Single-bond Torsion Research Articles

Post-Transition State Bifurcation Controls Torsional Selectivity in Radical Addition of Allenes.

Post-transition state bifurcation (PTSB) has received wide attention in the field of reaction mechanism research due to its role in producing nonstatistical reaction selectivity, which cannot be solely explained by transition state theory. Particularly, even subtle molecular motions such as bond torsion can precipitate PTSB, thereby significantly complicating the quantitative understanding of dynamic selectivity. In this work, we found that the radical addition of allenes is an elementary transformation that generally exhibits PTSB stereoselectivity, where a single radical addition transition state can lead to both Z- and E-allylic radicals via the post-transition state allylic single bond torsion. Interestingly, dynamic Z/E-selectivity favors the Z-allylic radicals, which contrasts the thermodynamic preference. Based on the dynamics study of twenty-five radical additions of mono-substituted allenes with diverse electronic and steric effects, we have identified that this dynamic stereoselectivity is synergistically controlled by the transition state structure and the differential trends within specific dimensions of the bifurcating reaction coordinates, which also holds true for di-substituted allene substrates. This study refines the mechanism of radical addition of allenes and underscores the importance of the differential trend of the reaction coordinates in controlling dynamic selectivity, offering a deeper insight into PTSB selectivity factors.

Photoisomerization mechanisms from trans, trans-1,4-diphenyl-1,3-butadiene: CASSCF on-the-fly trajectory surface hopping dynamic simulations.

We have employed the SA2-CAS(4,4)/6-31G ab initio method together with an on-the-fly global-switching trajectory surface hopping algorithm to simulate photoisomerization reaction dynamics from reactant trans, trans-1,4-diphenyl-1,3-butadiene (DPB) to products cis,trans-DPB and cis,cis-DPB. This topic has been extensively studied experimentally and the present theoretical study is the first to simulate DPB photoisomerization reaction dynamics as far as we know. With total 600 sampling trajectories, 300 actively contribute to isomerization reaction via two conical intersections between the electronic ground and the first excited states. Simulated quantum yields of photoisomerization to cis, trans-DPB and cis, cis-DPB are 0.09 and 0.045, which are in good agreement with the experimental values of 0.07-0.25 and 0.02, respectively. The lifetime of the first excited state is estimated as 702 fs. The present simulation has shown two reactive photoisomerization mechanisms, namely one bond twist (OBT) and bicycle pedal (BP), and two non-reactive photoisomerization mechanisms, namely single bond torsion (SBT) and reverse torsion (RT) with respect to the central backbone CC bonds. We believe that the present theoretical work can benefit the experiments on photoisomerization of DPB derivates.

Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods.

The photoisomerization of the retinal chromophore of visual pigments proceeds along a complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out-of-plane (HOOP) coordinate, a bond length alternation (BLA) coordinate, a single bond torsion and, finally, the reactive double bond torsion. These degrees of freedom are coupled with changes in the electronic structure of the chromophore and, therefore, the computational investigation of the photochemistry of such systems requires the use of a methodology capable of describing electronic structure changes along all those coordinates. Here, we employ the penta-2,4-dieniminium (PSB3) cation as a minimal model of the retinal chromophore of visual pigments and compare its excited state isomerization paths at the CASSCF and CASPT2 levels of theory. These paths connect the cis isomer and the trans isomer of PSB3 with two structurally and energetically distinct conical intersections (CIs) that belong to the same intersection space. MRCISD+Q energy profiles along these paths provide benchmark values against which other ab initio methods are validated. Accordingly, we compare the energy profiles of MRPT2 methods (CASPT2, QD-NEVPT2, and XMCQDPT2) and EOM-SF-CC methods (EOM-SF-CCSD and EOM-SF-CCSD(dT)) to the MRCISD+Q reference profiles. We find that the paths produced with CASSCF and CASPT2 are topologically and energetically different, partially due to the existence of a "locally excited" region on the CASPT2 excited state near the Franck-Condon point that is absent in CASSCF and that involves a single bond, rather than double bond, torsion. We also find that MRPT2 methods as well as EOM-SF-CCSD(dT) are capable of quantitatively describing the processes involved in the photoisomerization of systems like PSB3.

Native hydrogen bonding network of the photoactive yellow protein (PYP) chromophore: Impact on the electronic structure and photoinduced isomerization

The local hydrogen bonding network of the p-coumaric thio-ester chromophore in the photoactive yellow protein (PYP) has been studied in some detail from a theoretical point of view, using the ab initio coupled-cluster CC2 method. The main focus is put on the impact of the native H-bonds, donated by the Tyr42, Glu46 and Cys69 amino acids, on (i) the molecular and electronic structure of the chromophore in the ground and first excited state and (ii) the photoinduced torsion of the chromophore around its single and double carboncarbon bonds. The H-bonds of both the Tyr42/Glu46 pair and the Cys69 amino acid are shown to substantially stabilize the negative charge of the chromophore in the ground state but have a different influence on the excited state. The Tyr42/Glu46 H-bonds tend to suppress the single-bond torsion in the excited state, thereby stabilizing the double-bond torsion, whereas the Cys69 H-bond has an opposite effect. The stabilization of the double-bond torsion is shown to depend on the length of the Tyr42/Glu46 H-bonds. Shorter H-bonds can significantly enhance the stabilization, which is proposed to be an important factor for the successful trans–cis isomerization of the chromophore in the native protein.

Photoinduced Isomerization of the Photoactive Yellow Protein (PYP) Chromophore: Interplay of Two Torsions, a HOOP Mode and Hydrogen Bonding

We report on a detailed theoretical analysis, based on extensive ab initio calculations at the CC2 level, of the S(1) potential energy surface (PES) of the photoactive yellow protein (PYP) chromophore. The chromophore's photoisomerization pathway is shown to be fairly complex, involving an intimate coupling between single-bond and double-bond torsions. Furthermore, these torsional modes are shown to couple to a third coordinate of hydrogen out-of-plane (HOOP) type whose role in the isomerization is here identified for the first time. In addition, it is demonstrated that hydrogen bonding at the phenolate moiety of the chromophore can hinder the single-bond torsion and thus facilitates double-bond isomerization. These results suggest that the interplay between intramolecular factors and H-bonding determines the isomerization in native PYP.

Activation of Fluorescent Protein Chromophores by Encapsulation

Chromophores related to fluorescent proteins, when sequestered into the "octaacid" capsule, recover their fluorescence. The fluorescence recovery is related to the inhibition of torsional motions within the cavity, implicating the single-bond torsion as an important contributor to internal conversion within this important class of chromophores.

Meta Conjugation Effect on the Torsional Motion of Aminostilbenes in the Photoinduced Intramolecular Charge-Transfer State

The photochemical behavior of a series of trans-3-(N-arylamino)stilbenes (m1, aryl = 4-substituted phenyl with a substituent of cyano (CN), hydrogen (H), methyl (Me), or methoxy (OM)) in both nonpolar and polar solvents is reported and compared to that of the corresponding para isomers (p1CN, p1H, p1Me, and p1OM). The distinct propensity of torsional motion toward a low-lying twisted intramolecular charge-transfer (TICT) state from the planar ICT (PICT) precursor between the meta and para isomers of 1CN and 1Me reveals the intriguing meta conjugation effect and the importance of the reaction kinetics. Whereas the poor charge-redistribution (delocalization) ability through the meta-phenylene bridge accounts for the unfavorable TICT-forming process for m1CN, it is such a property that slows down the decay processes of fluorescence and photoisomerization for m1Me, facilitating the competition of the single-bond torsional reaction. In contrast, the quinoidal character for p1Me in the PICT state kinetically favors both fluorescence and photoisomerization but disfavors the single-bond torsion. The resulting concept of thermodynamically allowed but kinetically inhibited TICT formation could also apply to understanding the other D-A systems, including trans-4-cyano-4'-(N,N-dimethylamino)stilbene (DCS) and 3-(N,N-dimethylamino)benzonitrile (3DMABN).

Influence of the S0−T1 structural changes on the triplet–triplet sensitization of dienes

Abstract The triplet–triplet energy transfer properties of different dienes were examined through time-resolved laser spectroscopy, and the different structural changes between ground and triplet states were investigated by molecular modeling. It was found that these compounds exhibit very different behaviors depending on their molecular structure. The calculations of ground- and triplet-state potential energy surfaces (PESs) at the B3LYP/6-31+G(d) level clearly evidenced the crucial role of the thermal activation of a single bond torsion in order to decrease the energetic requirement for the transition. A recently developed model, that included the influence of such a torsional mode, was successfully used to support this hypothesis.

Role of Structural Changes in the Triplet−Triplet Energy Transfer Process to Oxime Derivatives

The triplet energy accepting properties of bridged hydroxy and methyl derivatives of acetophenone oxime were examined. Sandros and Agmon−Levine−Balzani (ALB) models were used to deduce the oxime triplet energies, , and the reorganizational intrinsic barriers, ΔG#(0), associated with the reaction. It is found for the first time that these compounds exhibit different degrees of nonvertical energy transfer (NVET) behavior, depending on their chemical structure. These structural properties have been investigated at both the AM1 and the B3LYP/6-31+G(d) levels of theory. The flexibility of the ground-state molecule and the structural changes occurring during the S0 → T1 sensitized transition seem to play crucial roles. It appears that two important rearrangements are involved, namely, rotation about the C−N double bond and a π system flattening associated with a torsion about the formal C−C single bond. To relate the NVET character to these structural changes, the energy variations associated with these latter were evaluated and successfully related to ΔG#(0). Moreover, the role of the thermal activation of the molecular coordinates is evidenced through the calculations of the ground and triplet potential energy surfaces (PESs) at DFT and CIS levels. A simple model, based on the Sandros equation, was derived to include the influence of such torsional modes on the energy-transfer behavior. Finally, the experimental quenching data were fitted to this model, leading to the conclusion that, although both C−N double bond and C−C single bond torsions occur during the sensitization, the thermal activation of C−C single bond torsion plays the major role in the NVET character of oxime derivatives.

Influence of solvent viscosity on the photoisomerization of a novel trans-stilbene derivative with hindered single bond torsion

Fluorescence life-time measurements were performed at elevated pressure and temperature to examine the viscosity dependence of the rate of photoinduced isomerization, k iso, in a stilbene derivative in which the single bond torsion is hindered by the introduction of CH 2 bridges. The results obtained with n-hexane and methylcyclohexane as solvents (0.2 mPa s< η<2 mPa s) could not be fitted satisfactorily on the basis of Kramers' expression. A good global fit was, however, achieved when applying the empirical relationship k iso= C·( η/mPa s) −a·exp(− E A/ RT). The value for a drops from about 0.30 in n-hexane to about 0.15 in methylcyclohexane thus pointing to solvent specific contributions to the friction. The derived activation energies E A are about 12.8 and 12.5 kJ mol −1 in n-hexane and methylcyclohexane, respectively.

‘Nonvertical’ triplet energy transfer to a severely non-planar 1,3-diene: proposal of a mechanism based on progressive endothermicity of vertical transfer to individual single-bond torsional levels

The 1,3-diene unit in trans-β-ionol exhibits extreme ‘nonvertical’ behaviour in accepting triplet energy from a series of donors, a result strongly supporting a mechanism herein presented, which depends on the modes of single-bond torsion available to non-planar molecules and the relative dispositions of their So and T1 surfaces with respect to such torsion.

‘Nonvertical’ triplet energy transfer to cyclooctatetraene: support for the single-bond torsion mechanism

The severely non-planar π-system of Cyclooctatetraene exhibits extreme ‘nonvertical’ behaviour in accepting triplet energy from a series of donors, a fact strongly supporting the proposal that ‘nonvertical’ behaviour is a consequence of single-bond torsional modes on the ground-state surface.

Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme

We have developed a new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates. This method, normal-mode dynamics, is particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories. The essential assumption and limitation of normal-mode analysis is that the molecular potential energy varies quadratically. Our study starts with energy minimization of the X-ray co-ordinates with respect to the single-bond torsion angles. The main technical task is the calculation of second derivative matrices of kinetic and potential energy with respect to the torsion angle co-ordinates. These enter into a generalized eigenvalue problem, and the final eigenvalues and eigenvectors provide a complete description of the motion in the basic 0.1 to 10 picosecond range. Thermodynamic averages of amplitudes, fluctuations and correlations can be calculated efficiently using analytical formulae. The general method presented here is applied to four proteins, trypsin inhibitor, crambin, ribonuclease and lysozyme. When the resulting atomic motion is visualized by computer graphics, it is clear that the motion of each protein is collective with all atoms participating in each mode. The slow modes, with frequencies of below 10 cm −1 (a period of 3 ps), are the most interesting in that the motion in these modes is segmental. The root-mean-square atomic fluctuations, which are dominated by a few slow modes, agree well with experimental temperature factors ( B values). The normal-mode dynamics of these four proteins have many features in common, although in the larger molecules, lysozyme and ribonuclease, there is low frequency domain motion about the active site.