Titanocene(II)-Catalyzed Hydroboration of Carbonyl Compounds

Titanocene bis­(catecholborane), [Cp₂Ti­(HBcat)₂] (<b>1</b>), catalyzes the room-temperature hydroboration of carbonyl compounds by pinacolborane (HBpin) rapidly, cleanly, and chemoselectively. Aryl aldehydes and ketones produced alkoxypinacolboronate esters in moderate to high yields in 2 h, and facile hydrolysis of alkoxypinacolboronate esters over silica occurred cleanly to afford alcohols in good yields. Complex <b>1</b> demonstrated a preference for CO bonds over CC bonds in both conjugated and nonconjugated enones. Kinetic studies of the catalytic hydroboration of a series of acetophenones showed that electron-poor substrates undergo the reaction more quickly than electron-rich substrates. This result is consistent with the proposed mechanism, in which stronger π-acids should undergo CO bond cleavage more readily. Computational studies using benzophenone and benzaldehyde showed that the hydroboration is spontaneous and likely proceeds via intermediates that are best described as Ti metallacycles whose structures are not significantly altered by substrate steric differences. This result indicates that similarities in the electronic properties of benzophenone and benzaldehyde supersede their steric differences in determining reaction outcomes

Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase

Combined quantum mechanics/molecular mechanics molecular dynamics simulations reveal that the M20 loop conformational dynamics of dihydrofolate reductase (DHFR) is severely restricted at the transition state of the hydride transfer as a result of the M42W/G121V double mutation. Consequently, the double-mutant enzyme has a reduced entropy of activation, i.e., increased entropic barrier, and altered temperature dependence of kinetic isotope effects in comparison with those of wild-type DHFR. Interestingly, in both wild-type DHFR and the double mutant, the average donor–acceptor distances are essentially the same in the Michaelis complex state (∼3.5 Å) and the transition state (2.7 Å). It was found that an additional hydrogen bond is formed to stabilize the M20 loop in the closed conformation in the M42W/G121V double mutant. The computational results reflect a similar aim designed to knock out precisely the dynamic flexibility of the M20 loop in a different double mutant, N23PP/S148A

Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads

Predictive modeling and understanding of chemical warhead reactivities have the potential to accelerate targeted covalent drug discovery. Recently, the carbanion formation free energies as well as other ground-state electronic properties from density functional theory (DFT) calculations have been proposed as predictors of glutathione reactivities of Michael acceptors; however, no clear consensus exists. By profiling the thiol-Michael reactions of a diverse set of singly- and doubly-activated olefins, including several model warheads related to afatinib, here we reexamined the question of whether low-cost electronic properties can be used as predictors of reaction barriers. The electronic properties related to the carbanion intermediate were found to be strong predictors, e.g., the change in the Cβ charge accompanying carbanion formation. The least expensive reactant-only properties, the electrophilicity index, and the Cβ charge also show strong rank correlations, suggesting their utility as quantum descriptors. A second objective of the work is to clarify the effect of the β-dimethylaminomethyl (DMAM) substitution, which is incorporated in the warheads of several FDA-approved covalent drugs. Our data suggest that the β-DMAM substitution is cationic at neutral pH in solution and promotes acrylamide’s intrinsic reactivity by enhancing the charge accumulation at Cα upon carbanion formation. In contrast, the inductive effect of the β-trimethylaminomethyl substitution is diminished due to steric hindrance. Together, these results reconcile the current views of the intrinsic reactivities of acrylamides and contribute to large-scale predictive modeling and an understanding of the structure–activity relationships of Michael acceptors for rational TCI design

Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads

Predictive modeling and understanding of chemical warhead reactivities have the potential to accelerate targeted covalent drug discovery. Recently, the carbanion formation free energies as well as other ground-state electronic properties from density functional theory (DFT) calculations have been proposed as predictors of glutathione reactivities of Michael acceptors; however, no clear consensus exists. By profiling the thiol-Michael reactions of a diverse set of singly- and doubly-activated olefins, including several model warheads related to afatinib, here we reexamined the question of whether low-cost electronic properties can be used as predictors of reaction barriers. The electronic properties related to the carbanion intermediate were found to be strong predictors, e.g., the change in the Cβ charge accompanying carbanion formation. The least expensive reactant-only properties, the electrophilicity index, and the Cβ charge also show strong rank correlations, suggesting their utility as quantum descriptors. A second objective of the work is to clarify the effect of the β-dimethylaminomethyl (DMAM) substitution, which is incorporated in the warheads of several FDA-approved covalent drugs. Our data suggest that the β-DMAM substitution is cationic at neutral pH in solution and promotes acrylamide’s intrinsic reactivity by enhancing the charge accumulation at Cα upon carbanion formation. In contrast, the inductive effect of the β-trimethylaminomethyl substitution is diminished due to steric hindrance. Together, these results reconcile the current views of the intrinsic reactivities of acrylamides and contribute to large-scale predictive modeling and an understanding of the structure–activity relationships of Michael acceptors for rational TCI design

Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads

Predictive modeling and understanding of chemical warhead reactivities have the potential to accelerate targeted covalent drug discovery. Recently, the carbanion formation free energies as well as other ground-state electronic properties from density functional theory (DFT) calculations have been proposed as predictors of glutathione reactivities of Michael acceptors; however, no clear consensus exists. By profiling the thiol-Michael reactions of a diverse set of singly- and doubly-activated olefins, including several model warheads related to afatinib, here we reexamined the question of whether low-cost electronic properties can be used as predictors of reaction barriers. The electronic properties related to the carbanion intermediate were found to be strong predictors, e.g., the change in the Cβ charge accompanying carbanion formation. The least expensive reactant-only properties, the electrophilicity index, and the Cβ charge also show strong rank correlations, suggesting their utility as quantum descriptors. A second objective of the work is to clarify the effect of the β-dimethylaminomethyl (DMAM) substitution, which is incorporated in the warheads of several FDA-approved covalent drugs. Our data suggest that the β-DMAM substitution is cationic at neutral pH in solution and promotes acrylamide’s intrinsic reactivity by enhancing the charge accumulation at Cα upon carbanion formation. In contrast, the inductive effect of the β-trimethylaminomethyl substitution is diminished due to steric hindrance. Together, these results reconcile the current views of the intrinsic reactivities of acrylamides and contribute to large-scale predictive modeling and an understanding of the structure–activity relationships of Michael acceptors for rational TCI design

Expression Stabilities of Candidate Reference Genes for RT-qPCR under Different Stress Conditions in Soybean

<div><p>Due to its accuracy, sensitivity and high throughput, real time quantitative PCR (RT-qPCR) has been widely used in analysing gene expression. The quality of data from such analyses is affected by the quality of reference genes used. Expression stabilities for nine candidate reference genes widely used in soybean were evaluated under different stresses in this study. Our results showed that <i>EF1A</i> and <i>ACT11</i> were the best under salinity stress, <i>TUB4</i>, <i>TUA5</i> and <i>EF1A</i> were the best under drought stress, <i>ACT11</i> and <i>UKN2</i> were the best under dark treatment, and <i>EF1B</i> and <i>UKN2</i> were the best under virus infection. <i>EF1B</i> and <i>UKN2</i> were the top two genes which can be reliably used in all of the stress conditions assessed.</p></div

Determination of the optimal number of reference genes for normalization by pairwise variation (V) using GeNorm.

<p>The pairwise variation(V) to determine the optimal number of reference gene for accurate normalization in all samples (A), NaCl-treated (B), PEG-treated (C), Dark-treated (D), Virus-treated (E). It is the representative of the V2/3, V3/4, V4/5, V5/6, V6/7, V7/8, V8/9 form one to seven.</p

Efficiency of designed primer pairs used for RT-qPCR amplification.

<p>Efficiency of designed primer pairs used for RT-qPCR amplification.</p

Primer sequences and related information for each candidate reference gene.

<p>Primer sequences and related information for each candidate reference gene.</p

Ranking of candidate reference genes in order of their expression stability as calculated by NormFinder.

<p>Ranking of candidate reference genes in order of their expression stability as calculated by NormFinder.</p