Structural-topological preferences and protonation sequence of aliphatic polyamines : a theoretical case study of tetramine trien

A large set of lowest and medium energy conformers of aliphatic tetramine trien was used to uncover structural-topological preferences of poliamines. Numerous common structural features among HL and H2L tautomers were identified, e.g., H-atoms of protonated functional groups are always involved in intramolecular NH•••N interactions and they result in as large and as many as possible rings in lowest energy conformers. Largest, 11-membered, molecular rings stabilize a molecule most and they appeared to be strain free whereas 5-memebred intramolecular rings were most strained (all formed due to NH•••N interactions). The CH•••HC interactions with QTAIM-defined atomic interaction lines were also found but, surprisingly, mainly in the lowest energy conformers of HL tautomers. According to the non-covalent interaction-based (NCI) analysis, 5- memebered rings formed by CH•••HC interactions are not strained and, in general, 3D NCI isosurfaces mimic those obtained for weaker NH•••N interactions. Also, 3D NCI isosurfaces found for NH•••N and CH•••HC interactions, regardless whether linked or not by an atomic interaction line, appeared to be indistinguishable. Using lowest energy conformers, theoretically predicted mixture of primary (HLp) and secondary (HLs) forms of trien was found to be in accord with the literature reports; using linear conformers resulted in predicting HLs as the only tautomer formed. In contrast to HF, the overall performance of B3LYP was found satisfactory for the purpose of the study.National Research Foundation of South Africa (Grant Numbers 87777) and the University of Pretoria.http://link.springer.com/journal/8942016-06-30hb201

Competition reaction-based prediction of polyamines' stepwise protonation constants: a case study involving 1,4,7,10-tetraazadecane (2,2,2-tet)

Theoretical prediction of four stepwise protonation constants of 1,4,7,10-tetraazadecane (2,2,2- tet) in correct order and with the smallest (largest) deviation of about 0.1 (–0.8) log unit from experimental values was achieved by an explicit application of a competition reaction (CRn) methodology in discrete-continuum solvation model involving four explicit water molecules. This methodology performs best when (i) tested (L(1)) and reference (L(2)) molecules are structurally similar, (ii) lowest energy conformers (LECs, selected from all possible tautomers) are used and (iii) a CRn, which assures a balanced charge distribution between reactants and products, Hn–1L(1) + HnL(2) = HnL(1) + Hn–1L(2), is implemented. A 5-step EEBGB-protocol was developed to effectively and in shortest time possible select LECs (E, B and G stands for electronic-energy-, Boltzmann-distribution- and Gibbs-free-energy-based stepwise selection of conformers). The EEBGB-protocol (i) reduced (by 94%) the number of conformers subjected to the frequency calculations (to obtain G-values) from 420 MM-selected to 25 used to compute four protonation constants and (ii) is of general-purpose as it is applicable to any flexible and poly-charged molecules. Moreover, in search for LECs, a rapid pre-screening protocol was developed and tested; it was found efficient for the purpose of this study. Additional research protocols, aimed at even better prediction of protonation constants, are also suggested.This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Numbers 87777) and the University of Pretoria.http://link.springer.com/journal/102672017-05-31hb2016Chemistr

Evaluating common QTAIM and NCI interpretations of the electron density concentration through IQA interaction energies and 1D cross-sections of the electron and deformation density distributions

Nine kinds of inter- and intramolecular interactions were investigated by exploring the topology of electron density in the interatomic regions using standard protocols of QTAIM, IQA and NCI techniques as well as in-house developed cross-sections of the electron and deformation density distributions. The first four methods provide the properties of the resultant density distribution in a molecular system whereas the later illustrates the process, inflow or outflow of density from fragments to the interatomic region of an interaction on its formation in a molecular system. We used (i) the QTAIM-defined atomic interaction line, AIL (presence or absence), (ii) IQA-defined interaction energy, EA;B int , and its components, classical VA;B cl and exchange–correlation VA;B XC term, (iii) NCI-defined isosurfaces to identify local regions of accumulated (k2 0) density relative to immediate environment, and (iv) deformation density for which Dq(r) > 0 indicates an inflow or otherwise an outflow of density on the interaction formation to explore the nature of the interactions. We found (i) AILs for highly attractive and repulsive interactions, regardless whether an inflow (Dq(r) > 0) or outflow of density into the interatomic region, (ii) no correlation between the signs of k2 and EA;B int ; both, highly repulsive and attractive, interactions might have locally depleted density and vice versa, (iii) locally accumulated density (k2 < 0) does not imply that this is the result of an inflow (Dq(r) > 0) of density and this equally applies to attractive and repulsive interactions either with or without an AIL. Results obtained demonstrate that the molecular environment can change the character of an interaction radically, from (i) attractive to repulsive, (ii) k2 0, or (iii) Dq(r) > 0 to Dq(r) < 0; hence, none of the topological indices used here, either separately or combined, can be used to definitely predict the (de)stabilizing nature of an interaction except highly repulsive ones for which the absence of AIL, interatomic density depletion and outflow of density on interaction formation are observed.The National Research Foundation of South Africa (Grant Number 87777) and the University of Pretoria.http://www.elsevier.com/locate/comptchb2016Chemistr

Exploring steric and electronic parameters of biaryl phosphacycles

Please read abstract in article.Research Centre for Synthesis and Catalysis (University of Johannesburg) and Sasol (Pty) Ltd as well as the Centre for High Performance Computing (CHPC), South Africa for providing computational resources.https://pubs.rsc.org/en/journals/journal/njhj2023Chemistr

2,2&amp;#8242;-(Piperazine-1,4-diyl)diethanaminium dibenzoate

The asymmetric unit of the title salt C8H22N42+&amp;#183;2C7H5O2&amp;#8722;, comprises two independent pairs of half a 2,2&amp;#8242;-(piperazine-1,4-diyl)diethanaminium dication plus a benzoate anion. The dications are symmetrical and lie across crystallographic centres of inversion. The crystal structure was refined as a two-component pseudo-merohedral twin using the twin law 001 0-10 100 [he domain fractions are 0.8645&amp;#8197;(8) and 0.1355&amp;#8197;(8)]. The anions and cations are linked by N&amp;#8212;H...O hydrogen bonds and weak N&amp;#8212;H...O intermolecular interactions to form infinite two-dimensional networks parallel to [101]. The conformation adopted by the cation in the crystal structure is very similar to that adopted by the same cation in the structures of the 2-hydroxybenzoate [Cukrowski et al. (2012). Acta Cryst, E68, o2387], the nitrate and the tetrahydrogen pentaborate salts

3,6-Diazaoctane-1,8-diaminium diiodide

The asymmetric unit of the title salt, C6H20N42+&amp;#183;2I&amp;#8722;, comprises half a 3,6-diazaoctane-1,8-diaminium dication plus an I&amp;#8722; anion. The dications are symmetrical and lie across crystallographic centres of inversion. In the crystal, the ions form a network involving mainly weak N&amp;#8212;H...I intermolecular interactions: two H atoms of the ammonium group form interactions with two I&amp;#8722; anions and the H atom of the secondary amine forms a weak interaction with a third I&amp;#8722; cation. The third ammonium H atom is hydrogen bonded to a secondary amine of an adjacent cation. The backbone of the cation does not form a uniformly trans chain, but is `kinked' [C&amp;#8212;N&amp;#8212;C&amp;#8212;C torsion angle = 71.5&amp;#8197;(2)&amp;#176;], probably to accommodate the direct hydrogen bond between the ammonium group and the secondary amine in an adjacent cation

2,2&amp;#8242;-(Piperazine-1,4-diyl)diethanaminium bis(2-hydroxybenzoate)

The asymmetric unit of the title salt, C8H22N42+&amp;#183;2C7H5O3&amp;#8722;, comprises half a 2,2&amp;#8242;-(piperazine-1,4-diyl)diethanaminium dication plus a 2-hydroxybenzoate anion. In the crystal, the anions and cations are linked by N&amp;#8212;H...O and O&amp;#8212;H...O hydrogen bonds to form infinite two-dimensional networks parallel with the a unit-cell face. The conformation adopted by the cation in the crystal is very similar to that adopted by the same cation in the structures of the nitrate and tetrahydrogen pentaborate salts

Non-specific cell-mediated immunity in Nigerian children with uncomplicated malaria

Non-specific cellular immunity was determined in 59 Nigerian children aged between 1-9 years with uncomplicated malaria and 93 age-matched uninfected controls using percentage migration index (%M.I) and Mantoux tuberculin skin test. The mean %M.I (using malaria Pf 155 antigen) was significantly lower in malaria subjects compared with the controls (

Non-specific cell-mediated immunity in Nigerian children with uncomplicated malaria

Non-specific cellular immunity was determined in 59 Nigerian children aged between 1-9 years with uncomplicated malaria and 93 age-matched uninfected controls using percentage migration index (%M.I) and Mantoux tuberculin skin test. The mean %M.I (using malaria Pf 155 antigen) was significantly lower in malaria subjects compared with the controls (p<0.05) while the mean diameter of tuberculin skin reaction (using Purified Protein Derivative of Mycobacterium butyricum ) was significantly lower in children with uncomplicated malaria compared with the controls (p<0.05). The mean total white blood cell count (TWBC) was also significantly reduced in the malaria subjects when compared with the controls (p<0.05). The results show that leucocytes of children with uncomplicated malaria exhibited effective adaptive immune response. This may help to combat initial contact with malaria parasites

Ab-initio investigation of the fundamental properties of metals (X = Be, Mg, and Ca) encapsulated CsXO3 tin-based perovskite materials

Perovskite material are widely used in Solar cell device due to it promising properties and power conversion efficiencies (PCE). Most importantly, properties of the absorber layer such as the band gap, electronic, optical, chemical composition and the grain size of the perovskite absorbed layer are very sacrosanct when determining efficacy of the material for such application. Thus, in this work, the optical, structural stability, electronic, and mechanical properties of non-halide cubic perovskite CsXO3 (X = Mg, Be and Ca) was extensively studied using the first principles Density functional theory (DFT) approach. The structural, electronic and optoelectronic properties was evaluated using Quantum Espresso Simulation Package (QESP) with the plane wave self-consistent field (PWscf) code. The structural computation reveals that the Lattice constant as well as total energy of CsXO3 (X = Be, Mg and Ca) increases as the size of cation X (X = Be, Mg and Ca) increases such that CsCaO3 possess the highest energy. Contrary, the fermi energy decreases with increase in cationic size, however, CsCaO3 has the highest lattice constant value 4.3743 eV. Electronic properties investigation shows that the studied perovskite has a metallic property with no forbidden band. zero band gap materials can adsorb photon across the entire solar spectrum, including lower-energy photons which is an advantage over a non-zero band gap which can only absorb photon with energies higher than the band gap energy can be absorbed and converted into electricity. This enables more efficient utilization of sunlight and increased overall energy conversion. To ascertain the effect of atomic exchange and orbital contribution in the formation of electronic properties, partial density of state (PDOS) was calculated and the result reveal that electron transition occurs mostly from p-orbital oxygen atom having major contribution on the valence band to the d-orbital of Caesium atom having major contribution on the conduction band and X-cation having minor contribution. CsXO3 (X = Be, Mg and Ca) also shows fascinating optical properties and thus can be used to improve solar cell device