Catalytic enantioselective [3 + 2]-cycloadditions of diazoketone-derived aryl-substituted carbonyl ylides

An evaluation of alpha-aryl-alpha-diazodiones in tandem carbonyl ylide formation-enantioselective [3 + 2]-cycloaddition reactions is described. Such substrates were designed to allow investigation of the electronic characteristics of the dipole upon asymmetric induction. Intramolecular cycloadditions (with a tethered alkene dipolarophile) were found to occur in good to quantitative yields, with a difference in ee exhibited by the two electronically different diazodiones 8 and 9. Intermolecular cycloadditions using diazodiones 12 and 13 with DMAD and arylacetylenes 16-18 again demonstrated that electronics play a key role in determining the outcome of the cycloaddition reactions. Enantioselectivities of up to 76% were observed.     

Vibrational projection analysis: New tool for quantitatively comparing vibrational normal modes of similar molecules

A new method for quantitatively comparing calculated vibrational modes is described that relies on projecting the vectors describing the normal modes of one molecule onto those of a basis molecule. The procedure virtually automates the assignment of vibrational modes from one molecule to a second, structurally similar one. We illustrate the concept by using the classical Wilson modes of benzene as a basis for describing normal modes of the monosubstituted benzene derivatives phenol, phenol-d5, and phenol radical cation. These examples demonstrate the method's power for accurately assigning and comparing the normal modes of molecules perturbed by chemical substitution, isotopic substitution, or oxidation state. The vibrational projection analysis method—a special case of vector projection analysis—is compared and contrasted with total energy distribution analysis, perhaps the most commonly used technique for quantitatively comparing vibrational modes, and is found superior in each case when comparing normal modes. Vibrational projection analysis need not be limited to single molecules and quantum calculations, because normal modes may be obtained for much larger systems using molecular mechanics or molecular dynamics techniques. The method should therefore prove useful for interpreting the normal modes of ordered periodic solids and structures perturbed by noncovalent contacts, including proteins and polymers. The method may also prove useful in evaluating new computational methods by allowing direct, quantitative comparison of the vibrational modes obtained from different techniques. The power of this technique will make vibrational projection analysis a valuable tool for computational chemists as well as those using calculations to complement vibrational spectroscopic measurements. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1663–1674, 1998     

Comparison of CID,ETD and metastable atom‐activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision‐induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom‐activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b‐/y‐type ions with abundant neutral losses of the phosphorylation modification. ETD produced c‐/z‐type ions in highest abundance but also showed numerous y‐type ions at a frequency about 50% that of the z‐type ions. The major peaks observed in the ETD spectra correspond to the charge‐reduced product ions and small neutral losses from the charge‐reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15–20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD. Copyright © 2012 John Wiley & Sons, Ltd.     

Redox chemistry of tellurium bis(tert-butylamido)cyclodiphosph(V)azane disulfide and diselenide systems: a spectroscopic and structural study

The redox chemistry of tellurium-chalcogenide systems is examined via reactions of tellurium(IV) tetrachloride with Li[(t)()BuN(E)P(mu-N(t)Bu)(2)P(E)N(H)(t)Bu] (3a, E = S; 3b, E = Se). Reaction of TeCl(4) with 2 equiv of 3a in THF generates the tellurium(IV) species TeCl(3)[HcddS(2)][H(2)cddS(2)] 4a [cddS(2) = (t)BuN(S)P(mu-N(t)Bu)(2)P(S)N(t)Bu] at short reaction times, while reduction to the tellurium(II) complex TeCl(2)[H(2)cddS(2)](2) 5a is observed at longer reaction times. The analogous reaction of TeCl(4) and 3b yields only the tellurium(II) complex TeCl(2)[H(2)cddSe(2)](2) 5b. The use of 4 equiv of 3a or 3b produces Te[HcddE(2)](2) (6a (E = S) or 6b (E = Se)). NMR and EPR studies of the 5:1 reaction of 3a and TeCl(4) in THF or C(6)D(6) indicate that the formation of the Te(II) complex 6a via decomposition of a Te(IV) precursor occurs via a radical process to generate H(2)cddS(2). Abstraction of hydrogen from THF solvent is proposed to account for the formation of 2a. These results are discussed in the context of known tellurium-sulfur and tellurium-nitrogen redox systems. The X-ray crystal structures of 4a.[C(7)H(8)](0.5), 5a, 5b, 6a.[C(6)H(14)](0.5), and 6b.[C(6)H(14)](0.5) have been determined. The cyclodiphosph(V)azane dichalcogenide ligand chelates the tellurium center in an E,N (E = S, Se) manner in 4a.[C(7)H(8)](0.5), 6a.[C(6)H(14)](0.5), and 6b.[C(6)H(14)](0.5) with long Te-N bond distances in each case. Further, a neutral H(2)cddS(2) ligand weakly coordinates the tellurium center in 4a small middle dot[C(7)H(8)](0.5) via a single chalcogen atom. A similar monodentate interaction of two neutral ligands with a TeCl(2) unit is observed in the case of 5a and 5b, giving a trans square planar arrangement at tellurium.     

Simultaneous detection of cadmium, copper, and lead using a carbon paste electrode modified with carbamoylphosphonic acid self-assembled monolayer on mesoporous silica (SAMMS)

A new sensor was developed for simultaneous detection of cadmium (Cd²⁺), copper (Cu²⁺), and lead (Pb²⁺), based on the voltammetric response at a carbon paste electrode modified with carbamoylphosphonic acid (acetamide phosphonic acid) self-assembled monolayer (SAM) on mesoporous silica (Ac-Phos SAMMS). The adsorptive stripping voltammetry (AdSV) technique involves preconcentration of the metal ions onto Ac-Phos SAMMS under an open circuit, then electrolysis of the preconcentrated species, followed by a square wave potential sweep towards positive values. Factors affecting the preconcentration process were investigated. The voltammetric responses increased linearly with the preconcentration time from 1 to 30 min or with metal ion concentrations ranging from 10 to 200 ppb. The responses also evolved in the same fashion as adsorption isotherm in the pH range of 2-6. The metal detection limits were 10 ppb after 2 min preconcentration and improved to 0.5 ppb after 20 min preconcentration.     

Characterizing bitterness: identification of key structural features and development of a classification model

This work describes the first approach in the development of a comprehensive classification method for bitterness of small molecules. The data set comprises 649 bitter and 13 530 randomly selected molecules from the MDL Drug Data Repository (MDDR) which are analyzed by circular fingerprints (MOLPRINT 2D) and information-gain feature selection. The feature selection proposes substructural features which are statistically correlated to bitterness. Classification is performed on the selected features via a na?ve Bayes classifier. The substructural features upon which the classification is based are able to discriminate between bitter and random compounds, and thus we propose they are also functionally responsible for causing the bitter taste. Such substructures include various sugar moieties as well as highly branched carbon scaffolds. Cynaropicrine contains a number of the substructural features found to be statistically associated with bitterness and thus was correctly predicted to be bitter by our model. Alternatively, both promethazine and saccharin contain fewer of these substructural features, and thus the bitterness in these compounds was not identified. Two different classes of bitter compounds were identified, namely those which are larger and contain mainly oxygen and carbon and often sugar moieties, and those which are rather smaller and contain additional nitrogen and/or sulfur fragments. The classifier is able to predict 72.1% of the bitter compounds. Feature selection reduces the number of false-positives while also increasing the number of false negatives to 69.5% of bitter compounds correctly predicted. Overall, the method presented here presents both one of the largest databases of bitter compounds presently available as well as a relatively reliable classification method.     

EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods

Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.     

Excited-state structural dynamics of 5-fluorouracil

5-Fluorouracil is an analogue of thymine and uracil, nucleobases found in DNA and RNA, respectively. The photochemistry of thymine is significant; UV-induced photoproducts of thymine in DNA lead to skin cancer and other diseases. In previous work, we have suggested that the differences in the excited-state structural dynamics of thymine and uracil arise from the methyl group in thymine acting as a mass barrier, localizing the vibrations at the photochemical active site. To further test this hypothesis, we have measured the resonance Raman spectra of 5-fluorouracil at wavelengths throughout its 267 nm absorption band. The spectra of 5-fluorouracil and thymine are very similar. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism suggests that, at most, 81% of the reorganization energy upon excitation is directed along photochemically relevant modes. This compares well with what was found for thymine, supporting the mass barrier hypothesis.     

Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Proton ionizable crown compounds. 18. Comparison of alkali metal transport in a H2O-CH2Cl2-H2O liquid membrane system by four proton-ionizable macrocycles containing the dialkylhydrogenphosphate moiety

The macrocycle-mediated fluxes of alkali, alkaline earth, and several transition metal cations have been determined and compared in a H₂O-CH₂Cl₂-H₂O liquid membrane system using four water-insoluble macrocycles containing a dialkylhydrogenphosphate moiety. Transport of alkali metal cations by these ligands was greatest from a source phase pH = 12 or above into an acid receiving phase (pH = 1.5). Very low fluxes were observed for the transport of the alkaline earth cations and all transition metal ions studied except Ag⁺ and Pb²⁺ which were transported reasonably well by these new macrocycles.Deceased: September 5, 1987.