Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization

Electrostatic interactions between localized integral charges make the stability and structure of highly charged small and rigid organics intriguing. Can σ/π-electron delocalization compensate reduced conformational freedom by lowering the repulsion between identical charges? The crystal structure of the title salt, C14H16N42+·2CF3SO3−, (2), is described and compared with that of the 2,2′′-bis(diphenylphosphanyl) derivative, (4). The conformations of the dications and their interactions with neighbouring trifluoromethanesulfonate anions are first analyzed from the standpoint of formal electrostatic effects. Neither cation exhibits any geometrical strain induced by the intrinsic repulsion between the positive charges. In contrast, the relative orientation of the imidazolium rings [i.e. antifor (2) andsynfor (4)] is controlled by different configurations of the interactions with the closest trifluoromethanesulfonate anions. The long-range arrangement is also found to be specific: beyond the formal electrostatic packing, C—H...O and C—H...F contacts have no definite `hydrogen-bond' character but allow the delineation of layers, which are either pleated or flat in the packing of (2) or (4), respectively.

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Polycarboxylate crown ethers from meso-tartaric acid

Canadian Journal of Chemistry ◽

10.1139/v91-003 ◽

1991 ◽

Vol 69 (1) ◽

pp. 12-19 ◽

Cited By ~ 5

Author(s):

Frank R. Fronczek ◽

Richard D. Gandour ◽

Thomas M. Fyles ◽

Philippa J. Hocking ◽

Susan J. McDermid ◽

...

Keyword(s):

Crystal Structure ◽

Crown Ether ◽

Tartaric Acid ◽

Crown Ethers ◽

Nmr Spectra ◽

Product Distribution ◽

Complexing Agents ◽

Triclinic Space Group ◽

The Stability ◽

Ether Synthesis

The synthesis of crown ethers derived from meso-tartaric acid was investigated. The sodium salt of the bis(dimethylamide) of meso-tartaric acid reacted with diethylene glycol ditosylate to give a mixture of 18-crown-6 tetraamide and 27-crown-9 hexaamide crown ethers. The 2R,3S,11S,12R 18-crown-6 isomer crystallized in triclinic space group [Formula: see text] (a = 7.557(2), b = 8.866(2), c = 10.4133(13) Å, α = 94.13(2), β = 95.86(2), γ = 99.26(2)°, R = 0.040 for 2090 observed of 3129 unique reflections). The structures of the remaining products were then assigned from the NMR spectra. The solution conformations of the amide crown ethers were examined by NMR, and provide a rationale for the product distribution obtained. One of the 18-crown-6 isomers and a mixture of the two 27-crown-9 isomers were hydrolyzed to the respective crown ether carboxylic acids, and the stability constants for complexation of cations were determined by potentiometric titration. The meso tetra- and hexacarboxylates are remarkably nonselective and inefficient cation complexing agents, compared to related crown ethers from R,R-(+)-tartaric acid, due to the unfavorable conformational control exerted by the tartaro units. Key words: crown ether synthesis, complexation, crown ether conformation, meso-tartaric acid, crystal structure.

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Solid-State and Theoretical Investigations of Some Banister-Type Macrocycles with 2,2’-Aldoxime-1,1’-Biphenyl Units

Frontiers in Chemistry ◽

10.3389/fchem.2021.750418 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ioan Stroia ◽

Ionuţ -Tudor Moraru ◽

Maria Miclăuş ◽

Ion Grosu ◽

Claudia Lar ◽

...

Keyword(s):

Crystal Structure ◽

Solid State ◽

Density Functional ◽

Alkali Metal Ions ◽

Functional Theory ◽

State Data ◽

Supramolecular Associations ◽

Theoretical Investigations ◽

The Stability ◽

Good Agreement

In the context of helical chirality, bridging of biphenyl units leads to banister-type compounds and the stability of the resulted atropisomers may increase dramatically if suitable changes are performed in the linker unit that coils around the biphenyl moiety. A rigorous density functional theory (DFT) study was conducted for macrocycles containing rigid oxime ether segments connected to the biphenyl backbone in order to determine how the rotation barriers are influenced by the presence of either a flexible oligoethyleneoxide or a more rigid m–xylylene component in the macrocycle. The calculated values for the racemization barrier were in good agreement with those obtained experimentally and confirm the benefit of introducing a more rigid unit in the macrocycle on the stability of atropisomers. Solid-state data were obtained and computed data were used to assess the contribution brought by supramolecular associations observed in the lattice to the stabilization of the crystal structure. Beside introducing rigidity in the linker, complexation of flexible macrocycles with alkali metal ions is also contributing to the stability of atropisomers, leading to values for the racemization barrier matching that of the rigid macrocycle. Using diethylammonium cation as guest for the macrocycle, a spectacular increase in the barrier to rotation was observed for the resulted pseudo[2]rotaxane.

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Synthesis and Complexation Properties of 2-Hydroxy-5-methoxyphenylphosphonic Acid (H3L1). Crystal Structure of the [Cu(H2L1)2(Н2О)2] Complex

Russian Journal of General Chemistry ◽

10.1134/s1070363221110074 ◽

2021 ◽

Vol 91 (11) ◽

pp. 2176-2186

Author(s):

G. S. Tsebrikova ◽

Yu. I. Rogacheva ◽

I. S. Ivanova ◽

A. B. Ilyukhin ◽

V. P. Soloviev ◽

...

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Methoxy Group ◽

Protonation Constants ◽

Water Molecules ◽

X Ray Diffraction ◽

X Ray ◽

The Stability ◽

Intramolecular Hydrogen ◽

Oxygen Atoms

Abstract 2-Hydroxy-5-methoxyphenylphosphonic acid (H3L1) and the complex [Cu(H2L1)2(H2O)2] were synthesized and characterized by IR spectroscopy, thermogravimetry, and X-ray diffraction analysis. The polyhedron of the copper atom is an axially elongated square bipyramid with oxygen atoms of phenolic and of monodeprotonated phosphonic groups at the base and oxygen atoms of water molecules at the vertices. The protonation constants of the H3L1 acid and the stability constants of its Cu2+ complexes in water were determined by potentiometric titration. The protonation constants of the acid in water are significantly influenced by the intramolecular hydrogen bond and the methoxy group. The H3L1 acid forms complexes CuL‒ and CuL24‒ with Cu2+ in water.

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Quantum Mechanical-Based Stability Evaluation of Crystal Structures for HIV-Targeted Drug Cabotegravir

Molecules ◽

10.3390/molecules26237178 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7178

Author(s):

Yanqiang Han ◽

Hongyuan Luo ◽

Qianqian Lu ◽

Zeying Liu ◽

Jinyun Liu ◽

...

Keyword(s):

Crystal Structure ◽

Ab Initio ◽

Crystal Structures ◽

Structure Prediction ◽

Hiv Infections ◽

Integrase Inhibitor ◽

Hiv Integrase ◽

Stability Evaluation ◽

The Stability ◽

Long Acting

The long-acting parenteral formulation of the HIV integrase inhibitor cabotegravir (GSK744) is currently being developed to prevent HIV infections, benefiting from infrequent dosing and high efficacy. The crystal structure can affect the bioavailability and efficacy of cabotegravir. However, the stability determination of crystal structures of GSK744 have remained a challenge. Here, we introduced an ab initio protocol to determine the stability of the crystal structures of pharmaceutical molecules, which were obtained from crystal structure prediction process starting from the molecular diagram. Using GSK744 as a case study, the ab initio predicted that Gibbs free energy provides reliable further refinement of the predicted crystal structures and presents its capability for becoming a crystal stability determination approach in the future. The proposed work can assist in the comprehensive screening of pharmaceutical design and can provide structural predictions and stability evaluation for pharmaceutical crystals.

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Modular protein-oligonucleotide signal exchange

Nucleic Acids Research ◽

10.1093/nar/gkaa405 ◽

2020 ◽

Vol 48 (12) ◽

pp. 6431-6444

Author(s):

Deepak K Agrawal ◽

Rebecca Schulman

Keyword(s):

Specific Protein ◽

Vascular Endothelial ◽

Complementary Dna ◽

Exchange Processes ◽

Dna Strand Displacement ◽

Specific Proteins ◽

Dna Strand ◽

Endothelial Growth Factor ◽

Signal Exchange

Abstract While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

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Microporous crystal structure of labuntsovite-Fe and high-pressure behavior up to 23 GPa

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s205252061700498x ◽

2018 ◽

Vol 74 (1) ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Sergey M. Aksenov ◽

Elena A. Bykova ◽

Ramiza K. Rastsvetaeva ◽

Nikita V. Chukanov ◽

Irina P. Makarova ◽

...

Keyword(s):

Crystal Structure ◽

High Pressure ◽

Single Crystal ◽

Cross Section ◽

Structure Refinement ◽

Alkaline Complex ◽

X Ray ◽

Cell Parameters ◽

Diamond Anvil ◽

The Stability

Labuntsovite-Fe, an Fe-dominant member of the labuntsovite subgroup, was first discovered in the Khibiny alkaline massif on Mt Kukisvumchorr [Khomyakov et al. (2001). Zap. Vseross. Mineral. Oba, 130, 36–45]. However, no data are published about the crystal structure of this mineral. Labuntsovite-Fe from a peralkaline pegmatite located on Mt Nyorkpakhk, in the Khibiny alkaline complex, Kola Peninsula, Russia, has been investigated by means of electron microprobe analyses, single-crystal X-ray structure refinement, and IR and Raman spectroscopies. Monoclinic unit-cell parameters of labuntsovite-Fe are: a = 14.2584 (4), b = 13.7541 (6), c = 7.7770 (2) Å, β = 116.893 (3)°; V = 1360.22 (9) Å3; space group C2/m. The structure was refined to final R 1 = 0.0467, wR 2 = 0.0715 for 3202 reflections [I > 3σ(I)]. The refined crystal chemical formula is (Z = 2): Na2K2Ba0.7[(Fe0.5Ti0.1Mg0.05)(H2O)1.3]{[Ti2(Ti1.9Nb0.1)(O,OH)4][Si4O12]2}·4H2O. The high-pressure in situ single-crystal X-ray diffraction study of the labuntsovite-Fe has been carried out in a diamond anvil cell. The labuntsovite-type structure is stable up to 23 GPa and phase transitions are not observed. Calculations using the BM3 equation of state resulted in the bulk modulus K = 72 (2) GPa, K′0 = 3.7 (2) and V 0 = 1363 (2) Å3. Compressing of the heteropolyhedral zeolite-like framework leads to the deformation of main structural units. Octahedral rods show the gradual increase of distortion and the wave-like character of rods becomes more distinct. Rod deformations result in the distortion of the silicon–oxygen ring which is not equal in different directions. Structural channels are characterized by a different ellipticity–pressure relationship: the cross-section of the largest channel I and channel II demonstrates the stability of the geometrical characteristics which practically do not depend on pressure: ∊channel I ≃ 0.85 (4) (cross-section is rather regular) and ∊channel II ≃ 0.52 (2) within the whole pressure range. However, channel III is characterized by the increasing of ellipticity with pressure (∊ = 0.40 → 0.10).

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Cloning and molecular analysis of promoter-like sequences isolated from the chromosomal DNA ofLactobacillus acidophilusATCC 4356

Canadian Journal of Microbiology ◽

10.1139/m97-009 ◽

1997 ◽

Vol 43 (1) ◽

pp. 61-69 ◽

Cited By ~ 18

Author(s):

G. Djordjevic ◽

B. Bojovic ◽

N. Miladinov ◽

L. Topisirovic

Keyword(s):

Lactococcus Lactis ◽

Molecular Analysis ◽

Lactobacillus Acidophilus ◽

Promoter Activity ◽

Lactobacillus Reuteri ◽

Bacterial Species ◽

Chromosomal Dna ◽

Complementary Dna ◽

E Coli ◽

Dna Strand

Promoter-like sequences from the chromosomal DNA of thermophilic strain Lactobacillus acidophilus ATCC 4356 were cloned. Analysis of the three DNA fragments showing promoter activity, designated P3, P6, and P15, were performed in Lactobacillus reuteri, Lactococcus lactis, and E. coli. The reporter cat-86 gene was expressed in all three bacterial species under control of the fragments P3 and P6. Fragment P15 showed promoter activity only in Lactobacillus reuteri and E. coli but not in Lactococcus lactis. The three host-specific transcriptional start points (TSPs) were used when transcription of the cat-86 gene was controlled by fragment P3 in Lactobacillus reuteri, E. coli, and Lactococcus lactis. Similarly, fragment P15 initiated transcription of the cat-86 gene at two distinctive sites in Lactobacillus reuteri and E. coli. Only within fragment P6, a common TSP was used in Lactobacillus reuteri and E. coli, but different from that used in Lactococcus lactis. Each TSP was preceded by the putative −35 and −10 hexamers. Computer analysis of the fragment P3 sequence revealed the existence of divergent promoterlike sequence (P3rev) located on the complementary DNA strand. Fragments P6 and P15 were also functional in Lactobacillus acidophilus ATCC 4356 from which chromosomal DNA they were originally cloned.Key words: Lactobacillus acidophilus, promoter-like sequences, regulation.

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