'Genome order index' should not be used for defining compositional constraints in nucleotide sequences

A “genome order index,” defined as S = a² + c² + t² + g², where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively, was used to suggest that there exist genome-specific constraints on nucleotide composition. We show that the “evidence” for constraint, S < 1/3, is in fact a mathematical property that is always true regardless of data. Moreover, we show that S is strictly equivalent to and derivable from the Shannon H-function and has no advantage over it.     

Structures of 3,3′-dicarbometoxy-2,2′-bipyridine complexes with silver(I) and copper(II) cations

The structures of 3,3′-dicarbometoxy-2,2′-bipyridine (dcmbpy) complexes with copper(II) and silver(I) cations have been determined using single crystal X-ray-diffraction. The crystals of Cu(dcmbpy)Cl₂ are monoclinic, C2/c, a = 16.966(3), b = 18.373(3), c = 13.154(2) Å, β = 126.543(3)°. The crystals of Ag(dcmbpy)NO₃ · H₂O are also monoclinic, C2/c, a = 16.7547(13), b = 11.0922(9), c = 18.7789(18) Å, β = 100.228(7)°. The results have been compared with the literature data on the complexes of dcmbpy and its precursors: 2,2′-bipyridine (bpy) and 3,3′-dicarboxy-2,2′-bipyridine (dcbpy). Two types of complexes of 3,3′-carboxy derivatives of bpy are distinguished: (1) with metal atom bonded to two N atoms of the same molecule and (2) with metal atom bonded to two N atoms of two different molecules. The Cu(dcmbpy)Cl₂ complex belongs to the first type, whereas Ag(dcmbpy)NO₃ · H₂O belongs to the second type.     

The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of complex peptide mixtures is often hampered by signal suppression effects as well as certain intrinsic properties of specific peptides that influence the desorption/ionization behavior. The present systematic study reports on the relationship between the occurrence of certain amino acids in peptides and the intensities of the related ions which appear during MALDI-MS analysis for both tryptic digests of proteins and synthetic peptide mixtures. The analysis of the tryptic digests revealed that the peptide sequences of the most intense peaks detected by MALDI-MS contained significantly higher proportions of arginine, phenylalanine, proline, and leucine than the average values for the measured proteins. The relationship between the relative signal intensities and amino acid compositions of peptides was studied in more detail by the partial least squares (PLS) method using equimolar mixtures of 144 well-characterized synthetic peptides. The regression coefficients clearly indicated that the presence of arginine, phenylalanine, leucine and proline tend to enhance the desorption/ionization process which results in higher MALDI-MS peak intensities. Furthermore, it was shown that the impact of arginine depends strongly on the identity of adjacent amino acids.     

Amperometric detection of cytochrome c by capillary electrophoresis at a sol–gel carbon composite electrode

Capillary electrophoresis (CE) was employed for the determination of cytochrome c using a wall-jet amperometric detector consisting a copper(I) oxide-modified sol–gel carbon composite electrode (CCE), which exhibits a sensitive electrocatalytic response for the oxidation of cytochrome c. The optimum conditions of separation and detection are 0.08 M NaOH for the separation solution, 12 kV for separation voltage and +0.60 V versus saturated calomel electrode (SCE) for the detection potential. Calibration was linear over the concentration range 1–600 μM with the limit of detection of 3.4 μM, based on a signal-to-noise ratio (S/N) of 3.     

The organic ligands as template: the synthesis, structures and properties of a series of the layered structure rare-earth coordination polymers

A series of new 2D-layered structural rare-earth coordination polymers with the general formal [Ln(C₈H₄O₅)(H₂O)₅]·(H₂O)·(C₈H₄O₅)_1/2 (Ln=Eu for (1); Gd for (2); Tb for (3); Dy for (4); and Er for (5)) have been yielded by hydrothermal synthesis. The coordination polymers crystallize in monoclinic space group C/2c with a=19.838(16), b=10.529(8), c=17.752(14) Å, β=107.503(14)° for (1), with a=19.823(7), b=10.552(4), c=17.762(6) Å, β=107.443(6)° for (2), with a=19.770(4), b=10.519(2), c=17.698(4) Å, β=107.52(3)° for (3), with a=19.632(2), b=10.492(2), c=17.617(3) Å, β=107.470(12)° for (4), with a=19.648(7), b=10.480(3), c=17.598(6) Å, β=107.502(6)° for (5), respectively. And the metal ions (Ln³⁺) are located in nine-member coordination environment. The carboxyl groups from 5-hydroxyisophthalate chelate the metal ions to form 1D helical cation chains. It is interesting that these helical cation chains are arranged to form 2D anion–cation layers by the uncoordinated ligands' anions as template. And the luminescence properties of the rare-earth ions are studied in the paper.     

Equilibrium diagram of KPO3–Y(PO3)3 system, chemical preparation and characterization of KY(PO3)4

Microdifferential thermal analysis (μ-DTA), X-ray diffraction (XRD) and infrared (IR) spectroscopy were used for the first time to investigate the liquidus and solidus relations in the KPO₃–Y(PO₃)₃ system. The only compound observed within the system was KY(PO₃)₄ melting incongruently at 1033 K. An eutectic appears at 13.5 mol% Y(PO₃)₃ at 935 K, the peritectic occurs at 1033 K and the phase transition for potassium polyphosphate KPO₃ was observed at 725 K. Three monoclinic allotropic phases of the single crystals were obtained. KY(PO₃)₄ polyphosphate has the P2₁ space group with lattice parameters: a=7.183(4) Å, b=8.351(6) Å, c=7.983(3) Å, β=91.75(3)° and Z=2 is isostructural with KNd(PO₃)₄. The second allotropic form of KY(PO₃)₄ belongs to the P2₁/n space group with lattice parameters: a=10.835(3) Å, b=9.003(2) Å, c=10.314(1) Å, β=106.09(7)° and Z=4 and is isostructural with TlNd(PO₃)₄. The IR absorption spectra of the two forms show a chain polyphosphates structure. The last modification of KYP₄O₁₂ crystallizes in the C2/c space group with lattice parameters: a=7.825(3) Å, b=12.537(4) Å, c=10.584(2) Å, β=110.22(7)° and Z=4 is isostructural with RbNdP₄O₁₂ and contains cyclic anions. The methods of chemical preparations, the determination of crystallographic data and IR spectra for these compounds are reported.     

Voltammetry of redox analytes at trace concentrations with nanoelectrode ensembles

Gold nanoelectrodes ensembles (NEEs) have been prepared by electroless plating of Au nanoelectrode elements within the pores of a microporous polycarbonate template membrane. Cyclic voltammograms recorded in (ferrocenylmethyl) trimethylammonium hexafluorophosphate (FA⁺ PF₆⁻) solutions showed that these NEEs operate in the “total-overlap” response regime, giving well resolved peak shaped voltammograms. Experimental results show that the faradaic/background currents ratios at the NEE are independent on the total geometric area of the ensemble, so that NEE can be enlarged or miniaturized at pleasure without influencing the very favorable signal/noise ratio. Differential pulse voltammetry (DPV) at the NEE is optimized for direct determinations at trace levels. DPV at NEE allowed the determination (with no preconcentration) of trace amounts of FA⁺, with a detection limit of 0.02 μM. The use of NEE and DPV in cytochrome c (cyt c) solutions showed the possibility to observe the direct electrochemistry of submicromolar concentration of the protein, even without the need of adding any promoter or mediator.     

Structural and theoretical studies of Xe(OChF5)2 and [XeOChF5][AsF6] (Ch = Se, Te)

The XeOSeF₅⁺ cation has been synthesized for the first time and characterized in solution by ¹⁹F, ⁷⁷Se and ¹²⁹Xe NMR spectroscopy and in the solid state by X-ray crystallography and Raman spectroscopy with AsF₆⁻ as its counter anion. The X-ray crystal structures of the tellurium analogue and of the Xe(OChF₅)₂ derivatives have also been determined: [XeOChF₅][AsF₆] crystallize in tetragonal systems, P4/n, a=6.1356(1) Å, c=13.8232(2) Å, V=520.383(14) Å³, Z=2 and R₁=0.0453 at −60°C (Te) and a=6.1195(7) Å, c=13.0315(2) Å, V=488.01(8) Å³, Z=2 and R₁=0.0730 at −113°C (Se); Xe(OTeF₅)₂ crystallizes in a monoclinic system, P2₁/c, a=10.289(2) Å, b=9.605(2) Å, c=10.478(2) Å, β=106.599(4)°, V=992.3(3) Å³, Z=4 and R₁=0.0680 at −127°C; Xe(OSeF₅)₂ crystallizes in a triclinic system, , a=8.3859(6) Å, c=12.0355(13) Å, V=732.98(11) Å³, Z=3 and R₁=0.0504 at −45°C. The energy minimized geometries and vibrational frequencies of the XeOChF₅⁺ cations and Xe(OChF₅)₂ were calculated using density functional theory, allowing for definitive assignments of their experimental vibrational spectra.     

Capillary electrophoresis—matrix-assisted laser-desorption ionization mass spectrometry of proteins

An “off-line” combination of capillary electrophoresis (CE) with matrix-assisted laser-desorption mass spectrometry (MALDI-MS) has been developed for the structural characterization of CE-separated peptides and proteins. Using a sheath flow interface, similar to that developed for “on-line” CE—fast atom bombardment MS and CE—electrospray MS, an efficient sample isolation procedure has been developed which is applicable to bioorganic compounds in aqueous buffer solutions. This isolation procedure, with subsequent transfer to the MALDI-MS sample target, has been successfully used for the direct analysis of CE-separated proteins of M _r up to 67 000, and a mixture of apolipoprotein AII monomer and homodimer, using sample amounts of less than 1 pmol.     

Hydrogenmaleato bridged supramolecular double chains via π–π stacking interactions: syntheses, crystal structures and magnetic properties of ∞[Cu(phen)X(HL)2/2] with X=Cl (1), NO3 (2) and H2L=maleic acid

Two novel hydrogen maleato (HL) bridged Cu(II) complexes _∞¹[Cu(phen)Cl(HL)_2/2] 1 and _∞¹[Cu(phen)(NO₃)(HL)_2/2] 2 were obtained from reactions of 1,10-phenanthroline, maleic acid with CuCl₂·2H₂O and Cu(NO₃)₂·3H₂O, respectively, in CH₃OH/H₂O (1:1 v/v) at pH=2.0 and the crystal structures were determined by single crystal X-ray diffraction methods. Both complexes crystallize isostructurally in the monoclinic space group P2₁/n with cell dimensions: 1 a=8.639(2) Å, b=15.614(3) Å, c=11.326(2) Å, β=94.67(3)°, Z=4, D_calc=1.720 g/cm³ and 2 a=8.544(1) Å, b=15.517(2) Å, c=12.160(1) Å, β=90.84(8)°, Z=4, D_calc=1.734 g/cm³. In both complexes, the square pyramidally coordinated Cu atoms are bridged by hydrogen maleato ligands into 1D chains with the coordinating phen ligands parallel on one side. Interdigitation of the chelating phen ligands of two neighbouring chains via π–π stacking interactions forms supramolecular double chains, which are then arranged in the crystal structures according to pseudo 1D close packing patterns. Both complexes exhibit similar paramagnetic behavior obeying Curie–Weiss laws χ_m(T−θ)=0.414 cm³ mol⁻¹ K with the Weiss constants θ=−1.45, −1.0 K for 1 and 2, respectively.     

Structural and spectral studies of N-2-(pyridyl)-, N-2-(3-, 4-, 5-, and 6-picolyl)- and N-2-(4,6-lutidyl)-N′-2-thiomethoxyphenylthioureas

Structures of the following compounds have been obtained: N-(2-pyridyl)-N′-2-thiomethoxyphenylthiourea, PyTu2SMe, monoclinic, P2₁/c, a=11.905(3), b=4.7660(8), c=23,532(6) Å, β=95.993(8)°, V=1327.9(5) ų and Z=4; N-2-(3-picolyl)-N′-2-thiomethoxyphenyl-thiourea, 3PicTu2SeMe, monoclinic, C2/c, a=22.870(5), b=7.564(1), c=16.941(4) Å, β=98.300(6)°, V=2899.9(9) ų and Z=8; N-2-(4-picolyl)-N′-2-thiomethoxyphenylthiourea, 4PicTu2SMe, monoclinic P2₁/a, a=9.44(5), b=18.18(7), c=8.376(12) Å, β=91.62(5)°, V=1437(1) ų and Z=4; N-2-(5-picolyl)-N′-2-thiomethoxyphenylthiourea, 5PicTu2SMe, monoclinic, C2/c, a=21.807(2), b=7.5940(9), c=17.500(2) Å, β=93.267(6)°, V=2893.3(5) ų and Z=8; N-2-(6-picolyl)-N′-2-thiomethoxyphenylthiourea, 6PicTu2SMe, monoclinic, P2₁/c, a=8.499(4), b=7.819(2), c=22.291(8) Å, β=90.73(3)°, V=1481.2(9) ų and Z=4 and N-2-(4,6-lutidyl)-N′-2-thiomethoxyphenyl-thiourea, 4,6LutTu2SMe, monoclinic, P2₁/c, a=11.621(1), b=9.324(1), c=14.604(1) Å, β=96.378(4)°, V=1572.4(2) ų and Z=4. Comparisons with other N-2-pyridyl-N′-arylthioureas having substituents in the 2-position of the aryl ring are included.     

Mesoscopic simulation of self-assembly in surfactant oligomers by dissipative particle dynamics

Self-assembling properties of surfactant oligomers in an aqueous medium is simulated by dissipative particle dynamics (DPD). The critical micellar concentration (CMC) of dimeric (oligomerization = 2) and trimeric (oligomerization = 3) surfactant is much lower than their single-chain counterpart. All surfactants form spherical micelles at the concentration not far above their CMC. The transition from spherical to cylindrical micelles exhibits with increasing surfactant concentration. Lamellar micelles will appear with further increasing the surfactant concentration. For dimeric and trimeric surfactants, cylindrical micelles transform into extremely long “wormlike” or “threadlike” micelles before the transition to lamellar micelles. These results are in qualitative agreement with laboratory experiment. Average aggregation numbers (AN) of micelles increase with a power law of AN  c when the surfactant concentration c CMC. The self-diffusion coefficients will drop with a power law of D  c⁻ when wormlike micelles are formed.     

Multifunctional nanoparticles composite for MALDI-MS: Cd2+-doped carbon nanotubes with CdS nanoparticles as the matrix, preconcentrating and accelerating probes of microwave enzymatic digestion of peptides and proteins for direct MALDI-MS analysis

For the first time, we utilized multifunctional nanoparticles composite (NPs composite) for matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis of peptides and proteins. Multiwalled carbon nanotubes doped with Cd(2+) ions and modified with cadmium sulfide NPs were synthesized by a chemical reduction method at room temperature. The multifunctional NPs composite applied for the analysis of peptides and microwave-digested proteins in the atmospheric pressure matrix-assisted laser desorption/ionization ion-trap and MALDI time-of-flight (TOF) mass spectrometry (MS) was successfully demonstrated. The maximum detection sensitivity for peptides in MALDI-MS was achieved by the adsorption of negatively charged peptides onto the surfaces of NP composite through electrostatic interactions. The optimal conditions of peptide mixtures were obtained at 20 min of incubation time using 1 mg of NPs composite when the pH of the sample solution was kept higher than the pI values of peptides. The potentiality of the NP composite in the preconcentration of peptides was compared with that of the individual NP by calculating the preconcentration factors (PF) and found that the NPs composite showed a 4-6 times of PF than the other NPs. In addition, the NPs composite was also applied as heat-absorbing materials for efficient microwave tryptic digestion of cytochrome c and lysozyme from milk protein in MALDI-TOF-MS analysis. We believe that the use of NPs composite technique would be an efficient and powerful preconcentrating tool for MALDI-MS for the study of proteome research.     

Combination of MALDI-TOF mass spectrometry with immobilized enzyme microreactor for peptide mapping

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been combined with immobilized enzyme microreactor for the rapid, sensitive, and accurate tryptic mapping of protein and polypeptides. The technique utilizes the trypsin microreactor by immobilized enzyme on the glycidyl methacrylate (GMA)-modified cellulose membrane. The membrane micro-reactor was used for the tryptic mapping of cytochrome C and the results were compared with those obtained by using free trypsin. A significant increase in the overall sensitivity of the process was observed using the membrane microreactor, as well as the elimination of background signals due to the autolysis of the trypsin. Further, membrane microreactor digestions were found to be rapid and convenient.     

Composition of N-linked carbohydrates from ovalbumin and co-purified glycoproteins

Analysis of commercial samples of chicken ovalbumin by reversed-phase high performance liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) showed the presence of several other co-purifying glycoproteins. These were isolated, subjected to tryptic digestion, and two of them were identified as ovomucoid and chicken riboflavin binding-protein following database matching of the peptide masses obtained by MALDI. The N-linked glycans were released from the glycoproteins and their structures were examined by MALDI-MS in combination with exoglycosidase digestion. Ovalbumin was found to be glycosylated mainly with high-mannose and hybrid structures, consistent with profiles obtained on the intact glycoprotein by electrospray. The other glycoproteins contained mainly larger, complex glycans with up to five antennae, many of which had earlier been associated with ovalbumin.     

Intermodulated fluorescence spectroscopy of caf AΠ-XΠ

The A ²Π-X²∑⁺ 0-0 transition of CaF has been examined by the technique of intermodulated fluorescence spectroscopy (“Lamb dip”). The hyperfine structure due to ¹⁹F and the spin-rotation fine structure of the X ²∑⁺ state was determined. Parameter values of b = 104.0 (9) MHz, c = 58(6) MHz and γ = 38.6(2) MHz were found for v = 0 of X²∑⁺     

C CP MAS NMR, FTIR, X-ray diffraction and PM3 studies of some N-(ω-carboxyalkyl)morpholine hydrohalides

N-(ω-carboxyalkyl)morpholine hydrochlorides, OC₄H₈N(CH₂)_nCOOH·HCl, n=1–5, were obtained and analyzed by ¹³C cross polarization (CP) magic angle spinning (MAS) NMR, FTIR and PM3 calculations. The structure of N-(3-carboxypropyl)morpholine hydrochloride (n=3) has been solved by X-ray diffraction method at 100 K and refined to the R=0.031. The crystals are monoclinic, space group P2₁/c, a=14.307(3), b=9.879(2), c=7.166(1) Å, β=93.20(3)°, V=1011.3(3) ų, Z=4. In this compound the nitrogen atom is protonated and two molecules form a centrosymmetric dimer, connected by two N⁺–HCl⁻ (3.095(1) Å) and two O–HCl⁻ (3.003(1) Å) hydrogen bonds. ¹³C CP MAS NMR spectra, contrary to the solution, showed non-equivalence of the ring carbon atoms. The PM3 calculations predict a molecular dimer without proton transfer for an HCl complex, while for an HBr complex an ion pairs with proton transfer, and reproduces correctly the conformation of both dimers but overestimates H-bond distances. Shielding constants calculated from the PM3 geometry of ion pairs gave a linear correlation with the ¹³C chemical shifts in solids.     

Crystal structure of Fe(η-C5H5BCMe3)2 a “problem structure”

The complex Fe(η⁶-C₅H₅CMe₃)₂ crystallizes in the centrosymmetric triclinic space group P (C_i¹; No. 2) with unit cell dimensions of a 8.770(1) Å, b 8.878(1) Å, c 11.991(1) Å, 107.56(1)°, β 90.85(1)°, γ 90.13(1)°, V 890.0(2) ų and Z = 2. A full sphere of data was collected on a four-circle diffractometer. The structure was solved and refined to R 7.93% for all 3155 independent reflections and R 4.98% for those 2002 data with | F₀ | > 6σ. | F₀ |. The molecules lie on crystallographic inversion centers at 0, 0, 0 and 1/2, 0, 1/2; the crystallographic asymmetric unit therefore consists of two independent half molecules. The molecule centered at 0, 0, 0 (molecule “A”) is ordered and well-defined; that centered on 1/2, 0, 1/2 (molecule “B”)is probably disordered, as indicated by larger “thermal parameters” and a greater range of apparent interatomic distances. Discussion em phasizes the geometry of molecule A, which has precise C_i symmetry with Fe(1A)-B(1A) 2.297(4) Å and Fe(1A)-C(ring) distances ranging from 2.057(6) Å to 2.138(4) Å.     

Improved matrix-assisted laser desorption/ionization mass spectrometric analysis of tryptic hydrolysates of proteins following guanidination of lysine-containing peptides

Analysis of tryptic digests of proteins using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry commonly results in superior detection of arginine-containing peptides compared with lysine-containing counterparts. The effect is attributable in part to the greater stability of the arginine-containing peptide ions associated with the sequestration of the single ionizing proton on the arginine side-chain. Reaction of peptides with O-methylisourea resulted in conversion of lysine to homoarginine residues with consequent improved detection during MALDI-MS. Analysis of the underivatized tryptic digest of the yeast protein, enolase, revealed peptides representing 20% of the protein; the corresponding figure after derivatization was 46%.     

Far infrared spectroscopy on hemoproteins: A model compound study from 1800–100 cm

Infrared spectroscopy measurements on different hemoproteins and models of the active side have been completed for the spectral range from 1800 to 100 cm⁻¹ giving an overview on the contributions expected in the low frequency range. Little is known of the low frequency contribution of proteins in infrared. In order to detect the contributions of heme centers and protein moiety, a systematic study of the infrared spectroscopic properties of the porphyrin ring, the ferric porphyrines with different ligands (hemine and hematine), a heme with 11 amino acids (microperoxidase-11), cytochrome c and cytochrome c oxidase are compared at different pD values and an overview on the relative contributions of hemes, their ligands and the protein site can be provided in the low frequency region. Beside the well know amide I and II modes, the low frequency range is found to be dominated by the amide IV and VI mode around 530/580 cm⁻¹ for cytochrome c and cytochrome c oxidase, as well as further proteins like ferrodoxin. Below 300 cm⁻¹ amide VII modes, doming modes of the heme site and hydrogen-bonding signatures overlap to a broad peak with covering 100–250 cm⁻¹. As clear markers for the iron ligands, bands can be depicted at 388/378 cm⁻¹ (FeN, histidine ligand) and 345 cm⁻¹ FeCl. Furthermore the ring vibration of the protonated histidine is determined at 623 cm⁻¹.