The Effect of Chlorine Substitution on Rotational Speed and Light Absorption of Second Generation Molecular Motors

TL;DR

This study investigates how chlorine substitution at the stereogenic center affects rotation speed and spectral selectivity in second-generation molecular motors. It combines climbing-image nudged elastic-band maps of THI and TI minimum energy paths for five base motors and their H→Cl or Me→CCl3 substitutions with DFT calculations (B3LYP/6-31G(d,p)) in ORCA and harmonic transition-state theory to obtain forward and backward rate constants, using $t_{1/2} = rac{ ln 2}{k_{ m THI}+k_{ m TI}}$. Spectral properties are probed with linear-response TDDFT to determine absorption wavelengths for the P and M isomers and the gap between them. Key findings show that substituting Me with CCl3 dramatically shortens the metastable state's lifetime by 2–5 orders of magnitude and preserves THI as the dominant forward step, yielding faster unidirectional rotation and a larger P/M spectral gap; by contrast, H→Cl reverses M vs P stability and raises the THI barrier above TI, quenching rotation, highlighting distinct design rules for speed and selectivity in chlorinated second-generation molecular motors.

Abstract

The effect of substituting a hydrogen atom by a chlorine atom or a methyl group by a trichloromethyl (CCl3) group at the stereogenic center of light-driven second generation molecular motors is calculated in order to assess the effect on rotational speed and the separation of the absorption peaks of the isomers. While experimental and theoretical studies have previously been carried out for fluorine substitution, this is the first study of chlorine substitution. Five well-characterized base molecules are studied and the trends are compared with the effect of fluorine substitution. The trichloromethyl substitution is found to accelerate the rotation more than a trifluoromethyl (CF3) substitution by reducing the life-time of the metastable state, due to larger steric hindrance in the metastable state than in the transition state for the thermal helix inversion (THI). A larger increase in the separation of the absorption peaks of the two isomers is also obtained. The Cl atom substitution, however, changes the energy landscape significantly, making the M isomer lower in energy than the P isomer, and raising the energy barrier for THI beyond that of the back transition, thus quenching the rotation.

Figures (5)

• Figure 1: The second-generation molecular motors studied here with substitutional site marked with an X. Two modifications are studied: H $\to$ Cl and Me $\to$CCl3.
• Figure 2: Front and top views of the optimized structures for the various states of molecule /molecules/3. (a and e) The stable P isomer. (b and f) The transition structure for the forward thermal helix inversion, THI. (c and g) The metastable M isomer. (d and h) The transition structure for the backward thermal isomerization, TI.
• Figure 3: (a-e) Minimum energy paths between the P and M isomers of the five base molecules where a methyl group and a hydrogen atom are at the X site (blue), as well as the chlorinated molecules with the methyl group substituted for a CCl3 group (red), or the H atom is substituted for a Cl atom (green). The zero of energy is taken to be the P state in each case. The energy maxima correspond to first order saddle points, i.e. transition structures, for the TI (left) and THI (right) transitions. For the CCl3 substitution, both energy barriers decrease and the THI barrier continues to be lower than that for TI. For the Cl substitution, the M isomer becomes more stable than P, and the THI energy barrier increases significantly. (f) Activation energy for the TI and THI transitions from the metastable state (the M isomer for the base (blue) and CCl3 substituted (red) molecules, but the P state for Cl substituted (green) molecules). The dashed red line separates molecules by their dominant thermal transition mechanism: THI for those above the line and TI for those below.
• Figure 4: Comparison of the half-life of the metastable M isomer of the molecules. The substitution of the methyl group for a $\ce{CCl3}$ group (blue) shortens the half-life and thereby increases the rotational speed, more so than the previously reported substitution by a $\ce{CF3}$ group. Data on fluorine and $\ce{CF3}$ substitution are from Ref. tambovtsevFineTuningRotational2025.
• Figure 5: Difference in excitation wavelength, $\Delta \lambda$, of the two isomers of the molecules with methyl (red), CCl3 (blue) and CF3 (purple) tambovtsevFineTuningRotational2025 groups at the stereogenic center. The substitution of the methyl for CCl3 consistently increases the gap and thereby would improve selectivity in the photoexcitation.