Application of the DFT Theory to Study Cobalamin Complexes

The aim of present study is to select the best methodology in the frame of the Density Functional Theory (DFT), which may be employed to study the cobalamin complexes. Our discussion is limited to two approaches, one in which hybrid B3LYP and UB3LYP functionals are used, and the second in which geometry parameters are calculated within LDA-VWN functional, and energies of the investigated systems are computed within RPBE functional. Results of performed calculations show that both methodologies can be successfully applied to study cobalamin derivatives. Probably because of the small ligand binding energies in the studied complexes, the B3LYP and UB3LYP functionals may be used only to predict the pattern of changes in the binding energies. The use of the RPBE functional, originally parameterized to reproduce in a proper way the chemisorption energies of the small molecules on the metallic surfaces, allows to improve their values so as they fit into experimental data. Geometry parameters of the investigated complexes computed within both approaches are in good agreement with the experimental values. Interatomic distances are a little overestimated while calculated within both hybrid functionals, what is in contrast to VWN functional results. The latter, in general, gives shorter distances as observed experimentally.     

Synthesis of some dibenzodiazepinone derivatives as potent and m2-selective antimuscarinic compounds

Two series of 5-[[4-[4-(dialkylamino)butyl]-l-cyclohexyl]acetyl], and 5-[(dialkylamino)acyl]-10,11-dihydro-5H- dibenzo[b,e][1,4]diazepin-11-ones were synthesized as potential m2-selective ligands 1,2. Their affinity and selectivity for the muscarinic cholinergic receptor m-AChR subtypes were determined. Replacing a nitrogen with CH in the piperidine ring of 5-[[4-[4-(dialkylamino)butyl]-l-piperidinyl]acetyl]-10,11-dihydro-5H-dibenzo-[b,e][1,4]diazepin-11-ones 3 significantly altered the affinity and selectivity to the muscarinic receptor subtypes.     

H-bonding dependent structures of (NH4+)3H+(SO4 2-)2. Mechanisms of phase transitions

The role of different H-bonds in phases II, III, IV, and V of triammonium hydrogen disulfate, (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), has been studied by X-ray diffraction and (1)H solid-state MAS NMR. The proper space group for phase II is C2/c, for phases III and IV is P2/n, and for phase V is P onemacr;. The structures of phases III and IV seem to be the same. The hydrogen atom participating in the O(-)-H(+).O(-) H-bond in phase II of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) at room temperature is split at two positions around the center of the crucial O(-)-H(+).O(-) H-bonding, joining two SO(4)(2)(-) tetrahedra. With decreasing temperature, it becomes localized at one of the oxygen atoms. Further cooling causes additional differentiation of possibly equivalent sulfate dimers. The NH(4)(+) ions participate mainly in bifurcated H-bonds with two oxygen atoms from sulfate anions. On cooling, the major contribution of the bifurcated H-bond becomes stronger, whereas the minor one becomes weaker. This is coupled with rotation of sulfate ions. In all the phases of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), some additional, weak but significant, reflections are observed. They are located between the layers of the reciprocal lattice, suggesting possible modulation of the host (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) structure(s). According to (1)H MAS NMR obtained for phases II and III, the nature of the acidic proton disorder is dynamic, and localization of the proton takes place in a broader range of temperatures, as can be expected from the X-ray diffraction data.     

Tungsten and Molybdenum Heteropolyanions with Different Central Ions—Correlation between Theory and Experiment

Density functional theory calculations were carried out to investigate the electronic structures of Keggin-typed [XMo₁₂O₄₀]ⁿ⁻ and [XW₁₂O₄₀]ⁿ⁻ anions with different heteroatoms (X = Zn²⁺, B³⁺, Al³⁺, Ga³⁺, Si⁴⁺, Ge⁴⁺, P⁵⁺, As⁵⁺, and S⁶⁺). The influence of solvent on redox properties of heteropolyanions was discussed. For [XW₁₂O₄₀]ⁿ⁻ systems two linear correlation: first, between the experimental redox potential and energies of LUMO orbital; and second, between the experimental redox potential and total energy interaction (calculated between internal tetrahedron (XO₄ⁿ⁻), and rest of Kegging anion skeleton, (W₁₂O₃₆)) were designated. Taking into account the similarity of XW₁₂O₄₀ⁿ⁻ and XMo₁₂O₄₀ⁿ⁻ systems (in geometry and electronic structure), the estimated redox potential of molybdenum heteropolyanions (with X being p block elements) in different solvent were proposed.     

Investigation of the low-frequency vibrations of crystalline tartaric acid using terahertz spectroscopy and solid-state density functional theory

The room temperature and cryogenic terahertz (THz) spectra (10-95 cm(-1)) of l-tartaric acid and dl-tartaric acid were investigated. At 293 K, the l-tartaric acid spectrum showed four absorption features at 36.4, 61.6, 78.7, and 87.3 cm(-1) in the experimental spectrum. Once cooled to 78 K, these features narrowed and shifted to 35.9, 63.4, 81.1, and 90.1 cm(-1). The THz spectrum of dl-tartaric acid is significantly different, containing only a single absorption at 79.9 cm(-1) at room temperature, which shifts to 82.9 cm(-1) at 78 K. Solid-state density functional theory calculations [B3LYP/6-311G(2d,2p)] were performed to simulate the crystalline structure of both molecular solids and to assign the observed spectral features to specific atomic motions. The THz spectrum of l-tartaric acid is particularly interesting in that it contains a theoretically unaccounted for spectral feature that may arise from second-order phonon processes and also exhibits an anomalous red-shifting absorption feature with cooling that is shown to originate from negative thermal expansion of the crystal.     

Terahertz spectroscopy and solid-state density functional theory simulations of the improvised explosive oxidizers potassium nitrate and ammonium nitrate

Terahertz spectroscopy provides a noninvasive and nondestructive method for detecting and identifying concealed explosives. In this work, the room-temperature and cryogenic terahertz spectra of two common improvised explosive oxidizers, namely, potassium nitrate (KN) and ammonium nitrate (AN), are presented, along with detailed solid-state density functional theory (DFT) analyses of the crystalline structures and spectral features. At both 294 and 78 K, KN exhibits two terahertz absorption features below 100 cm(-1) that have been assigned through DFT simulations to arise from hindered nitrate rotations in the KN-II crystalline polymorph. The terahertz spectrum of AN exhibits a pronounced temperature dependence. The 294 K spectrum is free of any absorptions, whereas the 78 K spectrum consists of several narrow and intense peaks. The origin of this large difference is the polymorphic transition that occurs during cooling of AN, where room-temperature AN-IV is converted to AN-V at 255 K. The 78 K terahertz spectrum of AN is assigned here to various ion rotations and translations in the AN-V polymorph lattice. The analysis of the room-temperature AN-IV terahertz spectrum proved to be more complicated. The solid-state DFT simulations predicted that the room-temperature crystal structure of AN is not very well described using the standard Pmmn space-group symmetry as previously believed. The AN-IV polymorph actually belongs to the Pmn2(1) space group, and the perceived Pmmn symmetry results from vibrational averaging through nitrate rotations. This newly observed Pmn2(1) crystal symmetry for room-temperature AN is the reason for the absence of absorption features in the 294 K terahertz spectrum of AN and provides new insight into the polymorphic transitions of this ionic solid.     

CP/MAS NMR in trans-β-carotene

CP/MAS NMR spectra of solid trans-β-carotene were assigned, compared with crystallographic data and discussed in terms of molecular motion.     

Raman Spectroscopy Studies of Reorientations in Isotropic Phase of Alkoxyazoxybenzenes

Abstract

Raman spectra for isotropic phase of PAA, PAP and HOAB were recorded. Three benzene rings vibrations were chosen for quantitative analysis and the choice is discussed for different PAA deuteration. The separation of vibrational and rotational relaxation was performed. Vibrational relaxation is a dominating process, but ca. 10% of total bandshape can be attributed to rotational relaxation. Rotational correlation times τ2 were calculated for all studied substances to be of the order 10^?11 s. τ2 is connected with the rotation around the long molecular axis and supports the correlation time τ₁ received from the dielectric relaxation measurements.