MO calculation level. In conclusion, it is expected that the NDDO‐SSRP method should become quite useful for dynamic and statistical applications to chemical reaction systems in solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Determination of the Apparent Michaelis Constant of Glucose Oxidase Immobilized on a Microelectrode with Respect to Oxygen

We report determination of the apparent Michaelis constant of glucose oxidase (GOx) immobilized on a microelectrode with respect to oxygen. We used a GOx‐modified microelectrode as a probe for scanning electrochemical microscopy. We detected hydrogen peroxide generated by the enzyme reaction at the microelectrode under controlling the oxygen concentration using water electrolysis at an interdigitated array (IDA) electrode. The response depends on the oxygen concentration, which is regulated by the microelectrode position and the potential applied to the IDA electrode. We estimated the apparent Michaelis constant with respect to oxygen in this experimental condition to be about 0.28 mM.     

Simultaneous analysis of photoinduced electron transfer in wild type and mutated AppAs

Photoinduced electron transfer (PET) from Tyr21 to isoalloxazine (Iso) in the excited state (Iso*) is considered to be an initial step of the photosensing function of the blue-light sensing using flavin adenine dinucleotide (BLUF) component of the anti-repressor of the photosynthetic regulation (AppA). The PET mechanism was investigated via fluorescence dynamics of AppA and Kakitani and Mataga (KM) theories as well as by molecular dynamic (MD) simulation. The local structures of both the Y21F and W104F mutant AppAs around the Iso binding sites were quite different from those of the wild type (WT) AppA. The distances between Iso and Trp104 in Y21F, and between Iso and Tyr21 in W104F were shorter by 0.06 nm and 0.02 nm, respectively, compared to the WT. The frequency factor, ν₀, in Tyr21 was 1.15-fold greater than that in Trp104. The critical distance between adiabatic and non-adiabatic PET processes, R₀, was found to be very long in the AppA Tyr21. The large values of ν₀ and R₀ for Tyr21 of AppA compared to those in a non photosensing flavoprotein, FMN binding protein (FBP), were elucidated by hydrogen bond (H bond) chain between Tyr21 and Iso through Gln63. Interaction energies among Iso*, Trp104, Tyr21 and Gln63 in WT were calculated using the semi-empirical PM3 method. The amount of the transferred charge from Trp104 to Iso* in the WT exhibited a maximum at an interaction energy of around ?20 kcal/mol, but decreased as the interaction energy (absolute value) increased.     

Novel solid-phase refolding method for preparation of scFv-immobilized polystyrene plates with high-antigen-binding activity

In the present study, we demonstrated site-specific immobilization and solid-phase refolding of single-chain Fv antibodies on hydrophilic polystyrene (phi-PS) plates that was mediated by novel polystyrene binding peptides (PS-tags: RIIIRRIRR), which were originally isolated and optimized in previous studies. Three PS-tag-fused scFvs, namely scFv-PS, scFv-(PS), and scFv-PSII, which were over-expressed in the insoluble fraction of Escherichia coli cells were denatured and site-specifically immobilized onto hydrophilic PS plates in the presence of 0.5~4 M urea and 0.1% Tween 20. The antigen-binding activity of the scFvs was efficiently recovered by washing the surface of the plate with PBS that contained 0.1% Tween 20 (PBST). The solid-phase refolding mediated by PS-tag was successfully applied to several scFvs such as mouse anti-CRP antibodies and an anti-RNase antibody, although further investigation of the versatility of scFv-PSII is needed. The maximal density of PS-tag-fused scFvs was increased more than 15-fold compared with a whole monoclonal antibody (mAb) immobilized on Maxisorp™ and, consequently, the sensitivity of PS-tag-fused scFvs for CRP in a sandwich ELISA was increased 25-fold. Thus, the novel, solid-phase, refolding method mediated by a PS-tag will be very useful for preparation of solid supports coated with recombinant antibody fragments, which can be used in immunoassays and immuno-separation.     

Scalable syntheses of both enantiomers of DNJNAc and DGJNAc from glucuronolactone: the effect of N-alkylation on hexosaminidase inhibition

The efficient scalable syntheses of 2-acetamido-1,2-dideoxy-D-galacto-nojirimycin (DGJNAc) and 2-acetamido-1,2-dideoxy-D-gluco-nojirimycin (DNJNAc) from D-glucuronolactone, as well as of their enantiomers from L-glucuronolactone, are reported. The evaluation of both enantiomers of DNJNAc and DGJNAc, along with their N-alkyl derivatives, as glycosidase inhibitors showed that DGJNAc and its N-alkyl derivatives were all inhibitors of α-GalNAcase but that none of the epimeric DNJNAc derivatives inhibited this enzyme. In contrast, both DGJNAc and DNJNAc, as well as their alkyl derivatives, were potent inhibitors of β-GlcNAcases and β-GalNAcases. Neither of the L-enantiomers showed any significant inhibition of any of the enzymes tested. Correlation of the in vitro inhibition with the cellular data, by using a free oligosaccharide analysis of the lysosomal enzyme inhibition, revealed the following structure-property relationship: hydrophobic side-chains preferentially promoted the intracellular access of iminosugars to those inhibitors with more-hydrophilic side-chain characteristics.     

Eight stereoisomers of homonojirimycin from D-mannose

Although there are 32 6-azidoheptitols, there are only 16 homonojirimycin (HNJ) stereoisomers. Two epimeric azidoalditols derived from d-mannose allow the synthesis in water of eight stereoisomers of HNJ.     

Ultrafast photoisomerization and its single-shot pump pulse efficiency of trans-azobenzene derivative: Compound for photosensitive DNA

The femtosecond photoisomerization processes of trans (T) 4-carboxy-2′,6′-dimethylazobenzen, which has been employed recently as an efficient photoregulator of DNA hybridization, were clarified by the rate equation analysis of measured transient absorbance changes with (350 nm) and without (380 nm) ground-state absorption of both the reactant (T) and photoproduct (cis: C) isomers under S₂^T-band excitation (360 nm, 150 fs pump): after excitation to the S₂^T state with a 450-fs lifetime, ~ 1.5% of the T-molecules in the S₂^T state are isomerized to the C-form within ~ 6 ps through the intermediate state (so called bottleneck state), but most of those return back to the T ground-state S₂^T via the internal conversion processes with an ultrafast kinetic rate of 2.2 × 10¹² s^? 1. Moreover, the rate equation analysis enables us to determine the T-to-C photoisomerization rate η^T,C per pump pulse to be 0.0011 at the pump energy of 80 nJ from the amplitude A_3,350 of the offset component in the 350-nm probe signal, and to obtain the photoisomerization quantum yield Φ^T,C = 0.094. The latter value is slightly lower than that of T-azobenzene, and well agrees with that (Φ^T,C = 0.097) measured by the conventional CW irradiation method using a photostationary state.     

A supramolecular photosynthetic triad of slipped cofacial porphyrin dimer, ferrocene, and fullerene

A supramolecular triad consisting of self-assembled imidazolyl-zinc-porphyrin dimer, ferrocene, and fullerene was successfully constructed, resulting in long-lived charge separated species after efficient photoinduced electron transfer and charge shift reactions.     

Ab initio theoretical study of temperature and density dependence of molecular and thermodynamic properties of water in the entire fluid region: autoionization processes

The temperature and density dependence of the molecular and thermodynamic properties of water is investigated theoretically by means of the ab initio electronic structure theory combined with the reference interaction site model method, so-called RISM-SCF. We consider the autoionization process (H2O + H2O right harpoon over left harpoon H3O+ + OH-) by regarding H2O, H3O+, and OH- as "solute" molecules in an aqueous solution and evaluate molecular geometry, electronic structure, solvation structure, and the ionic product of water (pKw) of these species as functions of thermodynamic conditions. In our previous paper, we calculated these properties by using essentially the same method in a wide range of density values (0.6-1.4 g/cm3). However, the calculation was limited at rather higher density (>0.6 g/cm3) due to the difficulty of convergence, which is inherent to the hypernetted-chain (HNC) closure. The problem is overcome in this study by employing the Kovalenko-Hirata (KH) closure which hybridizes the HNC and the mean-spherical approximation (MSA). Here, we present the results for the thermodynamic range of densities from 0.025 to 1.0 g/cm3 and for temperatures from 300 to 800 K including the supercritical point.