Computational and Experimental Evidence of Two Competing Thermal Electrocyclization Pathways for Vinylheptafulvene

The thermal electrocyclic ring‐closure reaction of vinylheptafulvene (VHF) to form dihydroazulene (DHA) is elucidated herein by using DFT and ¹H NMR spectroscopy. Two different transition states were found computationally; one corresponds to a disrotatory pathway, which is allowed according to the Woodward–Hoffmann selection rules, whereas the other corresponds to a conrotatory pathway. The conrotatory pathway is found to be zwitterionic in the transition state, whereas the disrotatory transition state varies in zwitterionic character depending on solvent and substituents in the molecular framework. The conrotatory and disrotatory transition states are found to have similar energy and their relative stability varies with solvent polarity and functionalization at the C1 position. To support these findings, we chemically ring‐opened diastereomerically pure 1‐(benzothiazol‐2‐yl)‐DHA to give the VHF form, then subsequently thermally reconverted the VHF to DHA in a range of solvents with various polarities. We found that, depending on solvent polarity, different ratios of anti‐ and syn‐diastereoisomers of DHA were formed in a systematic manner, which supports the existence of two distinct thermal ring‐closure pathways for VHF.     

Conservation of Orbital Symmetry can be Circumvented in Mechanically Induced Reactions

In first‐principles molecular dynamics simulations of the mechanically induced ring‐opening of substituted benzocyclobutene we observe both con‐ and disrotatory ring‐opening reactions. We show that this finding does not contradict the fundamental principle that the orbitals develop continuously in time. However, it constitutes an exception from the principle of the conservation of orbital symmetry and thus is indeed an exception from the Woodward–Hoffmann rules. In contrast, the ring‐opening of unsubstituted cyclobutene proceeds in a conrotatory fashion. This shows that the breaking of the Woodward–Hoffmann rules is significantly facilitated by the substituents.     

Embedding of the saddle point of index two on the PES of the ring opening of cyclobutene

The ring opening of cyclobutene is characterized by a competition of the two different pathways: a usual pathway over a saddle of index one (SP₁) along the conrotatory behavior of the end groups, as well as a “forbidden” pathway over a saddle point of index two (SP₂) along the disrotatory behavior of the end CH₂ groups. We use the system of ordinary differential equations for the method of the gentlest ascent dynamics (GAD) to determine saddle points of the potential energy surface (PES) of the ring opening of cyclobutene to cis‐butadiene. We apply generalized GAD formulas for the search of a saddle point of index two. To understand the relation of the different regions of the PES (around minimums, around SPs of index one or two) we also calculate valley‐ridge inflection (VRI) points on the PES using Newton trajectories (NT). VRIs and the corresponding singular NTs subdivide the regions of “attraction” of the different SPs. We calculate the connections of the SP₂ (in its different symmetry versions) with different SPs of index one of the PES by different “reaction pathways.” We compare the possibilities of the tool of the GAD curves for the exploration of PESs with these of NT. The barrier of the disrotatory SP₂ is somewhat higher than the barrier of the conrotatory SP₁, however, pathways across the slope to the SP₂ open additional reaction valleys. © 2015 Wiley Periodicals, Inc.     

A single‐molecule reaction cascade: First‐principles molecular dynamics simulation

The success of mechanochemistry is continued with the targeted organic synthesis of functional nano‐scale devices. In the present theoretical study, first principles molecular dynamics simulations are performed for a recently synthesized three‐ring system that functions as a molecular reaction cascade. Mechanochemical and photochemical reaction conditions are investigated. The system was designed in a way that three bonds would break consecutively in mechanochemical and sonochemical setups. We succeeded to simulate the reaction mechanisms with first‐principles molecular dynamics simulations and discuss the stereochemistry.     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Unraveling the Role of Water in the Stereoselective Step of Aqueous Proline‐Catalyzed Aldol Reactions

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self‐condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First‐principles molecular dynamics simulations were used to study the free‐energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high‐level static first‐principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths.     

Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two‐Step Pathway in the Frustrated Lewis Pair Reaction

The role solvent plays in reactions involving frustrated Lewis pairs (FLPs)—for example, the stoichiometric mixture of a bulky Lewis acid and a bulky Lewis base—still remains largely unexplored at the molecular level. For a reaction of the phosphorus/boron FLP and dissolved CO₂ gas, first principles (Born–Oppenheimer) molecular dynamics with explicit solvent reveals a hitherto unknown two‐step reaction pathway—one that complements the concerted (one‐step) mechanism known from the minimum‐energy‐path calculations. The rationalization of the discovered reaction pathway—that is, the stepwise formation of P?C and O?B bonds—is that the environment (typical organic solvents) stabilizes an intermediate which results from nucleophilic attack of the phosphorus Lewis base on CO₂. This finding is significant because presently the concerted reaction‐path paradigm predominates in the rationalization of FLP reactivity. Herein we point out how to attain experimental proof of our results.     

Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

The methanol‐to‐olefin process is a showcase example of complex zeolite‐catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H‐SAPO‐34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first‐principle molecular dynamics approach enables unprecedented insights into zeolite‐catalyzed reactions at the nanometer scale to be obtained.     

Electrocyclic ring opening of cis-bicyclo[m.n.0]alkenes: the anti-Woodward-Hoffmann quest

The dubbed anti-Woodward-Hoffmann ring-opening reaction of cis-bicyclo[4.2.0]oct-7-ene to yield cis,cis-cycloocta-1,3-diene has been intensively studied with robust, high-level computational methods. This reaction has been found to proceed through a conrotatory allowed pathway to afford cis,trans-cycloocta-1,3-diene followed by E to Z isomerization, instead of a disrotatory forbidden pathway, as suggested. Computational calculations of kinetic isotope effects are consistent with this interpretation and the experimental values. The study of lower bicyclic homologues with [3.2.0], [2.2.0] and [2.1.0] skeletons indicates the feasibility of a mechanistic change towards the anti-Woodward-Hoffmann disrotatory path. This is clearly favored for the ring opening of the highly strained cis-bicyclo[2.1.0]pent-2-ene and is highly competitive with the conrotatory path for cis-bicyclo[2.2.0]hex-2-ene. Therefore, the rearrangement of the smallest bicyclic cyclobutene is predicted computationally to be an anti-Woodward-Hoffmann disrotatory electrocyclic ring-opening reaction.     

ChemInform Abstract: First‐Principles Molecular Dynamics Investigation on Na3AlF6 Molten Salt.

The partial radial distribution function, coordination numbers, bond angles, F atoms type, self‐diffusion coefficient, viscosity, and ionic conduction of molten Na₃AlF₆ are investigated by first‐principles molecular dynamics simulation.     

Thermal isomerization of tricyclo[4.1.0.0(2,7)]heptane and bicyclo[3.2.0]hept-6-ene through the (E,Z)-1,3-cycloheptadiene intermediate

The thermal isomerization of tricyclo[4.1.0.0(2,7)]heptane and bicyclo[3.2.0]hept-6-ene was studied using ab initio methods at the multiconfiguration self-consistent field level. The lowest-energy pathway for thermolysis of both structures proceeds through the (E,Z)-1,3-cycloheptadiene intermediate. Ten transition states were located, which connect these three structures to the final product, (Z,Z)-1,3-cycloheptadiene. Three reaction channels were investigated, which included the conrotatory and disrotatory ring opening of tricyclo[4.1.0.0(2,7)]heptane and bicyclo[3.2.0]hept-6-ene and trans double bond rotation of (E,Z)-1,3-cycloheptadiene. The activation barrier for the conrotatory ring opening of tricyclo[4.1.0.0(2,7)]heptane to (E,Z)-1,3-cycloheptadiene was found to be 40 kcal mol(-1), while the disrotatory pathway to (Z,Z)-1,3-cyclohetpadiene was calculated to be 55 kcal mol(-1). The thermolysis of bicyclo[3.2.0]hept-6-ene via a conrotatory pathway to (E,Z)-1,3-cycloheptadiene had a 35 kcal mol(-1) barrier, while the disrotatory pathway to (Z,Z)-1,3-cyclohetpadiene had a barrier of 48 kcal mol(-1). The barrier for the isomerization of (E,Z)-1,3-cycloheptadiene to bicyclo[3.2.0]hept-6-ene was found to be 12 kcal mol(-1), while that directly to (Z,Z)-1,3-cycloheptadiene was 20 kcal mol(-1).     

The entry pathway of O2 into human ferritin

We study the entry pathway of dioxygen into human ferritin by means of both first principles and classical molecular dynamics techniques. Oxygen molecules, which behave hydrophobically in the water solvent, are found to interact with the Tyr 29 residue of human ferritin both directly via weak interactions and indirectly via hydrophobic forces. These interactions drive O₂ toward a narrow hydrophobic channel which connects the ferroxidase site of ferritin with the external environment. Diffusion of O₂ through the channel is observed using locally enhanced sampling techniques, and the enthalpy barrier to diffusion is calculated from first principles.     

Dynamical Dimension to the Hofmeister Series: Insights from First‐Principles Simulations

A systematic characterization of the competing kosmotropic and chaotropic effects of a series of divalent salts on the aqueous H‐bonding structure by means of first‐principles molecular dynamics simulations is presented. The structural properties are quantified by means of experimental and computed ¹H NMR chemical shifts, whereby the local environments of cations and anions can be discriminated. Complementary to the well‐established structural features, a dynamical aspect is added to the concept of kosmotropes and chaotropes. The H‐bond dynamics, quantified in terms of the H‐bonding autocorrelation functions, shows a good correlation with the structural kosmotropic and chaotropic modifications, which are commonly referred to as the Hofmeister series. The considerably enhanced (reduced) fluctuations of the H‐bonding network in the hydration shells around the anions (cations) are a complementary dynamical dimension to the concept of kosmotropic/chaotropic behavior of solvated ions.     

Cover Picture: Journal of the Chinese Chemical Society 5/2012

Oriented molecular beams provide us direct microscopic information on reaction dynamics in bimolecular as well as photodissociation systems. The oriented & crossed beam experiment of OH + HBr → H₂O + Br reveals the steric effect which clarifies branching mechanisms. Collisions at O‐end of OH lead to direct H₂O formation while H‐end of OH reacts via indirect migration mechanism. A roaming pathway is observed along with transition‐state pathway in photodissociation of methyl formate HCOOCH₃ which can be a unimolecular version of branching dynamics at the molecular level. For more details on this figure, please see pp 567～582 in this issue.     

A theoretical study of cyclohexyne addition to carbonyl-Cα bonds: allowed and forbidden electrocyclic and nonpericyclic ring-openings of strained cyclobutenes

The mechanism of cyclohexyne insertion into a C(O)-C(α) bond of cyclic ketones, explored experimentally by the Carreira group, has been investigated using density functional theory. B3LYP and M06-2X calculations were performed in both gas phase and THF (CPCM, UAKS radii). The reaction proceeds through a stepwise [2 + 2] cycloaddition of cyclohexyne to the enolate, followed by three disparate ring-opening possibilities of the cyclobutene alkoxide to give the product: (1) thermally allowed conrotatory electrocyclic ring-opening, (2) thermally forbidden disrotatory electrocyclic ring-opening, or (3) nonpericyclic C-C bond cleavage. Our computational results for the model alkoxide and potassium alkoxide systems show that the thermally allowed electrocyclic ring-opening pathway is favored by less than 1 kcal/mol. In more complex systems containing a potassium alkoxide (e-f), the barrier of the allowed conrotatory ring-opening is disfavored by 4-8 kcal/mol. This suggests that the thermodynamically more stable disrotatory product can be formed directly through a "forbidden" pathway. Analysis of geometrical parameters and atomic charges throughout the ring-opening pathways provides evidence for a nonpericyclic C-C bond cleavage, rather than a thermally forbidden disrotatory ring-opening. A true forbidden disrotatory ring-opening transition structure was computed for the cyclobutene alcohol; however, it was 19 kcal/mol higher in energy than the allowed conrotatory transition structure. An alternate mechanism in which the disrotatory product forms via isomerization of the conrotatory product was also explored for the alkoxide and potassium alkoxide systems.     

Theoretical studies on the electrocyclic reactions of bis(allene) and vinylallene. Role of allene group

The reaction mechanisms of the electrocyclic ring closure of bis(allene) and vinylallene were studied by ab initio MO methods. The conrotatory and disrotatory pathways of the electrocyclic reactions from bis(allene) to bis(methylene)cyclobutene were determined by a CASSCF method. The transition state on the conrotatory pathway is 26.8 kcal/mol above bis(allene) and about 23 kcal/mol lower than that on the disrotatory pathway at a MRMP calculation level. The activation energy on the conrotatory pathway is lower by 23 kcal/mol than that of the electrocyclic reaction of butadiene. This lower energy barrier comes from the interactions of the "side pi orbitals" of the allene group. The interaction of the "vertical pi orbitals" of the allene group is predominant at the early stage of the reaction. The activation energy of the electrocyclic reaction of vinylallene is about 8.5 kcal/mol higher than that on the conrotatory pathway of bis(allene).     

Color Polymorphism: Understanding the Diverse Solid‐State Packing and Color in Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate

Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular O?H???O and O?H???Cl hydrogen bonds. Time‐dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid‐state dispersion‐corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum‐energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two ?OH groups through a hybrid intermediate having one intramolecular O?H???O and one O?H???Cl bond. The LY form is shown to exist on the higher‐energy pathway involving a concerted Y→W transformation.     

The photochemical behavior of colchicone and thiocolchicone

The irradiation of colchicone 5 led to the formation of lumicolchicone 7. The same reaction cannot be obtained by using thiocolchicone 6 as substrate. Transient absorption spectroscopy of colchicone and beta-lumicolchicone showed that probably the photoisomerization occurred on colchicone in its first excited singlet state. The spectroscopic data are in agreement with the hypothesis that lumicolchicone was generated in the ground state from the S1 state of colchicone without the presence of any intermediate. Semiempirical calculations on colchicone and thiocolchicone showed that the highest single occupied molecular orbital and the lowest unoccupied molecular orbital of the singlet excited colchicone can give a disrotatory ring closure to 7, while thiocolchicone cannot give the same type of process.     

Temperature-dependent statistical behavior of single molecular conductance in aqueous solution

We have combined molecular dynamics simulations with first principles calculations to study electron transport in a single molecule of perylene tetracarboxylic diimide (PTCDI) sandwiched between two gold electrodes with an aqueous electrolyte. This combination has for the first time allowed one to reveal statistical behavior of molecular conductance in solution at different temperatures and to produce conductance histograms that can be directly compared with experiments. Our calculations show that experimentally observed temperature-dependent conductance can be attributed to the thermal effect on the hydrogen bonding network around the molecule and can be described by the radial distribution of water molecules surrounding the oxygen atom in the PTCDI molecule.