Perspective: Mechanochemistry of biological and synthetic molecules

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins

A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory. We show that the characteristic internal friction timescale is directly proportional to the timescale of hindered dihedral rotations within the polypeptide chain, with a proportionality coefficient b that is independent of the chain length. Such chain length independence of b provides experimentally testable evidence that internal friction arises from concerted, crankshaft-like dihedral rearrangements. In accord with phenomenological models of internal friction, we find the global reconfiguration timescale of a polypeptide to be the sum of solvent friction and internal friction timescales. At the same time, the time evolution of inter-monomer distances within polypeptides deviates both from the predictions of those models and from a simple, one-dimensional diffusion model.

Mechanochemical Kinetics in Elastomeric Polymer Networks: Heterogeneity of Local Forces Results in Nonexponential Kinetics

A common approach to inducing selective mechanochemical transformations relies on embedding the target molecules (called mechanophores) within elastomeric polymer networks. Mechanical properties of such elastomers can also be modulated through the mechanochemical response of the constituent polymer chains. The inherent randomness in the molecular structure of such materials leads to heterogeneity of the local forces exerted on individual mechanophores. Here we use coarse-grained simulations to study the force distributions within random elastomeric networks and show that those distributions are close to exponential regardless of the applied macroscopic load, entanglement effects, or network parameters. Exponential form of the distribution allows one to completely characterize the mechanophore kinetics in terms of the mean value of the force. At the same time, heterogeneity of the local force affects the kinetics qualitatively: While a narrow force distribution around the mean would lead to exponential kinetics, exponential force distribution results in highly nonexponential kinetics, with a fast kinetic phase involving highly loaded molecules, followed by a slow phase dominated by unloaded molecules.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Response to Comment on T. Stauch, A. Dreuw, “Stiff-stilbene photoswitch ruptures bonds not by pulling but by local heating”, Phys. Chem. Chem. Phys., 2016, 18, 15848

Computational analysis of mechanical stress energy revealed that photoisomerization of stiff-stilbene cannot initiate the ring opening of cyclobutene via a purely mechanical pathway.

Mechanically induced cis-to-trans isomerization of carbon–carbon double bonds using atomic force microscopy

Single molecule force spectroscopy can be used to induce cis-to-trans isomerization in carbon–carbon double bonds.