Single Enantiomer Versus Racemate: Chiral Distinction in the Proton Pump Inhibitors Omeprazole and Esomeprazole

Chiral distinction in the proton pump inhibitor drugs omeprazole and in its chiral‐switch esomeprazole magnesium was studied employing the Density Functional Theory (DFT) method. At B3LYP/6‐311G(d,p), the 6‐methoxy???6‐methoxy and 5‐methoxy???5‐methoxy homochiral and heterochiral dimers were calculated. The chiral distinction free energies (ΔΔG_{298,(RS‐SS)}) between the cyclic C₂‐(S,S)‐ and C_i‐(R,S)‐dimers with two intermolecular hydrogen bonds are 3.8, 1.9 (with BSSE counterpoise correction), and –6.9 (with D3 dispersion and BSSE counterpoise corrections) kJ/mol. Adding water as an implicit solvent (polarized continuum model [PCM] model) resulted in a chiral distinction energy of –3.3 kJ/mol, indicating a reversal of the order of the relative stabilities of C₂‐(S,S)‐ and C_i‐(R,S)‐dimers. The chiral distinction free energies between the corresponding (less stable) C₁‐dimers with one intermolecular hydrogen bond are –9.3, –5.8 (with BSSE CC), 17.6 (D3 + BSSE CC), and –3.2 (H₂O) kJ/mol. The results highlight the contention that omeprazole is not just a superposition of its enantiomer constituents. They are consistent with the pharmacological evidence of enantiomer–enantiomer interactions in omeprazole versus esomeprazole and the differences between the drugs omeprazole and esomeprazole magnesium and support the lodged application for regulatory supplementary protection certificate (SPC) exclusivity for the esomeprazole‐related combination drug Vimovo. Chirality 26:214–227, 2014. © 2014 Wiley Periodicals, Inc.     

Poly –N = N– linked 1,5-dihydro-1,5-diazocine,the two-dimensional polymer with Dirac insulator properties: ab initio study

A new material – the monolayered, π-conjugated, poly dinitrogen-linked 1,5-dihydro-1,5-diazocine – is proposed. Density functional theory calculations reveal that the material is a two-dimensional Dirac insulator with a direct band gap. The generalised gradient approximation (GGA) and the local density approximation (LDA) give band gaps of E _gap ^GGA = 0.045 eV and E _gap ^LDA = 0.035 eV. Anisotropy of the Dirac cones results in variation of Fermi velocities of the charge carriers: [0.85–5.30] × 10⁶ m/s (GGA) and [0.86–5.38] × 10⁶ m/s (LDA). Corresponding effective masses are ～10³ lower than that of a free electron. G₀W₀ calculations confirm the topology of density functional theory band structure and show band gap of E _gap = 0.121 eV. Cohesive energies are estimated at E _c ^GGA = 5.30 eV/atom and E _c ^LDA = 6.15 eV/atom. Thus, the results provide the first evidence for the existence of Dirac insulators among organic polymers.     

The Water Dimer: Post-Hartree-Fock and Density Functional Calculations on the Potential Energy Surface

Conventional ab initio and density functional methods with extended basis sets were employed in the study of a path on the water-dimer potential energy surface. The results show that density functional methods do depend strongly on the type of exchange-correlation potential employed, as well as on the quality of the basis sets – similarly to conventional ab initio methods – and on the density of the grid. Gradient-corrected methods behave, as expected, better than uncorrected ones, the Becke–Lee–Yang–Parr (BLYP) potential being the one that gives the best results. However, too large chemical- and hydrogen-bond lengths and absolute energies, as well as too small relative total and correlation energies demonstrate that even BLYP calculations with a relative large basis set are not good as MP2 calculations of the same size. Adiabatically connected functionals (ACM), represented in this work by B3PW91, provide an improvement on the whole surface. This revised version was published online in June 2006 with corrections to the Cover Date.     

DFT study of a substrate and inhibitors of 1-deoxy-2-xylulose-5-phosphate reductoisomerase – the potential novel target molecule for anti-malaria drug development

1-Deoxy-2-xylulose-5-phosphate (DOXP) reductoisomerase is a novel target for developing anti-malaria drugs. The determination of structural and electronic properties of the inhibitor molecules is of crucial importance for analyzing the interactions between DOXP-reductoisomerase and its inhibitors. Geometry-optimizations and single point calculations at the B3LYP/3-21G*//B3LYP/3-21G** and B3LYP/3-21G*//MP2/3-21G** levels were performed to determine the structures and charge distributions of an enzyme substrate (1-deoxy-D-xylulose 5-phosphate) and the two inhibitors (fosmidomycin and FR-900098). The theoretically derived bond lengths are in excellent agreement with the corresponding experimental values reported for similar structures. Partial charges and dipole moments are assigned using the Mulliken and natural population analyses. The calculated structures and partial charge distributions can readily be used for the further development of biologically active inhibitors of DOXP-reductoisomerase as well as parameters for docking experiments.Electronic Supplementary Material available.     

Degradation and racemization of zopiclone enantiomers in plasma and partially aqueous solutions

We investigated the degradation and racemization of zopiclone (ZOP) enantiomers in plasma and partially aqueous solutions (ethanol:phosphate buffer). Degradation and racemization increased with increasing pH and temperature. Degradation products were identified by means of mass spectrometry, which revealed hydrolysis of the carbamate function and opening of the pyrrolidone ring. In plasma, neither degradation nor racemization occurred after 6 months of storage at -20°C and subsequent extraction. © 1995 Wiley-Liss, Inc.     

FT-IR,FT-Raman spectra and DFT vibrational analysis of 2-aminobiphenyl

In this work, the Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 2-aminobiphenyl (2ABP) were recorded in the solid phase. The optimised geometry, frequency and intensity of the vibrational bands of 2ABP were obtained by the density functional theory (BLYP and B3LYP) methods with complete relaxation in the potential energy surface using 6-31G(d) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectrograms.     

Potentials for Molecular Dynamics Simulation of Silicate Glasses

A new potential model has been developed for the simulation of amorphous silica based on the ab initio potential model of Pyper. This model promises to be of value in the simulation of silica at high pressures.     

正常和反常PRION分子PrP~C和PrP~(Sc)的空间结构模建和电子结构计算

朊蛋白（ＰＲＩＯＮ）是一种不同于细菌,真菌,病毒的新的病原体。１９９６年英国“疯牛病”引起了对ＰＲＩＯＮ研究的高潮。ＰＲＩＯＮ分子生物学的关键是解释ＰＲＩＯＮ蛋白构象转换的生物不本质。本文从构象模建,量子化学整体从头算的水平上对两个构象的电子结构进行了计算比较,从中发现了ＰＲＩＯＮ蛋白分子电子结构上区别于其他分子的特异性,并对计算所得的活性部位进行了讨论。     

正常和反常PRION分子PrP~C和PrP~(Sc)的空间结构模建和电子结构计算

朊蛋白（ＰＲＩＯＮ） 是一种不同于细菌,真菌,病毒的新的病原体。１９９６ 年英国“疯牛病”引起了对ＰＲＩＯＮ 研究的高潮。ＰＲＩＯＮ 分子生物学研究的关键是解释ＰＲＩＯＮ 蛋白构象转换的生物学本质。本文从构象模建,量子化学整体从头算的水平上对两个构象的电子结构进行了计算比较,从中发现了ＰＲＩＯＮ 蛋白分子电子结构上区别于其他分子的特异性, 并对计算所得的活性部位进行了讨论。