A B3LYP and MP2(full) theoretical investigation into explosive sensitivity upon the formation of the molecule-cation interaction between the nitro group of 3,4-dinitropyrazole and H+, Li+, Na+, Be2+ or Mg2+

The explosive sensitivity upon the formation of molecule-cation interaction between the nitro group of 3,4-dinitropyrazole (DNP) and H⁺, Li⁺, Na⁺, Be²⁺ or Mg²⁺ has been investigated using the B3LYP and MP2(full) methods with the 6-311++G** and 6-311++G(2df,2p) basis sets. The bond dissociation energy (BDE) of the C3–N7 trigger bond has also been discussed for the DNP monomer and the corresponding complex. The interaction between the oxygen atom of nitro group and H⁺ in DNP…H⁺ is partly covalent in nature. The molecule-cation interaction and bond dissociation energy of the C3–N7 trigger bond follow the order of DNP…Be²⁺ > DNP…Mg²⁺ > DNP…Li⁺ > DNP…Na⁺. Except for DNP…H⁺, the increment of the trigger bond dissociation energy in comparison with the DNP monomer correlates well with the molecule-cation interaction energy, natural charge of the nitro group, electron density ρ _BCP(C3–N7), delocalization energy E ⁽²⁾ and NBO charge transfer. The analyses of atoms in molecules (AIM), natural bond orbital (NBO) and electron density shifts have shown that the electron density of the nitro group shifts toward the C3–N7 trigger bond upon the formation of the molecule-cation interaction. Thus, the trigger bond is strengthened and the sensitivity of DNP is reduced.     

DFT study of the interaction of cytidine and 2′-deoxycytidine with Li, Na, and K: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li⁺, Na⁺, and K⁺ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li⁺ to Na⁺ and K⁺ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1-C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids.     

Crystal structure and kinetics of the acid-catalysed decomposition of (N,N′-bis(2-pyridylmethylene)-1,3-diamino-2,2-dicarboxyethylpropane)copper(II)perchlorate

The crystal structure of the complex [CuL(OH)₂](ClO₄)₂·H₂O; L=N,N′-bis(2-pyridylmethylene)-1,3-diamino-2,2-dicarboxyethylpropane, determined for the first time, reveals a penta-coordinated copper(II) centre in a distorted square-pyramidal geometry with a weakly bonded axial water molecule. In order to assess possible routes to the putative free ligand N,N′-bis(2-pyridylmethylene)-1,3-diaminopropane-2-carboxylic acid the behaviour (stability) of the complex towards both acid and alkaline aqueous solution has been investigated. In 1.0 M acidic chloride media at 25 °C the complex undergoes slow decomposition in two stages giving 2-pyridylmethylammonium chloride, formaldehyde and diethylmalonate in addition to aqueous Cu²⁺. The initial fast stage has both H⁺-dependent (5.32±0.18×10⁻⁵ M⁻² s⁻¹) and independent (1.59±0.10×10⁻⁵ s⁻¹) paths, the latter believed to reflect rapid chloride equilibration at the labile axial site followed by rate determining isomerisation to place a CuNH bond at the axial site leading to CuN bond cleavage. The rate constant for the H⁺-dependent faster stage carries a [H⁺]² dependence suggesting that here protonation of both secondary NH groups occurs within the rate-determining step prior to decomposition. Assistance from the axial site is also proposed. Absorbance changes monitored as a function of [H⁺] for the ∼10× slower second stage suggest that it may involve intermediates resulting from the H⁺-independent initial step.     

Diastereomeric preference in 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononanelithium(I) and its sodium(I) analogue

In N,N-dimethylformamide (DMF), 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononane forms metal complexes, [M(S-thppc9)]⁺, for which log K (dm³ mol⁻¹)=3.01, 2.65, 2.66, 2.65, 2.42 and 7.59 (all±0.05) where M⁺=Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ and Ag⁺, respectively. Variable temperature ¹³C{¹H} NMR spectroscopy shows that the interchange between equivalent forms of a single diastereomer occurs for [Li(S-thppc9)]⁺ and [Na(S-thppc9)]⁺ characterised by: k=43±5 and 2900±100 s⁻¹, at 298.2 K, ΔH^‡=22.5±1.6 and 33.8±1.6 kJ mol⁻¹, and ΔS^‡=−133±5 and −59±6 J K⁻¹ mol⁻¹, respectively. Gas phase ab initio modelling shows these complexes and their K⁺ analogue to preferentially form distorted trigonal prismatic Λ, Δ, and Λ diastereomers, respectively.     

Synthesis and structural characterisation of the phenyl/scorpionate hybrid ligand [Ph(pz)BC5H10]

The new phenyl/scorpionate hybrid ligand [Ph(pz)BC₅H₁₀]⁻ has been synthesised and structurally characterised as K⁺ and Tl⁺ salt. The ligand is specifically designed to create half-sandwich complexes in which the metal ion is chelated by the π-electron system of the phenyl ring and by the electron lone pair of the pyrazolyl nitrogen atom. This structural motif is established both by K[Ph(pz)BC₅H₁₀] and by Tl[Ph(pz)BC₅H₁₀].     

Kinetic study of base-catalyzed asymmetric nitrogen conversion of cis-folded macrocyclic nickel(II) complex of 1,4,7,11-tetraazacyclotetradecane

In order to examine the effects of coordinated hydroxide ion and free hydroxide ion in configurational conversion of a tetraamine macrocyclic ligand complex, the kinetic of the cis-to-planar interconversion of cis-[Ni(isocyclam)(H₂O)₂]²⁺ (isocyclam = 1,4,7,11-tetraazacyclotetradecane) has been examined spectrophotometrically. All kinetic data have been satisfactorily fitted by the rate law, R = (k₁K_OH[OH⁻]² + k₂[OH⁻])(1 + K_OH[OH⁻])⁻¹(cis-[Ni(isocyclam)(H₂O)₂]²⁺ + [Ni(isocyclam)(OH)]⁺), where k₂ = (3.40 ± 0.12) × 10³ dm³ mol⁻¹ s⁻¹ is almost equal to k_OH determined in buffer solution (lowly basic media), K_OH = 22.7 ± 1.4 dm³ mol⁻¹ at I (ionic strength) = 0.10 mol dm⁻³ (NaClO₄ + NaOH) and 25.0 °C. Rate constants, k₂ and K_OH, are functions of ionic strength, giving a good evidence for an intermolecular pathway. The reaction follows a free-base-catalyzed mechanism where nitrogen inversion, solvation and ring conformational changes are occurred.     

Preparation, properties and crystal structure of two isomers of R,R,S,S- and R,S,R,S-[chloro(1,3,10,12,16,19-hexaazatetracyclo[17,3,1,1,0]tetracosane)copper(II)]

Two isomers (R,S,R,S- and R,R,S,S-) of five coordinate complex [Cu(L)Cl]⁺ have been separated and characterised. These two isomers have significantly different spectrochemical and electrochemical properties. Absorption maximum of R,S,R,S-[Cu(L)Cl]⁺ shifts to longer wavelength and its reduction potential shifts to more positive direction comparing those of R,R,S,S-[Cu(L)Cl]⁺. R,S,R,S-[Cu(L)Cl]⁺ is significantly distorted to trigonal-bipyramidal structure, whereas R,R,S,S-[Cu(L)Cl]⁺ retains almost square-planar geometry. The average bond distance of Cu-N in basal plane of R,S,R,S-[Cu(L)Cl]⁺ is longer by 0.024 Å than that of R,R,S,S-[Cu(L)Cl]⁺, whereas the bond distance of Cu-Cl in former is shorter by 0.200 Å than that in latter. The isolated square-planar complexes of R,R,S,S- and R,S,R,S-[Cu(L)](ClO₄)₂ are converted to the R,R,S,S- and R,S,R,S-[Cu(L)Cl]⁺ by the addition of Cl⁻ in nitromethane solution with the rate constants, k=1.70 (±0.02) and 8.31 (±0.07) M⁻¹ s⁻¹, respectively.     

Similar structural feature observed in the crystal packing of [Ni(dmit)2] salts of geometrical isomer of methoxycarbonyl pyridinium

The crystal structures of the C-H?O hydrogen-bonded, 1:1 complex salts of with [Ni(dmit)₂]⁻ 2MMP, 3MMP and 4MMP (ortho-, meta-, and para-methoxycarbonyl N-methyl-pyridinium, respectively) cations with have been investigated. All complex salts formed non-segregated stacks with the anions being sandwiched between layers or dimers of cations. Within these salts, the arrangement of the counter cations are structurally modulated by two weak intermolecular hydrogen bonds between the hydrogen of the pyridinium ring, methyl group or one of the two and the CO group of the cations. The alignment of Ni(dmit)₂ molecules is found to be mainly governed by the attached position of methoxycarbonyl group. Powders of (2MMP)[Ni(dmit)₂], (3MMP)[Ni(dmit)₂] and (4MMP)[Ni(dmit)₂] salts exhibited room temperature conductivities of 4.33 × 10⁻¹⁰, 1.80 × 10⁻⁶ and 5.60 × 10⁻⁶ S cm⁻¹, respectively.     

Tbx18 is essential for normal development of vasculature network and glomerular mesangium in the mammalian kidney

Tbx18 has been shown to be essential for ureteral development. However, it remains unclear whether it plays a direct role in kidney development. Here we addressed this by focusing on examining the pattern and contribution of Tbx18+ cells in the kidney and its role in kidney vascular development. Expression studies and genetic lineage tracing revealed that Tbx18 is expressed in renal capsule, vascular smooth muscle cells and pericytes and glomerular mesangial cells in the kidney and that Tbx18-expressing progenitors contribute to these cell types. Examination of Tbx18^−/− kidneys revealed large reduction in vasculature density and dilation of glomerular capillary loops. While SMA+ cells were reduced in the mutant, PDGFRβ+ cells were seen in early capillary loop renal corpuscles in the mutant, but fewer than in the controls, and further development of the mesangium failed. Analysis of kidney explants cultured from E12.5 excluded the possibility that the defects observed in the mutant were caused by ureter obstruction. Reduced proliferation in glomerular tuft and increased apoptosis in perivascular mesenchyme were observed in Tbx18^−/− kidneys. Thus, our analyses have identified a novel role of Tbx18 in kidney vasculature development.     

Ternary copper(II) complexes with hippurate derivatives and 1,10-phenanthroline: Synthesis and biological activity

Several new Cu-hippurate derivative-phenanthroline ternary complexes have been prepared. The X-ray structure of one of them, [Cu(hip)(phen)₂]⁺·(hip⁻) (2) (where hip is hippurate and phen is 1,10-phenanthroline) has been solved. The structure of this new compound shows important differences (3D-pattern) to other similar related complexes (2D-pattern). A study of the biological activity of [Cu(hip)(phen)₂]⁺·(hip⁻)·2H₂O (2), [Cu(BGG)(phen)₂]⁺·(BGG⁻)·6H₂O (3), [Cu(B^IGG)₂(phen)](H₂O) (4) and [Cu(I-hip)(bpy)₂]⁺·(I-hip⁻)·3.5H₂O (5) (where I-hip is ortho-iodohippurate, BGG corresponds to benzoylglycilglycine, and B^IGG is ortho-iodobenzoylglycilglycine) is included and compared with the anti-proliferative activity of [Cu(I-hip)(phen)₂]⁺·(I-hip⁻)·7H₂O (1) previously described, resulting in a greater cytotoxic activity of the compounds with 1,10-phenanthroline instead of those with 2,2′-bipyridyl, in the same way that removing iodine substitution or lengthening the peptidic chain diminishes the activity of compounds compared with 1. The presence of an ortho-iodine group and the direct bond between Ar-CO and glycine moieties yield to the best results.     

Theoretical studies on tetrahedral oxoanions MO4 (n=2, 3, 4; M=Cr, Mo, W)

The structure and bonding in MO₄ ⁿ⁻ (n=2, 3, 4; M=Cr, Mo, W) tetrahedral oxoanions have been investigated using density-functional methods. Good computational-experimental agreement for the geometrical parameters of the known species has been obtained which allowed the prediction of the cited parameters for those species that have not yet been isolated. The molecular-orbital analysis indicates that the chemical bonds mainly have d functions of the metal and p functions of oxygen. The electron affinities for the process MO₄ ⁿ⁻ + 1e → MO₄ ^(n + 1)− have also been calculated and their importance in relation with the preparation of the oxoanions MO₄ ⁿ⁻ (M=Mo, W; n=3, 4) not reported in the bibliography is discussed. Comparative studies of the electronic structures of oxoanions allow to explain their reactivities against nucleophilic and electrophilic attacks. The vibrational frequencies have been calculated and compared with the experimental values and the different relationships between the symmetric-stretching and antisymmetric-bending frequencies allow to confirm the assignations of the calculated spectra.     

The synthesis and toxicity of tripodal tricarbonyl rhenium complexes as radiopharmaceutical models

We report the synthesis and toxicity of a series of rhenium(I) tricarbonyl complexes incorporating the trisaminomethylethane (TAME) ligand. Compounds with the (TAME)Re(CO)₃⁺ cation were synthesized via several routes, including by use of Re(CO)₅X precursors as well as the aqueous cation Re(CO)₃(H₂O)₃⁺. Salts of the formula [(TAME)Re(CO)₃]X where X = Br⁻, Cl⁻, NO₃⁻, PF₆⁻ and ClO₄⁻ were evaluated using two cell lines: the monoclonal S3 HeLa line and a vascular smooth muscle cell line harvested from mice. All compounds have isostructural cations and differ only in the identity of the non-coordinating anion. None of the complexes exhibited any appreciable toxicity in the HeLa line up to the solubility limit. In the vascular smooth muscle cell line, the bromide salt exhibited some cytotoxicity, but this observation most likely results from the presence of bromide anion, which has been shown to have limited toxicity.     

Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

Conformational preferences of modified nucleoside, N(4)-acetylcytidine, ac⁴C have been investigated using quantum chemical semi-empirical RM1 method. Automated geometry optimization using PM3 method along with ab initio methods HF SCF (6-31G**), and density functional theory (DFT; B3LYP/6-31G**) have also been made to compare the salient features. The most stable conformation of N(4)-acetyl group of ac⁴C prefers “proximal” orientation. This conformation is stabilized by intramolecular hydrogen bonding between O(7)···HC(5), O(2)···HC2′, and O4′···HC(6). The “proximal” conformation of N(4)-acetyl group has also been observed in another conformational study of anticodon loop of E. coli elongator tRNA^Met. The solvent accessible surface area (SASA) calculations revealed the role of ac⁴C in anticodon loop. The explicit molecular dynamics simulation study also shows the “proximal” orientation of N(4)-acetyl group. The predicted “proximal” conformation would allow ac⁴C to interact with third base of codon AUG/AUA whereas the ‘distal’ orientation of N(4)-acetyl cytidine side-chain prevents such interactions. Single point energy calculation studies of various models of anticodon–codon bases revealed that the models ac⁴C₍₃₄₎(Proximal):G₃, and ac⁴C₍₃₄₎(Proximal):A₃ are energetically more stable as compared to models ac⁴C₍₃₄₎(Distal):G₃, and ac⁴C₍₃₄₎(Distal):A₃, respectively. MEPs calculations showed the unique potential tunnels between the hydrogen bond donor–acceptor atoms of ac⁴C₍₃₄₎(Proximal):G₃/A₃ base pairs suggesting role of ac⁴C in recognition of third letter of codons AUG/AUA. The “distal” conformation of ac⁴C might prevent misreading of AUA codon. Hence, this study could be useful to understand the role of ac⁴C in the tertiary structure folding of tRNA as well as in the proper recognition of codons during protein biosynthesis process.     

Antiport Mechanism for Cl/H in ClC-ec1 from Normal-Mode Analysis

ClC chloride channels and transporters play major roles in cellular excitability, epithelial salt transport, volume, pH, and blood pressure regulation. One family member, ClC-ec1 from Escherichia coli, has been structurally resolved crystallographically and subjected to intensive mutagenetic, crystallographic, and electrophysiological studies. It functions as a Cl⁻/H⁺ antiporter, not a Cl⁻ channel; however, the molecular mechanism for Cl⁻/H⁺ exchange is largely unknown. Using all-atom normal-mode analysis to explore possible mechanisms for this antiport, we propose that Cl⁻/H⁺ exchange involves a conformational cycle of alternating exposure of Cl⁻ and H⁺ binding sites of both ClC pores to the two sides of the membrane. Both pores switch simultaneously from facing outward to facing inward, reminiscent of the standard alternating-access mechanism, which may have direct implications for eukaryotic Cl⁻/H⁺ transporters and Cl⁻ channels.     

Spermatogonial exchange involving the X but not the y chromosome inDrosophila Melanogaster

Summary The distal uninverted portion of In(1)sc⁸, which carriesy ⁺ andac ⁺, is occasionally lost during spermatogonial divisions. This is accomplished by exchange between the protion of the proximal heterochromatin that has been removed distally by the inversion and some other heterochromatin in the complement (see alsoLindsley 1955b).. The majority of the recombiants recovered from males carrying In(1)sc⁸ arise through exchange with the Y chromosome (12/15). The majority of the recombinants recovered from males carring In(1)sc^8L, EN^R, which is characterized by a heterochromatic second arm, do not arise through exchange with the Y chromosome (18/22). The absolute frequencies of Y involvement with In(1)sc⁸ (7/105067) and In(1)sc^8L, EN^R,(2/38588), however, are comparable. The heterochromatic constitution of the recombinants examined is consistent with the hypothesis that an observed excess of recombinants recoverred from In(1)sc^8L, EN^R as compared with In(1)sc⁸ is accounted for by Y independent recombinants and is the consequence of exchange between the second heterochromatin arm of In(1)EN^R and the distal heterochromatin of In(1)sc^8L. A maximum of six different regions of exchange between these two regions may be inferred from the constitution of the recombinants. This inference is considered to support the hypothesis that pairing and exchange between heterochromatic regions are not strictly homologous.With 6 Figures in the TextOperated by Union Carbide Nuclear Company for the U.S. Atomic Energy Commission.Part of the material was presented to the Graduate School of the California Institute of Technology in partial fulfillment of requirements for the degree of Doctor of Philosophy supported by an Atomic Energy Commission predoctoral fellowship. Further experimentation has been pursued under a National Research Council postdoctoral fellowship at the University and under a National Science Foundation postdoctoral fellowship at the University of Missouri. Experimentation was completed at Oak Ridge.     

Magneto-structural relationships for a mononuclear Co(II) complex with large zero-field splitting

A mononuclear cobalt(II) complex, [Co(ac)₂(H₂O)₂(MeIm)₂], with heteroleptic coordination sphere possessing the {CoO₂O′₂N₂} chromophore has been prepared and structurally characterized. The magnetic data down to 2 K show an enhanced magnetic anisotropy manifesting itself in a large zero-field splitting (ZFS) parameter. As a consequence, the magnetization deviates substantially from the Brillouin-function behavior. A fit to the zero-field splitting model gave the following set of magnetic parameters: D/hc = +95 cm⁻¹, g_x = 2.530, zj/hc = −0.078, χ_TIP = 16.7 × 10⁻⁹ m³ mol⁻¹, (g_z = 2.0). The Griffith-Figgis model and the Generalized Crystal-Field model lie beyond the spin-Hamiltonian formalism; they gave analogous, although not identical ZFS parameters: D/hc = 109 cm⁻¹, and D/hc = 77 cm⁻¹, respectively. The absorption spectrum taken in the FAR-IR region exhibits manifold absorption peaks referring to the transitions among the crystal-field multiplets of the parent ⁴A_2g + ⁴E_g terms (D_4h), originating in a crystal-field splitting of the octahedral ⁴T_1g ground term.     

Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies

This report present the results of natural energy decomposition analysis (NEDA), natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM) calculations of three derivatives of biphenyl-1-aza-18-crown-6 ether and their 1:1 complexes with Cd²⁺. All calculations used the B3LYP density functional theory in combination with the 6-311G and WTBS basis sets for ligands and Cd²⁺ ion, respectively. Ligands 1 and 3 have a single 1-aza-18-crown-6, substituent; ligand 2 has two such substituents. The results show that, in the optimized geometries of the complexes, the distance between N and Cd²⁺ is greater than the distance between O and Cd²⁺. NBO and QTAIM data confirm these results. There was no stabilization energy or bond critical point for N · · · Cd²⁺ in NBO or QTAIM, respectively. Data show that the O · · · Cd²⁺ interaction is a kind of closed shell interaction. The trend of the calculated stabilization energy was similar to the experimental data. Different contributions of interaction energies for complex formation were analyzed by NEDA, and the results show that the main component of the interactions is accounted for by polarization.

     

Early postnatal development of the immune system in piglets: the redistribution of T lymphocyte subsets

In this study, we have characterised postnatal changes in T lymphocyte subsets, especially γδ T lymphocytes, in blood, spleen and lymph nodes. Detection was carried out using two-colour flow cytometry and three-colour immunohistochemistry. During ontogeny, there was a significant increase in the total percentage of γδ T cells in the spleen and blood. In the lymph nodes, there were no age-dependent changes in the total percentage of γδ T cells, but the percentage of the γδTCR⁺CD8⁺ subpopulation significantly increased. The tissue distribution of γδTCR⁺CD8⁺ and γδTCR⁺CD8⁻ cells in the lymph nodes is random and not collocated with a particular area of the organ. Furthermore, postnatal development was characterised by an increasing frequency of CD8⁺CD3⁺CD4⁻γδTCR⁻, which was compensated by a decreasing proportion of CD4⁺ lymphocytes. Double positive CD4⁺CD8⁺ lymphocytes were rare during the first month of life and a significant age-dependent increase of these cells was found in all the compartments monitored.