Zhongyue Yang

Distortion-Controlled Reactivity and Molecular Dynamics of Dehydro-Diels–Alder Reactions

We report density functional theory (M06-2X) studies of a series of dehydro-Diels-Alder (DDA) reactions. For these and the parent reaction, the stepwise mechanisms have similar barriers, whereas the barriers of the concerted mechanisms differ significantly. The reactivity of DDA reactions is controlled by distortion energy. The concerted and stepwise mechanisms of the hexadehydro-Diels-Alder (HDDA) reaction are competitive with activation barriers of ∼36 kcal/mol. This is because a large distortion energy (∼43 kcal/mol) is required to achieve the concerted transition state geometry. MD simulations reveal that productive concerted trajectories display a strong angle bending oscillation (∼25° oscillation amplitude), while the stepwise trajectories show only a chaotic pattern and less pronounced bending vibrations.

QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels–Alder Reaction

We describe a solvent-perturbed transition state (SPTS) sampling scheme for simulating chemical reaction dynamics in condensed phase. The method, adapted from Truhlar and Gaos ensemble-averaged variational transition state theory, includes the effect of instantaneous solvent configuration on the potential energy surface of the reacting system (RS) and allows initial conditions for the RS to be sampled quasiclassically by TS normal mode sampling. We use a QM/MM model with direct dynamics, in which QM forces of the RS are computed at each trajectory point. The SPTS scheme is applied to the acceleration of the Diels-Alder reaction of cyclopentadiene (CP) + methyl vinyl ketone (MVK) in water. We explored the effect of the number of SPTS and of solvent box size on the distribution of bond lengths in the TS. Statistical sampling of the sampling was achieved when distribution of forming bond lengths converged. We describe the region enclosing the partial bond lengths as the transition zone. Transition zones in the gas phase, SMD implicit solvent, QM/MM, and QM/MM+QM (3 water molecules treated by QM) vary according to the ability of the medium to stabilize zwitterionic structures. Mean time gaps between formation of C-C bonds vary from 11 fs for gas phase to 25 fs for QM/MM+QM. Mean H-bond lengths to O(carbonyl) in QM/MM+QM are 0.14 Å smaller at the TS than in MVK reactant, and the mean O(carbonyl)-H(water)-O(water) angle of H-bonds at the TS is 10° larger than in MVK reactant.

Molecular Dynamics of Dimethyldioxirane C-H Oxidation.

We report molecular dynamics simulations of the reaction of dimethyldioxirane (DMDO) with isobutane. The reaction involves hydrogen atom abstraction in the transition state, and trajectories branch to the oxygen rebound pathway, which gives tert-butanol and acetone, or a separated radical pair. In the gas phase, only 10% of the reactive trajectories undergo the oxygen rebound pathway, but this increases to 90% in simulations in an implicit acetone solvent (SMD) because the oxygen rebound becomes barrierless in solution. Short-lived diradical species were observed in the oxygen rebound trajectories. The time gap between C-H bond-breaking and C-O bond formation ranges from 30 to 150 fs, close to the <200 fs lifetime of radical pairs from DMDO hydroxylation of trans-1-phenyl-2-ethylcyclopropane measured by Newcomb.

SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis

Pericyclic reactions—which proceed in a concerted fashion through a cyclic transition state—are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon–carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels–Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-l-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels–Alder and hetero-Diels–Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme ‘toolboxes’. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.

Chronology of CH···O Hydrogen Bonding from Molecular Dynamics Studies of the Phosphoric Acid-Catalyzed Allylboration of Benzaldehyde

CH···O hydrogen bonds involving formyl groups have been invoked as a crucial factor controlling many asymmetric transformations. We conducted quasi-classical direct molecular dynamics simulations on the phosphoric acid-catalyzed allylboration of benzaldehyde to understand the synergy between the phosphoric acid OH···O hydrogen bond and the secondary CH···O formyl hydrogen bond as the reaction occurs. In the gas phase, both the CH···O and OH···O hydrogen bonds are enhanced from reactants to transition states. In toluene, the trend of H-bond enhancement is observed with a smaller magnitude because of solvent caging. The strength of the formyl hydrogen bond in the TS, a second CH···O interaction between the P═O oxygen and ortho-hydrogen of the phenyl ring and the OH···O hydrogen bond were determined using quantum mechanical calculations (4.6, 1.0, and 14.5 kcal mol-1, respectively).

A novel acetate selective chromogenic chemosensor based on phenanthroline.

A novel colorimetric anion-chemosensor based on 1,10-phenanthroline-2,9-dicarbonyl-p-nitro-phenylhydrazine has been synthesized. Among the different anions tested, it shows the best selectivity towards AcO(-). The addition of acetate causes the color to change from yellow to red, which could be detected with naked eyes. The binding ability of chemosensor 1 with anions has been investigated through UV-vis spectral titrations. In addition, (1)H NMR experiment was carried out to explore the nature of interaction between chemosensor 1 and acetate.

Mechanisms and Origins of Periselectivity of the Ambimodal [6 + 4] Cycloadditions of Tropone to Dimethylfulvene

The mechanisms and selectivities of the cycloadditions of tropone to dimethylfulvene have been investigated with M06-2X and B3LYP-D3 density functional theory (DFT) calculations and quasi-classical direct molecular dynamics simulations. The originally proposed reaction mechanism (Houk) involves a highly peri-, regio-, and stereoselective [6F + 4T] cycloaddition of tropone [4π] to dimethylfulvene [6π], followed by a [1,5] hydrogen shift, and, finally, a second [6 + 4] cycloaddition of tropone [6π] to the cyclopentadiene moiety [4π]. Paddon-Row and Warrener proposed an alternative mechanism: the initial cycloaddition involves a different [6T + 4F] cycloaddition in which fulvene acts as the 4π component, and a subsequent Cope rearrangement produces the formal [6F + 4T] adduct. Computations now demonstrate that the initial cycloaddition proceeds via an ambimodal transition state that can lead to both of the proposed [6 + 4] adducts. These adducts can interconvert through a [3,3] sigmatropic shift (Cope rearrangement). Molecular dynamics simulations reveal the initial distribution of products and provide insights into the time-resolved mechanism of this ambimodal cycloaddition. Competing [4 + 2] cycloadditions and various sigmatropic shifts are also explored.

Intramolecular Crossed [2+2] Photocycloaddition through Visible Light-Induced Energy Transfer

Herein, we present the intramolecular [2+2] cycloadditions of dienones promoted through sensitization, using a polypyridyl iridium(III) catalyst, to form bridged cyclobutanes. In contrast to previous examples of straight [2+2] cycloadditions, these efficient crossed additions were achieved under irradiation with visible light. The reactions delivered desired bridged benzobicycloheptanone products with excellent regioselectivity in high yields (up to 96%). This process is superior to previous syntheses of benzobicyclo[3.1.1]heptanones, which are readily converted to B-norbenzomorphan analogues of biological significance. Electrochemical, computational, and spectroscopic studies substantiated the mechanism of triplet energy transfer and explained the unusual regiocontrol.

Mechanism and Dynamics of Intramolecular C–H Insertion Reactions of 1-Aza-2-azoniaallene Salts

The 1-aza-2-azoniaallene salts, generated from α-chloroazo compounds by treatment with halophilic Lewis acids, undergo intramolecular C-H amination reactions to form pyrazolines in good to excellent yields. This intramolecular amination occurs readily at both benzylic and tertiary aliphatic positions and proceeds at an enantioenriched chiral center with retention of stereochemistry. Competition experiments show that insertion occurs more readily at an electron-rich benzylic position than it does at an electron-deficient one. The C-H amination reaction occurs only with certain tethers connecting the heteroallene cation and the pendant aryl groups. With a longer tether or when the reaction is intermolecular, electrophilic aromatic substitution occurs instead of C-H amination. The mechanism and origins of stereospecificity and chemoselectivity were explored with density functional theory (B3LYP and M06-2X). The 1-aza-2-azoniaallene cation undergoes C-H amination through a hydride transfer transition state to form the N-H bond, and the subsequent C-N bond formation occurs spontaneously to generate the heterocyclic product. This concerted two-stage mechanism was shown by IRC and quasi-classical molecular dynamics trajectory studies.

2-Hydroxy-naphth-1-aldehyde phenyl-thiosemicarbazone: effective thiourea-based sensor for acetate anion

A novel urea-based sensor displaying selective recognition for AcO− had been designed and synthesized. Experiments showed that sensor 1 can selectively recognize acetate in DMSO. The evaluation of the sensor’s interaction with a variety of structurally different anions was performed by UV–vis titration experiments in DMSO. In addition, the nature of interaction between sensor 1 and AcO− was investigated by 1H NMR titrations.