Molecular structure and vibrational and chemical shift assignments of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione by DFT and <Emphasis Type="Italic">ab initio</Emphasis> HF calculations

The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values and several thermodynamic parameters of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Also, calculated ¹H chemical shift values compared with the experimental ones. The data of the title compound display significant molecular structure and IR, NMR analysis provide the basis for future design of efficient materials having the of 1,2,4-triazole core.     

Electronic structure modeling of dinuclear copper(II)-methacrylic acid complex by density functional theory

A dinuclear centrosymmetric copper(II) complex with the formula [Cu₂(μ-maa)₄(maaH)₂] has been synthesized and experimentally characterized by IR, electronic spectroscopy, and X-ray single-crystal diffractometry. Starting from experimental X-ray geometry and using antiferromagnetic singlet ground state, gas phase geometry optimization was performed by density functional hybrid (B3LYP) method with 6-31G(d) and LANL2DZ basis sets. Gas-phase vibrational frequencies and single point energy (SPE) calculations have been carried out at the geometry-optimized structure. Molecular electrostatic potential calculated at the optimized geometry and natural bond orbital analysis data have been extracted from SPE output. The gas-phase electronic transitions of the title complex were investigated by the time dependent-density functional theory (TD-DFT) approach with the same theory employing LANL2DZ basis set. Also the calculated UV-Vis based upon TD-DFT results and IR spectra were simulated for comparison with the experimental ones.     

Novel Pt(II) and Pt(IV) complexes with 3-amino-5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione. Synthesis, physicochemical, chemometric and pharmacological investigation

Platinum(II) and platinum(IV) complexes with 3-amino-5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione (L) with general formulaе cis-[PtL₂X₂]·nH₂O and [PtL₂Cl₄], where X = Cl⁻, Br⁻, I⁻ and n = 2-4) were synthesized. The novel compounds were fully characterized by elemental analysis, IR, ¹H, ¹³C, ¹⁹⁵Pt NMR spectra, thermal analysis and molar conductivity. The geometry of Pt(II) complexes and of the organic ligand in the gas phase were optimized using the hybrid DFT method B3LYP with LANL2DZ and 6-31G** basis sets. Some physicochemical parameters as dipole moment, HOMO, LUMO energies and ESP charges were calculated. The comparison of the bond length and angles, obtained from the X-ray analysis and DFT calculations is realized. The cytotoxic effects of these complexes in human T-cell leukemia KE-37 (SKW-3) are reported.     

Complexes of DNA bases and Watson–Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study

We study the binding of the neutral Ag_n (n = 8, 10, 12) to the DNA base-adenine (A), guanine (G) and Watson–Crick –adenine-thymine, guanine-cytosine pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential was used for silver and 6–31 + G^** was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Ag_n–A,G/WC complexes were also studied using time-dependent density functional theory. The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Ag_n–WC complexes. The vertical ionization potential, vertical electron affinity, hardness, and electrophilicity index of Ag_n–DNA/WC complexes have also been discussed.     

G6PD lozere and trinacria-like

Summary Two new G6PD variants have been found in red blood cells of the members of a French family originating from Lozere. The father is hemizygous for an electrophoretically fast variant with mild enzyme deficiency (50–60% of normal). The abnormal paternal G6PD gene is segregating in his daughter who is double heterozygous for maternal and paternal variants. This mutant enzyme, different from previously described variants is designated as Gd Lozère. The mother is heterozygous for another G6PD variant. Two sons are hemizygous for this latter mutant enzyme characterized by a moderate deficiency (25–30% of normal) and slower electrophoretic mobility with some slightly altered kinetic properties. This G6PD has been identified as Gd Trinacria like.These two abnormal enzymes are not associated with any hemolytic problem. Case reported is the first showing the segregation of two new mutant enzymes, distinct from common G6PD variants, among the members of the same family.     

An ab initio study of di- and trifluorobenzene–benzene complexes as relevant to carbonic anhydrase II–drug interactions

Ab initio calculations at the MP2/6-31G* level have shown that variously substituted di- and trifluorobenzenes form non-covalent complexes with benzene that adopt either aromatic–aromatic or H---F binding, the choice being determined by the pattern of fluorination. The binding energies of these structures are from 3.4 to 4.5 kcal mol^–1. This range is large enough to account for observed variations in the binding affinity of a library of fluoroaromatic inhibitors of carbonic anhydrase. This enzyme has an aromatic amino acid at a central position in the active site. The diverse modes of binding of the dimers also suggest that aggregates of fluorobenzenes might adopt specified 3-dimensional shapes in the solid state. Figure Observed structure for 1,2-difluorobenzene     

Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine

Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu–O(aqua) interactions were estimated to be about 60 kcal mol^–1 and for Cu–N7 bonding in the range of 75–83 kcal mol^–1. The broad range in Cu–N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.     

Peptides from the N-terminus of the atrial natriuretic factor prohormone enhance guanylate cyclase activity and increase cyclic GMP levels in a wide variety of tissues

The 98 amino acid (a. a.) N-terminus of the 126 a. a. atrial natriuretic factor (ANF) prohormone contains three peptides consisting of a. a. 1–30 (proANF 1–30), a. a. 31–67 (proANF 31–67) and a. a. 79–98 (proANF 79–98) with blood pressure lowering, sodium and/or potassium excreting properties similar to atrial natriuretic factor (a. a. 99–126, C-terminus of prohormone). ProANF 1–30 and proANF 31–67 have separate and distinct receptors from ANF in both vasculature and in the kidney to help mediate the above effects. At the cellular level proANFs 1–30, 31–67, and 79–98 as well as ANF's effects are mediated by enhancement of the guanylate cyclase (EC 4.6.1.2) — cyclic GMP system in vasculature and in the kidney. These peptides from the N-terminus of the ANF prohormone circulate normally in man and in all animal species tested. The object of the present investigation was to determine if these peptides have the ability to enhance either guanylate cyclase and/or adenylate cyclase in a variety of other tissues in addition to kidney and vasculature. ProANF 1–30, proANF 31–67, proANF 79–98, and ANF all increased rat lung, liver, heart and testes, but not spleen, particulate guanylate cyclase 2- to 3-fold at their 100 nM concentrations. Dose response curves revealed that maximal stimulation of particulate guanylate cyclase activity by these newly discovered peptides was at their 1 M concentrations, with no further increase in activity above their 1 M concentrations. Half-maximal (EC₅₀) enhancement of particulate guanylate cyclase occurred at 0.15 ± 0.01, 0.3 ± 0.02, 0.5 ± 0.03, and 0.9 ± 0.03 nM for proANF 1–30, proANF 31–67, proANF 79–98 and ANF, respectively. ProANFs 1–30, 31–67, 79–98, and 99–126 (i.e., ANF) each increased cyclic GMP but not cyclic AMP levels in tissue slices of liver, lung, small intestine, heart, and testes. None of these peptides enhanced either adenylate cyclase or the soluble 100,000 G form of guanylate cyclase. The ability of these N-terminal peptides to enhance particulate guanylate cyclase activity in a wide variety of tissues suggests that they may have effects in a much wider variety of tissues than presently thought.     

The structure of the cold-stable kinetochore fiber in metaphase PtK1 cells

When metaphase PtK₁ cells are cooled to 6–8 ° C for 4–6 h the free, polar, and astral spindle microtubules (MTs) disassemble while the MTs of each kinetochore fiber cluster together and persist as bundles of cold-stable MTs. These cold-stable kinetochore fibers are similar to untreated kinetochore fibers in both their length (i.e., 5–6 m) and in the number of kinetochore-associated MTs (i.e., 20–45) of which they are comprised. Quantitative information concerning the lengths of MTs within these fibers was obtained by tracking individual MTs between serial transverse sections. Approximately 1/2 of the kinetochore MTs in each fiber were found to run uninterrupted into the polar region of the spindle. It can be inferred from this and other data that a substantial number of MTs run uninterrupted between the kinetochore and the polar region in untreated metaphase PtK₁ cells.     

Description of the oöcysts of three new species of coccidia (Apicomplexa: Eimeriidae) from lizards in Namibia

Three new species of coccidian were recovered from the intestinal contents and faeces of lizards in Namibia, southwest Africa. Oöcysts of Eimeria barnardi n. sp. are described from Rhoptropus barnardi (Gekkonidae) and are ellipsoidal, 24.3 × 19.9 (21–26.5 × 16–22) m; shape index (length/width) 1.22 (1.12–1.30). A micropyle and oöcyst residuum are absent but a fragmented polar granule is present. Sporocysts are subspherical, 9.2 × 8.3 (8–11 × 7.5–9) m; shape index 1.11 (1.02–1.27). Oöcysts of Eimeria pachybibroni n. sp. were found in Pachydactylus bibroni (Gekkonidae) and are ellipsoidal, 26.2 × 18.2 (21.5–28 × 16–19) m; shape index 1.44 (1.30–1.52). A micropyle and oöcyst residuum are absent but a polar granule is present. Sporocysts are subspherical, 8.9 × 8.0 (8–9.5 × 7–8.5) m; shape index 1.12 (1.03–1.20). Oöcysts of Isospora spilogaster n. sp. are reported from Mabuya spilogaster (Scincidae) and are subspherical, 27.4 × 26.0 (21.5–35 × 21–35) m; shape index 1.05 (1.00–1.13). Micropyle, oöcyst residuum and polar granules are absent. Sporocysts are ellipsoidal, 13.2 × 9.7 (10.5–15 × 9–11) m; shape index 1.36 (1.08–1.50).     

Theoretical investigation of the triphosphate forms of azidothymidine and thymidine

In this paper we investigate (using AM1 semi-empirical as well as HF methods at the STO-3G, 3-21G, 6-31G, 6-31G* and 6-31+G** level) the conformations, geometrical parameters, Mulliken charges, and solvation effects of the triphosphate form of AZT (AZTTP), as well as the thymidine nucleotide (dTTP) structure. Our calculated geometrical parameters and Mulliken charges, with and without solvation effects, are correlated with recent experimental results.     

Stability of Glucose 6-Phosphate Dehydrogenase Complexed with Its Substrate or Cofactor in Aqueous and Micellar Environment

Inactivation of glucose 6-phosphate dehydrogenase (G6PDH) complexed with its substrate, glucose 6-phosphate (GP), or cofactor, NADP⁺, has been studied within the range 20–40°C in three media: (a) 0.04 M NaOH–glycine buffer (pH 9.1); (b) Aerosol OT (AOT) reversed micelles in octane; and (c) Triton X-100 micelles in octane supplemented with 10% hexanol. The enzyme inactivation was characterized quantitatively by first order rate constants, k _in(s^–1). In the case of G6PDH–NADP⁺complexes, the values of k _inwere independent of the initial concentrations of G6PDH, either in aqueous medium or AOT micelles. The values of k _infor the complex G6PDH–GP were inversely related to the initial concentration of the enzyme, in both aqueous and micellar media. When inactivation of both complexes were studied in AOT micelles, minimum values of k _incorresponded to the degree of hydration W ₀= 16.7; at W ₀> 16.7 and W ₀< 16.7, k _inincreased. Within the range 20–40°C, the values of k _inmeasured for both complexes in aqueous medium were significantly lower than those measured in AOT micelles. Temperature dependences of k _inwere characterized by inflections in Arrhenius plots, which corresponded, depending on the medium, to certain temperatures from 33.6°C to 40°C. In all media studied, NADP⁺complexes of the enzyme exhibited higher stability than their GP counterparts. The parameters of G6PDH and G6PDH–NADP⁺melting, measured by differential scanning microcalorimetry (maximum temperature and half-width of the transition, enthalpy of denaturation, and van't Hoff enthalpy), provided unequivocal evidence of the higher stability of the complex as compared to that of the enzyme. In addition, this approach demonstrated that G6PDH undergoes destabilization in AOT micelles.     

Conformational studies on chiral rhodium complexes by ECD and VCD spectroscopy

This article reports vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic studies in acetonitrile on the chiral Rh(2)(O-Phe-Cbz)(1)(OAc)(3) and Rh(2)(O-Phe-Ac)(1)(OAc)(3) complexes (abbreviated Rh(2)Z(1) and Rh(2)Ac(1) , respectively; Phe, L-phenylalanine; Cbz, benzyloxycarbonyl; Ac, acetyl) supported by theoretical calculations. The ECD spectra of the complexes depend on temperature that indicates the conformational mobility of the chiral ligands. Calculations of the VCD spectra were performed at ab initio (DFT) level of theory using Gaussian 03 [B3LYP functional combined with the LANL2DZ basis set for the dirhodium core and the 6-31G(d) basis set for other atoms]. The population-weighted sums of the computed VCD spectra of the conformers are in excellent agreement with the experimental VCD spectra. The combination of the VCD and ECD spectroscopic methods led us to the structural characterization of the complexes.     

Charge calculations in molecular mechanics 6: the calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing.

A previously described scheme for the direct calculation of the partial atomic charges in molecules (CHARGE2) is applied to the nucleic acid bases. It is shown that inclusion of the omega-technique for the calculation of HMO derived pi charges is of particular importance for these highly polar systems. The molecular dipole moments obtained for the resulting charges are in very good agreement with the observed values for a variety of substituted purine and pyrimidine bases. The partial atomic charges for cytosine, thymine, guanine and adenine (as the 1-methyl and 9-methyl forms) are given and compared with values calculated by a variety of molecular orbital and empirical schemes. All the schemes reproduce the same general trends, with the possible exception of those calculated by the Del Re method, though the charges given by Kollman are in general somewhat larger than the others. The electrostatic contribution to the Watson-Crick base pair interaction energies are calculated using these partial atomic charges. The electrostatic contributions obtained from the M.O. derived atomic charges are less than half the observed values, as are those obtained by the Gasteiger method. The electrostatic contributions calculated from the CHARGE2 atomic charges and those of Kollman are in reasonable agreement with the observed values. The influence of a distant-dependent dielectric constant is examined, but no clear pattern emerges.     

Molecular modeling studies of poly lactic acid initiation mechanisms

The two possible routes to synthesize poly (lactic acid) are polycondensation of the lactic acid and ring opening polymerization (ROP) of the lactide. This work involves molecular modeling of the polymerization initiation mechanisms using different initiators a) H₂SO₄ for polycondensation b) aluminum isopropoxide for coordination-insertion ROP c)methyl triflate for cationic ROP, and d) potassium methoxide for anionic ROP. For molecular modeling of PLA, we have benchmarked our approach using Ryner’s work on ROP of L-lactide using stannous (II) 2-ethylhexanoate (Sn(Oct)₂) and methanol as initiators. Our values of -15.2 kcal mol^-1 and -14.1 kcal mol^-1 for enthalpy changes in the two steps of activated complex formation match with Ryner’s. Geometric and frequency optimizations have been done on Gaussian’03 using B3LYP density functional theory along with the basis sets LANL2DZ for metal atoms and 6–31G* and 6–31G** for non metal atoms. The kinetic rate constant for each mechanism has been calculated using the values of energy of activation, change in enthalpy, Gibbs free energy, entropy and the partition functions from the Gaussian’03 output. Our polycondensation rate constant value of 1.07 × 10^–4 se^-1 compares well with 1.51 × 10^–4 se^-1 as reported by Wang. However, ROP rate constants could not be validated due to lack of experimental data. Figure Cationic Ring Opening Polymerization of L-Lactide

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Pronuclear synthesis of DNA in fertilized and parthenogenetically activated mouse eggs : A cytophotometric study

Mouse one-cell embryos were taken 1, 1.5, 2, 3, 4, 6, 8, 10, 13 and 18 h after insemination. One-cell parthenogenones were induced by treatment of mouse eggs obtained 20 h after HCG injection with hyaluronidase and cultured for 0.5, 1, 3, 4.5, 6, 8, 10, 12 and 24 h. Some parthenogenones were pulse-labelled with tritiated thymidine, cut and autoradiographed. Both the embryos and parthenogenones were Feulgen-stained, and integrated relative optical absorption of either pronuclei or nuclei of polar bodies was measured with a cytophotometer. In some fertilized eggs and parthenogenones the DNA synthesis sets in 4–6 h after either insemination or parthenogenetic stimulus. Between the 8th and 13th hour after insemination the fraction of DNA synthesizing embryonic pronuclei remained at the level 30–40%. Most parthenogenones duplicated their DNA content between the 8th and 12th hour after hyaluronidase treatment. The DNA synthesis time in pronuclei of embryos was determined to be 3.5–4.0 h and that of pronuclei of parthenogenones approx. 4 h. The minimal time of the G2 phase was estimated to be 3–5 h. The first labelled pronuclei of parthenogenones were detected 6 h after stimulus. Male pronuclei started and ended DNA synthesis earlier than female pronuclei. Differences in the DNA content between pronuclei of the parthenogenones (when there are two in one parthenogenone) were observed beginning with the 10th h after hyaluronidase treatment.The DNA content in the nuclei of the second polar bodies (PB) of embryos increased slowly between the 8th and 22nd hour after insemination, up to an overall value of 1.4 C. That of the nuclei of the polar bodies of parthenogenones accompanied the synthesis of DNA in pronuclei to the 10th hour after hyaluronidase treatment, up to an overall value of 1.4 C.     

Simultaneous assay of morphine, morphine-3-glucuronide and morphine-6-glucuronide in human plasma using normal-phase liquid chromatography–tandem mass spectrometry with a silica column and an aqueous organic mobile phase

Morphine (MOR) is an opioid analgesic used for the treatment of moderate to severe pain. MOR is extensively metabolized to morphine-3-glucuronide (M3G) and morphine-6-glucuronide (M6G). A rapid and sensitive method that was able to reliably detect at least 0.5 ng/ml of MOR and 1.0 ng/ml of M6G was required to define their pharmacokinetic profiles. An LC–MS–MS method was developed in our laboratory to quantify all three analytes with the required sensitivity and a rapid turnaround time. A solid-phase extraction (SPE) was used to isolate MOR, M3G, M6G, and their corresponding deuterated internal standards from heparinized plasma. The extract was injected on a LC tandem mass spectrometer with a turbo ion-spray interface. Baseline chromatographic separation among MOR, M3G, and M6G peaks was achieved on a silica column with an aqueous organic mobile phase consisting of formic acid, water, and acetonitrile. The total chromatographic run time was 3 min per injection, with retention times of 1.5, 1.9 and 2.4 min for MOR, M6G, and M3G, respectively. Chromatographic separation of M3G and M6G from MOR was paramount in establishing the LC–MS–MS method selectivity because of fragmentation of M3G and M6G to MOR at the LC–MS interface. The standard curve range in plasma was 0.5–50 ng/ml for MOR, 1.0–100 ng/ml for M6G, and 10–1000 ng/ml for M3G. The inter-day precision and accuracy of the quality control (QC) samples were <7% relative standard deviation (RSD) and <6% relative error (R.E.) for MOR, <9% RSD and <5% R.E. for M6G, and <3% RSD and <6% R.E. for M3G. Analyte stability during sample processing and storage were established. Method ruggedness was demonstrated by the reproducible performance from multiple analysts using several LC–MS–MS systems to analyze over one thousand samples from clinical trials.     

High activity of glucose-6-phosphate dehydrogenase in Kupffer cells isolated from rat liver

Summary Sinusoidal cells in the rat liver react intensively for G6DPH activity after appropriate incubation (Rieder et al. 1978). After isolation and purification of the sinusoidal Kupffer and endothelial cells, it was demonstrated that Kupffer cells exhibit a 5–8 times higher G6PDH activity on a per cell basis by comparison with endothelial cells, while the specific G6PDH activity was 3–4 times higher in Kupffer cells. The Kupffer cells can be divided into two groups which differ significantly in G6PDH activity calculated on a per cell basis. In histochemical studies, G6PDH can be used as a marker for Kupffer cell identification.     

Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations

The human APOBEC3G (A3G) protein is a cellular polynucleotide cytidine deaminase that acts as a host restriction factor of retroviruses, including HIV-1 and various transposable elements. Recently, three NMR and two crystal structures of the catalytic deaminase domain of A3G have been reported, but these are in disagreement over the conformation of a terminal β-strand, β2, as well as the identification of a putative DNA binding site. We here report molecular dynamics simulations with all of the solved A3G catalytic domain structures, taking into account solubility enhancing mutations that were introduced during derivation of three out of the five structures. In the course of these simulations, we observed a general trend towards increased definition of the β2 strand for those structures that have a distorted starting conformation of β2. Solvent density maps around the protein as calculated from MD simulations indicated that this distortion is dependent on preferential hydration of residues within the β2 strand. We also demonstrate that the identification of a pre-defined DNA binding site is prevented by the inherent flexibility of loops that determine access to the deaminase catalytic core. We discuss the implications of our analyses for the as yet unresolved structure of the full-length A3G protein and its biological functions with regard to hypermutation of DNA.     

C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives

We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ~5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ~12. ¹³C substitution at C5′ in dAdo yields ¹³C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-¹³C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated ¹³C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.