DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC)

2016 ◽  
Vol 72 (6) ◽  
pp. 780-788 ◽  
Author(s):  
Arunachalam Thirugnanasambandam ◽  
Selvam Karthik ◽  
Gunanithi Artheswari ◽  
Namasivayam Gautham
Keyword(s):  
Metal Ion ◽  
Helical Structure ◽  
Mixed Population ◽  
Helical Conformation ◽  
Cd Spectra ◽  
X Ray ◽  
X Ray Crystallography ◽  
Double Helical Structure ◽  
Flexible Molecule ◽  
Dna Fragment

High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs.

One-pot synthesis of 5-(8-ethoxycarbonyl-1-naphthyl)-10,15,20-triphenyl porphyrin (ENTPP) and spontaneous resolution upon crystallization

2011 ◽  
Vol 15 (03) ◽  
pp. 197-201 ◽  
Author(s):  
Juanxia Yang ◽  
Jiaxun Jiang ◽  
Weiguang Fang ◽  
Xiaoxu Kai ◽  
Chuanjiang Hu ◽  
...  
Keyword(s):  
Soret Band ◽  
Ester Group ◽  
Spontaneous Resolution ◽  
Cd Spectra ◽  
One Pot ◽  
Nmr Spectrum ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Entire Structure

5-(8-ethoxycarbonyl-1-naphthyl)-10,15,20-triphenyl porphyrin (ENTPP) has been synthesized in a one-pot reaction, and the corresponding chiral crystalline samples have been obtained by spontaneous resolution. 1 H NMR spectrum suggests it is mononaphthyl substituted species and an ethyl group is over the porphyrin plane. The structure has been further confirmed by X-ray crystallography. ENTPP·C6H14 (C57H50N4O2 ): monoclinic, P21, a = 10.707(2) Å, b = 12.203(2) Å, c = 17.858(4) Å, β = 103.06(3)°, V = 2272.8(8) Å3, Z = 2. The 8-position substituent, ester group, lies above the porphyrin plane and leads to the conformational chirality. The entire structure is built up with homochiral molecules, which leads to a chiral crystal through packing in P21 space group. Circular dichroism (CD) spectra have exhibited remarkable absorptions in the Soret band region, which further confirms the homochirality of the crystalline samples.

scholarly journals Helix-sense-selective Polymerization of 3,5-bis(hydroxymethyl)phenylacetylene Rigidly Bearing Galvinoxyl Residues and Their Chiroptical Properties

Polymers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1877 ◽  
Author(s):  
Shi ◽  
Wang ◽  
Teraguchi ◽  
Aoki ◽  
Kaneko
Keyword(s):  
Main Chain ◽  
Helical Structure ◽  
Intramolecular Hydrogen Bonding ◽  
Catalyst System ◽  
Static Stability ◽  
Cotton Effect ◽  
Helical Conformation ◽  
Cd Spectra ◽  
Cotton Effects ◽  
Intramolecular Hydrogen

Four kinds of newly synthesized achiral phenylacetylenes bearing a phenylhydrogalvinoxyl residue at 4-position were polymerized by using a chiral rhodium catalyst system, [Rh(nbd)B(C6H5)4] or [Rh(nbd)Cl]2 catalysts in the presence of chiral (R)-(+)- or (S)-(–)-1-phenylethylamine ((R)- or (S)-PEA) cocatalysts. Poly(m-HGDHPA) and poly(m-HGTHPA) in THF showed Cotton signals at the absorption regions of the main chain and hydrogalvinoxyl in the circular dichroism (CD) spectra. It indicated that excess of one-handed helical polyacetylene backbone was induced by helix-sense-selective polymerization (HSSP) under the asymmetric conditions despite the achiral monomer, and the hydrogalvinoxyl moieties were also arranged to form one-handed helical structure. However, there was no Cotton effect for poly(p-HGDHPA) and poly(p-HGTHPA) because the intramolecular hydrogen bonding did not act well to stabilize the helical conformation. The hydrogalvinoxyl units of poly(m-HGDHPA) and poly(m-HGTHPA) were converted to the corresponding galvinoxyl radicals after treatment with PbO2. In the CD spectra of the polyradicals, the Cotton effects decreased depending on their static stability of helical conformation, suggesting that reversal conformation of the polymer chain arose.

Preparation and characterization of Tl(1,2-C2H4Cl2)B(OTeF5)4: a metal complex of a least coordinating solvent and a least coordinating anion

1992 ◽  
Vol 70 (3) ◽  
pp. 726-731 ◽  
Author(s):  
Paul K. Hurlburt ◽  
Oren P. Anderson ◽  
Steven H. Strauss
Keyword(s):  
Metal Ion ◽  
Chelate Ring ◽  
Ion Solvation ◽  
Crystalline Compound ◽  
Triclinic Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Solid Salt ◽  
Solvent Metal

Addition of B(OTeF5)3 to TIOTeF5 in the weakly coordinating solvents dichloromethane, 1,2-dichloroethane, and 1,1,2-trichlorotrifluoroethane produces solutions of M(solv)x+B(OTeF5)4−. When the solvent was 1,2-dichloroethane, the crystalline compound Tl(1,2-C2H4Cl2)B(OTeF5)4 was isolated and studied by X-ray crystallography: triclinic, space group [Formula: see text], a = 9.221 (4), b = 11.396(5), c = 12.538 (4) Å, α = 110.75 (3)°, β = 101.72(3)°, γ = 99.74 (3)°, Z = 2, T = −116 °C. The Tl(1,2-C2H4Cl2)+ cation contains a five-membered chelate ring with Tl—Cl distances of 3.138 (4) and 3.179 (3) Å. The metal ion is weakly bonded to four B(OTeF5)4− counterions, with nine Tl—F interactions that range from 2.950 (5) to 3.981 (8) Å. When the solvent is dichloromethane or 1,1,2-trichlorotrifluoroethane, only the unsolvated solid salt TlB(OTeF5)4 can be isolated by crystallization. This salt is thermally unstable, slowly forming TlOTeF5 and volatile B(OTeF5)3. Keywords: noncoordinating anion, noncoordinating solvent, metal ion solvation.

New homodinuclear tris(3-alkylpyrazolyl)borate complexes of CoIIand NiIIwith a tetraacetylethane dianion as a bridging ligand

2016 ◽  
Vol 72 (11) ◽  
pp. 777-785
Author(s):  
Elena A. Mikhalyova ◽  
Swiatoslaw Trofimenko ◽  
Matthias Zeller ◽  
Anthony W. Addison ◽  
Vitaly V. Pavlishchuk
Keyword(s):  
Metal Ions ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Molecular Structures ◽  
Polynuclear Complexes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Coordination Sites ◽  
Borate Complexes ◽  
Capping Ligands

Polynuclear complexes and coordination polymers of 3dmetals have attracted significant interest evoked by a number of their unique properties. One of the most common approaches to the directed synthesis of coordination polymers is the linking of pre-prepared discrete coordination units by polydentate ligands. The formation of polynuclear complexes is usually a spontaneous process and precise prediction of the products of such reactions is virtually impossible in most cases. Tris(pyrazolyl)borates (Tp) act as tripodal `capping' ligands which form stable complexes with 3dmetal ions. In such 1:1 compounds, three metal-ion coordination sites are occupied by N atoms from a Tp anion. This limits the number of remaining coordination sites, and thus the number of additional ligands which may coordinate, and opens an attractive approach for the directed design of desirable structures by exploiting ligands with appropriate composition and topology. In the present study, Tp anions with neopentyl [TpNp, tris(3-neopentylpyrazolyl)borate] and cyclohexyl [TpCy, tris(3-cyclohexylpyrazolyl)borate] substituents were used as `capping' ligands and the dianion of tetraacetylethane (3,4-diacetylhexa-2,4-diene-2,5-diolate, tae2−) was employed as a bridge. The dinuclear complexes (μ-3,4-diacetylhexa-2,4-diene-2,5-diolato-κ4O2,O3:O4,O5)bis{[tris(3-cyclohexyl-1H-pyrazol-1-yl-κN2)borato]cobalt(II)} acetonitrile disolvate, [Co2(C27H40BN6)2(C10H12O4)]·2CH3CN, (I)·2CH3CN, and (μ-3,4-diacetylhexa-2,4-diene-2,5-diolato-κ4O2,O3:O4,O5)bis{[tris(3-neopentyl-1H-pyrazol-1-yl-κN2)borato]nickel(II)}, [Ni2(C24H40BN6)2(C10H12O4)], (II), were synthesized by the reaction of the mononuclear complexes TpCyCoCl or TpNpNiCl with H2tae (3,4-diacetylhexane-2,5-dione or tetraacetylethane) in the presence of NEt3as base. Compounds (I) and (II) were characterized by mass spectrometry, elemental analysis, and X-ray crystallography. They possess similar molecular structures, X-ray diffraction revealing them to be dinuclear in nature and composed of discrete Tp–Munits in which two metal ions are linked by a tae2−dianion. Each metal ion possesses a five-coordinate square-pyramidal environment. The interplanar angles between the acetylacetonate fragments are significantly smaller than the near-90° values commonly observed.

Address of the President Sir Alan Hodgkin, O. M. at the Anniversary Meeting, 1 December 1975

1976 ◽  
Vol 192 (1109) ◽  
pp. 371-391
Keyword(s):  
Molecular Biology ◽  
Coiled Coil ◽  
Helical Structure ◽  
X Ray Diffraction ◽  
Helical Structures ◽  
X Ray ◽  
Double Helical Structure ◽  
Leading Role ◽  
Replication Scheme ◽  
Related Proteins

The Copley Medal is awarded to Dr F. H. C. Crick, F. R. S. In 1953 Crick and Watson proposed the double-helical model for DNA, in which the bases are arranged in complementary pairs so that the molecule is capable of self-replication and is thus the essential carrier of genetic information in living cells. This proposal was based on an inspired interpretation of the results of X-ray diffraction analysis of DNA carried out by Wilkins, Franklin and their collaborators, and on the chemical analyses of Chargaff and others. The replication scheme inherent in the double-helical structure of DNA made it possible for the first time to discuss the mechanism of heredity in molecular terms; it has been the most fruitful concept in the whole of biology during the past 25 years, and has been the basis for the explosive development of molecular biology. Besides his part in this dramatic discovery, Crick played a very important part in increasing our understanding of the way in which the genetic message is carried on DNA (the ‘coding’ problem), and of the mechanisms by which it is translated into specific sequences of amino acids in the proteins synthesized by the cell. He has also continued to play a leading rôle in many other aspects of molecular biology, and has made important contributions to X-ray studies of crystalline proteins, fibrous proteins and viruses. These include the theory of diffraction from helical structures, the coiled-coil model of α-keratin and related proteins, the structure of collagen, and the theoretical basis of the construction of ‘spherical’ viruses. More recently, Crick has had an important influence on work in the fields of development and of chromosome structure.

Solution Conformation of Konjac Glucomannan Single Helix

2011 ◽  
Vol 197-198 ◽  
pp. 96-104 ◽  
Author(s):  
Chao Wang ◽  
Yu Zhang ◽  
Hong Xia Huang ◽  
Mao Bin Chen ◽  
Dong Sheng Li
Keyword(s):  
Congo Red ◽  
Helical Structure ◽  
Konjac Glucomannan ◽  
Helical Conformation ◽  
Urea Solution ◽  
Cd Spectra ◽  
Solution Conformation ◽  
Random Coils ◽  
The Stability ◽  
Single Helix

The possibility of the existence of konjac glucomannan (KGM) single helix in dilute solution was discussed finely by ultraviolet-visible spectrophotometer (UV-Vis) with Congo red complex, viscosimetry and circular dichroism (CD). KGM bound to Congo red and the λmaxcharacteristic shifted markedly to longer wavelength (514 nm) in 0.25 M aq NaOH. The shifts of λmaxand intrinsic viscosity were also compared in different mediums, such as different concentrations of KGM, NaOH, urea solutions or temperatures. The results indicated that KGM had an ordered, single-helical conformation in neutral, slight NaOH (<0.15 M) and urea (<3.0 M) solutions or at a moderate temperature (T<55ºС ), while it was transformed disorder, random coils in high NaOH (>0.45 M), urea (>4.0 M) solutions or at a high temperature (T>60ºС ). So it can be conclude that the outside factors play an important role on the stability of the single-helix conformation for KGM solution. The induced CD spectra by Congo red and the CD spectra of KGM in aqueous and urea solution indicated further that KGM had a single-helical structure. The new conclusion laid the foundation of determining helical radius, pitch and length of KGM in the future studies.

Open-Framework Solids with Diamond-Like Structures Prepared from Clusters and Metal-Organic Building Blocks

1994 ◽  
Vol 371 ◽  
Author(s):  
Omar M. Yaghi ◽  
D. A. Richardson ◽  
G. Li ◽  
C. E. Davis ◽  
T. L. Groy
Keyword(s):  
Metal Ion ◽  
Building Blocks ◽  
Diamond Structure ◽  
Tetrahedral Cluster ◽  
X Ray ◽  
Open Framework ◽  
X Ray Crystallography ◽  
Metal Organic ◽  
Channel Systems ◽  
Cu And Zn

AbstractThe tetrahedral cluster Ge4S104- and the rodlike ligand 4,4′-bipyridine are utilized in addition copolymerization reactions with the metal (II) ions of Mn, Fe, Co, Cu, and Zn in the preparation of 3-D open-framework solids, MxCol-xGe4S10-2(CH3)4N (x = 0.86, M = Mn; x = 1, M = Mn, Fe, Co, and Zn), 1, and Cu(4,4′-bpy)2. PF6, 2, having diamond-like structures. These structures are viewed in terms of the cubic diamond structure, where the carbon atoms have been replaced by either a cluster or a metal ion and the C-C bond by a sulfide or the 4,4′-bpy. These compounds have been fully characterized by single crystal x-ray crystallography and their composition was confirmed by elemental analysis; they contain 3-D channel systems where cations or anions reside to balance the charge on the framework.

scholarly journals Mixed Chirality α-Helix in a Stapled Bicyclic and a Linear Antimicrobial Peptide Revealed by X-Ray Crystallography

2021 ◽  
Author(s):  
stéphane Baeriswyl ◽  
Hippolyte Personne ◽  
Ivan Di Bonaventura ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Md Simulations ◽  
Isobutyric Acid ◽  
Cd Spectra ◽  
X Ray ◽  
X Ray Crystallography ◽  
Left Handed ◽  
Amino Isobutyric Acid ◽  
Α Helix ◽  
Protein Environment

<p></p><p>The peptide α-helix is right-handed when containing amino acids with L-chirality, and left-handed with D-chirality, however mixed chirality peptides generally do not form α-helices unless the non-natural residue amino-isobutyric acid is used as helix inducer. Herein we report the first X-ray crystal structures of mixed chirality α-helices in short peptides comprising only natural residues at the example of a stapled bicyclic and a linear membrane disruptive amphiphilic antimicrobial peptide (AMP) containing seven L- and four D-residues, as complexes of fucosylated analogs with the bacterial lectin LecB. The mixed chirality α-helices are superimposable to their parent homochiral α-helices and form under similar conditions as shown by CD spectra and MD simulations but are resistant to proteolysis. The observation of mixed chirality α-helix with only natural residues in the protein environment of LecB suggests a vast unexplored territory of α-helical mixed chirality sequences and their possible use for optimizing bioactive α-helical peptides.</p><br><p></p>

scholarly journals On the control of secondary carbanion structure utilising ligand effects during directed metallation

2012 ◽  
Vol 8 ◽  
pp. 50-60 ◽  
Author(s):  
Andrew E H Wheatley ◽  
Jonathan Clayden ◽  
Ian H Hillier ◽  
Alison Campbell Smith ◽  
Mark A Vincent ◽  
...  
Keyword(s):  
Short Distance ◽  
Metal Ion ◽  
Organic Anion ◽  
Lewis Base ◽  
Aromatic System ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ligand Effects ◽  
Directing Group ◽  
Bond Character

N,N-Diisopropyl-2-propylbenzamide 6-H undergoes lateral deprotonation by t-BuLi in the presence of the Lewis base PMDTA (N,N,N′,N″,N″-pentamethyldiethylenetriamine) to give a benzyllithium 6-Li l ·PMDTA that incorporates a trigonal planar secondary carbanion. In the solid state, the amide directing group and the PMDTA additive work together to abstract the metal ion from the deprotonated α-C of the propyl group (4.107(4) Å). A short distance of 1.376(3) Å is observed between the deprotonated carbon centre and a planar aromatic system that shows a pattern of bond lengths which contrasts with that reported for related tertiary carbanion systems. Analogous benzylic deprotonation is seen if 6-H is treated with t-BuLi in the presence of diglyme to give 6-Li l ·DGME. X-ray crystallography now shows that the metal ion more closely approaches the tertiary carbanion (2.418(6) Å) but that the planarity of the deprotonated carbon centre and the bonding pattern in the organic anion seen in the PMDTA complex are retained. DFT analysis corroborates both the short distance between aromatic ring and carbanion centre and the unperturbed nature of aromaticity in 6-Li l ·L (L = Lewis base). The observation of two structure-types for the carbanion in solution is explained theoretically and by NMR spectroscopy in terms of cis and trans isomerism imparted by partial double bond character in the arene–(α-C) bond.

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