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 N1-methyladenosine, 5-methylcytosine, and pseudouridine (Ψ) via bisulfite treatment of RNA provides a key advance to locate these important modifications. The locations of Ψ 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 Ψ was explored to identify six isomers of bisulfite adducted to Ψ. We found four of these adducts involved the heterocyclic ring, similar to the reaction with other pyrimidines. The remaining two adducts were bonded to the 1' carbon, which resulted in opening of the ribose ring. The utilization of complementary 1D- and 2D-NMR, Raman, and electronic circular dichroism spectroscopies led to the assignment of the two ribose adducts being the constitutional isomers of an S- and an O-adduct of bisulfite to the ribose, and these are the final products after heating. A mechanistic proposal is provided to rationalize chemically the formation and stereochemistries of all six isomeric bisulfite adducts to Ψ; conversion of intermediate adducts to the two final products is proposed to involve E2, SN2', and [2,3]-sigmatropic shift reactions. Lastly, a synthetic RNA template with Ψ at a known location was treated with bisulfite, leading to a deletion signature after reverse transcription, supporting the RBS-Seq report. This classical bisulfite reaction used for epigenomic and epitranscriptomic sequencing diverges from the C nucleoside Ψ to form stable bisulfite end products that yield signatures for next-generation sequencing.

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. This state is absent when one of the two G residues is substituted by 8-oxo-7,8-dihydroguanine, a modification that is suggested to disrupt base stacking, while maintaining base pairing. These findings demonstrate that a nucleobase tetramer arranged as two stacked base pairs accurately captures the interplay between intrastrand and interstrand decay channels. The similar signals seen in the miniduplexes and longer sequences suggest that excited states in the latter rapidly localize on two adjacent base pairs.

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 = 10.1 in which dGh was favored at low pH and dIa was favored at high pH. The structures for these isomers were confirmed by UV-vis, MS, and (1)H and (13)C NMR. Additionally, the UV-vis and NMR experimental results are supported by density functional theory calculations. A mechanism is proposed to support the pH dependency of the isomerization reaction. Next, we noted the hydantoin ring of dGh mimics thymine, while the iminohydantoin ring of dIa mimics cytosine; consequently, a dGh/dIa site was synthesized in a DNA template strand, and standing start primer extension studies were conducted with Klenow fragment exo(-). The dATP/dGTP insertion ratio opposite the dGh/dIa site as a function of pH was evaluated from pH 6.5-9.0. At pH 6.5, only dATP was inserted, but as the pH increased to 9.0, the amount of dGTP insertion steadily increased. This observation supports dGh to dIa isomerization in DNA with a transition pH of ∼8.2.

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.

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 (2Ih). The 2Ih free base enantiomers were synthesized from 2'-deoxyguanosine oxidized with a Cu(II)/H2O2 oxidant system followed by hydrolysis of the N-glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations. Time-dependent density functional theory calculations of the expected spectra were completed in both the gas phase and with solvent modeling in order to interpret the experimental spectra and provide the absolute configuration assignments.

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. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

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. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

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. Sumanene has bowl shaped curvature in its natural conformation and indenofluoranthene is planar in its natural conformation, which led us to examine how altering the curvature affects the chemical shifts in relation to those of C(60). Using X-ray structures of both sumanene and indenofluoranthene as our starting model, we calculate the energy and chemical shielding tensors and compare these data with those collected utilizing the (13)C ssNMR FIREMAT experiment. We define curvature of sumanene and indenofluoranthene using the pi-orbital axis vector (POAV) pyramidalization angle (theta(p)). We calculate the energy of varying conformations of indenofluoranthene versus their theta(p) associated with each deformed conformation.

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. The exchange between the free and complexed cation in these reactions is fast on an NMR timescale resulting in a single lithium peak which is a concentration-weighted average of the free and bound species. Solvent effects show that the 1:1 complex is much more stable in acetonitrile than in propylene carbonate or in the propylene carbonate dimethyl carbonate mixture. Anion effects for a given solvent were small. Optimized geometries of the free ligands and the 1:1 and 1:2 (sandwich) metal-ligand complexes were predicted by hybrid-density functional theory using the Gaussian 03 software package. Results were compared to literature values for 1:1 stability constants found by microcalorimetry for several of these systems and are found to be in good agreement. Although microcalorimetry only considered the formation of 1:1 complexes, (7)Li NMR shows evidence that both 1:1 and 1:2 complexes should be considered.

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.

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. The self-assembly of the amphiphilic macrocycle at the air-water interface has been investigated through Langmuir-trough techniques. The study indicates the possible formation of surface micelle-like aggregates. The disparity between the experimental molecular areas and those derived from molecular models support the idea of aggregation. AFM images of the surface aggregates show the formation of a flat topology with arbitrary ridgelike patterns. Reasonable molecular-packing arrangements are proposed to explain the molecular organization within the observed structures.

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. Atomic force microscopy on the transferred Langmuir-Schaefer films reveals spontaneous formation of wormlike micellar aggregates. A shear-induced transition and alignment are proposed for the observed effects.

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. Instead, larger than usual differences are observed between the experimental chemical shift components and the chemical shielding tensor components calculated on a single molecule of 4,7-di-t-butylacenaphthene, with a root mean square (rms) error of +/-7.0 ppm. The greatest deviation is concentrated in the component perpendicular to the aromatic plane, with the largest value being a 23 ppm difference between experiment and theory for the 13CH2 carbon delta11 component. These differences are attributed to an intermolecular chemical shift that arises from the graphitelike, stacked arrangement of molecules found in the crystal structure of 4,7-di-t-butylacenaphthene. This conclusion is supported by a calculation on a trimer of molecules, which improves the agreement between experiment and theory for this component by 14 ppm and reduces the overall rms error between experiment and theory to 4.0 ppm. This intermolecular effect may be modeled with the use of nuclei independent chemical shieldings (NICS) calculations and is also observed in the isotropic 1H chemical shift of the CH2 protons as a 4.2 ppm difference between the solution value and the solid-state chemical shift measured via a 13C-1H heteronuclear correlation experiment.

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. The best cluster model includes three cadmium acetate dihydrate and gives an RMS result of 4.4 ppm. The EIM method, which uses point charges to account for the intermolecular effects, achieves an RMS of 7.7 ppm on individual anions alone. A combination of the two, the EIM/cluster method, shows that the only necessary atom to explicitly add is the nearest cadmium; this addition results in an RMS of 4.1 ppm. These results are also discussed in terms of the computational cost of the different calculations.

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.

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. Compound 1 exhibited potent cytotoxicity against HCT-116 cells in vitro. Cell cycle analysis showed that treatment of cells with compound 1 arrested cells in the S-phase.

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. The naked vertex appears to be in position 12 since the material reacts instantaneously with alcohols and ethers to form the 12-alkoxy anions 12-CB(11)Me(11)OR. It reacts with many other nucleophiles to yield more complex mixtures containing similar products. DFT calculations for the four CB(11)Me(11) isomers give closed-shell ground-state electronic structures. For the isomer with naked vertex 12, a DFT computational search failed to reveal any skeletal dimers, apparently due to excessive methyl-methyl repulsions, and only a cyclic dimer bound through weak interactions of one of the 7-methyl hydrogen atoms on each cage with the empty exocyclic orbitals on B12 of the other cage was found. Natural hybrid orbital populations suggest that the three possible isomers of monomeric boronium ylides are close to true singlet ylides, with triplet states approximately 50 kcal/mol higher. The calculated electronic structure of the carbonium ylide is close to a singlet carbene, with a triplet state approximately 16 kcal/mol higher. An attempted preparation of Me(3)C(+)CB(11)Me(12)(-) yielded neopentane and products consistent with a sequential loss of methyl groups from the carborane cage with a transient formation of similar boronium ylides. Probable mechanisms of these methyl transfer reactions are considered, and the possibly quite general role of "ylide" structures in Lewis acid induced substitution reactions on the boron vertices of carboranes and boranes is noted.

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. From the measured components, it was found that the behavior of the isotropic chemical shift, delta(iso), for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, delta(22). Additionally it was found that the smallest shift component, delta(33), for the L -lactic acid ( L -Lac) and D -alpha-hydroxyisovaleric acid ( D -Hyi) C(alpha)-O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the delta(33) component that governs the behavior of delta(iso) in these alpha carbons.

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. Further considerable improvement in the correlation is achieved by utilizing the embedded ion method, which was recently developed to include electrostatic crystal potentials in chemical shift tensor calculations on ionic compounds. Similarities and differences in the chemical shift tensor orientations and principal values of the trigonal sp2 carbon atoms in the carbonate and thiocarbonate anions are compared with those known for condensed polyaromatic hydrocarbons.