Structural Elucidation of Bisulfite Adducts to Pseudouridine That Result in Deletion Signatures during Reverse Transcription of RNA.

The recent report of RBS-Seq to map simultaneously the epitranscriptomic modifications -methyladenosine, 5-methylcytosine, and pseudouridine () via bisulfite treatment of RNA provides a key advance to locate these important modifications. The locations of were found by a deletion signature generated during cDNA synthesis after bisulfite treatment for which the chemical details of the reaction are poorly understood. In the present work, the bisulfite reaction with was explored to identify six isomers of bisulfite adducted to .

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations.

UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes.

The excited-state dynamics of two cyclic DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrared spectroscopy. As in longer DNA duplexes, intrastrand electron transfer induced by UV excitation triggers interstrand proton transfer in the alternating miniduplex containing two out-of-phase G·C base pairs. The resulting excited state decays on a time scale of several tens of picoseconds.

pH-Dependent Equilibrium between 5-Guanidinohydantoin and Iminoallantoin Affects Nucleotide Insertion Opposite the DNA Lesion.

Four-electron oxidation of 2'-deoxyguanosine (dG) yields 5-guanidinohydantoin (dGh) as a product. Previously, we hypothesized that dGh could isomerize to iminoallantoin (dIa) via a mechanism similar to the isomerization of allantoin. The isomerization reaction was monitored by HPLC and found to be pH dependent with a transition pH = 10.

Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin.

Oxidation of the guanine heterocycle by two electrons can yield the chiral product 5-carboxamido-5-formamido-2-iminohydantoin (). The free base enantiomers were synthesized from 2'-deoxyguanosine oxidized with a Cu(II)/HO oxidant system followed by hydrolysis of the -glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations.

Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine.

Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin.

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph.

Solid-state 13C NMR investigations of 4,7-dihydro-1H-tricyclopenta[def,jkl,pqr]triphenylene (sumanene) and indeno[1,2,3-cd]fluoranthene: Buckminsterfullerene moieties.

4,7-Dihydro-1H-tricyclopenta[def,jkl,pqr]triphenylene (sumanene) and indeno[1,2,3-cd]fluoranthene (indenofluoranthene) are structural moieties related to Buckminsterfullerene (C(60)). As such, understanding their structural characteristics is of great interest because of the insight they shed upon C(60). Hence, solid-state NMR (ssNMR) and ab initio quantum mechanical calculations with Gaussian03 are used in order to understand and to better characterize the molecular conformation and properties of sumanene and indenofluoranthene.

7Li NMR chemical shift titration and theoretical DFT calculation studies: solvent and anion effects on second-order complexation of 12-crown-4 and 1-aza-12-crown-4 with lithium cation in several aprotic solvents.

(7)Li NMR titration was used to determine stepwise complexation constants for the second-order complexation of lithium cation with 12-crown-4 in acetonitrile, propylene carbonate and a binary mixture of propylene carbonate and dimethyl carbonate. The anions used were perchlorate, hexaflurophosphate and trifluromethanesulfonate. A second ligand 1-aza-12-crown-4 was similarly investigated.

Self-assembly of a triangle-shaped, hexaplatinum-incorporated, supramolecular amphiphile in solution and at interfaces.

The self-assembly and characterization of a novel supramolecular amphiphile built from a new 60 degree amphiphilic precursor that incorporates hydrophilic platinum(II) metals and hydrophobic dioctadecyloxy chains is reported. The amphiphilic macrocycle and its precursor compound have been characterized by multinuclear NMR spectroscopy, ESI-MS, and other standard techniques. The coacervate morphology of the amphiphile at the liquid-liquid interface has been studied by using confocal optical microscopy and in situ Raman spectroscopy.

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.

Giant micelles of organoplatinum(II) gemini amphiphiles.

Organoplatinum(II) gemini amphiphiles with two different chain lengths are synthesized and characterized. Self-assembly at the air-water interface is investigated as a function of chain length and reduction in surface area by using Langmuir-trough techniques. The Langmuir-trough experiments lead to a conjecture that surface aggregates may be the adsorbing units.

Ring current effects in crystals. Evidence from 13C chemical shift tensors for intermolecular shielding in 4,7-di-t-butylacenaphthene versus 4,7-di-t-butylacenaphthylene.

13C chemical shift tensor data from 2D FIREMAT spectra are reported for 4,7-di-t-butylacenaphthene and 4,7-di-t-butylacenaphthylene. In addition, calculations of the chemical shielding tensors were completed at the B3LYP/6-311G** level of theory. While the experimental tensor data on 4,7-di-t-butylacenaphthylene are in agreement with theory and with previous data on polycyclic aromatic hydrocarbons, the experimental and theoretical data on 4,7-di-t-butylacenaphthene lack agreement.

The role of asynchronous bond formation in the diastereoselective epoxidation of cyclic enol ethers: a density functional theory study.

Density functional theory (DFT) (Becke3LYP functional and the D95 basis set) was used to study the influence of substitution on the dimethyldioxirane epoxidation reaction of six- and seven-membered cyclic enol ethers. In agreement with our previously reported experimental results, the calculations predict that substitution on the cyclic enol ether influences the level of diastereoselectivity. Apparent only from the calculations is that the degree of synchronicity in the transition state is important in the diastereoselectivity.

CB11Me11 boronium ylides: carba-closo-dodecaboranes with a naked boron vertex.

In pentane solution, 2 equiv of the icosahedral CB(11)Me(12)(*) radical cleaves the Si-Si bond of hexaalkyldisilanes by boron to silicon methyl transfer with formation of 2 equiv of methyltrialkylsilanes. The loss of a methyl radical converts the CB(11)Me(12)(*) radical into an internally charge-compensated "boronium ylide" CB(11)Me(11) with a naked vertex, which can be formally viewed as a deprotonated hypercloso carborane. It has been isolated as an air-sensitive solid, stable only below approximately -60 degrees C.

Tedanolide C: a potent new 18-membered-ring cytotoxic macrolide isolated from the Papua New Guinea marine sponge Ircinia sp.

Cytotoxicity-guided fractionation of the crude methanol extract of a marine sponge, Ircinia sp., yielded tedanolide C (1), a new 18-membered macrolide. The structure was solved by interpreting NMR and MS data, and the relative stereochemistry was determined from a combination of homo- and heteronuclear coupling constants in conjunction with molecular modeling.

Revisiting the calculation of (13)C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods.

The chemical shift tensors of the acetate anions in cadmium acetate dihydrate are calculated using a cluster approach, the embedded ion method (EIM), and a combination of the two in the EIM/cluster method. The results of these calculations are compared with those completed on the isolated acetate anion and show the need for the inclusion of intermolecular interactions. The RMS difference between experiment and theory improves from over 60 ppm when the calculation is completed on an isolated anion, to below 10 ppm when interactions to nearby atoms are included.

Metal cation-methyl interactions in CB11Me12(-) salts of Me3Ge+, Me3Sn+, and Me3Pb+.

Oxidation of Me(6)M(2) (M = Ge, Sn) and Me(4)Pb with the CB(11)Me(12)(*) radical in alkane solvents produced the insoluble salts Me(3)M(+)CB(11)Me(12)(-), characterized by CP-MAS NMR and EXAFS. The cations interact with methyl groups of CB(11)Me(12)(-) with coordination strength increasing from Pb to Ge. Density functional theory (DFT) calculations for the isolated ion pairs, Me(3)M(+)CB(11)Me(12)(-) (M = Ge, Sn), revealed three isomers with the cation above methyl 2, 7, or 12, and not above a BB edge or a BBB triangle.

Modeling solid-state effects on NMR chemical shifts using electrostatic models.

This paper presents a comparison of the embedded ion method (EIM) and the surface charge representation of the electrostatic embedding potential (SCREEP) method, two methods which can be used to calculate solid-state effects on NMR chemical shifts. The results in a selected group of compounds with known single-crystal solid-state NMR data and neutron diffraction structures, confirm that these effects are important in both (13)C and (15)N chemical shifts. The solid-state effects calculated by both methods are similar and of equal statistical quality when compared with the experimental data.

13C NMR chemical shifts of the triclinic and monoclinic crystal forms of valinomycin.

Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state (13)C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment.

Carbonates, thiocarbonates, and the corresponding monoalkyl derivatives: III. The 13C chemical shift tensors in potassium carbonate, bicarbonate and related monomethyl derivatives.

The principal values of the 13C chemical shift tensors in potassium carbonate (K2CO3), trithiocarbonate (K2CS3), bicarbonate (KHCO3), methylcarbonate (KO2COCH3), S-methyl-monothiocarbonate (KO2CSCH3), O-methyl-monothiocarbonate (KOSCOCH3), S-methyl-dithiocarbonate (KOSCSCH3), and O-methyl-dithiocarbonate (KS2COCH3), were measured in solid-state nuclear magnetic resonance experiments. Chemical shift tensor calculations on the corresponding isolated anions were used to assign the chemical shift tensor orientations in the molecular frames of all anions. The correlation between experimental and calculated principal values improves significantly when the calculations are performed on isolated anions with proton-optimized X-ray geometries rather than on isolated anions with fully optimized geometries.