Half Of Molecules Research Articles

The development of biochemistry and molecular biology in China

The development of biochemistry and molecular biology in China

Bis[2-(2H-benzotriazol-2-yl)-4-methylphenolato]palladium(II)

In the title complex, [Pd(C13H10N3O)2], the PdII atom is tetra­coordinated by two N atoms and two O atoms from two bidentate 2-(2H-benzotriazol-2-yl)-4-methylphenolate ligands, forming a square-planar environment. The asymmetric unit contains one half mol­ecule in which the Pd atom lies on a centre of symmetry.

Bovine lactoferrin region responsible for binding to bifidobacterial cell surface proteins

Bovine lactoferrin promotes bifidobacterial growth. Its binding to bifidobacteria is thought to be responsible for such action. After separating the bovine lactoferrin half molecule and extraction of surface proteins from bifidobacteria, binding profiles were observed by immunoblotting. No binding appeared when lactoferrin C-lobe was reacted with the cell surface proteins on a polyvinylidene difluoride membrane. Conversely, a 50-kDa band appeared when the surface proteins were reacted with either intact or nicked bovine lactoferrin. This result strongly suggests that the binding region could be lactoferrin N-lobe. Interestingly, despite the absence of binding, C-lobe enhanced bifidobacterial growth.

Conjugation in 1,4-diphenylbutadiyne and 1,2-diphenylacetylene: A combined experimental and theoretical study

We have performed a combined experimental and theoretical study of the molecular system of 1,4-diphenylbutadiyne and compared with previously reported 1,2-diphenylacetylene. 1,4-Diphenylbutadiyne exists as a half molecule in the asymmetric unit. Experimental charge density analysis of the molecule showed that the acetylenic linkers have triple bond character close to an ideal triple bond, in clear contrast to the situation 1,2-diphenylacetylene, where the charge density parameters resemble more closely those of a double bond due to extended conjugation. The influence of the reduced conjugation on the transport characteristics has been obtained using the Landauer’s formalism. Thus, 1,4-diphenylbutadiyne is found less conducting than 1,2-diphenylacetylene.

A new polymorph of poly[bis(μ2-perchlorato-κ2O:O′)(2,2′:6′,2′′-terpyridine-κ3N,N′,N′′)lead(II)] with a greatly extended chain repeat distance

In the title compound, [Pb(ClO(4))(2)(C(15)H(11)N(3))](n), two molecules occupy general positions while the third lies on a crystallographic twofold axis, giving a total of two and a half molecules per asymmetric unit. Each metal centre is coordinated equatorially by three 2,2':6',2''-terpyridine (terpy) N-donor atoms and axially by two perchlorate O-donor atoms. The distorted pentagonal bipyramidal geometry is completed by two equatorial O-donor atoms from two perchlorate anions which bridge to two different adjacent metal centres. The coordination about each metal centre is very similar to that seen at the unique Pb(II) centre in the previously published polymorph [Engelhardt, Harrowfield, Miyamae, Patrick, Skelton, Soudi & White (1996). Aust. J. Chem. 49, 1135-1146], but the new polymorph differs from it by the insertion on each side of an existing [bis(perchlorato)(terpy)lead(II)] molecule of two additional such units. Pairs of asymmetrically bridging perchlorate anions link irregularly spaced Pb(II) centres into undulating chains parallel to [201] which exhibit a repeat distance of 26.280 (4) A. The significance of this new polymorph lies in the fact that, while it is chemically identical to the known polymorph, it is structurally distinct from it.

3-(2-Aminoethyl)-2-(4-chloroanilino)quinazolin-4(3H)-one methanol 0.75-solvate

In the asymmetric unit of the title compound, C16H15ClN4O·0.75CH3OH, there are two independent quinazolin-4(3H)-one mol­ecules and one and a half methanol mol­ecules. One of the methanol mol­ecules is disordered over two positions with equal occupancies. The dihedral angles between the quinazoline ring system and the chloro­benzene ring in the two quinazolin-4(3H)-one mol­ecules are essentially the same, at 39.83 (1) and 39.84 (1)°. Intra­molecular N—H⋯N and O—H⋯O, and inter­molecular N—H⋯O and N—H⋯N hydrogen bonds are observed. In addition, π–π stacking inter­actions, with centroid-to-centroid distances of 3.654 (1), 3.766 (1) and 3.767 (1) Å, and weak C—H⋯π inter­actions, are observed.

(m-Phenylenedimethylene)diammonium dichloride

The asymmetric unit of the title compound, C8H14N2 2+·2Cl−, contains one and a half of the dications and three chloride anions. The half molecule is completed by crystallographic twofold symmetry with two C atoms lying on the rotation axis. The two ammonium groups in each cation adopt a trans conformation with respect ot the benzene ring. The ammonium groups and chloride anions are involved in the formation of a three-dimensional N—H⋯Cl hydrogen-bonding network, which stabilizes the crystal packing.

Diaqua(2,2′-bipyridine-5,5′-dicarboxylato-κ2N,N′)(ethylenediamine-κ2N,N′)copper(II) 2.5-hydrate

In the mol­ecule of the title compound, [Cu(C12H6N2O4)(C2H8N2)(H2O)2]·2.5H2O, the CuII atom is six-coordinated in a distorted octa­hedral configuration by two N atoms from a 2,2′-bipyridine-5,5′-dicarboxyl­ate anion, two N atoms from ethyl­enediamine and two O atoms from two water mol­ecules. There are also two and a half water mol­ecules in the asymmetric unit. The planar five-membered ring is nearly coplanar with the adjacent pyridine rings, while the other five-membered ring adopts a twisted conformation, probably due to hydrogen bonding. In the crystal structure, intra- and inter­molecular N—H⋯O and O—H⋯O hydrogen bonds link the mol­ecules.

Photoreductive Self-Assembly from [MoVI7O24]6− to Anti-Tumoral [H2MoV12O28(OH)12(MoVIO3)4]6− in Aqueous Media

Abstract The long-term photolysis of [iPrNH3]6[Mo7O24]·3H2O in aqueous solutions at pH 5–6 is found to provide the formation of anti-tumoral [H2MoV12O28(OH)12(MoVIO3)4]6− species (1a), the core of which is a well-known ε-isomer ({ε-MoV12}) of the Keggin anion showing edge-shared MoVO6 octahedra in the arrangement of six diamagnetic MoV2-pairs with a MoV–MoV bond distance of 2.6 Å. To obtain structural insight of 1a in aqueous solutions from a viewpoint of the pharmaceutical mechanism, 95Mo NMR, electronic absorption, IR, and electrospray ionization mass (ESI-MS) spectrometries of 1a are investigated and indicate that the {ε-MoV12} core remains intact at pH 5–9 and that a detachment of the MoVIO3 unit from 1a proceeds at high pH level with an accompanying increase in the electronic transition of the MoV2 pairs. Highly positive and negative potentials (0.8–0.9 and −1.1– −1.2 V) of oxidation and reduction current peaks for the MoV2 pairs of 1a assist the structural stability of the ε-Keggin {MoV12} framework in aerobic solutions. A plausible mechanism of the photoreductive self-assembly of [MoVI7O24]6− to 1a through two- and four-electron reduction species, [MoV2Mo5O22(OH)2]6− ({MoV2MoVI5}) and [MoV4Mo3O20(OH)4]6− ({MoV4MoVI3}), is proposed in terms of the formation of a half molecule ([HMoV6O18(OH)6(MoVIO3)2]11−) of 1a, which is suggested by ESI-MS spectrometry of the photolytes.

Tetra-μ-benzoato-bis[(3-methylquinoline)copper(II)](Cu—Cu)

In the title compound, [Cu2(C7H5O2)4(C10H9N)2], the paddle-wheel-type dinuclear complex mol­ecule contains four bridging benzoate groups and two terminal 3-methyl­quinoline ligands. The asymmetric unit contains one and a half mol­ecules with a total of three independent Cu atoms; there is an inversion center at the mid-point of the Cu⋯Cu bond in one molecule. The octa­hedral coordination of each Cu atom, with four O atoms in the equatorial plane, is completed by an N atom of a 3-methyl­quinoline ligand [Cu—N = 2.190 (4)–2.203 (3) Å] and by another Cu atom [Cu⋯Cu = 2.667 (1) and 2.6703 (7) Å]. The Cu atoms are all ca 0.22 Å out of the plane of the four bonded O atoms.

Catena-Poly[[[μ-cyanido-1:2κ2 C:N-tricyanido-1κ3 C-bis(ethylenediamine)-2κ4 N,N′-copper(II)iron(II)]-μ-cyanido-κ2 C:N-[bis(ethylenediamine-κ2 N,N′)copper(II)]-μ-cyanido-κ2 N:C] 4.5-hydrate

The asymmetric unit of the title compound, {[Cu2Fe(CN)6(C2H8N2)4]·4.5H2O}n, consists of two [Cu(C2H8N2)2]2+ cations, one [Fe(CN)6]4− anion, four water mol­ecules and a half water mol­ecule that lies on a twofold rotation axis. The FeII atom is coordinated by six C atoms from three terminal and three doubly bridging CN− ligands. The bridging CN− ligands connect the anion to a five-coordinate [Cu(C2H8N2)2]2+ cation and to two symmetry-related six-coordinate [Cu(C2H8N2)2]2+ cations, forming a one-dimensional polymer in the ab plane. Inter­molecular hydrogen bonds connect the polymer units into a three-dimensional network.

Molecular structure of hydrated complex of 1,4-dimethylpiperazine di-betaine with l-tartaric acid

1,4-Dimethylpiperazine di-betaine (DBPZ) forms a crystalline complex with l-tartaric acid (TA) and two and a half water molecules. The crystals are monoclinic, space group P2 1. The piperazine has a chair conformation with the methyl groups in the equatorial positions and the axial CH 2COO substituents. One of the CH 2COO group is protonated and forms with the neighboring DBPZ molecule the COO H⋯OOC hydrogen bond of the length 2.476(3) Å, which links them into a chain. The semi-tartrate anions, form a chain through the symmetrical, short COO⋯H⋯OOC hydrogen bond of 2.464(3) Å. The crystals have a layer structure, where hydrogen-bonded sheets of TA and water molecules are separated by the chains of DBPZ; no H-bonds between water and DBPZ are present. In the optimized molecules in the B3LYP/6-31G(d,p) approach, the tartaric acid interacts with the tartrate di-anions through the COO H⋯OOC hydrogen bonds of 2.506 Å, while the DBPZ has the same conformation as in the crystals. The FTIR spectrum of the solid complex is consistent with the X-ray results.

Structural Diversity in Organotin Compounds Derived from Bulky Monoaryl Phosphates: Dimeric, Tetrameric, and Polymeric Tin Phosphate Complexes

AbstractMonoaryl phosphates with a bulky aryl substituent have been used to synthesize new organotin clusters and polymers. The equimolar reaction between 2,6‐diisopropylphenylphosphate (dipp‐H2) and Me2SnCl2 in ethanol at 25 °C leads to the formation of [Me2Sn(μ3‐dipp)]n (1), while the reaction of 2,6‐dimethylphenylphosphate (dmpp‐H2) with Me2SnCl2 in either a 1:1 or 2:1 molar ratio proceeds to produce exclusively [Me2Sn(μ‐dmpp‐H)2]n·nH2O (2). Compounds 1 and 2 are 1D polymers with different architectures. In compound 1, the tin atom is five‐coordinate (trigonal bipyramidal). Each dipp ligand bridges three different tin atoms to form an infinite ladder‐chain structure. In 2, each six‐coordinate (octahedral) tin atom is surrounded by four phosphate oxygen atoms originating from four different bridging dmpp‐H ligands, thus forming a spirocyclic coordination polymeric chain. The use of nBu2SnO as the diorganotin source in its reaction with dipp‐H2 leads to the isolation of dimeric [nBu2Sn(μ‐dipp‐H)(dipp‐H)]2 (4), which contains a central Sn2O4P2 unit. There are two chemically different half molecules of 4 in the asymmetric part of the unit cell and hence it actually exists as a 1:1 mixture of [nBu2Sn(μ‐dipp‐H)(dipp‐H)]2 and [nBu2Sn(μ‐dipp)(dipp‐H2)]2 in the solid state. The reaction of the monoorgano tin precursor nBuSn(O)(OH)·xH2O with dipp‐H2 takes place in acetone at room temperature to yield the tetrameric cluster 5, which has different structures in the solution and in the solid state. 31P NMR spectroscopy clearly suggests that 5 has the formula [nBu4Sn4(μ‐O)2(μ‐dipp‐H)8] in solution. The single‐crystal X‐ray diffraction studies in the solid state, however, reveal that compound 5 exists as [nBu4Sn4(μ‐OH)2(μ‐dipp‐H)6(μ‐dipp)2]. The use of compounds 1–4 as possible precursors for the preparation of ceramic tin phosphate materials has been investigated. The thermolysis of 1 at 500 °C leads to the formation of quantitative amounts of Sn2P2O7, while the thermolysis of 2, 3, and 4 under similar conditions results in the formation of SnP2O7. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Crystal Structure of N,N'-Bis(3-methoxysalicylidene)-1,4-diaminocyclohexane

The structure of the title compound, C22H26N2O4, was prepared by the reaction of 3-methoxysalicylaldehyde and trans-1,2-diaminocyclohexane in ethanol. There is a half molecule in the asymmetric unit, and the other half at the symmetry position (2-x, -y, 1-z). It belongs to the space group P21/n with cell parameters a = 6.3312(11), b = 23.967(3), c = 6.775(6)A, β = 108.918(10)°.

Small Nuclear RNAs U11 and U12 Modulate Expression of TNR-CFTR mRNA in Mammalian Kidneys

TNR-CFTR, discovered as a splice variant of CFTR (Cystic Fibrosis Transmembrane conductance Regulator), is distributed in different tissues such as human and rat kidney, trachea, lungs etc and is a functional chloride channel. In Kidneys, our findings show TNR-CFTR to have an unique distribution pattern with low levels of expression in renal cortex and high levels of expression in renal medulla. As shown by us previously, TNR-CFTR mRNA lacks 145 bp corresponding to segments of exons 13 and 14. This deletion causes a frame shift mutation leading to reading of a premature termination codon in exon 14. Premature termination of translation produces a functional half molecule of CFTR; TNR-CFTR. Our analysis of TNR mRNA has shown that the putative alternatively spliced intron has in its 5'' and 3'' conserved element CT and AC, respectively, that can be recognized by snRNAs U11 and U12. With these findings, we hypothesize that TNR-CFTR mRNA alternative splicing is probably mediate by splicing pathways utilizing U11 and U12 snRNAs. In this study, we have determined sequences of snRNAs U11 and U12 derived from rat kidney, which show significant homology to human U11 and U12 snRNAs. We show that there is significantly lower expression of U11 and U12 snRNAs in renal cortex compared to renal medulla in both humans and rats. This renal pattern of distribution of U11 and U12 snRNAs in both humans and rats closely follows distribution pattern of renal TNR-CFTR. Further, we have shown that blocking U11 and/or U12 mRNAs, by using antisense probes transfected in Immortalized Rat Proximal Tubule Cell line (IRPTC), decreases TNR-CFTR mRNA expression but not wild-type CFTR mRNA expression. Our results suggest that expression of U11 and/or U12 snRNAs is important for non-conventional alternative splicing process that gives rise to mRNA transcript coding for TNR-CFTR.

Studies on RNA-protein interactions and enzyme activity by mutational analysis of telomerase

The protein component of telomerase (TERT: telomerase reverse transcriptase) contains a domain (RID2: RNA interaction domain 2), which interacts with the RNA component of telomerase (TR: telomerase RNA). RID2 includes a telomerase-specific motif (T-motif), which is highly conserved among species. But, the role of T-motif is not clearly understood. To elucidate the role of T-motif in the telomerase activity and the TERT-TR interaction, we designed two systems including full-length human TERT (hTERT) proteins for telomerase activity and RID2 domain peptides for binding activity. Variants of hTERT, in which a highly conserved amino acid residue in T-motif was replaced with an alanine residue, were expressed in the in vitro translation system of rabbit reticulocyte lysate. We examined telomerase activity of the hTERT variants by the stretch-PCR method. T564A, E565A, and W581A variants did not show remarkably decreased activity suggesting that these amino acid residues are not important for the enzymatic activity, although they are conserved with 89-100% identity. Next, we tried construction of an experimental system for examination of RNA-binding activity of RID2 variants with the same mutations in T-motif. The wild-type RID2 peptide with His-tags was prepared by expression in an E. coli system and purified with an affinity column. The binding activity to human TR (hTR) was examined by the EMSA (electrophoretic mobility shift assay) method. The RID2 (aa 300-617) peptide showed binding to the 3'half molecule of hTR but not to the 5'-half molecule. The RID2 variants are being prepared and analyzed in this system.

Bis(methyl 2,4,6-tri-O-acetyl-β-D-allofuranosid-3-yl)sulfane

The title compound, C26H38O16S, crystallizes with two unique half molecules in the asymmetric unit, where the central S atom in each of the unique molecules is positioned on a twofold rotation axis. The only major conformational difference between the two molecules concerns one of the acetyl groups. Except for that acetyl group, the atoms of the two different molecules, in an overlay of one molecule on the other, differ on average by only 0.06 (6) Å from each other.

A novel single pot synthesis of binuclear copper(II) complexes of macrocyclic and macroacyclic compartmental ligands: Structures and magnetic properties

Two binuclear copper(II) complexes one (complex 1) with a macrocyclic ligand (H 2L1) and other (complex 2) with a macroacyclic (end-off type) compartmental ligand (HL2) have been synthesized from single pot template synthesis involving copper(II) nitrate, 1,2-diaminoethane, 4-methyl-2,6-diformylphenol, and sodium azide. Structure analysis of complex 1 reveals that there are actually two half molecules present in the asymmetric unit and so two complexes (molecule-I and molecule-II) are present in unit cell, although they show slight differences. The two Cu(II) centers are in distorted square pyramidal coordination environment with two endogenous phenoxo bridges provided by the phenolate of H 2L1 having Cu–Cu separations of 2.9133(10) Å and 2.9103(10) in the two molecules. In complex 2 the coordination environments around two Cu(II) centers are asymmetric, Cu1 is in distorted square pyramidal environment whereas, the coordination environment around Cu2 is distorted octahedral. The two Cu(II) centers in complex 2 are connected by two different kinds of bridges, one is endogenous phenoxo bridge provided by the phenolate of the ligand HL2 and the other is exogenous azido bridge (μ −1,1 type) with Cu–Cu distance of 3.032(10) Å. Variable temperature magnetic studies show that two Cu(II) centers in both the complexes are strongly antiferromagnetically coupled with J = −625 ± 5 cm −1 and J = −188.6 ± 1 cm −1 for complex 1 and 2, respectively.

Structure of double Keggin-Ti/W-mixed polyanion [(A-β-GeTi 3W 9O 37) 2O 3] 14− and multielectron-transfer-based photocatalyic H 2-generation

[(A-β-GeW 9Ti 3O 37) 2O 3] 14− ( 1a) is isolated as K +/Na +/H + salt, K 9NaH 4[(β-GeW 9Ti 3O 37) 2O 3]·40.5H 2O ( 1), and characterized by single-crystal X-ray structural and 183W NMR spectral analyses in comparison with [(A-α-GeW 9Ti 3O 37) 2O 3] 14− ( 2a) previously isolated as K 9H 5[(α-GeW 9Ti 3O 37) 2O 3]·16H 2O ( 2). Two isomers of 1a and 2a have local symmetry of D 3h and are stable in aqueous solutions at least at pH values of ≤7. The photocatalytic H 2-formation for the dehydrogenative oxidation of methanol (CH 3OH → H 2 + HCHO) with 1 and 2 is investigated with a help of electronic and ESR spectra and electrochemistry, and is explained in terms of the two-electron reduction of protons at the central Ti III–O–Ti III linkage of the corner-shared TiO 6 octahedra connecting two half molecules.

TRNA regulation of gene expression: Interactions of an mRNA 5′-UTR with a regulatory tRNA

Many genes encoding aminoacyl-tRNA synthetases and other amino acid-related products in Gram-positive bacteria, including important pathogens, are regulated through interaction of unacylated tRNA with the 5'-untranslated region (5'-UTR) of the mRNA. Each gene regulated by this mechanism responds specifically to the cognate tRNA, and specificity is determined by pairing of the anticodon of the tRNA with a codon sequence in the "Specifier Loop" of the 5'-UTR. For the 5'-UTR to function in gene regulation, the mRNA folding interactions must be sufficiently stable to present the codon sequence for productive binding to the anticodon of the matching tRNA. A model bimolecular system was developed in which the interaction between two half molecules ("Common" and "Specifier") would reconstitute the Specifier Loop region of the 5'-UTR of the Bacillus subtilis glyQS gene, encoding GlyRS mRNA. Gel mobility shift analysis and fluorescence spectroscopy yielded experimental Kds of 27.6 +/- 1.0 microM and 10.5 +/- 0.7 microM, respectively, for complex formation between Common and Specifier half molecules. The reconstituted 5'-UTR of the glyQS mRNA bound the anticodon stem and loop of tRNA(Gly) (ASL(Gly)(GCC)) specifically and with a significant affinity (Kd = 20.2 +/- 1.4 microM). Thus, the bimolecular 5'-UTR and ASL(Gly)(GCC) models mimic the RNA-RNA interaction required for T box gene regulation in vivo.