Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide‐and‐conquer,density‐functional tight‐binding,and massively parallel computation

The linear‐scaling divide‐and‐conquer (DC) quantum chemical methodology is applied to the density‐functional tight‐binding (DFTB) theory to develop a massively parallel program that achieves on‐the‐fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC‐DFTB potential energy surface are implemented to the program called DC‐DFTB‐K. A novel interpolation‐based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC‐DFTB‐K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC‐DFTB‐K program, a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc.     

Characterization of the complex formation of 1,6‐anhydro‐β‐maltotriose with potassium using 1H and 39K NMR spectroscopy

The ¹H and ³⁹K longitudinal relaxation times (T₁) and ¹H diffusion coefficients were measured to investigate the complex formation of 1,6‐anhydro‐β‐maltotriose and potassium ions. Although the ¹H‐T₁ values of H3′, H5′, H1″ and H4″ decreased in the presence of potassium ions, ¹H chemical shifts and ¹H diffusion coefficients did not show significant changes. The long‐range coupling constants of ³J_C?H around the glycosyl bonds did not show significant changes either. In the measurements of ³⁹K spectra, the ³⁹K signal obviously broadened and the ³⁹K‐T₁ values decreased in the presence of 1,6‐anhydro‐β‐maltotriose, indicating the complex formation of 1,6‐anhydro‐β‐maltotriose and potassium ions. These results indicate that the conformation and molecular volume were unaffected in the complex formation. Copyright © 2009 John Wiley & Sons, Ltd.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Development and validation of a LC‐MS/MS method for the in vitro analysis of 1‐hydroxymidazolam in human liver microsomes: application for determining CYP3A4 inhibition in complex matrix mixtures

Complementary and alternative medicines (CAM) can affect the pharmacokinetics of anticancer drugs by interacting with the metabolizing enzyme cytochrome P450 (CYP) 3A4. To evaluate changes in the activity of CYP3A4 in patients, levels of 1‐hydroxymidazolam in plasma are often determined with liquid chromatography–quadrupole mass spectrometry (LC‐MS/MS). However, validated LC‐MS/MS methods to determine in vitro CYP3A4 inhibition in human liver microsomes are scarce and not optimized for evaluating CYP3A4 inhibition by CAM. The latter is necessary because CAM are often complex mixtures of numerous compounds that can interfere with the selective measurement of 1‐hydroxymidazolam. Therefore, the aim was to validate and optimize an LC‐MS/MS method for the adequate determination of CYP3A4 inhibition by CAM in human liver microsomes. After incubation of human liver microsomes with midazolam, liquid–liquid extraction with tert‐butyl methyl ether was applied and dried samples were reconstituted in 50% methanol. These samples were injected onto a reversed‐phase chromatography consisting of a Zorbax Extend‐C₁₈ column (2.1 × 150 mm, 5.0 µm particle size), connected to a triple quadrupole mass spectrometer with electrospray ionization. The described LC‐MS/MS method was validated over linear range of 1.0–500 nm for 1‐hydroxymidazolam. The results revealed good inter‐assay accuracy (≥85% and ≤115%) and within‐day and between‐day precisions (coefficient of variation ≤ 4.43%). Furthermore, the applicability of this assay for the determination of CYP3A4 inhibition in complex matrix mixtures was successfully demonstrated in an in vitro experiment in which CYP3A4 inhibition by known CAM (β‐carotene, green tea, milk thistle and St. John's wort) was determined. Copyright © 2013 John Wiley & Sons, Ltd.