Density and wave function analysis of actinide complexes: what can fuzzy atom, atoms-in-molecules, Mulliken, Lowdin, and natural population analysis tell us?

Recent advances in computational methods have made it possible to calculate the wave functions for a wide variety of simple actinide complexes. Equally important is the ability to analyze the information contained therein and produce a chemically meaningful understanding of the electronic structure. Yet the performance of the most common wave function analyses for the calculation of atomic charge and bond order has not been thoroughly investigated for actinide systems. This is particularly relevant because the calculation of charge and bond order even in transition metal complexes is known to be fraught with difficulty. Here we use Mulliken, Lowdin, natural population analysis, atoms-in-molecules (AIM), and fuzzy atom techniques to determine the charges and bond orders of UO(2)(2+), PuO(2)(2+), UO(2), UO(2)Cl(4)(2-), UO(2)(CO)(5)(2+), UO(2)(CO)(4)(2+), UO(2)(CN)(5)(3-), UO(2)(CN)(4)(2-), UO(2)(OH)(5)(3-), and UO(2)(OH)(4)(2-). This series exhibits a clear experimental and computational trend in bond lengths and vibrational frequencies. The results indicate that Mulliken and Lowdin populations and bond orders are unreliable for the actinyls. Natural population analysis performs well after modification of the partitioning of atomic orbitals to include the 6d in the valence space. The AIM topological partitioning is insensitive to the electron donating ability of the equatorial ligands and the relative atomic volume of the formally U(VI) center is counterintuitively larger than that of O(2-) in the UO(2)(2+) core. Lastly, the calibrated fuzzy atom method yields reasonable bond orders for the actinyls at significantly reduced computational cost relative to the AIM analysis.     

Thermal characterization and kinetic analysis of nesquehonite,hydromagnesite, and brucite,using TG–DTG and DSC techniques

Nesquehonite, hydromagnesite, and brucite are important precursors for the preparation of high-purity magnesia (MgO) using magnesium resources from salt lake as raw materials. In this paper, TG–DTG and DSC were used to investigate the thermal decomposition behaviors of the three precursors. Decomposition kinetic parameters at each stage were evaluated based on the TG data using the iso-conversional method. Decomposition mechanisms were determined using the master-plots method. The decomposition temperature range, heat absorption, and kinetic parameters of the three phases were then compared. The most probable mechanism of each stage from the perspective of crystal structure was found to be consistent with the calculation results from the master-plots method. Results led to the conclusion that nesquehonite is the most appropriate precursor for the preparation of high-purity MgO. Further studies on precursor selection and calcining condition selection for the preparation of MgO using bischofite will benefit from this research.     

Quantitative analysis of geraniol,nerol, linalool,and α-terpineol in wine

A mixture of [(2)H(7)]-geraniol, [(2)H(7)]-nerol, [(2)H(7)]-linalool and [(2)H(7)]-alpha-terpineol was prepared for use as internal standards in a rapid and accurate analytical method, employing gas chromatography-mass spectrometry (GC/MS), to determine the concentration of geraniol, nerol, linalool and alpha-terpineol in wine. The method avoids the possible formation, degradation and interconversion of these compounds during their analysis.     

Nano ES GEMMA and PDMA,new tools for the analysis of nanobioparticles—Protein complexes,lipoparticles, and viruses

Differential mobility analysis (DMA) is a technique suited for size analysis as well as preparative collection of airborne nanosized airborne particles. In the recent decade, the analysis of intact viruses, proteins, DNA fragments, polymers, and inorganic nanoparticles was possible when combining this method with a nano-electrospray charge-reduction source for producing aerosols from a sample solution/suspensions. Mass analysis of high molecular weight noncovalent complexes is also possible with this methodology due to the linear correlation of the electrophoretic mobility diameter and the molecular mass. In this work, we present the analysis (size and molecular mass) of high molecular weight multimers (noncovalent functional homocomplex) of Jack bean urease in a mass range from 275 kDa up to 2.5 MDa, with mainly present tri- and hexamers but also higher oligomers of the 91 kDa monomer subunit. In a second experiment, the size analysis of intact very-low-density (approximately 35 nm), low-density ( approximately 22 nm) and high-density lipoparticles (approximately 10 nm), which are heterocomplexes consisting of cholesterol, lipids, and proteins in different ratios, is presented. Results from mobility analysis were in excellent agreement with particle diameters found in literature. The last presented experiment demonstrates size analysis of a rod-like virus and selective sampling of a selected size fraction of electrosprayed, singly-charged tobacco mosaic virus particles. Sampling and subsequent transmission electron microscopic investigations of a specific size fraction (40 nm electrophoretic mobility diameter) revealed the folding of virus particles during the electrospray and charge reduction (electrical stress) as well as solvent evaporation (mechanical stress) process, leading to an observed geometry of 150 (length) x 35 (width) nm (average cylindrical geometry of unsprayed intact virus 300 x 18 nm).     

Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how?

The standard procedure adopted up to the present in proteome analysis calls for just reduction prior to the isoelectric focusing/immobilized pH gradient (IEF/IPG) step, followed by a second reduction/alkylation step in between the first and second dimension, in preparation for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) step. This protocol is far from being optimal. It is here demonstrated, by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry, that failure to reduce and alkylate proteins prior to any electrophoretic step (including the first dimension) results in a large number of spurious spots in the alkaline pH region, due to "scrambled" disulfide bridges among like and unlike chains. This series of artefactual spots comprises not only dimers, but an impressive series of oligomers (up to nonamers) in the case of simple polypeptides such as the human alpha- and beta-globin chains, which possess only one (alpha-) or two (beta-) -SH groups. As a result, misplaced spots are to be found in the resulting two-dimensional (2-D) map, if performed with the wrong protocol. The number of such artefactual spots can be impressively large. In the case of analysis of complex samples, such as human plasma, it is additionally shown that failure to alkylate proteins results in a substantial loss of spots in the alkaline gel region, possibly due to the fact that these proteins, at their pI, regenerate their disulfide bridges with concomitant formation of macroaggregates which become entangled with and trapped within the polyacrylamide gel fibers. This strongly quenches their transfer in the subsequent SDS-PAGE step.     

Integration of sample pretreatment, μPCR,and detection for a total genetic analysis microsystem

Since the emergence of lab-on-a-chip technology, a variety of chemical and biochemical assays were successfully implemented on microdevice platforms. Among the chip-based applications, genetic analysis based on the polymerase chain reaction (PCR) has been extensively developed in order to accomplish the goal of cheap, rapid, high-throughput, and point-of-care DNA testing. We are summarizing here several formats of the miniaturized PCR systems including the integration of units for sample pretreatment and downstream analytical detection. The various sections cover (a) miniaturized PCR systems, (b) integrated sample pretreatment-PCR microsystems, (c) integrated PCR-detection microsystems, and (d) integrated sample pretreatment-PCR-detection microsystems. Respective microdevices were successfully introduced recently in the form of a fully integrated microsystem for genetic analysis with sample-in-answer-out capability. Contains 120 references. Figure

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Mass spectrometry based analysis of nucleotides, nucleosides, and nucleobases—application to feed supplements

In this work, accurate MS-based methods for quantitative profiling of nucleotides, nucleosides, and nucleobases in yeast extracts used as additives in animal feedstuff are presented. Reversed-phase chromatography utilizing a stationary phase compatible with 100% aqueous mobile phases resulted in superior analytical figures of merit than HILIC or ion-pair reversed-phase separation. The novel separation method was combined with both molecular and elemental mass spectrometry. By use of RP-LC-MS-MS, excellent limits of detection <1 μmol L(-1) could be obtained for all the compounds investigated. The elemental speciation analysis approach enabled determination of nucleotides by phosphorus detection. Sensitivity of LC-ICP-MS was 1-2 orders of magnitude lower than that of LC-MS-MS. Quantitative analysis of yeast products using complementary MS detection furnished values in good agreement.     

Fluorescent β-cyclodextrins modified by isomeric aminobenzamides: synthesis, conformational analysis, and fluorescent behaviors

Three isomeric fluorescent β-cyclodextrins bearing 2-, 3-, and 4-(2-aminoethyl)amino-N-butylbenzamide, respectively (1-3) have been synthesized. The conformations of these fluorescent CDs have been investigated by 2D NMR and induced circular dichromism. It is confirmed that the ortho isomer 1 takes a butyl-included conformation, while the other two isomers 2 and 3 display a phenyl-included conformation, respectively. The three fluorescent CDs 1-3 exhibited totally different self- and guest-inclusion fluorescence behavior. In the presence of adamantane carboxylate sodium (ADA) or deoxycholate sodium (DCA), the fluorescence intensity of 1 showed an enhancement over 1-fold, while 2 exhibited dramatic fluorescence quenching. Interestingly, the fluorescent responses of 3 toward two guests respectively were highly distinguishable. The fluorescence intensity of 3 only showed a slight increase upon the addition of ADA, but the addition of DCA led to a large decrease in fluorescence intensity. The investigations have been further carried out by 2D NMR, induced circular dichromism, fluorescence spectroscopy and molecular modeling to explore the relationships between the conformations and the fluorescence characteristics of CDs 1-3 in the absence and presence of guest molecules. On the basis of the above investigations, the origins for the different fluorescence behaviors have been proposed.     

Mixed ligand complexes of β-diketonates: synthesis,characterization, and FAB mass spectral analysis

Complexes of the type MLL′ · nB (where M = Ni(II) and Cu(II); LH and L′H = 2,4-pentanedione (acacH), 1-phenyl-1,3-butanedione (bacH), and 1,3-diphenyl-1,3-propanedione (dbmH); n = 0 to 2 and B = water or pyridine) have been synthesized and characterized. IR spectra are consistent with uninegative bidentate ligands. Magnetic moments and electronic spectral studies reveal high-spin octahedral geometry for nickel(II) complexes and distorted octahedral stereochemistry for copper(II) complexes. Frozen chloroform solution ESR spectra of the copper(II) complexes display significant Jahn–Teller distortion and dimeric behavior of the complexes in solution. FAB mass spectra of the copper(II) complexes also exhibit peaks corresponding to dimers. Molecular, pseudo-molecular, dimeric pseudo-molecular, and fragment ion peaks in unit resolution mass spectra have been identified with the help of their isotope distribution pattern expected due to natural abundances of the ⁶³Cu and ⁶⁵Cu isotopes. All the FAB mass spectral peaks from the fragment ions containing copper have been interpreted on the basis of isotope distribution pattern.     

Advances and trends in the design, analysis, and characterization of polymer–protein conjugates for “PEGylaided” bioprocesses

In addition to their use as therapeutics and because of their enhanced properties, PEGylated proteins have potential application in fields such as bioprocessing. However, the use of PEGylated conjugates to improve the performance of bioprocess has not been widely explored. This limited additional industrial use of PEG-protein conjugates can be attributed to the fact that PEGylation reactions, separation of the products, and final characterization of the structure and activity of the resulting species are not trivial tasks. The development of bioprocessing operations based on PEGylated proteins relies heavily in the use of analytical tools that must sometimes be adapted from the strategies used in pharmaceutical conjugate development. For instance, to evaluate conjugate performance in bioprocessing operations, both chromatographic and non-chromatographic steps must be used to separate and quantify the resulting reaction species. Characterization of the conjugates by mass spectrometry, circular dichroism, and specific activity assays, among other adapted techniques, is then required to evaluate the feasibility of using the conjugates in any operation. Correct selection of the technical and analytical methods in each of the steps from design of the PEGylation reaction to its final engineering application will ensure success in implementing a "PEGylaided" process. In this context, the objective of this review is to describe technological and analytical trends in developing successful applications of PEGylated conjugates in bioprocesses and to describe potential fields in which these proteins can be exploited.     

Theoretical investigation of the nature and strength of simultaneous interactions of π–π stacking and halogen bond including NMR,SAPT, AIM and NBO analysis

Ab initio MP2/aug-cc-pVDZ calculations were performed to investigate mutual effect between π–π stacking and halogen bond interactions in X-ben||pyr···Cl–F complexes (X = CN, F, Cl, Br, CH₃, OH and H where || and ··· denote π–π stacking and halogen bonds). The results indicate the cooperativity of π–π stacking and halogen bonds in these complexes. This effect was discussed in terms of the energetic, geometrical parameters and charge-transfer properties of the complexes. To explore on the two-bonded spin–spin coupling constant ^2X J(N–F) across ¹⁵N···³⁵Cl–¹⁹F halogen bond in X-ben||pyr···Cl–F complexes, NMR calculations were performed at PBE0/aug-cc-pVDZ levels of theory. To get more insight into the physical nature of the binding energies, Symmetry Adapted Perturbation Theory calculations were carried out. Energy decomposition indicates that the percentage of the electrostatic term in the halogen bonding system constitutes approximately half of the total attractive binding energies, while the percentage of the dispersion term in the π–π stacking complexes constitutes approximately half of the attractive binding energies. In addition, atoms in molecules, natural bond orbital and molecular electrostatic potential were also used to probe the π–π stacking interactions and halogen bonding strengths.     

Quantum chemical investigation on the structural and electronic properties of α-, β-, and γ-cyclodextrin complexes: DFT and QTAIM analysis

To characterize the structural, thermochemical and electronic aspects in complexes of leucine, vanillin and mechlorethamine with α-, β-, and γ-cyclodextrins (CDs), a density functional theory (DFT) study has been conducted in combination with quantum theory of atoms in molecules (QTAIM) analysis. The QTAIM method has been utilized to explore the nature of various possible interactions between leucine, vanillin and mechlorethamine with CDs in terms of bond critical points (BCPs). HOMO and LUMO and atomic charges studies show charge transfer occurs between drugs and cyclodextrins. This behavior has been also investigated via QTAIM charge analysis. On the other hand, based on QTAIM electronic energy indicators we have discussed electrostatic character of interactions between vanillin, leucine and mechlorethamine with inner surface CDs in the coordination sphere.     

Cloning, differential expression, and association analysis with fat traits of porcine IDH3γ gene

Mitochondrial NAD⁺-dependent isocitrate dehydrogenase (IDH3) catalyzes the allosterically regulated rate-limiting step of the tricarboxylic acid cycle activated. In pigs, very little is known about this gene. Here, we cloned 1,346 bp full-length cDNA and 8,778 bp genomic sequence of porcine γ subunit of IDH3 (IDH3γ). IDH3γ contains 12 exons separated by 11 introns. Real-time PCR revealed that IDH3γ mRNA were upregulated in backfat of Large White compared with Meishan and F1 hybrids, and most abundant in small intestine via tissue distribution profile. A microsatellite (“GT” repeats) in second intron was found. The selected pigs were genotyped at this microsatellite. The IDH3γ genotypes showed a significant effect on backfat thickness at thorax–waist (P < 0.05), backfat thickness at sixth to seventh thorax (P < 0.01), and average backfat thickness (P < 0.05). This site seemed to be significantly dominant in action (P < 0.05 for backfat thickness at sixth to seventh thorax, backfat thickness at thorax–waist, and average backfat thickness), and allele B was associated with increase of thickness values of these traits. This locus is possibly considered as a marker for adipose deposition traits.     

DFT, NBO, and NRT analysis of alkyl and benzyl β-silyl substituted cations: carbenium ion vs. silylium ion

The effect of β-trimethylsilyl (TMS) substituent on the structure, stability, natural charges, electrostatic potential map, natural bond orders, rotational energy barrier, and hyperconjugative interactions of five acyclic β-silyl carbocation derivatives of RR′C⁺–CH₂Si(Me)₃ including α-dimethyl 1 (R,R′ = Me), α-methyl phenyl 2 (R = Me, R′ = Ph), α-methyl para-aminophenyl 3 (R = Me, R′ = p-NH₂Ph), α-methyl para-nitrophenyl 4 (R = Me, R′ = p-NO₂Ph) and diphenyl 5 (R,R′ = Ph) was investigated in the gas phase and in solution using polarized continuum model (PCM) at B3LYP/6-311 ++G** level of theory. The resonance structures weighting of cations 1–5 were determined using natural resonance theory (NRT). The contribution of carbenium ion (RR′C⁺–CH₂Si(Me)₃) and silylium ion (RR′C=CH₂ Si(Me) ₃ ⁺ ) to the stability depend upon substituents. The former form dominants when R,R′ = Ph, but the latter is major the contributor when R,R′ = Me. The weighting of carbocation forms of β-silyl benzyl cation overwhelms silylium cation due to the delocalization of positive charge on the phenyl ring. The calculated molecular orbital (MO) diagrams, energy decomposition analysis (EDA) and ²⁹Si and ¹³C nuclear magnetic resonance (NMR) chemical shifts complement these predictions.     

Na,Rb‖F,Br three-component reciprocal system and analysis of the Na,M‖F,Br (M = K,Rb, and Cs) series

Solid-phase reactions were studied by differential thermal analysis and X-ray powder diffraction in a sample whose composition corresponds to the complete conversion point K of the Na,Rb‖F,Br three-component reciprocal system. A stable diagonal and a metastable diagonal were studied, and the parameters of two ternary eutectics were determined.     

Na,Ba∥F,Br three-component reciprocal system and analysis of the Na,Ba∥F,Hal (Hal=Cl, Br, and I) series

A set of isopleths was studied using differential thermal analysis (DTA), the liquidus surface projection on the concentration square was plotted, and parameters were determined for the alloys corresponding to two ternary eutectics and one peritectic of the Na,Ba∥F,Br three-component reciprocal system. Solid-phase reactions in a sample containing 66.7% BaBr2+33.3% (NaF) ₂ were also studied by DTA. The results were used to analyze the entire series of the Na,Ba∥F,Hal (Hal = Cl, Br, and I) systems.