Transition State Region Research Articles

Examining Ionic Liquid Effects on Mononuclear Rearrangement of Heterocycles Using QM/MM Simulations.

The mononuclear rearrangement of heterocycles (MRH) reaction of the Z-phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole into 4-benzoylamino-2,5-diphenyl-1,2,3-triazole derives a sizable rate enhancement in the 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4] ionic liquid as compared to the hexafluorophosphate-based [BMIM][PF6] and conventional organic solvents. However, the origin of the rate difference between [BMIM][BF4] and [BMIM][PF6] has proven difficult to rationalize as no experimental trend relates the physical properties of the solvents, e.g., polarity and viscosity, to the rates of reaction. QM/MM calculations in combination with free-energy perturbation theory and Monte Carlo sampling have been carried out for the MRH reaction to elucidate the disparities in rates when using ionic liquids, methanol, and acetonitrile. Activation barriers and solute-solvent interactions have been computed for both an uncatalyzed and a specific base-catalyzed mechanism. Energetic and structural analyses determined that favorable π+-π interactions between the BMIM cation, the substrate phenyl rings, and the bicyclic quasi-aromatic 10π oxadiazole/triazole transition state region imposed a preordered geometric arrangement that enhanced the rate of reaction. An ionic liquid clathrate formation enforced a coplanar orientation of the phenyl rings that maximized the electronic effects exerted on the reaction route. In addition, site-specific electrostatic stabilization between the ions and the MRH substrate was more prevalent in [BMIM][BF4] as compared to [BMIM][PF6].

Optimized Markov state models for metastable systems.

A method is proposed to identify target states that optimize a metastability index amongst a set of trial states and use these target states as milestones (or core sets) to build Markov State Models (MSMs). If the optimized metastability index is small, this automatically guarantees the accuracy of the MSM, in the sense that the transitions between the target milestones is indeed approximately Markovian. The method is simple to implement and use, it does not require that the dynamics on the trial milestones be Markovian, and it also offers the possibility to partition the system's state-space by assigning every trial milestone to the target milestones it is most likely to visit next and to identify transition state regions. Here the method is tested on the Gly-Ala-Gly peptide, where it is shown to correctly identify the expected metastable states in the dihedral angle space of the molecule without a priori information about these states. It is also applied to analyze the folding landscape of the Beta3s mini-protein, where it is shown to identify the folded basin as a connecting hub between an helix-rich region, which is entropically stabilized, and a beta-rich region, which is energetically stabilized and acts as a kinetic trap.

Chemical potential and reaction electronic flux in symmetry controlled reactions

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc.

Transition state region in the A-Band photodissociation of allyl iodide--A femtosecond extreme ultraviolet transient absorption study.

Femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy based on a high-harmonic generation source is used to study the 266 nm induced A-band photodissociation dynamics of allyl iodide (CH2 =CHCH2I). The photolysis of the C-I bond at this wavelength produces iodine atoms both in the ground ((2)P3/2, I) and spin-orbit excited ((2)P1/2, I*) states, with the latter as the predominant channel. Using XUV absorption at the iodine N4/5 edge (45-60 eV), the experiments constitute a direct probe of not only the long-lived atomic iodine reaction products but also the fleeting transition state region of the repulsive nIσ(∗) C-I excited states. Specifically, three distinct features are identified in the XUV transient absorption spectrum at 45.3 eV, 47.4 eV, and 48.4 eV (denoted transients A, B, and C, respectively), which arise from the repulsive valence-excited nσ(∗) states and project onto the high-lying core-excited states of the dissociating molecule via excitation of 4d(I) core electrons. Transients A and B originate from 4d(I) → n(I) core-to-valence transitions, whereas transient C is best assigned to a 4d(I) →σ(∗)(C-I) transition. The measured differential absorbance of these new features along with the I/I* branching ratios known from the literature is used to suggest a more definitive assignment, albeit provisional, of the transients to specific dissociative states within the A-band manifold. The transients are found to peak around 55 fs-65 fs and decay completely by 145 fs-185 fs, demonstrating the ability of XUV spectroscopy to map the evolution of reactants into products in real time. The similarity in the energies of transients A and B with analogous features observed in methyl iodide [Attar et al. J. Phys. Chem. Lett. 6, 5072, (2015)] together with the new observation of transient C in the present work provides a more complete picture of the valence electronic structure in the transition state region. The results provide a benchmark for theoretical calculations on the nature of core-excited states in halogenated hydrocarbons, especially in the transition state region along the C-I reaction coordinate.

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.

Despite the enormous increase in computer power, it is still extremely challenging to obtain computationally converging sampling of ab initio QM/MM (QM(ai)/MM) free energy surfaces in condensed phases. The sampling problem can be significantly reduced by the use of the reference potential paradynamics (PD) approach, but even this approach still requires major computer time in studies of enzymatic reactions. To further reduce the sampling problem we developed here a new PD version where we use an empirical valence bond reference potential that has a minimum rather than a maximum at the transition state region of the target potential (this is accomplished conveniently by shifting the EVB of the product state). Hence, we can map the TS region in a more efficient way. Here, we introduce and validate the inverted EVB PD approach. The validation involves the study of the S(N)2 step of the reaction catalyzed by haloakene dehalogenase (DhlA) and the GTP hydrolysis in the RasGAP system. In addition, we have also studied the corresponding reaction in water for each of the systems described here and the reaction involving trimethylsulfonium and dimethylamine in solution. The results are encouraging and the new strategy appears to provide a powerful way of evaluating QM(ai)/MM activation free energies.

Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C–C bond-alternation (D4h↔D8h↔D4h) and ring-inversion (D2d↔D4h↔D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT− revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

Direct Observation of the Transition-State Region in the Photodissociation of CH3I by Femtosecond Extreme Ultraviolet Transient Absorption Spectroscopy.

Femtosecond extreme ultraviolet (XUV) pulses produced by high harmonic generation are used to probe the transition-state region in the 266 nm photodissociation of CH3I by the real-time evolution of core-to-valence transitions near the iodine N-edge at 45-60 eV. During C-I bond breaking, new core-to-valence electronic states appear in the spectra, which decay concomitantly with the rise of the atomic iodine resonances of I((2)P3/2) and I*((2)P1/2). The short-lived features are assigned to repulsive valence-excited transition-state regions of (3)Q0 and (1)Q1, which can connect to transient core-excited states via promotion of 4d(I) core electrons. A simplified one-electron transition picture is described that accurately predicts the relative energies of the transient states observed. The transition-state resonances reach a maximum at ∼40 fs and decay to complete C-I dissociation in ∼90 fs, representing the shortest-lived chemical transition state observed by core-level, XUV, or X-ray spectroscopy.

Theoretical Study of FH2– Electron Photodetachment Spectra on New Ab Initio Potential Energy Surfaces.

The FH2– anion has a stable structure that resembles a configuration in the vicinity of the transition state for neutral reaction F + H2 → HF + H. Electron photodetachment spectra of the FH2– anion reveal the neutral reaction dynamics in the critical transition-state region. Accurate quantum dynamics simulations of the photodetachment spectra using highly accurate new ab initio potential energy surfaces for both anionic and neutral FH2 are performed and compared with all available experimental results. The results provide reliable interpretations for the experimental observations of FH2– photoelectron detachment and reveal a detailed picture of the molecular dynamics around the transition state of the F + H2 reaction. The latest high-resolution photoelectron detachment spectra [Kim et al. Science, 2015, 349, 510-513] confirm the high accuracy of our new potential energy surface for describing the resonance-enhanced reactivity of the neutral F + H2 reaction.

Transition state ensemble optimization for reactions of arbitrary complexity.

In the present work, we use Variational Transition State Theory (VTST) to develop a practical method for transition state ensemble optimization by looking for an optimal hyperplanar dividing surface in a space of meaningful trial collective variables. These might be interatomic distances, angles, electrostatic potentials, etc. Restrained molecular dynamics simulations are used to obtain on-the-fly estimates of ensemble averages that guide the variations of the hyperplane maximizing the transmission coefficient. A central result of our work is an expression that quantitatively estimates the importance of the coordinates used for the localization of the transition state ensemble. Starting from an arbitrarily large set of trial coordinates, one can distinguish those that are indeed essential for the advance of the reaction. This facilitates the use of VTST as a practical theory to study reaction mechanisms of complex processes. The technique was applied to the reaction catalyzed by an isochorismate pyruvate lyase. This reaction involves two simultaneous chemical steps and has a shallow transition state region, making it challenging to define a good reaction coordinate. Nevertheless, the hyperplanar transition state optimized in the space of 18 geometrical coordinates provides a transmission coefficient of 0.8 and a committor histogram well-peaked about 0.5, proving the strength of the method. We have also tested the approach with the study of the NaCl dissociation in aqueous solution, a stringest test for a method based on transition state theory. We were able to find essential degrees of freedom consistent with the previous studies and to improve the transmission coefficient with respect to the value obtained using solely the NaCl distance as the reaction coordinate.

Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562.

The folding kinetics of Rd-apocytochrome b562 is two-state, but native-state hydrogen exchange experiments show that there are discrete partially unfolded (PUF) structures in equilibrium with the native state. These PUF structures are called hidden intermediates because they are not detected in kinetic experiments and they exist after the rate-limiting step. Structures of the mimics of hidden intermediates of Rd-apocytochrome b562 are resolved by NMR. Based upon their relative stability and structural features, the folding mechanism was proposed to follow a specific pathway (unfolded → rate-limiting transition state → PUF1 → PUF2 → native). Investigating the roles of equilibrium PUF structures in folding kinetics and their interrelationship not only deepens our understanding of the details of folding mechanism but also provides guides in protein design and prevention of misfolding. We performed molecular dynamics simulations starting from a hidden intermediate and the native state of Rd-apocytochrome b562 in explicit solvent, for a total of 37.18 μs mainly with Anton. We validated our simulations by detailed comparison with experimental data and other computations. We have verified that we sampled the post rate-limiting transition state region only. Markov state model was used to analyze the simulation results. We replace the specific pathway model with a network model. Transition-path theory was employed to calculate the net effective flux from the most unfolded state towards the most folded state in the network. The proposed sequential folding pathway via PUF1 then more stable, more native-like PUF2 is one of the routes in our network, but it is not dominant. The dominant path visits PUF2 without going through PUF1. There is also a route from PUF1 directly to the most folded state in the network without visiting PUF2. Our results indicate that the PUF states are not necessarily sequential in the folding. The major routes predicted in our network are testable by future experiments such as single molecule experiment.

Dynamical resonances in chemical reactions

Gas-phase chemical reactions occur when one reactant collides with another followed by rearrangements of the atoms in the activated complex. This process is typically described by the reaction coordinate leading from the reactants to products via a transition state. In general, the transition state is only a whistle-stop for the reactive flux. However, an activated complex can sometimes be transiently trapped in the transition-state region as metastable quantum states. Such dynamical resonances can profoundly influence the dynamics of a chemical reaction. As a result, it has attracted much attention in the field of chemical dynamics over the past 30 years. Although signatures of dynamical resonances have been detected in several reactions [1–4], only the F + H2(HD) resonances have been elucidated [1–3]. It is thus exciting when a research team led by Profs Xueming Yang and Dong Hui Zhang in State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, unequivocally proved the existence of dynamical resonances in the Cl + HD (v = 1) → DCl + H reaction and elucidate them clearly through the state-of-the-art crossed molecular beams experiment and quantum dynamics calculations [5]. Experimentally, the first application of stimulated Raman pumping of HD molecules to the vibrationally excited v= 1 state in a crossed molecular beams study, in combination with the so-called differential cross-sections backward scattering spectroscopy method developed in their own laboratory, is Reaction coordinate Feshbach resonance pathway Shape resonance pathway

Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.

Intrinsically disordered regions of proteins can gain structure by binding to a partner. This process, of coupled folding and binding (CFaB), is a fundamental part of many important biological processes. Structure-based models have proven themselves capable of revealing fundamental aspects of how CFaB occurs, however, typical methods to enhance the sampling of these transitions, such as replica exchange, do not adequately sample the transition state region of this extremely rare process. Here, we use a variant of Umbrella Sampling to enforce sampling of the transition states of CFaB of HdeA monomers at neutral pH, an extremely rare process that occurs over timescales ranging from seconds to hours. Using high resolution sampling in the transition state region, we cluster states along the principal transition path to obtain a detailed description of coupled binding and folding for the HdeA dimer, revealing new insight into the ensemble of states that are accessible to client recognition. We then demonstrate that exchanges between umbrella sampling windows, as done in previous work, significantly improve relaxation in variables orthogonal to the restraints used. Altogether, these results show that Window-Exchange Umbrella Sampling is a promising approach for systems that exhibit flexible binding, and can reveal transition state ensembles of these systems in high detail. © 2015 Wiley Periodicals, Inc.

Vibrationally Coherent Preparation of the Transition State for Photoisomerization of the Cyanine Dye Cy5 in Water

Femtosecond pump-continuum probe spectroscopy with impulsive excitation was employed to observe coherent wavepacket motions of the cyanine dye Cy5 in water that promote photoisomerization after optical preparation of the first excited singlet state, S1. The chief component in the excited-state vibrational coherence is a resonance Raman-inactive, 273 cm(-1) mode of mixed carbon-carbon bond length alternation and out-of-plane or twisting character. The ultrafast (30 fs) damping of these motions arises from trajectories that irreversibly cross the transition state barrier; after several recurrences to the transition state region, vibrational cooling traps a significant fraction of the excited-state molecules in the planar, Franck-Condon region of the potential energy surface. Motion in the 273 cm(-1) promoting mode is apparently launched by a change in conformation of the conjugated polyene backbone during the first few vibrations of the high-frequency C-C and C═C bond length alternation coordinates that principally contribute to the initial displacement from the Franck-Condon structure. To our knowledge, this work provides the first direct observations of the intramolecular redistribution of excited-state potential energy into reactive motions that are rapidly damped by transition state barrier-crossing events leading to photoisomerization in a conjugated polyene. These results provide insight into the vibrational dynamics that contribute to the photoisomerization of retinal protonated Schiff bases in the rhodopsins and to the formation of intramolecular charge transfer character in carotenoids in photosynthetic light-harvesting proteins.

First-principles simulations of transition state spectra of the I + HI and I + DI reactions and vibrational bonding in IMuI

The lowest three potential energy surfaces for the I(2P3/2,2P1/2)+HI(X1Σ) reaction have been developed using extensive ab initio electronic structure calculations including the spin–orbit interaction. Using the ab initio potential energy surfaces, we simulate experimentally-observed transition state spectra for the I+HI and I+DI reactions by calculating photodetachment spectra of the IHI− and IDI− anions. Very good agreement was obtained between theory and experiment. When the hydrogen atom is replaced by Mu, which is a very light isotope of hydrogen, it was found that the I+MuI reaction system has a bound vibrational-bonding state whose wavefunction is highly localized around the transition state region on the ground-state potential energy surface. All other systems containing heavier hydrogen isotopes show only a van der Waals bonding feature.

Surface chemistry. Probing the transition state region in catalytic CO oxidation on Ru.

Femtosecond x-ray laser pulses are used to probe the carbon monoxide (CO) oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and oxygen (O) on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC-O bond lengths close to the transition state (TS). After 1 ps, 10% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.

Direct production of OH radicals upon CH overtone activation of (CH3)2COO Criegee intermediates.

Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH3)2COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol(-1)) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features, indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X(2)Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH3)2COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn-CH3CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science 345, 1596 (2014)].

Does the "reef structure" at the ozone transition state towards the dissociation exist? New insight from calculations and ultrasensitive spectroscopy experiments.

Since the discovery of anomalies in ozone isotope enrichment, several fundamental issues in the dynamics linked to the shape of the potential energy surface in the transition state region have been raised. The role of the reeflike structure on the minimum energy path is an intricate question previously discussed in the context of chemical experiments. In this Letter, we bring strong arguments in favor of the absence of a submerged barrier from ultrasensitive laser spectroscopy experiments combined with accurate predictions of highly excited vibrations up to nearly 95% of the dissociation threshold.

Non-oscillatory flux correlation functions for efficient nonadiabatic rate theory.

There is currently much interest in the development of improved trajectory-based methods for the simulation of nonadiabatic processes in complex systems. An important goal for such methods is the accurate calculation of the rate constant over a wide range of electronic coupling strengths and it is often the nonadiabatic, weak-coupling limit, which being far from the Born-Oppenheimer regime, provides the greatest challenge to current methods. We show that in this limit there is an inherent sign problem impeding further development which originates from the use of the usual quantum flux correlation functions, which can be very oscillatory at short times. From linear response theory, we derive a modified flux correlation function for the calculation of nonadiabatic reaction rates, which still rigorously gives the correct result in the long-time limit regardless of electronic coupling strength, but unlike the usual formalism is not oscillatory in the weak-coupling regime. In particular, a trajectory simulation of the modified correlation function is naturally initialized in a region localized about the crossing of the potential energy surfaces. In the weak-coupling limit, a simple link can be found between the dynamics initialized from this transition-state region and an generalized quantum golden-rule transition-state theory, which is equivalent to Marcus theory in the classical harmonic limit. This new correlation function formalism thus provides a platform on which a wide variety of dynamical simulation methods can be built aiding the development of accurate nonadiabatic rate theories applicable to complex systems.

How frustrated Lewis acid/base systems pass through transition-state regions: H2 cleavage by [tBu3P/B(C6F5)3

We investigate the transition-state (TS) region of the potential energy surface (PES) of the reaction tBu3P + H2 + B(C6F5)3 → tBu3P-H(+) + (-)H-B(C6F5)3 and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane⋅⋅⋅borane pocket involving heavy tBu3P and B(C6F5)3 species and features of the PES E(P⋅⋅⋅H, B⋅⋅⋅H | B⋅⋅⋅P) as a function of P⋅⋅⋅H, B⋅⋅⋅H, and B⋅⋅⋅P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi-bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane⋅⋅⋅borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi-bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.

Quantum localization/delocalization of muonium in the glycine–K+ complex

Previous electronic structure studies have revealed that the glycine–K+ complex has a low-barrier intramolecular proton-transfer pathway between zwitterionic and neutral forms. We have theoretically calculated quantum molecular structures of this complex including the proton-transfer process using a path-integral molecular dynamics technique on an interpolated potential energy surface developed at the B3LYP level of theory. When the transferring proton is substituted by muon, it was found that the muonium atom showed a broad distribution around the proton(muon)-transfer transition state region between the neutral and zwitterionic structures due to extreme nuclear quantum effects of a very light particle although the distribution peak is slightly deviated from the transition state. The present study demonstrates that Mu can be employed to probe transition-state regions of potential energy surfaces of proton-transfer chemical reactions.