Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics.

Lignocellulosic biomass is an abundant, rich source of aromatic compounds, but direct utilization of raw lignin has been hampered by both the high heterogeneity and variability of linking bonds in this biopolymer. Ab initio steered molecular dynamics (AISMD) has emerged both as a fruitful direct computational screening approach to identify products that occur through mechanical depolymerization (i.e., in sonication or ball-milling) and as a sampling approach. By varying the direction of force and sampling over 750 AISMD trajectories, we identify numerous possible pathways through which lignin depolymerization may occur in pyrolysis or through catalytic depolymerization as well. Here, we present eight unique major depolymerization pathways discovered via AISMD for the recently characterized spirodienone lignin branching linkage that may comprise around 10% weight of all lignin in some softwoods. We extract representative trajectories from AISMD and carry out reaction pathway analysis to identify energetically favorable pathways for lignin depolymerization. Importantly, we identify dynamical effects that could not be observed through more traditional calculations of bond dissociation energies. Such effects include thermodynamically favorable recovery of aromaticity in the dienone ring that leads to near-barrierless subsequent ether cleavage and hydrogen-bonding effects that stabilize newly formed radicals. Some of the most stable spirodienone fragments that reside at most 1 eV above the reactant structure are formed with only 2 eV barriers for C-C bond cleavage, suggesting key targets for catalyst design to drive targeted depolymerization of lignin.

Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness.

Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.

Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways.

The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting fragments that are formed during depolymerization of lignin oligomers containing two to six monomers. We have developed a chemical discovery technique to identify the chemically relevant putative fragments in eight known polymeric linkage types of lignin. Obtaining these structures is a crucial precursor to the development of any further kinetic modeling. We have developed this approach by adapting steered molecular dynamics calculations under constant force and varying the points of applied force in the molecule to diversify the screening approach. Key observations include relationships between abundance and breaking frequency, the relative diversity of potential pathways for a given linkage, and the observation that readily cleaved bonds can destabilize adjacent bonds, causing subsequent automatic cleavage.

A remote stereochemical lever arm effect in polymer mechanochemistry.

Molecular mechanisms by which to increase the activity of a mechanophore might provide access to new chemical reactions and enhanced stress-responsive behavior in mechanochemically active polymeric materials. Here, single-molecule force spectroscopy reveals that the force-induced acceleration of the electrocyclic ring opening of gem-dichlorocyclopropanes (gDCC) is sensitive to the stereochemistry of an α-alkene substituent on the gDCC. On the ∼0.1 s time scale of the experiment, the force required to open the E-alkene-substituted gDCC was found to be 0.4 nN lower than that required in the corresponding Z-alkene isomer, despite the effectively identical force-free reactivities of the two isomers and the distance between the stereochemical permutation and the scissile bond of the mechanophore. Fitting the experimental data with a cusp model provides force-free activation lengths of 1.67 ± 0.05 and 1.20 ± 0.05 Å for the E and Z isomers, respectively, as compared to 1.65 and 1.24 Å derived from computational modeling.

Mechanically triggered heterolytic unzipping of a low-ceiling-temperature polymer.

Biological systems rely on recyclable materials resources such as amino acids, carbohydrates and nucleic acids. When biomaterials are damaged as a result of aging or stress, tissues undergo repair by a depolymerization-repolymerization sequence of remodelling. Integration of this concept into synthetic materials systems may lead to devices with extended lifetimes. Here, we show that a metastable polymer, end-capped poly(o-phthalaldehyde), undergoes mechanically initiated depolymerization to revert the material to monomers. Trapping experiments and steered molecular dynamics simulations are consistent with a heterolytic scission mechanism. The obtained monomer was repolymerized by a chemical initiator, effectively completing a depolymerization-repolymerization cycle. By emulating remodelling of biomaterials, this model system suggests the possibility of smart materials where aging or mechanical damage triggers depolymerization, and orthogonal conditions regenerate the polymer when and where necessary.

The charge transfer problem in density functional theory calculations of aqueously solvated molecules.

Recent advances in algorithms and computational hardware have enabled the calculation of excited states with time-dependent density functional theory (TDDFT) for large systems of O(1000) atoms. Unfortunately, the aqueous charge transfer problem in TDDFT (whereby many spuriously low-lying charge transfer excited states are predicted) seems to become more severe as the system size is increased. In this work, we concentrate on the common case where a chromophore is embedded in aqueous solvent. We examine the role of exchange-correlation functionals, basis set effects, ground state geometries, and the treatment of the external environment in order to assess the root cause of this problem. We conclude that the problem rests largely on water molecules at the boundary of a finite cluster model, i.e., "edge waters." We also demonstrate how the TDDFT problem can be related directly to ground state problems. These findings demand caution in the commonly employed strategy that rests on "snapshot" cutout geometries taken from ground state dynamics with molecular mechanics. We also find that the problem is largely ameliorated when the range-separated hybrid functional LC-ωPBEh is used.