5α-Androst-3-en-17β-yl acetate

In the crystal structure of the title compound, C21H32O2, ring A is highly distorted, with a conformation inter­mediate between 10β-sofa and 1α,10β-half chair; rings B and C have slightly flattened chair conformations. Ring D assumes an unusual 13β-envelope conformation, probably induced by the acet­oxy substituent. Cohesion of the crystal structure is due only to weak van der Waals inter­actions

Androstane-3β,5α,6β,17β-tetrol tri­hydrate

The title hydrated tetrol, C19H32O4·3H2O, was synthesized by stereoselective reduction of the compound 3β,5α,6β-trihy­droxy­androstan-17-one. All rings are fused trans. The organic mol­ecules are connected head-to-tail along the c axis via O—H⋯O hydrogen bonds. Layers of water mol­ecules in the ab plane inter­connect these chains. A quantum chemical ab initio Roothan Hartree–Fock calculation of the isolated mol­ecule gives values for the mol­ecular geometry close to experimentally determined ones, apart from the C—O bond lengths, whose calculated values are significantly smaller than the measured ones, probably a consequence of the involvement of the C—OH groups in the hydrogen-bonding network

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

A reparameterization of the torsional parameters for the glycosidic dihedral angle, χ, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99χ. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99χ force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99χ force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) 1H, steady-state 1D 1H nuclear Overhauser effect (NOE), and transient 1D 1H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2′-endo sugar puckering of the pyrimidines, while the AMBER99χ force field’s predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310° for the base orientation of purines. The AMBER99χ force field prefers anti conformations around 185°, which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99χ force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures