Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods.

Autoxidation of drugs and drug-like molecules is a major concern in the development of safe and effective therapeutics. Because active pharmaceutical ingredients (APIs) that contain sulfur atoms can form sulfoxides under oxidative stress, predicting oxidative susceptibilities within an organic molecule can have a major impact in accelerating the compound's stability assessment. For investigation of a sulfur atom's oxidative stability, density functional theory (DFT) methods were applied to accurately predict S-O estimated bond dissociation enthalpies (BDEs) of sulfoxides.

Practical Synthesis of Terminal Vinyl Fluorides.

The synthesis of di- and trisubstituted vinyl fluorides with high isomeric purity remains a challenge for organic synthesis. While many methods exist to access these compounds, the separation of the desired isomer from the minor isomer and/or starting materials often is difficult. Herein, we report a practical method to access di- and trisubstituted vinyl fluorides via a selective Horner-Wadsworth-Emmons olefination/hydrolysis, which provides crystalline 2-fluoroacrylic acids in high (>98%) -isomeric purity.

N-oxidation Regioselectivity and Risk Prediction Using DFT-ALIE Calculations.

Introduction: The formation of N-oxide degradants is a major concern in development of new drugs due to potential effects on a compound's pharmacological activity. Such effects include but are not limited to solubility, stability, toxicity, and efficacy. In addition, these chemical transformations can impact physicochemical properties that affect drug manufacturability.

Deconvolution of fast exchange equilibrium states in NMR spectroscopy using virtual reference standards and probability theory.

A methodology for deconvolution of fast exchange equilibrium states in NMR spectroscopy (DFEQNMR) was developed based on DFT-GIAO NMR chemical shift prediction and a probability theory algorithm. Proof-of-concept studies were performed to estimate the protonation state of N-containing organic molecules involving fast proton exchange equilibrium and evaluate the solution tautomerism of a purine derivative. DFT-GIAO calculations were optimized to achieve good accuracy in C, H and N chemical shift prediction for protonated species.

D iCE: Diastereomeric in Silico Chiral Elucidation, Expanded DP4 Probability Theory Method for Diastereomer and Structural Assignment.

NMR chemical shift prediction at the B3LYP/cc-pVDZ level of theory was used to develop a highly accurate probability theory algorithm for the determination of the stereochemistry of diastereomers as well as the regiochemistry. DFT-GIAO calculations were performed for each conformer using geometry optimization and a CPCM solvent model. Boltzmann averaged shielding constants were converted to chemical shifts for H and C, using the generalized linear scaling terms determined in four different solvents for H and C and extended to N in DMSO.

Rhodium-Catalyzed Addition of Aryl Boronic Acids to 2,2-Disubstituted Malononitriles.

β-Ketonitriles bearing a quaternary carbon at the 2-position were prepared through Rh-catalyzed addition of aryl boronic acids to 2,2-disubstituted malononitriles. In contrast to the previously described transnitrilative cyanation of aryl boronic acids with dialkylmalononitriles, the present reaction avoids retro-Thorpe collapse of the intermediate addition product through the use of a milder base. The reaction was amenable to a variety of aryl boronic acids and disubstituted malononitriles, providing a diverse array of β-ketonitriles.

Development of a C NMR Chemical Shift Prediction Procedure Using B3LYP/cc-pVDZ and Empirically Derived Systematic Error Correction Terms: A Computational Small Molecule Structure Elucidation Method.

An accurate and efficient procedure was developed for performing C NMR chemical shift calculations employing density functional theory with the gauge invariant atomic orbitals (DFT-GIAO). Benchmarking analysis was carried out, incorporating several density functionals and basis sets commonly used for prediction of C NMR chemical shifts, from which the B3LYP/cc-pVDZ level of theory was found to provide accurate results at low computational cost. Statistical analyses from a large data set of C NMR chemical shifts in DMSO are presented with TMS as the calculated reference and with empirical scaling parameters obtained from a linear regression analysis.

Systematic investigation of DFT-GIAO N NMR chemical shift prediction using B3LYP/cc-pVDZ: application to studies of regioisomers, tautomers, protonation states and N-oxides.

The calculation of N NMR chemical shifts has been systematically investigated using density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/cc-pVDZ level of theory. General linear regression terms for N chemical shift predictions were calculated for nitromethane and liquid ammonia references in DMSO. Both aliphatic and aromatic nitrogens were studied using a diverse set of molecular scaffolds.

Diastereoselective Synthesis of α-Quaternary Aziridine-2-carboxylates via Aza-Corey-Chaykovsky Aziridination of N-tert-Butanesulfinyl Ketimino Esters.

A general, scalable, and highly diastereoselective aziridination of N-tert-butanesulfinyl ketimino esters is described. The methodology has been utilized to provide straightforward access to previously unobtainable, biologically relevant α-quaternary amino esters and derivatives starting from readily available precursors.

Three-dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model.

The three-dimensional solution conformation of teicoplanin aglycone was determined using NMR spectroscopy. A combination of NOE and dihedral angle restraints in a DMSO solvation model was used to calculate an ensemble of structures having a root mean square deviation of 0.17 Å.

A mild dihydrobenzooxaphosphole oxazoline/iridium catalytic system for asymmetric hydrogenation of unfunctionalized dialins.

Air-stable P-chiral dihydrobenzooxaphosphole oxazoline ligands were designed and synthesized. When they were used in the iridium-catalyzed asymmetric hydrogenation of unfunctionalized 1-aryl-3,4-dihydronaphthalenes under one atmosphere pressure of H2 , up to 99:1 e.r.

Facile entry to an efficient and practical enantioselective synthesis of a polycyclic cholesteryl ester transfer protein inhibitor.

An efficient enantioselective synthesis of the chiral polycyclic cholesteryl ester transfer protein (CETP) inhibitor 1 has been developed. The synthesis was rendered practical for large scale via the development of a modified Hantzsch-type reaction to prepare the sterically hindered pyridine ring, enantioselective hydrogenation of hindered ketone 6 utilizing novel BIBOP-amino-pyridine derived Ru complex, efficient ICl promoted lactone formation, and a BF3 mediated hydrogenation process for diastereoselective lactol reduction. This efficient route was successfully scaled to produce multikilogram quantities of challenging CETP drug candidate 1.

Automated Solid Phase Extraction (SPE) LC/NMR Applied to the Structural Analysis of Extractable Compounds from a Pharmaceutical Packaging Material of Construction.

Unlabelled: The structural analysis (i.e., identification) of organic chemical entities leached into drug product formulations has traditionally been accomplished with techniques involving the combination of chromatography with mass spectrometry.

Carbamoyl anion addition to N-sulfinyl imines: highly diastereoselective synthesis of α-amino amides.

Carbamoyl anions, generated from N,N-disubstituted formamides and lithium diisopropylamide, add with high diastereoselectivity to chiral N-sulfinyl aldimines and ketimines to provide α-amino amides. The methodology enables the direct introduction of a carbonyl group without the requirement of unmasking steps as with other nucleophiles. The products may be converted to α-amino esters or 1,2-diamines.

Development of a large scale asymmetric synthesis of the glucocorticoid agonist BI 653048 BS H3PO4.

The development of a large scale synthesis of the glucocorticoid agonist BI 653048 BS H3PO4 (1·H3PO4) is presented. A key trifluoromethyl ketone intermediate 22 containing an N-(4-methoxyphenyl)ethyl amide was prepared by an enolization/bromine-magnesium exchange/electrophile trapping reaction. A nonselective propargylation of trifluoromethyl ketone 22 gave the desired diastereomer in 32% yield and with dr = 98:2 from a 1:1 diastereomeric mixture after crystallization.

Asymmetric methallylation of ketones catalyzed by a highly active organocatalyst 3,3'-F2-BINOL.

(S)-3,3'-F2-BINOL has been synthesized for the first time and demonstrated as a highly active organocatalyst for asymmetric methallylation of ketones. Up to 98:2 enantioselectivity and 99% yield were obtained with 5 mol % catalyst loading. The catalyst (S)-3,3'-F2-BINOL could be easily recovered and reused.

Probing the cation binding modes of macrocyclic HCV protease inhibitor BILN 2061 by multinuclear NMR.

The ability of the macrocyclic HCV protease inhibitor BILN 2061 to bind different classes of cations has been studied by (15)N, (13)C, and (1)H NMR. (15)N NMR experiments were performed at natural abundance or with isotopically labeled materials. Three classes of cations: alkali metals, alkaline earth metals, and transition metals, were examined, using two members of each class.

Chromatographic Separation and NMR An Integrated Approach in Pharmaceutical Development.

Over the past 10 years, major improvements in the performance of LC-NMR have been realized. The addition of postcolumn SPE, advances in probe technology including cryogenic probes and microcoil probes, improved solvent suppression pulse sequences, and shielded magnets with better homogeneity have all contributed to rapid advancements in this technology. Application of LC-NMR to problems in pharmaceutical development has had a major impact on structure elucidation studies.

Ambient temperature hydrophosphination of internal, unactivated alkynes and allenyl phosphineoxides with phosphine borane complexes.

Phosphine boranes have been found to hydrophosphinate internal, unactivated alkynes at room temperature under basic conditions without the need for catalysts or radical initiators. The use of air-sensitive secondary phosphines is avoided in this facile process. Broad scope in both the phosphine borane and alkyne partners leads to excellent diversity in the phosphine products.

1H and 13C NMR assignments of all three isomeric o-fluoronaphthaldehydes and three o-fluorophenanthrene aldehydes.

Three isomeric o-fluoronaphthaldehydes, 9-fluorophenanthrene, and three previously unreported o-fluorophenanthrene aldehydes were analyzed in detail by multiple NMR techniques to provide unambiguous assignment of structures and resonances. The six aldehydes serve as the key starting materials for novel chiral ligands used in highly enantioselective rhodium-catalyzed asymmetric hydrogenation reactions.

(31)P solid state NMR study of structure and chemical stability of dichlorotriphenylphosphorane.

Solid state (31)P NMR spectroscopy was used to examine, monitor and quantify the compound integrity of the chemical reagent dichlorotriphenylphosphorane. Comparison was also made with solution (31)P NMR spectra which showed that this highly reactive species could be observed in dry benzene prior to conversion to the hydrolyzed product. This is the first reported solid state NMR study of the stability and reactivity of dichlorotriphenylphosphorane and the first account of its observation and comparison in the solution state.

The design, structure, and clinical update of small molecular weight matrix metalloproteinase inhibitors.

Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes involved in the degradation and remodeling of extracellular matrix proteins. Under normal physiological conditions, the activities of these enzymes are well-regulated by endogenous tissue inhibitors of metalloproteinases (TIMPs). Chronic stimulation of MMP activities due to an imbalance in the levels of MMPs and TIMPs has been implicated in the pathogenesis of a variety of diseases such as cancer, osteoarthritis, and rheumatoid arthritis.