A theoretical study of internal rearrangements and open channels for fission and mass exchanges in Xe n + clusters

In a previous work the equilibrium geometrical and electronic structures of Xe _n ⁺ clusters had been established using a non-empirical model hamiltonian. The same model is used to determine the energetic barriers between the nearly degenerate isomers; the movement of the neutral atoms around the Xe ₃ ⁺ or Xe ₄ ⁺ ionized linear cores are quite easy (ΔE?0.9 kcal/mole), the changes from a Xe ₃ ⁺ to a Xe ₄ ⁺ core are more difficult (ΔE?2.0 kcal/mole). The energetically possible fissions from a vertical photoionization \(Xe_n \xrightarrow{{h v}}Xe_n^{v + } \to Xe_p^ + + Xe_{n - p} \) forn≦19,p=1–9 and 12–14 and mass exchanges Xe _p ⁺ +Xe _q →Xe _p+m ⁺ +Xe _q?m (m=1,2,3) from relaxed Xe _p ⁺ clusters are given forp+m≦9 and 12–14 andq≦19. Surprisingly the reverse reactions are shown to occur for some values ofp andq. Numerous processes lead to Xe ₁₃ ⁺ , which is especially stable.     

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

Background

The inorganic (P_i) phosphate transporter (PiT) family comprises known and putative Na⁺- or H⁺-dependent P_i-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with P_i to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na⁺-dependent P_i (NaP_i) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins.

Results

We show that the human PiT2 histidine, H₅₀₂, and the human PiT1 glutamate, E₇₀, - both conserved in eukaryotic PiT family members - are critical for P_i transport function. Noticeably, human PiT2 H₅₀₂ is located in the C-terminal PiT family signature sequence, and human PiT1 E₇₀ is located in ProDom domains characteristic for all PiT family members. A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR₂₅₄-V₄₈₃), was found to be a fully functional P_i transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL₁₈₃-V₄₈₃) did also support P_i transport albeit at very low levels.

Conclusions

The results suggest that the overall structure of the P_i-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship.     

Ultratrace voltammetric method for the detection of DNA sequence related to human immunodeficiency virus type 1

An ultra-trace voltammetric method was developed for the determination of single strand DNA (ss-DNA) related to the human immunodeficiency virus type 1 (HIV-1). It is based on the signal amplification of carbon nanotubes loaded with silver nanoparticles and placed on a gold microelectrode. The capture ss-DNA (a 21-mer) possessing a thiol group at the 3?? end was self-assembled onto the surface of the gold microelectrode. It was then hybridized with target HIV-1 ss-DNA (a 42-mer) and further hybridized with the electrochemical probe (a 18-mer ss-DNA) tagged with multiwall carbon nanotubes and loaded with silver nanoparticles. The resulting formation of a DNA sandwich conjugate led to a strong electrochemical oxidation signal that was linearly proportional to the concentration of HIV-1 ss-DNA in the range from 1.0 to 100?pM. The detection limit was 0.5?pM (at an S/N of 3). This was equivalent to 0.05?fmol of HIV-1 ss-DNA in a volume of 20???L. The relative standard deviation was 4.0% at 1.0?pM (n?=?11). Non-complementary ss-DNA of HIV-1 ss-DNA was effectively discriminated. This work demonstrates that the employment of the microelectrode and a sandwich hybridization model is promising in terms of sensitive and selective electrochemical detection of DNA.

Molecular geometry and electronic structures of stable organic derivatives of divalent germanium and tin [(\operatorname{Me} _3 \operatorname{Si} )_2 \operatorname{N} {\kern 1pt} ---{\kern 1pt} Me_2 ]_n (M = Ge, n = 1; M = Sn, n = 2): a theoretical study

The molecular geometry and electronic structure of stable organic derivatives of divalent germanium and tin, [(Me₃Si)₂N-M-OCH₂CH₂NMe₂]_n (M = Ge (4), n = 1; M = Sn (5), n =2) and their isomers with broken (4a, 5a) and closed (4b, 5b) intramolecular coordination bonds M←NMe₂, were studied by the density functional (PBE/TZ2P/SBK-JC) and NBO methods. Factors responsible for stability of their dimers 4c and 5c were established. Dimerization of 5b in the gas phase is a thermodynamically favorable process (ΔG ⁰ = ?2.1 kcal mol^?1) while that of 4b is thermally forbidden (ΔG ⁰ = 10.1 kcal mol^?1), which is consistent with experimental data. The M←NMe₂ coordination bond energies, ΔE ⁰, were found to be ?5.3 and ?8.6 kcal mol^?1 for M = Ge and Sn, respectively. NBO analysis showed that the metal atoms M in molecules 4 and 5 are weakly hybridized. The lone electron pairs of the M atoms have strong s-character while vacant orbitals of these atoms, LP* M, are represented exclusively by the metal np_z-AOs. The strongest orbital interactions between subunits in dimers 4c and 5c involve electron density donation from the lone electron pairs of oxygen atoms (LP O) to the LP* M orbitals.     

On the stability of single-walled carbon nanotubes and their binding strengths

The series of rhenium (I) tricarbonyl mixed-ligand complexes ReCl(CO)₃(H_nbpydt) (n?=?2, 1; n?=?4, 2; bpy?=?bispyridine, dt?=?1,3-dithiole) and ReCl(CO)₃(H_nbpyTTF) (n?=?2, 3; n?=?3, 4; TTF?=?Tetrathiafulvalene) have been investigated theoretically to explore the effect of COOH functional group on their electronic structures, spectroscopic properties and their properties as dye in a solar cell. The calculated geometry structure and absorption spectrum of 1 and 3 are generally consistent with the experimental results. By attaching the COOH groups on both bpy and dt (TTF in 4) moiety in 2, the nature of LUMO is also contributed by both π*(bpy) and π*(dt) (π*(TTF) in 4), and the absorptions have an obvious red shift compared with 1 and 3. In addition, it can be found that the transition terminates at the orbital populated by the COOH-appended moieties, and the performance of 2 and 4 in the dye-sensitized solar cell can be enhanced as compared with 1 and 3.     

Adsorption and aggregation properties of novel star-shaped gluconamide-type cationic surfactants in aqueous solution

The adsorption and aggregation behavior of novel star-shaped gluconamide-type cationic surfactants N-dodecyl-N,N-bis[(3-D-gluconylamido)propyl]-N-alkylammonium bromide (C_nDBGB, where n represents hydrocarbon chain lengths of 10, 12, and 14) has been studied on the basis of static/dynamic surface tension, conductivity, dynamic light scattering (DLS), and transmission electron microscopy (TEM) data. The static surface tension of the C_nDBGB aqueous solution measured at the critical micelle concentration (CMC) is observed to be significantly lower than that of the corresponding monomeric surfactants. The dynamic surface tension results indicate that adsorption process of above CMC is a mixed diffusion–kinetic adsorption mechanism. From the results of temperature dependent conductivity measurements, we could obtain the degree of counterion binding (β) and the thermodynamic parameters such as standard free energy (ΔG _mic ⁰ ), enthalpy (ΔH _mic ⁰ ), and entropy (ΔS _mic ⁰ ) of aggregation. With a combination of the DLS and TEM data, a size transformation of the micelles is suggested to occur with an increase in the concentration.     

A novel view of modelling interactions between synthetic and biological polymers via docking

Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic polymers with flexible chains. The application of flexible docking to these polymers as whole macromolecule ligands is also limited by too many possible conformations. We propose to solve this problem via stepwise flexible docking. Step 1 is docking of separate polymer components: (1) backbone units (BU), multi-repeated along the chain, and (2) side groups (SG) consisting of functionally active elements (SG _F ) and bridges (SG _B ) linking SG _F with BU. At this step, probable binding sites locations and binding energies for the components are scored. Step 2 is docking of component-integrating models: [BU] _m , SG = SG _F –SG _B , BU–SG, BU–BU(SG)–BU, BU(SG)–[BU] _m –BU(SG), and [BU _var (SG _var )] _m . Every modelling level yields new information, including how the linkage of various components influences on the ligand—target contacts positioning, orientation, and binding energy in step-by-step approximation to polymeric ligand motifs. Step 3 extrapolates the docking results to real-scale macromolecules. This approach has been demonstrated by studying the interactions between hetero-SG modified anionic polymers and the N-heptad repeat region tri-helix core of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp41, the key mediator of HIV-1 fusion during virus entry. The docking results are compared to real polymeric compounds, acting as HIV-1 entry inhibitors in vitro. This study clarifies the optimal macromolecular design for the viral fusion inhibition and drug resistance prevention.     

The protein kinase DYRK1A phosphorylates the splicing factor SF3b1/SAP155 at Thr434, a novel in vivo phosphorylation site

Background

Diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the acyl-CoA-dependent acylation of sn-1, 2-diacylglycerol to generate triacylglycerol and CoA. The deduced amino acid sequence of cDNAs encoding DGAT1 from plants and mammals exhibit a hydrophilic N-terminal region followed by a number of potential membrane-spanning segments, which is consistent with the membrane-bound nature of this enzyme family. In order to gain insight into the structure/function properties of DGAT1 from Brassica napus (BnDGAT1), we produced and partially characterized a recombinant polyHis-tagged N-terminal fragment of the enzyme, BnDGAT1_(1–116)His₆, with calculated molecular mass of 13,278 Da.

Results

BnDGAT1_(1–116)His₆ was highly purified from bacterial lysate and plate-like monoclinic crystals were grown using this preparation. Lipidex-1000 binding assays and gel electrophoresis indicated that BnDGAT1_(1–116)His₆ interacts with long chain acyl-CoA. The enzyme fragment displayed enhanced affinity for erucoyl (22:1cis^Δ13)-CoA over oleoyl (18:1cis^Δ9)-CoA, and the binding process displayed positive cooperativity. Gel filtration chromatography and cross-linking studies indicated that BnDGAT1_(1–116)His₆ self-associated to form a tetramer. Polyclonal antibodies raised against a peptide of 15 amino acid residues representing a segment of BnDGAT1_(1–116)His₆ failed to react with protein in microsomal vesicles following treatment with proteinase K, suggesting that the N-terminal fragment of BnDGAT1 was localized to the cytosolic side of the ER.

Conclusion

Collectively, these results suggest that BnDGAT1 may be allosterically modulated by acyl-CoA through the N-terminal region and that the enzyme self-associates via interactions on the cytosolic side of the ER.     

Extraction of palladium with thiacalix[4]arenes from nitric acid nitrate-nitrite solutions

Calix[4]arene 1, thiacalix[4]arenes 2(LH₄), and calix[4]arenethioether 3 were compared in palladium extraction from nitric acid solutions; D _Pd for 2 was shown to be 2?C3 orders of magnitude larger than for 1 at pH > 3 (comparable with 3) because of cation-exchange and coordination extraction of palladium. It was shown by extraction methods and IR spectroscopy that thiacalixarenes 2 extract complex species [Pd _n L _m H_{4 ? 2n} ] (m = 1, n = 1 and 2) and [(PdA₂) _n L _m H₄] (A = m = 1, n = 1?C4) from nitric acid solutions at pH 3. Extraction constants for these palladium species that satisfactorily describe experimental data were calculated. As distinct from 3, thiacalixarenes 2 are promising for the combined extraction of palladium and silver from alkaline solutions and the selective extraction of fission palladium from nitric acid solutions. Phosphorylated at the upper rim thiacalixarenes 2 can be considered as bifunctional extractants for the separation of fission radionuclides.     

Theoretical study on the substitution reactions of fluorosilylenoid H2SiLiF with SiH3XH n−1 (X = F,Cl, Br,O, N; n = 1, 1, 1, 2, 3)

The substitution reactions of H₂SiLiF (A) with SiH₃XH _n?1 (X = F, Cl, Br, O, N; n = 1, 1, 1, 2, 3) have been studied using DFT and ab initio methods. The results indicate that the substitution reactions of A with SiH₃XH _n?1 proceed via two reaction paths, I and II. The following conclusions emerge from this work. (i) The substitutions of A with SiH₃XH _n?1 are nucleophilic reactions and occur in a concerted manner. Path I is more favorable than path II. The substitution barriers of A with SiH₃XH _n?1 for path I decrease with the increase of the atomic number of X for the same period systems, whereas the barriers increase with the increase of the atomic number of X for the same family systems. (ii) The substitution products are H₂SiFSiH₃ and LiXH _n?1. If the H atoms in SiH₃ of SiH₃XH _n–1 are substituted by different atoms or groups, silanes H₂SiFSiH₃ obtained via paths I and II would be enantiomers. (iii) All the substitution reactions of A with SiH₃XH _n?1 are exothermic.     

Construction of [Cu n I n ]-based coordination polymers via flexible benzimidazolyl-based ligands

Four new [Cu _n I _n ]-based coordination polymers, [{ Cu₄(µ₃-I)₄(mbbm)₂}·2DMF] _n (1), [(CuI)₂(mbbm)₂] _n (2), [{Cu₂(µ-I)₂-(ebbm)₂}·2MeCN] _n (3), and [Cu₂(µ-I)₂(prbbm)₂] _n (4), were prepared from solvothermal reactions of CuI with three flexible ligands [(bzim)(CH₂) _n (bzim)] (bzim = benzimidazole; n = 1, mbbm; n = 2, ebbm; n = 3, prbbm). These compounds were characterized by elemental analysis, IR and X-ray crystallography. 1 consists of cubanelike [Cu₄(µ₃-I)₄] fragments that link the neighboring ones via mbbm bridges to form a 1D ladder-type chain. 2 contains mononuclear [CuI] fragments that are bridged by mbbm ligands to yield a 1D zigzag chain. 3 or 4 contains a [Cu₂(µ-I)₂] dimeric fragment, which works as a four-connecting node to link its four equivalent ones to form a 2D (4,4) network (3) or acts as a two-connecting node to connect its two equivalent ones via two pairs of prbbm bridges to form a 1D double chain (4). The photoluminescent properties of 1–4 in the solid state at ambient temperature were investigated.     

Cluster cations ejected from liquid metal ion source: alkali metals (Li,Na) and group IV elements (Si,Ge, Sn,Pb)

Cluster abundance of Li _n ⁺ (n≤19), Na _n ⁺ (n≤25), Si _n ^z+ (n≤8 forz=1, 3≤n≤7 forz=2), Ge _n ^z+ (n≤11 forz=1, 3≤n≤9 forz=2,n=4 forz=3), Sn _n ^z+ (n≤7 forz=1, 3≤n≤9 forz=2,n=4 forz=3) and Pb _n ^z+ (n≤6 forz=1, 5≤n≤7 forz=2) ejected from a liquid metal ion source has been investigated by mass spectrometry. The abundance spectra of alkali metal clusters showed distinct maxima and steps atn=3, 7, 9, 13 and 19 for Li, and atn=3, 5, 11, 13 and 19 for Na. Mass spectra of Si, Ge and Sn clusters were very similar each other, showing intensity drops aftern=4 and 6 (and alson=10 for Ge) for singly charged clusters. The magic numbers observed are discussed in terms of stability of charged clusters.     

Photoelectron spectroscopy of silicon and germanium-fluorine binary cluster anions (SinF m − , GenF m − )

Electronic properties of silicon-fluorine and germanium-fluorine cluster anions (Si_nF _m ^? n = 1–9, m = 1–3, Ge_nF _m ^? ; n =1–9, m = 1–3) were investigated by photoelectron spectroscopy using a magnetic-bottle type electron spectrometer. The binary cluster anions were generated by a laser vaporization of a silicon/germanium rod in an He carrier gas mixed with a small amount of SiF₄ or F₂ gas. Comparison between photoelectron spectra of Si_nF^?/Ge_nF^? and Sin /Gen (n = 4–9) gives the insight that the doped F atom can remove one electron from the corresponding Sin _n ^? /Ge _n ^? cluster without any serious rearrangement of Sin/Gen framework, because only the first peak of Si _n ^? /Ge _n ^? , corresponding singly occupied molecular orbital (SOMO), disappears and other successive spectral features are unchanged with the F atom doping     

Photoemission from tin and lead cluster anions

Photoelectrons from mass-identified jet-cooled tin and lead cluster anions (Sn _n ^? , Pb _n ^? ) are detached by ultraviolet laser light (hν=3.68 eV). The photoelectron energy spectra give the detachment energies of ground state cluster anions (electron affinities) as well as excitation energies of neutral clusters in the geometry of the anions. The energy spectra for Sn _n ^? are dominated by flat thresholds with ann-dependence similar to that of other group IV clusters. In contrast, for Pb _n ^? we find pronounced narrow lines close to threshold, generally followed by a 0.3–1.4 eV gap which indicates closed-shell behaviour of Pb _n ^? for nearly alln.     

Synthesis, crystal structure, and properties of triphenylguanidinium perrhenate hemihydrate

Triphenylguanidinium perrhenate hemihydrate, [(C₆H₅NH)₃C]ReO₄ · 0.5H₂O (I), is synthesized, and its crystal structure and some properties are studied. The colorless extended plate-like crystals of compound I are triclinic (space group $P\bar 1$ , Z = 4, 293 K, a = 9.8716(17), b = 14.093(2), c = 15.439(3)Å, α = 99.632(9)^○, β = 101.802(9)^○, γ = 95.361(10)^○). Compound I has no isostructural analogs, and the conformations of both crystallographically independent triphenylguanidinium cations differ by a higher symmetry (C _3h ) from those for cations of this type in all other structurally studied compounds. The following parameters are determined: the upper limit of the temperature stability of compound I (383 K), the melting point of anhydrous [(C₆H₅NH)₃C]ReO₄ (Ia) of 441 K, the enthalpy of dehydration of compound I (ΔH _dehydr ^{(383 K)} = 10.0(8) kJ/mol), and the enthalpy of melting of anhydrous Ia (ΔH _m ^{(441 K)} = 16.6(9) kJ/mol).     

FTMS studies of sputtered metal cluster ions (IV): size-selective effects in the chemistry of Fe n + with NH3 and Pd n + with D2 or C2H4

Fe _n ⁺ and Pd _n ⁺ clusters up ton=19 andn=25, respectively, are produced in an external ion source by sputtering of the respective metal foils with Xe⁺ primary ions at 20 keV. They are transferred to the ICR cell of a home-built Fourier transform mass spectrometer, where they are thermalized to nearly room temperature and stored for several tens of seconds. During this time, their reactions with a gas leaked in at low level are studied. Thus in the presence of ammonia, most Fe _n ⁺ clusters react by simply adsorbing intact NH₃ molecules. Only Fe ₄ ⁺ ions show dehydrogenation/adsorption to Fe₄(NH) _m ⁺ intermediates (m=1, 2) that in a complex scheme go on adsorbing complete NH₃ units. To clarify the reaction scheme, one has to isolate each species in the ion cell, which often requires the ejection of ions very close in mass. This led to the development of a special isolation technique that avoids the use of isotopically pure metal samples. Pd _n ⁺ cluster ions (n=2...9) dehydrogenate C₂H₄ in general to yield Pd _n (C₂H₂)⁺, yet Pd ₆ ⁺ appear totally unreactive. Towards D₂, Pd ₇ ⁺ ions seem inert, whereas Pd ₈ ⁺ adsorb up to two molecules.     

The extraction of Yb(III) and Lu(III) with chloroform from aqueous solutions in the presence of cupferron

The equilibrium of distribution of Yb(III) and Lu(III) between chloroform and the aqueous phase in the presence of cupferron (the ammonium salt of N-nitrosophenylhydroxylamine) were studied as apH function of the aqueous phase and the concentration of N-nitrosophenylhydroxylamine (HL). The stability constants for theLnL _n ^3–n ) complexes (n=1÷3) being formed in the aqueous phase were established, as well as the equilibrium constants of the extraction reaction $$Ln(H_2 O)_m^{3 + } + 3HL_{(O)} \mathop \rightleftharpoons \limits^{K_{ex} } LnL_{3(O)} + 3H^ + + mH_2 O(Ln^{3 + } = Yb,Lu),$$ two-phase stability constants for theLnL ₃ complexes,pH _0.5 and the separation factor Lu(III) from Yb(III).     

Hydration Energies of Protonated and Sodiated Thiouracils

Hydration reactions of protonated and sodiated thiouracils (2-thiouracil, 6-methyl-2-thiouracil, and 4-thiouracil) generated by electrospray ionization have been studied in a gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH ^o n, ΔS ^o n, and ΔG ^o n, for the hydrated systems were obtained by equilibrium measurements. The water binding energies of protonated thiouracils, [2SU]H⁺ and [6Me2SU]H⁺, were found to be of the order of 51 kJ/mol for the first, and 46 kJ/mol for the second water molecule. For [4SU]H⁺, these values are 3–4 kJ/mol lower. For sodiated complexes, these energies are similar for all studied systems, and varied between 62 and 68 kJ/mol for the first and between 48 and 51 kJ/mol for the second water molecule. The structural aspects of the precursors for hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract

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