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The development of asymmetric catalysts is typically driven by the experimental screening of potential catalyst designs. Herein, we demonstrate the design of asymmetric propargylation catalysts through computational screening. This was done using our computational toolkit AARON (automated alkylation reaction optimizer for N-oxides), which automates the prediction of enantioselectivities for bidentate Lewis base catalyzed alkylation reactions. A systematic screening of 59 potential catalysts built on 6 bipyridine N,N′-dioxide-derived scaffolds results in predicted ee values for the propargylation of benzaldehyde ranging from 45% (S) to 99% (R), with 12 ee values exceeding 95%. These data provide a broad set of experimentally testable predictions. Moreover, the associated data revealed key details regarding the role of stabilizing electrostatic interactions in asymmetric propargylations, which were harnessed in the design of a propargylation catalyst for which the predicted ee exceeds 99%.

The generation of platinum-containing carbonyl ylides from acyclic γ,δ-ynones and the cycloaddition of these ylides with electron-rich alkenes have been explored computationally to explain the experimentally observed regio- and stereoselectivity. Three pathways for the reaction of ylides with methyl vinyl ether have been investigated. Two of these involve [3+2] cycloadditions, whereas the third involves a [4+2] cycloaddition. Results indicate that the operative reaction pathway depends on the substitution pattern of the acyclic γ,δ-ynone. For an acyclic γ,δ-ynone without a methyl substituent at the propargylic position, we predict that both [3+2] cycloaddition pathways are more favorable than the [4+2] cycloaddition pathway, which leads to two products. On the other hand, for an acyclic γ,δ-ynone with a methyl substituent at the propargylic position, one of the [3+2] pathways is predicted to dominate, which exclusively affords an exo product. This feature arises from the hyperconjugative stabilization effect of the methyl group. Further analysis indicates that steric interactions between the chlorine atom of the catalyst and the methyl group of the vinyl ether lead to the observed exo selectivity. In all cases, the cycloaddition is the rate determining step, whereas for chiral PtCl2(bisphosphine)-catalyzed reactions it is also stereodetermining, the high degree of enantioselectivity arises from differences in both noncovalent dispersion interactions and extent of partial bond formation in the key transition states for the [3+2] cycloaddition.

The impact of solvent on the enantioselectivity of the allylation of aromatic aldehydes catalyzed by a bipyridine-N,N'-dioxide [(S)-bis-1,1′-(5,6,7,8-tetrahydro-3-phenylisoquinoline)-N,N'-dioxide] has been studied using modern density functional theory methods. The computational results confirm that the pronounced changes in the enantioselectivity originate from changes in the operative mechanism depending on the solvent used. In CH3CN, CH2Cl2 and CHCl3, the allylation of aldehydes proceeds along the ionic dissociative route, which favors the formation of the (R)-alcohol. However, in PhCl and PhCH3, a neutral non-bonded mechanism is favored and the (S)-alcohol is formed predominantly. In each case, electrostatic interactions, π-stacking interactions, and steric repulsion between the catalyst and the substrates all contribute to the enantioselectivity. The present data rationalize the experimental findings and unveil the crucial role of non-covalent interactions in the enantioselectivity of these Lewis-base promoted asymmetric allylations of aldehydes.

The mechanisms of Selectfluor-mediated Au-catalyzed intramolecular Csp3–Csp2 cross-coupling reaction involving direct aryl Csp2–H functionalization have been investigated theoretically. Several pathways involving the oxidation of alkylgold(I) (Cycle I), phosphine Au(I) precatalyst (Cycle II), gold(I) π–alkene complex (Cycle III) and arylgold(I) (Cycle IV) by Selectfluor, respectively, were examined. Our calculation results suggested the following: (1) Cycles I and II are preferred over Cycles III and IV, and the reaction would undergo the energy favored pathways (Cycles I and II), which is further confirmed by stereochemical analysis; (2) Cycle I is competitive with Cycle II, and the rate-determining steps of these two cycles are oxidation of Au(I) species by Selectfluor; (3) water has been found to participate in the catalytic reaction and decrease the activation energy barrier of the reductive elimination.

Stereoselectivities were predicted for the allylation of benzaldehyde using allyltrichlorosilanes catalyzed by 18 axially chiral bipyridine N,N′-dioxides. This was facilitated by the computational toolkit AARON (Automated Alkylation Reaction Optimizer for N-oxides), which automates the optimization of all of the required transition-state structures for such reactions. Overall, we were able to predict the sense of stereoinduction for all 18 of the catalysts, with predicted ee’s in reasonable agreement with experiment for 15 of the 18 catalysts. Curiously, we find that ee’s predicted from relative energy barriers are more reliable than those based on either relative enthalpy or free energy barriers. The ability to correctly predict the stereoselectivities for these allylation catalysts in an automated fashion portends the computational screening of potential organocatalysts for this and related reactions. By studying a large number of allylation catalysts, we were also able to gain new insight into the orig...

Matile et al. introduced the concept of anion-π catalysis [Angew. Chem., Int. Ed. 2013, 52, 9940; J. Am. Chem. Soc. 2014, 136, 2101], reporting naphthalene diimide (NDI)-based organocatalysts for the Kemp elimination reaction. We report computational analyses of the operative noncovalent interactions, revealing that anion-π interactions actually increase the activation barriers for some of these catalyzed reactions. We propose new catalysts that are predicted to achieve significant lowering of the activation energy through anion-π interactions.

We present detailed computational analyses of the binding of four dinucleotides to a highly sequence-selective single-stranded DNA (ssDNA) binding antibody (ED-10) and selected point mutants. Anti-DNA antibodies are central to the pathogenesis of systemic lupus erythematosus (SLE), and a more complete understanding of the mode of binding of DNA and other ligands will be necessary to elucidate the role of anti-DNA antibodies in the kidney inflammation associated with SLE. Classical molecular mechanics based molecular dynamics simulations and density functional theory (DFT) computations were applied to pinpoint the origin of selectivity for the 5'-nucleotide. In particular, the strength of interactions between each nucleotide and the surrounding residues were computed using MMGBSA as well as DFT applied to a cluster model of the binding site. The results agree qualitatively with experimental binding free energies, and indicate that π-stacking, CH/π, NH/π, and hydrogen-bonding interactions all contribute to 5'-base selectivity in ED-10. Most importantly, the selectivity for dTdC over dAdC arises primarily from differences in the strength of π-stacking and XH/π interactions with the surrounding aromatic residues; hydrogen bonds play little role. These data suggest that a key Tyr residue, which is not present in other anti-DNA antibodies, plays a key role in the 5'-base selectivity, while we predict that the mutation of a single Trp residue can tune the selectivity for dTdC over dAdC.

Computational studies to determine the origin of enantioselectivity in the (1R,2R)-1,2-diphenylethane-1,2-diamine (DEPN)–Bronsted acid catalyzed epoxidation of 2-cyclohexen-1-one have been performed using density functional theory. Transition states for conjugate addition and ring closure steps of the epoxidations catalyzed by three different catalyst systems were characterized. Our calculations show that the Csp2H⋯O H-bond interaction between the benzene ring of the catalyst and H2O is mainly responsible for the chiral discrimination observed. The Bronsted acid counterion plays a very important role in ensuring high enantioselectivity by improving the rigidity of the transition state structures to allow the efficient formation of the Csp2H⋯O H-bond. Moreover, we explain why these two diamine catalysts (1S,2S)-DACH and (1R,2R)-DPEN display consistent enantioselectivities in the catalytic epoxidation of 2-cyclohexen-1-one when combining with three different cocatalysts; achiral TFA, and chiral (R)- and (S)-TRIP.

A simple electrostatic model explains the enhanced stereoselectivity of N-oxide catalyzed allylations compared to propargylations, which in turn explicates the dearth of stereoselective N-oxide propargylation catalysts. These results suggest that N-oxide catalysts that are effective for both allylations and propargylations can be designed by targeting inherently stereoselective ligand configurations and through the manipulation of distortion effects in the operative transition states.

Theoretical investigations of three equilibrium structures and two associated isomerization reactions of the GeCH(2) - HGeCH - H(2)GeC system have been systematically carried out. This research employed ab initio self-consistent-field (SCF), coupled cluster (CC) with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] wave functions and a wide variety of correlation-consistent polarized valence cc-pVXZ and cc-pVXZ-DK (where X = D, T, Q) basis sets. For each structure, the total energy, geometry, dipole moment, harmonic vibrational frequencies, and infrared intensities are predicted. Complete active space SCF (CASSCF) wave functions are used to analyze the effects of correlation on physical properties and energetics. For each of the equilibrium structures, vibrational second-order perturbation theory (VPT2) has been utilized to obtain the zero-point vibration corrected rotational constants, centrifugal distortion constants, and fundamental vibrational frequencies. The predicted rotational constants and anharmonic vibrational frequencies for 1-germavinylidene are in good agreement with available experimental observations. Extensive focal point analyses, including CCSDT and CCSDT(Q) energies and basis sets up to quintuple zeta, are used to obtain complete basis set (CBS) limit energies. At all levels of theory employed in this study, the global minimum of the GeCH(2) potential energy surface (PES) is confirmed to be 1-germavinylidene (GeCH(2), 1). The second isomer, germyne (HGeCH, 2) is predicted to lie 40.4(41.1) ± 0.3 kcal mol(-1) above the global minimum, while the third isomer, 2-germavinylidene (H(2)GeC, 3) is located 92.3(92.7) ± 0.3 kcal mol(-1) above the global minimum; the values in parentheses indicate core-valence and zero-point vibration energy (ZPVE) corrected energy differences. The barriers for the forward (1→2) and reverse (2→1) isomerization reactions between isomers 1 and 2 are 48.3(47.7) ± 0.3 kcal mol(-1) and 7.9(6.6) ± 0.3 kcal mol(-1), respectively. On the other hand, the barriers of the forward (2→3) and reverse (3→2) isomerization reactions between isomers 2 and 3 are predicted to be 55.2(53.2) ± 0.3 kcal mol(-1) and 3.3(1.6) ± 0.3 kcal mol(-1), respectively.

Three equilibrium structures and two associated isomerization transition states for the SiCH 2 –HSiCH–CSiH 2 system have been theoretically investigated using highly correlated ab initio methods combined with the correlation-consistent polarized core-valence basis sets. Vibrational second-order perturbation theory (VPT2) has been employed to obtain the zero-point vibration corrected rotational constants, centrifugal distortion constants, and fundamental vibrational frequencies for each equilibrium structure. The comparison of the theoretically predicted rotational constants and fundamental frequencies for silylidene (SiCH 2 ) with existing experimental observations shows excellent agreement. The CH 2 (CD 2 ) rocking modes ( ν 6 ) are the most anharmonic among the six vibrational modes, consistent with limited experimental observations. The five stationary point structures and their relative energies on the ground state potential energy surface (PES) are accurately determined using the focal point extrapolation technique. Silylidene (SiCH 2 ) has been confirmed to be the global minimum. Silaacetylene (HSiCH) with a trans -bent structure is located 34.8 ± 0.3 kcal mol −1 (with zero-point vibrational energy, scalar relativistic effects, and DBOC corrections) above the global minimum. The barrier height for the critical reverse isomerization process [HSiCH → SiCH 2 ] is predicted to be 4.1 ± 0.3 kcal mol −1 . The third isomer silavinylidene (CSiH 2 ) is predicted to lie 84.6 ± 0.3 kcal mol −1 above the global minimum, with the barrier height for the reverse isomerization process [CSiH 2 → HSiCH] being only 2.6 ± 0.3 kcal mol −1 . The present research should assist the future experimental characterization of silylidene (SiCH 2 ) isomers.

The equilibrium structures of P(2)H(2) isomers and the associated isomerization transition states have been investigated systematically starting from self-consistent-field theory and proceeding to coupled cluster methods using a wide range of basis sets. For each structure, the geometry, energy, dipole moment, harmonic vibrational frequencies, and infrared intensities have been predicted. The global minimum has been confirmed to be planar trans-HPPH diphosphene, lying 3.2 kcal mol(-1) below cis-HPPH with the aug-cc-pVQZ CCSD(T) method upon inclusion of zero-point vibrational energy corrections. Diphosphinylidene, which has the connectivity PPH(2) and C(2v) symmetry, lies 25.2 kcal mol(-1) above the global minimum. The trans-cis isomerization reaction occurs via internal rotation with a barrier of 35.2 kcal mol(-1) using the cc-pVQZ Mk-MRCCSD (2e/2MO) method. This transition state exhibits multireference character and consequently properties were evaluated using CASSCF, MRCI, CASPT2, and Mk-MRCCSD methods with various basis sets. At the aug-cc-pVQZ CCSD(T) level, the transition state for the isomerization reaction between trans-HPPH and diphosphinylidene (planar PPH(2)) is predicted to be nonplanar with a torsional angle of 101.1 degrees . The corresponding barrier is estimated to be 48.2 kcal mol(-1).

Computational analyses of the first catalytic asymmetric Fischer indolization (J. Am. Chem. Soc. 2011, 133, 18534) reveal that enantioselectivity arises from differences in hydrogen bonding and CH/π interactions between the substrate and catalyst in the operative transition states. This selectivity occurs despite strong π-stacking interactions that reduce the enantioselectivity.

Enantioselectivities for the allylation and propargylation of benzaldehyde catalyzed by bipyridine N,N′-dioxides were predicted using popular DFT methods. The results reveal deficiencies of several DFT methods while also providing a new explanation for the stereoselectivity of these reactions. In particular, even though many DFT methods provide accurate predictions of experimental ee's for these reactions, these predictions sometimes stem from qualitatively incorrect transition states. Overall, B97-D/TZV(2d,2p) provides the best compromise between accurate predictions of low-lying transition states and stereoselectivities for these reactions. The origin of stereoselectivity in these reactions was also examined, and arises from electrostatic interactions within the chiral electrostatic environment of a hexacoordinate silicon intermediate; the previously published transition state model for these reactions is flawed. Ultimately, these results suggest two strategies for the design of highly stereoselective catalysts for the propargylation of aromatic aldehydes, and pave the way for the computational design of novel catalysts for these reactions.

Detailed kinetic analyses of inverse electron-demand Diels–Alder cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition reactions were conducted and the reactions were applied for rapid protein bioconjugation. When reacted with a tetrazine or a diaryl nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics. To apply these “click” reactions for site-specific protein labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pair. Proteins bearing these noncanonical amino acids were successively labeled with a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro and in living cells.

The pairing of transition metal catalysis with the reagent Selectfluor (F-TEDA-BF4) has attracted considerable attention due to its utility in myriad C-C and C-heteroatom bond-forming reactions. However, little mechanistic information is available for Selectfluor-mediated transition metal-catalyzed reactions and controversy surrounds the precise role of Selectfluor in these processes. We present herein a systematic investigation of homogeneous Au-catalyzed oxidative C-O bond-forming reactions using density functional theory calculations. Currently, Selectfluor is thought to serve as an external oxidant in Au(I)/Au(III) catalysis. However, our investigations suggest that these reactions follow a newly proposed mechanism in which Selectfluor functions as an electrophilic fluorinating reagent involved in a fluorination/defluorination cycle. We have also explored Selectfluor-mediated gold-catalyzed homocoupling reactions, which, when cyclopropyl propargylbenzoate is used as a substrate, lead to an unexpected byproduct.

The Diels-Alder cycloaddition of anthracene and nitrostyrene catalyzed by the squaramide-derived aminocatalysts (Sq) recently reported by Jorgensen and co-workers (Angew. Chem. 2012, 124, 10417; Angew. Chem. Int. Ed. 2012, 51, 10271) has been studied by using modern tools of computational quantum chemistry. This catalyst is compared with analogous urea-, thiourea-, and thiosquaramide-derived aminocatalysts. Ultimately, a thiosquar-amide-derived catalyst is predicted to result in the lowest free-energy barrier, while retaining the same high degree of enantioselectivity as Sq. This stems in part from the superior hydrogen-bonding ability of thiosquaramides, compared to squaramides and (thio)ureas. We also examine the hydrogen-bonding ability of (thio)ureas and (thio)-squaramides in model complexes. In contrast to previous work, we show that aromaticity does not contribute significantly to the enhanced hydrogen-bonding interactions of squaramides. Overall, thiosquaramide, which has not been explored in the context of either organocatalysis or molecular recognition, is predicted to lead to strong, co-planar hydrogen bonds, and should serve as a potent hydrogen-bonding element in a myriad of applications.

The existing potential energy surfaces for the Li + HF system have been challenged by the experiments of Loesch, Stienkemeier, and co-workers. Here a very accurate potential energy surface has been obtained with rather rigorous theoretical methods. Methods up to full CCSDT have been pursued with basis sets as large as core correlated quintuple ζ. Reported here are the reactants, products, two transition states, and three intermediate complexes for this reaction. These reveal one previously undiscovered equilibrium geometry. The stationary point relative energies are very sensitive to level of theory. The reaction has a classical endothermicity of 2.6 kcal mol(-1). The complex Li···HF in the entrance valley lies 6.1 kcal/mol below the reactants. The expected transition state Li···H···F is bent with an angle of 72.2° and lies 4.5 kcal/mol above the reactants. The latter predicted classical barrier should be no more than one kcal/mol above the exact barrier. Not one but two product complexes lie 1.6 and 2.2 kcal/mol above reactants, respectively. Between the two product complexes, a second transition state, very broad, is found. The vibrational frequencies and zero-point vibrational energies (ZPVE) of all stationary points are reported, and significantly affect the relative energies.

The enantioselective propargylation of aromatic aldehydes with allenyltrichlorosilanes catalyzed by bipyridine N-oxides was explored using density functional theory. Low-lying transition states for a highly enantioselective helical bipyridine N-oxide catalyst [Org. Lett. 2011, 13, 1654] were characterized at the B97-D/TZV(2d,2p) level of theory. Predicted free energy barrier height differences are in agreement with experimental ee's for the propargylation of benzaldehyde and substituted analogues. The origin of enantioselectivity was pinpointed through distortion-interaction analyses. The stereoselectivity arises in part from through-space electrostatic interactions of the carbonyl carbon with the Cl ligands bound to Si, rather than noncovalent aryl-aryl interactions between the aromatic aldehyde and the helix as previously proposed. Moreover, aryl-aryl interactions between the aldehyde and helix are predicted to favor transition states leading to the R enantiomer, and ultimately reduce the enantioselectivity of this reaction. (S)-2,2'-bipyridine N-oxide was studied as a model catalyst in order to quantify the inherent enantioselectivity arising from different chiral arrangements of ligands around the hexacoordinate silicon in the stereocontrolling transition state for these reactions. The predicted selectivities arising from different chiral octahedral silicon complexes provide guidelines for the development of transition state models for N-oxide-based alkylation catalysts.

Elucidating catalytic reaction mechanisms is often a challenge, and these difficulties are compounded in the case of enantioselective catalysts. The ability of a catalyst to preferentially form one enantiomer over the other often hinges on the balance of many attractive and repulsive nonbonded interactions that occur in competing transition states. On page 737 of this issue, Milo et al. ( 1 ) combine physical organic and computational quantum chemistry with modern data analysis techniques to identify these interactions. Their predictive mathematical models elucidate the underlying reaction mechanism and the role of nonbonded interactions in these enantioselective reactions, facilitating the rational design of more effective catalysts.

In this research, six low-lying triplet states of diphosphene (HPPH) and disphosphinylidene (PPH(2)) are systematically investigated starting from self-consistent field theory and proceeding to multireference coupled cluster methods using a wide range of basis sets. For each structure, the geometry, energy, dipole moment, harmonic vibrational frequencies, and infrared intensities are predicted. The triplet potential energy surface (PES) of P(2)H(2) is presented, based on systematically extrapolated coupled cluster energies and accounting for core-valence correlation, zero-point vibrational energy, and diagonal Born-Oppenheimer effects. Both (3)A'' pyramidal PPH(2) and (3)B skewed HPPH are minima on the triplet PES and lie 27.4 ± 0.3 and 32.4 ± 0.3 kcal mol(-1) above the global minimum structure closed-shell (1)A(g) trans-HPPH, respectively. The energy barrier for the isomerization reaction [(3)B skewed HPPH → (3)A'' pyramidal PPH(2)] is predicted to be 16.4 ± 0.3 kcal mol(-1). On this triplet PES, two equivalent (3)B skewed HPPH are converted via the (3)B(u) trans-HPPH transition state with a barrier of 9.1 ± 0.3 kcal mol(-1) or via the (3)B(2) cis-HPPH transition state with a barrier of 11.1 ± 0.3 kcal mol(-1). Moreover, the two equivalent (3)A'' pyramidal PPH(2) structures are connected through the (3)A(2) planar PPH(2) transition state with a barrier of 18.6 ± 0.3 kcal mol(-1). The energy crossing of the singlet and triplet adiabatic PES is studied using Mukherjee multireference coupled cluster method with the cc-pVQZ basis set, which predicts that the (3)B skewed HPPH is 1.4 kcal mol(-1) lower in energy than the corresponding (1)A skewed HPPH at the (3)B skewed HPPH optimized geometry.

We demonstrate the patterning of silica substrates with thymine (Thy-PS) and positively charged N-methylpyridinium (PVMP) polymers using photolithography and the subsequent orthogonal modification of these surfaces using diaminopyridine-functionalized polystyrene (DAP-PS) and carboxylate-derivatized CdSe/ZnS core-shell nanoparticles (COO-NP) through diamidopyridine-thymine three-point hydrogen bonding and pyridinium-carboxylate electrostatic interactions, respectively. This two-component orthogonal surface modification was accomplished in a self-sorting, single-step fashion, providing a versatile tool for the rapid and efficient creation of complex materials.

The global minimum on the Si(2)CH(2) electronic singlet potential energy surface has been theoretically predicted to be a peculiar hydrogen bridged (Si···H···Si) disilacyclopropenylidene structure (Si(2)CH(2)). An accurate quartic force field for Si(2)CH(2) has been determined employing ab initio coupled-cluster theory with single and double excitations and a perturbative treatment for triple excitations [CCSD(T)], in combination with the correlation consistent core-valence quadruple zeta (cc-pCVQZ) basis set. The vibration-rotation coupling constants, equilibrium and zero-point vibration corrected rotational constants, centrifugal distortion constants, and harmonic and fundamental vibrational frequencies for six isotopologues of Si(2)CH(2) are predicted using vibrational second-order perturbation theory (VPT2). The anharmonic corrections for the vibrational motions involving the H bridged bonds are found to be more than 5% with respect to the corresponding harmonic vibrational frequencies. In this light, an experimental detection and characterization of disilacyclopropenylidene (Si(2)CH(2)) is highly desired.