Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid · polyuridylic acid and polyinosinic acid · polycytidylic acid

1973 ◽  
Vol 81 (2) ◽  
pp. 107-122 ◽  
Author(s):  
Struther Arnott ◽  
D.W.L. Hukins ◽  
S.D. Dover ◽  
W. Fuller ◽  
A.R. Hodgson
Keyword(s):  
X Ray Diffraction ◽  
Molecular Conformations ◽  
X Ray ◽  
Polycytidylic Acid ◽  
Polyinosinic Acid ◽  
Polyadenylic Acid ◽  
Polyuridylic Acid

Ultraviolet circular dichroism studies on synthetic polynucleotides

1969 ◽  
Vol 47 (6) ◽  
pp. 637-642 ◽  
Author(s):  
Fred H. Wolfe ◽  
Kimio Oikawa ◽  
Cyril M. Kay
Keyword(s):  
Circular Dichroism ◽  
Wavelength Region ◽  
Ph Values ◽  
Polycytidylic Acid ◽  
Naturally Occurring ◽  
Polyinosinic Acid ◽  
Polyadenylic Acid ◽  
Polyuridylic Acid ◽  
Extreme Sensitivity ◽  
Circular Dichroïsm

The ultraviolet circular dichroism spectra of polyadenylic acid, polyguanylic acid, polycytidylic acid, polyinosinic acid, and polyuridylic acid have been examined at neutral and acidic pH values, and at moderate and low ionic strengths, over the wavelength range 300–185 mμ. Increased resolution of spectra below 225 mμ has revealed heretofore unexamined ellipticity bands in the low wavelength region, which are sensitive to conformational alterations for those polynucleotides which exhibit both single and multistranded secondary structures. It is concluded that these ellipticity bands, in view of their extreme sensitivity to conformation, will be of significance in increasing the usefulness of the homopolynucleotides as model compounds in conformational studies of naturally occurring RNAs.

scholarly journals The interaction of aflatoxin B1 with polynucleotides and its effect on ribonucleic acid polymerase

1969 ◽  
Vol 114 (4) ◽  
pp. 679-687 ◽  
Author(s):  
A. M. Q. King ◽  
B. H. Nicholson
Keyword(s):  
Ionic Strength ◽  
Aflatoxin B1 ◽  
Polycytidylic Acid ◽  
Spectral Shifts ◽  
Bivalent Cations ◽  
Polyinosinic Acid ◽  
Polyadenylic Acid ◽  
Polyuridylic Acid ◽  
Calf Thymus

1. The interaction of aflatoxin B1 with different polynucleotides was studied spectrophotometrically. Equations were derived that enable the degree of binding to be determined without first determining the extinction coefficient of the bound form. 2. The interaction with calf thymus DNA obeys first-order relationships with an association constant of 0·40mm−1, but there is some evidence for a secondary binding process from results obtained at 390nm. 3. The spectral shifts decreased in the order polyadenylic acid+polyuridylic acid>DNA>polyadenylic acid>polyadenylic acid+polyinosinic acid. Polycytidylic acid, polyuridylic acid, polyinosinic acid (both single- and triple-stranded), AMP, CMP, GMP and UMP did not interact with aflatoxin. It was concluded that there is a requirement for the amino group of adenine (or possibly guanine) for binding of aflatoxin to polynucleotides to occur. 4. Binding is reversed by increasing ionic strength, and by Mn2+ and Mg2+ in the concentration range studied (0–5mm). The effect of the Mn2+ or Mg2+ was far greater than would be expected on the basis of their ionic strength. With both the bivalent cations and sodium chloride the reversal is greatest with double-stranded polynucleotides. 5. Inhibition in vitro of the DNA-dependent RNA polymerase of Escherichia coli by aflatoxin B1 was detected only in the absence of Mg2+ and at concentrations of Mn2+ below the optimum for RNA synthesis in vitro. 6. The degree of inhibition (maximally 30%) was dependent on the concentration of Mn2+ and decreased during incubation.

Structural studies on monofluorinated derivatives of the phytohormone indole-3-acetic acid (auxin)

1996 ◽  
Vol 52 (4) ◽  
pp. 651-661 ◽  
Author(s):  
A. Antolić ◽  
B. Kojić-Prodić ◽  
S. Tomić ◽  
B. Nigović ◽  
V. Magnus ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Side Chain ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Molecular Conformations ◽  
X Ray ◽  
Structure Activity ◽  
Planar Conformation ◽  
Derivatives Of ◽  
Indole 3 Acetic Acid

As part of the molecular recognition studies on the phytohormone indole-3-acetic acid (IAA) a series of fluorinated IAA's has been examined. The phenyl ring substitution at positions 4, 5, 6 and 7 resulted in four compounds, which were analyzed. Structure–activity correlation includes the analysis of their molecular conformations, based on the X-ray diffraction and computational chemistry results, and bioactivity determinations in the Avena coleoptile and the Pisum sativum stem straight-growth tests, lipophilicity and UV absorbance. The conformations of monofluorinated IAA's and a free hormone are defined by rotations about two bonds: one describes the relative orientation of a side chain towards the indole plane and the second the orientation of the carboxylic group. The results of X-ray structure analysis revealed the folded shape of the molecules in all compounds studied. Molecular mechanics and dynamics located the folded conformation as the local minimum, but failed to detect the planar conformation as one of the local minima, which according to ab initio results on IAA and 4-CI-IAA could also be possible. Crystal data at 295 K for 4-F-IAA and at 297 K for 5-F-IAA, and at 100 K for 6-F-IAA and 7-F-IAA using Mo Kα radiation (λ = 0.71073 Å) and Cu Kα (λ = 1.5418 Å, for 7-F-IAA), are as follows: 4-F-IAA, C10H8NO2F, Mr = 193.18, monoclinic, C2/c, a = 17.294 (5), b = 13.875 (4), c = 7.442 (4) Å, β = 103.88 (6)°, V = 1734 (1) Å3, Z = 8, Dx = 1.480 g cm−3, μ = 1.1 cm−1, F(000) = 800, R = 0.043, wR = 0.044 for 823 symmetry-independent [I ≥ 3σ(I)] reflections; 5-F-IAA, C10H8NO2F, monoclinic, P21/c, a = 19.284 (5), b = 5.083 (4), c = 9.939 (4) Å, β = 117.28 (6)°, V = 865.9 (1) Å3, Z = 4, Dx = 1.482 g cm−3, μ = 1.1  cm−1, F(000) = 400, R = 0.062, wR = 0.057 for 729 symmetry-independent [I ≥ 3σ(I)] reflections; 6-F-IAA, C10H8NO2F, monoclinic, P21/a, a = 9.360 (1), b = 5.167 (4), c = 17.751 (4) Å, β = 93.75 (1)°, V = 856.7 (8) Å3, Z = 4, Dx = 1.498 g cm−3, μ = 1.1 cm−1, F(000) = 400, R = 0.048, wR = 0.048 for 1032 symmetry-independent [I ≥ 2σ(I)] reflections; 7-F-IAA, C10H8NO2F, monoclinic, P21/a, a = 9.935 (5), b = 5.0059 (4), c = 17.610 (1) Å, β = 102.13 (1)°, V = 856.3 (1) Å3, Z = 4, Dx = 1.498 g cm−3, μ = 9.8 cm−1 (Cu Kα, F(000) = 400, R = 0.035, wR = 0.040 for 1504 symmetry-independent [I ≥ 2σ(I)] reflections.

Synthesis and crystallographic, spectroscopic and computational characterization of 3,3′,4,4′-substituted biphenyls: effects of OR substituents on the intra-ring torsion angle

2020 ◽  
Vol 76 (3) ◽  
pp. 366-377
Author(s):  
Nahir Vadra ◽  
Sebastian A. Suarez ◽  
Leonardo D. Slep ◽  
Veronica E. Manzano ◽  
Emilia B. Halac ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Torsion Angle ◽  
Liquid State ◽  
Molecular Conformation ◽  
X Ray Diffraction ◽  
Aromatic Rings ◽  
Molecular Conformations ◽  
X Ray ◽  
Selection Of

Presented here are the synthesis, characterization and study (using single crystal X-ray diffraction, Raman scattering, quantum mechanics calculations) of the structures of a series of biphenyls substituted in positions 3, 3′, 4 and 4′ with a variety of R (R = methyl, acetyl, hexyl) groups connected to the biphenyl core through oxygen atoms. The molecular conformation, particularly the torsion angle between aromatic rings has been extensively studied both in the solid as well as in the liquid state. The results show that the compounds appearing as rigorously planar in the solid present instead a twisted conformation in the melt. The solid versus melt issue strongly suggests that the reasons for planarity are to be found in the packing restraints. A `rule of thumb' is suggested for the design of biphenyls with different molecular conformations, based on the selection of the OR substituent.

Intermolecular interaction energies and molecular conformations in N-substituted 4-aryl-2-methylimidazoles with promising in vitro antifungal activity

2019 ◽  
Vol 75 (6) ◽  
pp. 1197-1207 ◽  
Author(s):  
Nerith-Rocio Elejalde ◽  
Estefanía Butassi ◽  
Susana Zacchino ◽  
Mario A. Macías ◽  
Jaime Portilla
Keyword(s):  
Antifungal Activity ◽  
High Resolution Mass Spectrometry ◽  
X Ray Diffraction ◽  
One Pot ◽  
Molecular Conformations ◽  
X Ray ◽  
The Difference ◽  
Molecule Interactions ◽  
In Vitro Antifungal Activity

A convenient one-pot synthesis of 4-aryl-2-methyl-N-phenacylimidazoles (4) through a microwave-assisted pseudo-tricomponent reaction of α-bromoacetophenones (1) with acetamidine hydrochloride (2) is reported. Ketones (4) were successfully used as substrates for the preparation of the respective N-(2-hydroxyethyl)imidazoles (5) with yields up to 87%. The synthesized compounds were characterized by NMR and high-resolution mass spectrometry analyses, and several structures were confirmed and studied by single-crystal X-ray diffraction. The analysis of the whole-of-molecule interactions shows that, despite the difference in the atom–atom contacts forming the crystals, dispersion energies make the largest contribution to the formation of the solids, giving an isotropic tendency in the topology of the energy framework diagrams for pairs of molecules. In addition, the in vitro antifungal activity of both families of compounds [ketones (4) and alcohols (5)] against Candida albicans and Cryptococcus neoformans was evaluated, where the 2,4-dichlorophenyl-substituted alcohol (5f), an isomer of the drug miconazole, showed the highest activity (IC50 = 7.8 µg ml−1 against C. neoformans).

A solid state NMR and X-ray crystallographic investigation of dynamic disorder in solid tetrahydronaphthalene derivatives

1996 ◽  
Vol 74 (10) ◽  
pp. 1844-1851 ◽  
Author(s):  
Glenn A. Facey ◽  
Terrence J. Connolly ◽  
Corinne Bensimon ◽  
Tony Durst
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
X Ray Diffraction ◽  
Molecular Conformations ◽  
Dynamic Disorder ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Deuterated Analog ◽  
Naphthoic Acid

The solid state disorder of two tetrahydronaphthalene derivatives, N-methyl-N-methoxy-5,6,7,8-tetrahydro-1-naphthamide and 5,6,7,8-tetrahydro-1-naphthoic acid, was studied by solid state NMR and single crystal X-ray diffraction. The X-ray crystal structure of N-methyl-N-methoxy-5,6,7,8-tetrahydro-1-naphthamide was obtained at 123 K. It indicated the presence of two distinct molecular conformations. Solid state 13C CP/MAS NMR data using the dipolar dephasing technique revealed that the two conformations of the molecule are dynamically disordered, while solid state 2H NMR data, collected on a specifically deuterated analog, were used to determine the populations of each conformation as well as an apparent activation energy. Solid state NMR experiments were also used to show that 5,6,7,8-tetrahydro-1-naphthoic acid possesses the same type of dynamic disorder. Key words: deuterium NMR, solid state NMR, dynamic disorder. X-ray, tetrahydronaphthalene derivatives

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