Theoretical and experimental mechanistic study of water molecule involvement in the Prilezhaev reaction.

The Prilezhaev reaction produces epoxides using alkenes and peroxy acids such as m-chloroperoxybenzoic acid (mCPBA). The reaction proceeds via a concerted mechanism in one step. Although the mCPBA used in organic syntheses contains water because of its explosive nature, the effects of water on the reaction have not been considered. To investigate the effects of water on the reaction mechanism, we determined the thermodynamic parameters for the Prilezhaev reaction between styrene and mCPBA. The activation free energies, including solvent effects, were calculated using the SMD and QM/MC/FEP methods. The calculated thermodynamic parameters for the reaction directly involving two water molecules were in better agreement with the experimental data than those for the concerted mechanism. This result indicated that water molecules are involved in the progression of the mCPBA-mediated Prilezhaev reaction in solvents containing water molecules.

Effects of an autoinducer analogue on antibiotic tolerance in Pseudomonas aeruginosa.

Objectives: Antibiotic tolerance causes chronic, refractory and persistent infections. In order to advance the development of a new type of drug for the treatment of infectious diseases, we herein investigated the effects of a newly synthesized analogue of the Pseudomonas aeruginosa quorum-sensing autoinducer named AIA-1 ( a uto i nducer a nalogue) on antibiotic tolerance in P. aeruginosa . Methods: A P. aeruginosa luminescent strain derived from PAO1 was injected into neutropenic ICR mice and bioluminescence images were acquired for a period of time after treatments with antibiotics and AIA-1. In vitro susceptibility testing and killing assays for the planktonic and biofilm cells of PAO1 were performed using antibiotics and AIA-1. The expression of quorum-sensing-related genes was examined using real-time PCR. Results: In vivo and in vitro assays showed that AIA-1 alone did not exert any bactericidal effects and also did not affect the MICs of antibiotics. However, the combined use of AIA-1 and antibiotics exerted markedly stronger therapeutic effects against experimental infection than antibiotics alone. The presence of AIA-1 also enhanced the killing effects of antibiotics in planktonic and biofilm cells. Although AIA-1 did not inhibit the expression of lasB and rhlA genes, which are directly regulated by quorum sensing, it clearly suppressed expression of the rpoS gene. Conclusions: The new compound, AIA-1, did not alter the antibiotic susceptibility of P. aeruginosa by itself; however, its addition enhanced the antibacterial activity of antibiotics. AIA-1 did not inhibit quorum sensing, but reduced the antibiotic tolerance of P. aeruginosa by suppressing rpoS gene expression.

Role of psl Genes in Antibiotic Tolerance of Adherent Pseudomonas aeruginosa.

Bacteria attached to a surface are generally more tolerant to antibiotics than their planktonic counterparts, even without the formation of a biofilm. The mechanism of antibiotic tolerance in biofilm communities is multifactorial, and the genetic background underlying this antibiotic tolerance has not yet been fully elucidated. Using transposon mutagenesis, we isolated a mutant with reduced tolerance to biapenem (relative to that of the wild type) from adherent cells. Sequencing analysis revealed a mutation in the pslL gene, which is part of the polysaccharide biosynthesis operon. The Pseudomonas aeruginosa PAO1ΔpslBCD mutant demonstrated a 100-fold-lower survival rate during the exposure of planktonic and biofilm cells to biapenem; a similar phenotype was observed in a mouse infection model and in clinical strains. Transcriptional analysis of adherent cells revealed increased expression of both pslA and pelA, which are directly regulated by bis-(3',5')-cyclic dimeric GMP (c-di-GMP). Inactivation of wspF resulted in significantly increased tolerance to biapenem due to increased production of c-di-GMP. The loss of pslBCD in the ΔwspF mutant background abolished the biapenem-tolerant phenotype of the ΔwspF mutant, underscoring the importance of psl in biapenem tolerance. Overexpression of PA2133, which can catalyze the degradation of c-di-GMP, led to a significant reduction in biapenem tolerance in adherent cells, indicating that c-di-GMP is essential in mediating the tolerance effect. The effect of pslBCD on antibiotic tolerance was evident, with 50- and 200-fold-lower survival in the presence of ofloxacin and tobramycin, respectively. We speculate that the psl genes, which are activated by surface adherence through elevated intracellular c-di-GMP levels, confer tolerance to antimicrobials.

A Pseudomonas aeruginosa Quorum-Sensing autoinducer analog enhances the activity of antibiotics against resistant strains.

In this study, we have investigated the effects of the newly synthesized analog of Pseudomonas aeruginosa quorum-sensing autoinducer named AIA-1 (autoinducer analog) against antibiotic-resistant bacteria. In vitro susceptibility and killing assays for P. aeruginosa PAO1ΔoprD mutant and clinical isolates were performed by using antibiotics and AIA-1. In an in vivo assay, a luminescent carbapenem-resistant strain derived from PAO1ΔoprD was injected into neutropenic ICR mice and bioluminescence images were acquired after the treatment with antibiotics and AIA-1. Additionally, we investigated the effects of the combination use against carbapenem-resistant Enterobacteriaceae (CRE). Using killing assays in P. aeruginosa, the survival rates in the presence of antibiotics and AIA-1 significantly decreased in comparison with those with antibiotics alone. Furthermore, dual treatment of biapenem and AIA-1 was more effective than biapenem alone in a mouse infection model. AIA-1 did not change the MICs in P. aeruginosa, suggesting that AIA-1 acts on the mechanism of antibiotic tolerance. Conversely, the MICs of antibiotics decreased in the presence of AIA-1 in some CRE strains, indicating that AIA-1 may require additional mechanism to act on CRE. In conclusion, AIA-1 may be a potent drug for clinical treatment of infections caused by antibiotic-resistant bacteria. J. Med. Invest. 64: 101-109, February, 2017.

Theoretical study on the stability of double-decker type metal phthalocyanines, M(Pc)2 and M(Pc)2(+) (M = Ti, Sn and Sc): a critical assessment on the performance of density functionals.

We report the results of theoretical calculations on the optimized structures and relative energies between the D4d and D2 symmetry structures for double-decker type phthalocyanine compounds, Ti(Pc)2, Ti(Pc)2(+), Sn(Pc)2, Sn(Pc)2(+), Sc(Pc)2 and Sc(Pc)2(+), using eighteen types of functionals: B3LYP, B3PW91, B3P86, PBE1PBE, BHandHLYP, BPW91, BP86, M06, M06-2x, M06-HF, M06L, LC-BPW91, LC-ωPBE, CAM-B3LYP, B97D, ωB97, ωB97X and ωB97XD. Two phthalocyanine moieties are stacked in a face-to-face configuration in the D4d structure, but they are stapled by two σ-bonds in the D2 one. We found that the molecular symmetry of M(Pc)2 and M(Pc)2(+) depends on the balance between stabilization due to electron delocalization and exchange repulsion of π-electrons in the phthalocyanine moieties. We assessed the performance of the well-established functionals to select the appropriate functional for calculations on M(Pc)2 and M(Pc)2(+), and several important aspects came out. Generally, the hybrid GGA and hybrid meta-GGA functionals with 20-27% of the HF exchange term would give the molecular structures consistent with the experimental expectations for the double-decker type phthalocyanine compounds. Pure GGA and pure meta-GGA functionals (BPW91, BP86, M06L and B97D) have the tendency to overestimate the stability of the D4d structure. On the other hand, functionals including HF exchange for 50% and over or including long-range corrections (BHandHLYP, M06, M06-2x, M06-HF, LC-BPW91, LC-ωPBE, CAM-B3LYP, ωB97, ωB97X and ωB97XD) tend to overestimate the stability of the D2 structure. It should be emphasized that the B3LYP functional, one of the most commonly used hybrid GGA functionals with 20% HF exchange, cannot estimate the relative stability between the two molecular structures of Ti(Pc)2 appropriately. The calculation for the systems considered in this article required well-balanced treatment of the HF exchange with the accompanied exchange-correlation functional. Thus, as has been pointed out rigorously and frequently, the selection of the functional is a crucial point for reliability of the calculations.

Theoretical and experimental investigation on the electronic properties of the shuttlecock shaped and the double-decker structured metal phthalocyanines, MPc and M(Pc)2 (M = Sn and Pb).

The molecular geometries, electronic structures, and excitation energies of tin and lead phthalocyanine compounds, SnPc, PbPc, Sn(Pc)(2), and Pb(Pc)(2), were investigated using the B3LYP method within a framework of density functional theory (DFT). The geometries of SnPc, PbPc, Sn(Pc)(2), and Pb(Pc)(2) were optimized under C(4v), C(4v), D(4d), and D(4d) molecular symmetries, respectively. The excitation energies of these molecules were computed by the time-dependent DFT (TD-DFT) method. The calculated results for the excited states of three compounds other than the unknown Pb(Pc)(2) corresponded well with the experimental results of electronic absorption spectroscopy. The non-planar C(4v) molecular structure of SnPc and PbPc influences especially on the orbital energy of the HOMO-1 through mixing of the s-type atomic orbital of the central metal atom to the π system of the Pc ring in an anti-bonding way; however, the HOMO and the LUMO have little effect of the deviation from the planar structure because they have no contribution from the atomic orbital of the central metal. This orbital mixing pushes up the orbital energy of the HOMO-1, and reduces the energy of the metal-to-ligand charge transfer band of SnPc and PbPc. The calculated results also reproduced well the excitation profile of Sn(Pc)(2), which was quite different from that of SnPc. The strong interactions between the π-type orbitals of two Pc moieties altered the electronic structure resulting in the characteristic excitation profile of Sn(Pc)(2). In addition, this caused a reduction of about 0.8 eV in the ionization potential as compared to usual MPcs including SnPc, which was consistent with the experimental results.

Theoretical and experimental study on the excited states of the X-, α- and ß-forms of lithium phthalocyanine.

The electronic structures and absorption spectra for three different types (X, α and ß) of model dimers of lithium phthalocyanine (LiPc) were investigated by the density functional theory (DFT) and compared with a LiPc monomer. We quantitatively investigated the excited states of the three LiPc dimers using time-dependent DFT calculations. The differences and similarities of the observed absorption spectra in the solution and the polymorphic solids of LiPc were clearly interpreted by the calculated excited states of the monomer and dimers. The calculated results for the dimers presumed that the X-form showed a different electronic spectral pattern from the monomer and the other two forms, whereas the α- and ß-forms presented similar electronic absorption profiles to each other and to the monomer. The calculated excited states also explained the differences in absorption profiles between LiPc and typical phthalocyanine compounds. These characteristic features of LiPc would be closely related to its molecular orbitals, especially those which originated from the singly occupied molecular orbital (SOMO) of the LiPc monomer. It was shown that the next highest occupied π-type orbital to the SOMO of the monomer reduced the energy of the low-lying excited states, which corresponded to the Q- and B-bands of the dimers.

Theoretical study on the molecular structures of X-, α-, and ß-types of lithium phthalocyanine dimer.

We report here the results from theoretical calculations of the potential energy curves, the geometry optimizations, and the electronic structures for three dimers of lithium phthalocyanine (LiPc) by using three types of functional systems: PBE1PBE, B3LYP, and M06. The results were discussed in comparison with those obtained for the dimers of magnesium phthalocyanine (MgPc). The long-range dispersive interactions were considered in part using these functional systems in the increasing order of PBE1PBE, B3LYP, and M06. The mechanism whereby the dispersive interactions affect the geometric and electronic structures of the LiPc and MgPc dimers is discussed. The calculated results provide insight into the computational methods for both open- and closed-shell metal phthalocyanine (MPc) dimers: Although the PBE1PBE and B3LYP functional systems cannot evaluate a weak dispersion interaction appropriately, the M06 functional can estimate a weak dispersion interaction well in both open- and closed-shell MPc dimers. Basis set superposition error (BSSE) corrections play an important role for the quantitative analysis; however, the calculation results without BSSE corrections may be sufficient for the qualitative discussion on the properties of these dimers such as geometries, stabilities, electronic structures, and so on.

Theoretical investigation of the molecular structures and excitation spectra of triphenylamine and its derivatives.

The molecular geometries, electronic structures, and excitation energies of NPh(3), NPh(2)Me, NPhMe(2), and NMe(3), were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region.

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.

This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free-energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free-energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels-Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG( sol)‡ values of 20.1 and 21.4 kcal mol(-1) in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free-energy surfaces for the Cope elimination of N,N-dimethyl-3-phenylbutan-2-amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6-hydroxybenzo-isoxazole-3-carboxylic acid in aqueous, dimethyl sulfoxide, and CH(3) CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol(-1) from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute-solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG (sol)‡ value similar to the experimental values, as well as that for a small droplet with 34 molecules.

Towards the development of synthetic routes using theoretical calculations: an application of in silico screening to 2,6-dimethylchroman-4-one.

This study describes an attempt to develop a synthetic route using theoretical calculations, i.e., in silico synthesis route development. The KOSP program created four potential synthetic routes for generating 2,6-dimethylchroman-4-one. In silico screening of these four synthetic routes was then performed. In silico screening involves theoretical analysis of synthetic routes prior to actual experimental work. A synthetic route using the Mitsunobu reaction had already been reported by Hoddgets et al. Theoretical investigations were also conducted on two S(N)Ar reactions as well as a Michael reaction before they were examined experimentally. In silico screening using DFT calculations indicated that only the Michael reaction was likely to produce the target. Experimental work confirmed that the target was obtained in a yield of 76.4% using the Michael reaction. The other two routes, except for the Mitsunobu reaction, failed to generate the target. Our results demonstrate that theoretical calculations can be used to narrow down the number of experiments that need to be conducted when developing novel synthetic routes.

F-18 FDG PET-CT findings in Mikulicz disease and systemic involvement of IgG4-related lesions.

A 72-year-old woman with Mikulicz disease with pathogically proven sclerosing sialadenitis showed systemic abnormal F-18 FDG uptake in the bilateral lacrimal and submandibular glands, pancreas, abdominal aortic wall, and a retroperitoneal fibroid mass on PET/CT scan, with marked elevation of the serum IgG4 level. This case supports Mikulicz disease being included as 1 of the disorders associated with a new clinical entity of systemic IgG4-related plasmacytic syndrome. A whole-body FDG-PET/CT scan can be expected as a useful tool for detecting systemic involvement in systemic IgG4-related plasmacytic syndrome.

F-18 FDG PET/CT monitoring of radiation therapeutic effect in hepatic epithelioid hemangioendothelioma.

We report the F-18 FDG PET/CT findings in a 59-year-old man with a rare hepatic tumor of malignant epithelioid hemangioendothelioma, who was treated with radiotherapy (RT). This patient had multifocal discrete hepatic tumors, and PET/CT images showed intense FDG uptake in these nodules, regardless of poor enhancement on contrast-enhanced computed tomography. Seven months after RT to the 2 relatively large nodules, the intense FDG uptake disappeared in these nodules, while the remaining untreated nodule showed persistently intense uptake. RT is one of the options for treatment of hepatic epithelioid hemangioendothelioma. F-18 FDG PET/computed tomography appears to be useful for monitoring the effect of RT in this neoplasm.

Hybridization-promoted and cytidine-selective activation for cross-linking with the use of 2-amino-6-vinylpurine derivatives.

Recently, we have proposed a new concept for cross-linking agents with inducible reactivity, in which the highly reactive cross-linking agent, the 2-amino-6-vinylpurine nucleoside analogue (1), can be regenerated in situ from its stable precursors, the phenylsulfide (4) and the phenylsulfoxide (3) derivatives, by a hybridization-promoted activation process with selectivity to cytidine. The phenylsulfide precursor (4) exhibited cross-linking ability despite its high stability toward strong nucleophiles such as amines and thiols. In this study, we investigated the substituent effects of the phenylsulfide group on the cross-linking reaction, and determined the 2-carboxy substituent of the phenylsulfide derivative (11k) as an efficient cross-linking agent with inducible reactivity. Detailed investigations have shown that the phenylsulfoxide (3) and phenylsulfide (4) precursors produce the 2-amino-6-vinylpurine nucleoside (1) as the common reactive species. It has been concluded that the nature of the inducible reactivity of the precursors (3 and 4) is acceleration of their elimination to the 2-amino-6-vinylpurine nucleoside (1) through the selective process in the duplex with the ODN having cytidine at the target site.