Virtual Issue on New Physical Insights

Virtual Issue on New Physical Insight

Virtual Issue on New Physical Insights

Virtual Issue on New Physical Insight

Theoretical Investigation of Charge Transfer in Metal Organic Frameworks for Electrochemical Device Applications

For electrochemical device applications metal organic frameworks (MOFs) must exhibit suitable conduction properties. To this end, we have performed computational studies of intermolecular charge transfer in MOFs consisting of hexa-Zr^IV nodes and tetratopic carboxylate linkers. This includes an examination of the electronic structure of linkers that are derived from tetraphenyl benzene <b>1</b>, tetraphenyl pyrene <b>2</b>, and tetraphenyl porphyrin <b>3</b> molecules. These results are used to determine charge transfer propensities in MOFs, within the framework of Marcus theory, including an analysis of the key parameters (charge transfer integral <i>t</i>, reorganization energy λ, and free energy change Δ<i>G</i>⁰) and evaluation of figures of merit for charge transfer based on the chemical structures of the linkers. This qualitative analysis indicates that delocalization of the HOMO/LUMO on terminal substituents increases <i>t</i> and decreases λ, while weaker binding to counterions decreases Δ<i>G</i>⁰, leading to better charge transfer propensity. Subsequently, we study hole transfer in the linker <b>2</b> containing MOFs, <b>NU-901</b> and <b>NU-1000</b>, in detail and describe mechanisms (hopping and superexchange) that may be operative under different electrochemical conditions. Comparisons with experiment are provided where available. On the basis of the redox and catalytic activity of nodes and linkers, we propose three possible schemes for constructing electrochemical devices for catalysis. We believe that the results of this study will lay the foundation for future experimental work on this topic

Osmolytic Co-Solute Perturbing the Surface Enhancement of Halide Ions

We have investigated the variation in the surface binding free energy with the choice of halide ion, F^–, Cl^–, Br^–, and I^–, in water–glycerol binary mixtures with varying glycerol concentrations using umbrella sampling with a polarizable force field. We have found that halide surface adsorption is significantly perturbed by glycerol. At no or low glycerol concentration, the surface preference follows the Hofmeister series (I^– > Br^– > Cl^– > F^–). However, at the highest concentration, Br^– is preferentially stabilized. Decomposition of the free energy indicates that the halide surface adsorption is dominated by enthalpy and, specifically, by the solvent–solvent polarization interaction. The differences in this interaction between the chaotropic halides are reduced by glycerol addition, which is in line with a recent measurement of the solvent excess enthalpy for the same systems studied here. Moreover, our calculations indicate that the effect of an osmolyte (glycerol) on surface ion concentrations parallels the known effect of osmolytes on protein folding

Free Energy Profile and Mechanism of Self-Assembly of Peptide Amphiphiles Based on a Collective Assembly Coordinate

By combining targeted molecular dynamics (TMD) simulations, umbrella sampling, and the weighted histogram analysis method (WHAM), we have calculated the potential of mean force (PMF) for the transition between the bound and free states of 90 peptide amphiphiles (PAs) in aqueous solution, with the bound state corresponding to a cylindrical micelle fiber. We specifically consider a collective reaction coordinate, the radius of gyration of the PAs, to describe assembly in this work. It is found that the free energy, enthalpy, and entropy differences between the free and bound states are −126 kcal/mol, −185 kcal/mol, and −190 cal/(mol K), respectively, for the self-assembly process. This indicates that the driving force to form the micelle structure is enthalpic. The enthalpic driving forces originate from several factors, including the conformational energy of PAs and the electrostatic and van der Waals interaction energy between solvent molecules and between solvent and PAs. Among these interactions, the solvent electrostatic interaction is the dominating one, contributing 54% of the total driving force. The PMF profile can be recognized as involving two stages of assembly: (1) PAs initially approach each other in mostly random configurations and loosely aggregate, resulting in significant desolvation and initiation of head–tail conformational reorganization; (2) PAs undergo a conformational disorder-to-order transition, including forming secondary structures that include more β-sheets and fewer random coils, along with tail–head core–shell alignment and condensation that leads to total exclusion of water from the core. The PMF decreases slowly in the first stage, but rapidly in the second. This study demonstrates a hierarchy of assembly steps in which PA structural changes, solvation, and redistribution of solvent molecules play significant roles in the PA self-assembly process

Advantages of Conical Pores for Ion Pumps

Nanofabricated synthetic channels have been able to mimic the transport properties of their biological counterparts. But it is still nontrivial to make artificial ion pumps. Recent research on conical pores with charged surfaces has demonstrated significant ionic current rectification, which suggests the possibility of employing conical pores for pumping ions. In this work, salt pumping through conical pores driven by an external potential is studied including a consideration of both static and dynamic surface charges. Because of asymmetry of the structure and a charged inner surface, even conical pores with static surface charges are able to selectively pump ions whose charge is opposite the surface charge. Consequently, a mixture of both negatively and positively charged conical pores is able to pump salt (both cations and anions) with an oscillating external potential. Moreover, if the surface charge can be controlled dynamically, more efficient salt pumping can be achieved and the pumping flux is several times larger than that for cylindrical pores with fixed charges. We also find a reverse rectification effect when the length of the conical pore is shortened and angle is sufficiently large. The origin of reverse rectification is explained by evolution of the concentration profile at the tip side of the cone, with the rectification ratio depending on length and angle of the pore. Numerical simulations also suggest that the radius of the pore should be designed carefully to balance the net pumping flux and pumping–leakage ratio

Free-Energy Landscape for Peptide Amphiphile Self-Assembly: Stepwise versus Continuous Assembly Mechanisms

The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis, a cluster analysis of the time dependence of PA assembly and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semifiber structure. We also find that head group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated, and the pillar-like intermediate structure was also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of nanoseconds, the PA self-assembly process can be recognized as involving two steps, (a) transition from the disordered state to the noncylindrical pillar-like intermediate and (b) pillar-like to final semifiber transition. These results are important to the further design of PAs as functional nanostructures

Tensile Mechanics of α‑Helical Polypeptides

We have developed a statistical mechanical model of the force–extension behavior of α-helical polypeptides, by coupling a random-coil polypeptide elastic model of an inhomogeneous partially freely rotating chain, with the latest version of the helix–coil transition model AGADIR. The model is capable of making quantitatively accurate predictions of force–extension behavior of a given polypeptide sequence including its dependence on pH, temperature and ionic strength. This makes the model a valuable tool for single-molecule protein unfolding experimental studies. Our model predicts the highly reversible unraveling of α-helical structures at small forces of about 20 pN, in good agreement with recent experimental studies

Mechanisms of Formaldehyde and C₂ Formation from Methylene Reacting with CO₂ Adsorbed on Ni(110)

Methylene (CH₂) is thought to play a significant role as a reaction intermediate in the catalysis of methane dry reforming as well as in converting synthesis gas to light olefins via Fischer–Tropsch synthesis. Here, we report high quality Born–Oppenheimer molecular dynamics (BOMD) simulations of the reaction mechanisms associated with CH₂ impinging on a Ni(110) surface with CO₂ adsorbed at 0.33 ML coverage. The results show the formation of formaldehyde, carbon monoxide, C₂ species such as H₂C–CO₂, and others. Furthermore, we provide real-time demonstration of both Eley–Rideal (ER) and hot atom (HA) reaction mechanisms. The ER mechanism mostly happens when CH₂ directly collides with an oxygen of CO₂, while CH₂ attacks the carbon of CO₂, dominantly following the HA mechanism. If CH₂ reaches the Ni surface, it can easily break one C–H bond to form CH and H on the surface. The mechanistic details of H₂CO, H/CO, C₂, and H/CH formation are illuminated through the study of bond breaking/formation, charge transfer, and spin density of the reactants and catalytic surface. This illuminates the key contribution of geometry and electronic structure of catalytic surface to the reaction selectivity. Moreover, we find that ³CH₂ switches to surfaces of ¹CH₂ character as soon as the methylene and nickel/CO₂ orbitals show significant interaction, and as a result the reactivity is dominated by low barrier mechanisms. Overall, the BOMD simulations provide dynamical information that allows us to monitor details of the reaction mechanisms, confirming and extending current understanding of CH₂ radical chemistry in the dry reforming of methane and Fischer–Tropsch synthesis

Mechanisms of Formaldehyde and C₂ Formation from Methylene Reacting with CO₂ Adsorbed on Ni(110)

Methylene (CH₂) is thought to play a significant role as a reaction intermediate in the catalysis of methane dry reforming as well as in converting synthesis gas to light olefins via Fischer–Tropsch synthesis. Here, we report high quality Born–Oppenheimer molecular dynamics (BOMD) simulations of the reaction mechanisms associated with CH₂ impinging on a Ni(110) surface with CO₂ adsorbed at 0.33 ML coverage. The results show the formation of formaldehyde, carbon monoxide, C₂ species such as H₂C–CO₂, and others. Furthermore, we provide real-time demonstration of both Eley–Rideal (ER) and hot atom (HA) reaction mechanisms. The ER mechanism mostly happens when CH₂ directly collides with an oxygen of CO₂, while CH₂ attacks the carbon of CO₂, dominantly following the HA mechanism. If CH₂ reaches the Ni surface, it can easily break one C–H bond to form CH and H on the surface. The mechanistic details of H₂CO, H/CO, C₂, and H/CH formation are illuminated through the study of bond breaking/formation, charge transfer, and spin density of the reactants and catalytic surface. This illuminates the key contribution of geometry and electronic structure of catalytic surface to the reaction selectivity. Moreover, we find that ³CH₂ switches to surfaces of ¹CH₂ character as soon as the methylene and nickel/CO₂ orbitals show significant interaction, and as a result the reactivity is dominated by low barrier mechanisms. Overall, the BOMD simulations provide dynamical information that allows us to monitor details of the reaction mechanisms, confirming and extending current understanding of CH₂ radical chemistry in the dry reforming of methane and Fischer–Tropsch synthesis