Observation of electron orbital signatures of single atoms within metal-phthalocyanines using atomic force microscopy.

Resolving the electronic structure of a single atom within a molecule is of fundamental importance for understanding and predicting chemical and physical properties of functional molecules such as molecular catalysts. However, the observation of the orbital signature of an individual atom is challenging. We report here the direct identification of two adjacent transition-metal atoms, Fe and Co, within phthalocyanine molecules using high-resolution noncontact atomic force microscopy (HR-AFM). HR-AFM imaging reveals that the Co atom is brighter and presents four distinct lobes on the horizontal plane whereas the Fe atom displays a "square" morphology. Pico-force spectroscopy measurements show a larger repulsion force of about 5 pN on the tip exerted by Co in comparison to Fe. Our combined experimental and theoretical results demonstrate that both the distinguishable features in AFM images and the variation in the measured forces arise from Co's higher electron orbital occupation above the molecular plane. The ability to directly observe orbital signatures using HR-AFM should provide a promising approach to characterizing the electronic structure of an individual atom in a molecular species and to understand mechanisms of certain chemical reactions.

Preferential interactions between lithium chloride and glucan chains in N,N-dimethylacetamide drive cellulose dissolution.

Naturally occurring cellulose is crystalline as a consequence of the strong interactions between the glucan chains that comprise it and therefore is insoluble in most solvents. One of the few solvent systems able to dissolve cellulose is lithium chloride (LiCl) dissolved in N,N-dimethylacetamide (DMA). By an integrated application of all-atom molecular dynamics (MD) simulations, reaction path optimization, free-energy calculations, and a force-matching analysis of coarse-grained atomistic simulations, we establish that DMA-mediated preferential interactions of Li(+) cations and Cl(-) anions with glucan chains enable cellulose dissolution in LiCl/DMA. The relatively weak solvation of Li(+), Cl(-), and glucan chains by DMA results in strong effective interactions of Li(+) and Cl(-) ions with the glucans, leading to cellulose dissolution. The small size of the Li(+) cations allows them to strongly couple to multiple interaction sites on the glucan chains of cellulose, including the spatially restricted regions around the ether linkages connecting neighboring glucose residues. Li(+) cations were thus identified as the main component responsible for driving cellulose dissolution. The mechanism for explaining the solubility of cellulose in the LiCl/DMA system deduced from the analysis of atomistic-scale simulations conducted in this work is also consistent with most of the empirical observations related to cellulose dissolution in salt/amide solvent systems.

Degree of polymerization of glucan chains shapes the structure fluctuations and melting thermodynamics of a cellulose microfibril.

A Staggered LATtice (SLAT) model is developed for modeling cellulose microfibrils. The simple representation of molecular packing and interactions employed in SLAT allows simulations of structure fluctuations and phase transition of cellulose microfibrils at sufficiently long and large scales for comparison with experiments. Glucan chains in the microfibril are modeled as connected monomers, each corresponding to a cellobiose subunit, and the surrounding space around the cellulose is composed of solvent cells. Interaction parameters of monomer-monomer interactions were parametrized based on the results of atomistic molecular dynamics simulations. The monomer-solvent interaction was optimized to give a melting temperature of ∼695 K for the 36-glucan chain model cellulose microfibril, which is consistent with the estimation based on experimental data. Monte Carlo simulations of the SLAT model also capture experimentally measured X-ray diffraction patterns of cellulose as a function of temperature, including the region of melting transition, as well as predict the highly flexible regions in the microfibril. Beyond the diameter of ∼3 nm, we found that melting temperature of the cellulose microfibril is not significantly shifted by changing the thickness. On the other hand, a slight decrease in the degree of polymerization of glucan chains is shown to enhance structure fluctuations through the ends of glucan chains, i.e., the defect sites, and thereby significantly reduce the melting temperature. Analysis of the sizes, densities, and lifetimes of defect structures in the microfibril indicates a significant extent of fluctuations on the surfaces even at room temperature and that defect statistics are strong but distinct functions of temperature and solvent quality. The SLAT model is the first of its kind for simulating cellulosic materials, and this work shows that it can be used to incorporate information obtained from atomistic simulations and experimental data to enable the aforementioned findings through computation.

Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride.

The entropic driving forces of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride (BmimCl) are investigated via molecular dynamics simulations and the two-phase thermodynamic model. An atomistic model of cellulose was simulated at a dissociated state and a microfibril state to represent dissolution. The calculated values of entropy and internal energy changes between the two states inform the interplay of energetic and entropic driving forces in cellulose dissolution. In both water and BmimCl, we found that the entropy associated with the solvent degrees of freedom (DOF) decreases upon cellulose dissolution. However, solvent entropy reduction in BmimCl is much smaller than that in water and counteracts the entropy gain from the solute DOF to a much lesser extent. Solvent entropy reduction in water also plays a major role in making the free energy change of cellulose dissolution unfavorable at room temperature. In BmimCl, the interaction energies between solvent molecules and glucan chains and the total entropy change both contribute favorably to the dissolution free energy of cellulose. Calculations at different temperatures in the two solvents indicate that changes in total internal energy are a good indicator of the sign of the free energy change of cellulose dissolution.

Thermodynamics of cellulose solvation in water and the ionic liquid 1-butyl-3-methylimidazolim chloride.

Cellulose is present in biomass as crystalline microfibrils held together by a complex network of intermolecular interactions making it difficult to initiate its hydrolysis and conversion to fuels. While cellulose is insoluble in water and most organic solvents, complete dissolution of cellulose can be achieved in certain classes of ionic liquids (ILs). The present study was undertaken to analyze the thermodynamic driving forces of this process and to understand how the anions and cations comprising an IL interact with the different moieties of glucose residues to cause dissolution. All-atom molecular dynamics (MD) simulations were performed at two extreme states of cellulose dissolution: a crystalline microfibril and a dissociated state in which all the glucan chains of the microfibril are fully separated from each other by at least four solvation shells. MD simulations of the two states were carried out in water and in the IL 1-butyl-3-methylimidazolium chloride (BmimCl) to provide a comprehensive analysis of solvent effects on cellulose dissolution. The results reveal two important molecular aspects of the mechanism of cellulose dissolution. The first is that the perturbation of solvent structures by the dissolved glucan chains can be a crucial factor in determining solubility, particularly for the insolubility of cellulose in water at 300 K. Second, both the Cl(-) and the Bmim(+) ions of BmimCl interact with the moieties of glucan residues that form intersheet contacts, the most robust component of the interaction network of crystalline cellulose. Cl(-) anions can form hydrogen bonds (HBs) with the hydroxyl groups of glucan chains from either the equatorial or the axial directions. For Bmim(+) cations, the calculated density profiles reveal that the contacts with glucan chains along the axial directions are closer than those along the equatorial directions. On the basis of the results of atomistic MD simulations, we propose that interacting with glucan chains along axial directions and disrupting the intersheet contacts of cellulose is an important ability of cellulose pretreatment solvents.

Dissecting force interactions in cellulose deconstruction reveals the required solvent versatility for overcoming biomass recalcitrance.

Pretreatment for deconstructing the multifaceted interaction network in crystalline cellulose is a limiting step in making fuels from lignocellulosic biomass. Not soluble in water and most organic solvents, cellulose was found to dissolve in certain classes of ionic liquids (ILs). To elucidate the underlying mechanisms, we simulated cellulose deconstruction by peeling off an 11-residue glucan chain from a cellulose microfibril and computed the free-energy profile in water and in 1-butyl-3-methylimidazolium chloride (BmimCl) IL. For this deconstruction process, the calculated free-energy cost/reduction in water/BmimCl is ∼2 kcal/mol per glucose residue, respectively. To unravel the molecular origin of solvent-induced differences, we devised a coarse graining scheme to dissect force interactions in simulation models by a force-matching method. The results establish that solvent-glucan interactions are dependent on the deconstruction state of cellulose. Water couples to the hydroxyl and side-chain groups of glucose residues more strongly in the peeled-off state but lacks driving forces to interact with sugar rings and linker oxygens. Conversely, BmimCl demonstrates versatility in targeting glucose residues in cellulose. Anions strongly interact with hydroxyl groups, and the coupling of cations to side chains and linker oxygens is stronger in the peeled-off state. Other than enhancing anion-hydroxyl group coupling, coarse-grain analysis of force interactions identifies configuring cations to target side chains and linker oxygens as a useful design strategy for pretreatment ILs. Furthermore, the state dependence of solvent-glucan interactions highlights specific stabilization and/or frustration of the different structure states of cellulose as important design parameters for pretreatment solvents.

On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils.

Biomass recalcitrance is a fundamental bottleneck to producing fuels from renewable sources. To understand its molecular origin, we characterize the interaction network and solvation structures of cellulose microfibrils via all-atom molecular dynamics simulations. The network is divided into three components: intrachain, interchain, and intersheet interactions. Analysis of their spatial dependence and interaction energetics indicate that intersheet interactions are the most robust and strongest component and do not display a noticeable dependence on solvent exposure. Conversely, the strength of surface-exposed intrachain and interchain hydrogen bonds is significantly reduced. Comparing the interaction networks of I(ß) and I(α) cellulose also shows that the number of intersheet interactions is a clear descriptor that distinguishes the two allomorphs and is consistent with the observation that I(ß) is the more stable form. These results highlight the dominant role of the often-overlooked intersheet interactions in giving rise to biomass recalcitrance. We also analyze the solvation structures around the surfaces of microfibrils and show that the structural and chemical features at cellulose surfaces constrict water molecules into specific density profiles and pair correlation functions. Calculations of water density and compressibility in the hydration shell show noticeable but not drastic differences. Therefore, specific solvation structures are more prominent signatures of different surfaces.