Histidine Protonation States Regulate the State Transition from R State Hemoglobin.

The objective of our work is to investigate the impact of pH on the structural changes of hemoglobin that affect its O2 affinity, known as the Bohr effect. We conducted molecular dynamics (MD) simulations to explore the transition between various hemoglobin states based on the protonation states (PSs) of two histidine residues (ßHis143 and ßHis146). We conducted the MD simulations from the R and R2 states with three sets of PSs assuming pH values of 7.0, 6.5, and 5.5, aiming to investigate the influence of pH on hemoglobin behavior. Our results demonstrated that the protonated His residues promote the state transition from the R state to the R2 state and encourage elongation of the distance between the ß1-ß2 subunits by weakening the inter-subunit interactions in the R state. These observations, aligning with the experimental evidence, indicate that the R2 state typically crystallizes under low pH conditions. Our findings suggest that the relationship between the PSs and the structural stability of the R state plays a role in the acid and alkaline Bohr effect.

Atomistic Chemical Elucidation of the Higher-Rate Reaction Mechanism in Hf-Pyridyl Amido-Catalyzed Copolymerization of Ethene and 1-Octene: Application of Red Moon Simulation with Polymer Propagation Diagrams.

The Hf-pyridyl amido complex ((pyridylamido)Hf(IV)) is a cationic catalyst activated by ion-pairing with auxiliary catalyst B(C6F5)4 to show high activity for α-olefin polymerization. Previously, it was experimentally observed that the consumption rate of 1-octene in the 1-octene/ethene copolymerization is 3-fold compared to the 1-octene homopolymerization in coordinative chain transfer polymerization using the catalyst HfCat+-B(C6F5)4- ion pair (IP) and the chain transfer agent (CTA) ZnEt2. In the present study, we have performed atomistic chemical simulations of the IP-catalyzed homopolymerization of 1-octene and copolymerization of 1-octene and ethene on the basis of the Red Moon (RM) methodology. Using the analysis by polymer propagation diagrams (PPDs), in the 1-octene homopolymerization and the 1-octene/ethene copolymerization with the 1-octene-inserted catalyst (oHfCat), it is theoretically shown that the propagation reactions intermittently pause due to the steric hindrance of two hexyl groups of the oHfCat and the 1-octene inserted adjacent to the Hf atom. On the other hand, in the polymerizations with the ethene-inserted catalyst (eHfCat), it is reasonably recognized that the propagation reactions occur smoothly at a constant rate, and the polymerization continuously proceeds due to the relatively smaller steric hindrance. In conclusion, it was shown, for the first time, that the RM method can be used to reveal the microscopic effects of monomers and substituents in the polymerization reaction processes. Therefore, our current work using PPDs demonstrates the promising potential of the RM methodology in studying catalytic olefin polymerizations and complex chemical reaction systems in general.

Microscopic Analysis of the Mechanical Stability of an SEI Layer Structure Depending on the FEC Additive Concentration in Na-Ion Batteries: Maximum Appearance in Vickers Hardness at Lower FEC Concentrations.

The stability of the solid electrolyte interphase (SEI) layer during the charging-discharging cycles is reasonably related to its microscopic elasticity. For the first time, it was theoretically revealed that each component of the elastic moduli takes a maximum at an optimal concentration of 1.0 vol % of fluoroethylene carbonate (FEC) for the SEI layer formed in the FEC-added NaPF6/PC-based electrolyte. The elastic constants indicated that the SEI layer formed at lower FEC concentrations is more resistant to tensile and shear deformations. The optimal hardness is sensitive in the lower FEC concentrations although it simply decreases as the FEC concentration increases. This is due to the formation of a denser SEI structure with small cavities in the lower concentrations. The results are excellently consistent with the experimental one, justifying the microscopic understanding of the FEC additive effect on the mechanical stability of the SEI layers designed through the Red Moon simulation.

(Pyridylamido)Hf(IV)-Catalyzed 1-Octene Polymerization Reaction Interwoven with the Structural Dynamics of the Ion-Pair-Active Species: Bridging from Microscopic Simulation to Chemical Kinetics with the Red Moon Method.

We performed the atomistic simulation of 1-octene polymerization reaction catalyzed by the ionic pair (IP) consisting of the cationic active species of (pyridylamido)Hf(IV) catalyst, HfCatPn+, and different counteranions (CAs), B(C6F5)4- and MeB(C6F5)3-, at different monomer concentrations. Using a hybrid Monte Carlo/molecular dynamics method, that is, the Red Moon (RM) method, the reaction progress measured by the "RM cycle" was transformed into effective real time using the time transformation theory. Then, the degree of polymerization was found to be consistent with that in the chemical kinetics, a macroscopic theory, and experimental ones. Remarkably, the current simulation has revealed the different dynamical features in the polymerization behavior originating from the CA. Namely, the HfCatPn+-B(C6F5)4- IP mainly forms an outer-sphere IP (OSIP) throughout the polymerization. The HfCatPn+-MeB(C6F5)3- IP, on the other hand, forms an inner-sphere IP (ISIP) in the initial stage of polymerization, and the ratio of ISIP steeply drops after the first monomer insertion because the IP interaction is reduced by the steric hindrance between the inserted monomers and the CA. In conclusion, we have shown that the microscopic IP dynamics interwoven with the polymerization reaction can be computationally observed in the real-time domain by using the RM method. Therefore, our current work demonstrates the promising potential of the RM method in studying catalytic olefin polymerization and complex chemical reaction systems.

Verification for Temperature Dependence of Tacticity in Polystyrene Radical Polymerization with the Combination of Reaction Pathway Analysis and Red Moon Methodology.

Radical polymerization is an economic and practical polymerization method over ionic and coordination polymerizations and is widely used for polymer production. Although many efforts have been made to improve the convenience and controllability of radical polymerization, it is still a challenge to directly observe the microbehaviors of propagation, which may provide inspiration for the development of polymerization processes. In this study, we focused on the tacticity of polystyrene produced by bulk radical polymerization since there is a debate over the temperature dependence. The propagation process is simulated via Red Moon methodology, which is a cost-effective method for handling complex chemical reaction systems. By the multiple pathway analysis for the propagation reaction model composed of the dimer radical and the monomer using density functional theory, we obtained the relative energies in multiple transition states, whose energy differences are partly explained by the π-π stacking interactions. Via performing Red Moon simulations from 30 to 190 °C, we confirmed that meso contents moderately increase as the temperature increases, which is explained by the influence of temperature on the probability density of the reaction conformations of each pathway. The successful prediction and explanation for tacticity demonstrate the potential of Red Moon methodology in unveiling the microbehaviors of propagation.

Chloride Ions Stabilize Human Adult Hemoglobin in the T-State, Competing with Allosteric Interaction of Oxygen Molecules.

In the context of a molecular-level understanding of the allostery mechanisms, human adult hemoglobin (HbA) has been extensively studied for over half a century. Chloride ions (Cl-) have been known as one of HbA allosteric effectors, which stabilizes the T-state preferable to release oxygen molecules. The functional mechanisms were individually proposed by Ueno and Perutz several decades ago. Ueno considered that the site-specific Cl- binding is essential, while Perutz proposed the non-site-specific interaction between HbA and Cl-. Each speculation explains the mechanism plausibly since each was tightly associated with its reasonable experimental observation. However, both mechanisms themselves still seem to make their speculations controversial. In the present study, we have theoretically reconsidered these apart from their approaches. Our atomistic molecular dynamics simulations then showed that the increase of Cl- concentration suppresses the conformational conversion from the T-state. Interestingly, chloride ions loosely interact with the amino acid residues inside the HbA central cavity, suggesting that both Perutz's and Ueno's speculations are involved in understanding the microscopic roles of Cl-. In conclusion, we theoretically certified that the effect of Cl- competes against that of solvated O2, i.e., the destabilization of T-state through the non-site-specific interaction, implying the concerted regulation of HbA under physiological conditions.

Frontiers in Theoretical Analysis of Solid Electrolyte Interphase Formation Mechanism.

Solid electrolyte interphase (SEI) is an ion conductive yet electron-insulating layer on battery electrodes, which is formed by the reductive decomposition of electrolytes during the initial charge. The nature of the SEI significantly impacts the safety, power, and lifetime of the batteries. Hence, elucidating the formation mechanism of the SEI layer has become a top priority. Conventional theoretical calculations reveal initial elementary steps of electrolyte reductive decomposition, whereas experimental approaches mainly focus on the characterization of the formed SEI in the final form. Moreover, both theoretical and experimental methodologies could not approach intermediate or transient steps of SEI growth. A major breakthrough has recently been achieved through a novel multiscale simulation method, which has enriched the understanding of how the reduction products are aggregated near the electrode and influence the SEI morphologies. This review highlights recent theoretical achievements to reveal the growth mechanism and provides a clear guideline for designing a stable SEI layer for advanced batteries.

Atomistic Simulation of the Polymerization Reaction by a (Pyridylamido)hafnium(IV) Catalyst: Counteranion Influence on the Reaction Rate and the Living Character of the Catalytic System.

Atomistic simulation of the 1-octene polymerization reaction by a (pyridylamido)Hf(IV) catalyst was conducted on the basis of Red Moon (RM) methodology, focusing on the effect of the counteranions (CAs), MeB(C6F5)3-, and B(C6F5)4-, on the catalyst activity and chain termination reaction. We show that RM simulation reasonably reproduces the faster reaction rate with B(C6F5)4- than with MeB(C6F5)3-. Notably, the initiation of the polymerization reaction with MeB(C6F5)3- is comparatively slow due to the difficulty of the first insertion. Then, we investigated the free energy map of the ion pair (IP) structures consisting of each CA and the cationic (pyridylamido)Hf(IV) catalyst with the growing polymer chain (HfCatPn+), which determines the polymerization reaction rates, and found that HfCatPn+-MeB(C6F5)3- can keep forming "inner-sphere" IPs even after the polymer chain becomes sufficiently bulky, while HfCatPn+-B(C6F5)4- forms mostly "outer-sphere" IPs. Finally, we further tried to elucidate the origin of the broader molecular weight distribution (MWD) of the polymer experimentally produced with B(C6F5)4- than that with MeB(C6F5)3-. Then, through the trajectory analysis of the RM simulations, it was revealed that the chain termination reaction would be more sensitive to the IP structures than the monomer insertion reaction because the former involves a more constrained structure than the latter, which is likely to be a possible origin of the MWDs dependent on the CAs.

A Constant-pH Hybrid Monte Carlo Method with a Configuration-Selection Scheme Using the Zero Energy Difference Condition: Elucidation of Molecular Diffusivity Correlated with a pH-Dependent Solvation Shell.

We have proposed a new constant-pH (CpH) hybrid Monte Carlo (MC) method with a configuration-selection (CS) scheme, called the CS-CpH method, to obtain pH-dependent physical properties within a framework of atomistic molecular simulation. The CS-CpH method consists of carrying out a short equilibrium molecular dynamics (MD) and a searching MD coupled with thermostats and barostats to generate physically plausible configurations with changed protonation states (PSs) that are subsequently accepted or rejected according to the Metropolis MC procedure. As an example, we have applied it to glutamic acid in aqueous solution and have demonstrated that it can work to generate reasonably the pH-dependent microscopic configuration ensemble compatible with the experimental pKa value and also to show interestingly the molecular diffusivity correlated with pH-dependent solvation shell. In conclusion, we believe that the present CS-CpH method becomes a quite useful tool to study the microscopic origin of various pH-dependent phenomena, interpreting them in the atomistic chemical processes.

Development of advanced electrolytes in Na-ion batteries: application of the Red Moon method for molecular structure design of the SEI layer.

This review aims to overview state-of-the-art progress in the collaborative work between theoretical and experimental scientists to develop advanced electrolytes for Na-ion batteries (NIBs). Recent investigations were summarized on NaPF6 salt and fluoroethylene carbonate (FEC) additives in propylene carbonate (PC)-based electrolyte solution, as one of the best electrolytes to effectively passivate the hard-carbon electrode with higher cycling performance for next-generation NIBs. The FEC additive showed high efficiency to significantly enhance the capacity and cyclability of NIBs, with an optimal performance that is sensitive at low concentration. Computationally, both microscopic effects, positive and negative, were revealed at low and high concentrations of FEC, respectively. In addition to the role of FEC decomposition to form a NaF-rich solid electrolyte interphase (SEI) film, intact FECs play a role in suppressing the dissolution to form a compact and stable SEI film. However, the increase in FEC concentration suppressed the organic dimer formation by reducing the collision frequency between the monomer products during the SEI film formation processes. In addition, this review introduces the Red Moon (RM) methodology, recent computational battery technology, which has shown a high efficiency to bridge the gap between the conventional theoretical results and experimental ones through a number of successful applications in NIBs.

Theoretically predicting the feasibility of highly-fluorinated ethers as promising diluents for non-flammable concentrated electrolytes.

The practical application of nonflammable highly salt-concentrated (HC) electrolyte is strongly desired for safe Li-ion batteries. Not only experimentalists but also theoreticians are extensively focusing on the dilution approach to address the limitations of HC electrolyte such as low ionic conductivity and high viscosity. This study suggests promising highly-fluorinated ethers to dilute the HC electrolyte based on non-flammable trimethyl phosphate (TMP) solvent. According to the quantum mechanical and molecular dynamics calculations, the fluorinated ether diluents showed a miscibility behavior in HC TMP-based electrolyte. While such miscibility behavior of the diluent with TMP solvent has been significantly enhanced by increasing its degree of fluorination, i.e., the "fluorous effect", it is remarkable that the self-diffusion constant of Li+ and the ionic conductivity should be significantly improved by dilution with bis(1,1,2,2-tetrafluoro ethyl) ether (B2E) and bis(pentafluoro ethyl) ether (BPE) compared to other common hydrofluoroether diluents. In addition, the fluorinated-ether diluents have high ability to form a localized-concentrated electrolyte in HC TMP-based solution, leading to high expectation for the formation of a stable and a compact inorganic SEI film.

Theoretical analysis of electrode-dependent interfacial structures on hydrate-melt electrolytes.

Aqueous electrolytes have the potential to overcome some of the safety issues associated with current Li-ion batteries intended for large-scale applications such as stationary use. We recently discovered a lithium-salt dihydrate melt, viz., Li(TFSI)0.7(BETI)0.3·2H2O, which can provide a wide potential window of over 3 V; however, its reductive stability strongly depends on the electrode material. To understand the underlying mechanism, the interfacial structures on several electrodes (C, Al, and Pt) were investigated by conducting molecular dynamics simulation under the constraint of the electrode potential. The results showed that the high adsorption force on the surface of the metal electrodes is responsible for the increased water density, thus degrading the reductive stability of the electrolyte. Notably, the anion orientation on Pt at a low potential is unfavorable for the formation of a stable anion-derived solid electrolyte interphase, thus promoting hydrogen evolution. Hence, the interfacial structures that depend on the material and potential of the electrode mainly determine the reductive stability of hydrate-melt electrolytes.

Scalable and Precise Synthesis of Armchair-Edge Graphene Nanoribbon in Metal-Organic Framework.

Graphene nanoribbons (GNRs), narrow and straight-edged stripes of graphene, attract a great deal of attention because of their excellent electronic and magnetic properties. As of yet, there is no fabrication method for GNRs to satisfy both precision at the atomic scale and scalability, which is critical for fundamental research and future technological development. Here, we report a methodology for bulk-scale synthesis of GNRs with atomic precision utilizing a metal-organic framework (MOF). The GNR was synthesized by the polymerization of perylene (PER) or its derivative within the nanochannels of the MOF. Molecular dynamics simulations showed that PER was uniaxially aligned along the nanochannels of the MOF through host-guest interactions, which allowed for regulated growth of the nanoribbons. A series of characterizations of the GNR, including NMR, UV/vis/NIR, and Raman spectroscopy measurements, confirmed the formation of the GNR with well-controlled edge structure and width.

Microscopic Origin of the Solid Electrolyte Interphase Formation in Fire-Extinguishing Electrolyte: Formation of Pure Inorganic Layer in High Salt Concentration.

A highly salt-concentrated (HC) electrolyte based on the nonflammable solvent trimethyl-phosphate (TMP) has recently shown an attractive self-extinguishing property in addition to an excellent charge-discharge performance. However, the microscopic understanding of its solid electrolyte interphase (SEI) layer remains an open question. In this Letter, the red moon (RM) method was used to investigate the molecular mechanism of SEI layer formation depending on lithium bis(fluorosulfonyl)amide (LiFSA) salt concentration in a TMP-based electrolyte and was able to reproduce successfully the experimental observations, i.e., the "bottom-up" formation mechanism with a thinner and denser SEI layer mainly based on salt reduction in the HC electrolyte. The results showed that a pure dense inorganic layer is formed in the HC electrolyte, which should considerably improve the SEI layer stability leading to a longer lifetime in charge-discharge performance. This new microscopic finding should provide an important guide in designing an effective nonflammable electrolyte to develop advanced, safe secondary batteries.

Vibrational Spectroscopy in Solution through Perturbative ab Initio Molecular Dynamics Simulations.

We have developed a method that allows computing the vibrational spectra at a high quantum mechanical level for molecules in solution or other complex systems. The method is based on the use of configurational samplings from combined QM/MM molecular dynamics simulations and the use of perturbation theory to calculate accurate molecular properties. Such calculations provide in addition accurate free energy gradient vectors and Hessian matrices and thus open the door for the characterization of stationary points in free energy landscapes and the study of chemical reaction mechanisms in large disordered systems. The vibrational spectrum of the water molecule in liquid water has been computed as a test case. It has been obtained using a weighted average of instantaneous signals assuming the instantaneous normal modes approach. Vibrational frequencies are also computed by diagonalizing the Hessian of the free energy surface. Comparison is made with experimental data and with calculations using the Fourier transform of the time autocorrelation function of the dipole moment. The discussion emphasizes the advantages of the developed methodology compared to other techniques in terms of the accuracy/computational cost ratio.

Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian-based constant potential molecular dynamics simulation study.

Computational models including electrode polarization can be essential to study electrode/electrolyte interfacial phenomena more realistically. We present here a constant-potential classical molecular dynamics simulation method based on the extended Lagrangian formulation where the fluctuating electrode atomic charges are treated as independent dynamical variables. The method is applied to a graphite/ionic liquid system for the validation and the interfacial kinetics study. While the correct adiabatic dynamics is achieved with a sufficiently small fictitious mass of charge, static properties have been shown to be almost insensitive to the fictitious mass. As for the kinetics study, electrical double layer (EDL) relaxation and ion desorption from the electrode surface are considered. We found that the polarization slows EDL relaxation greatly whereas it has little impact on the ion desorption kinetics. The findings suggest that the polarization is essential to estimate the kinetics in nonequilibrium processes, not in equilibrium. © 2019 Wiley Periodicals, Inc.

Impact of cis- versus trans-Configuration of Butylene Carbonate Electrolyte on Microscopic Solid Electrolyte Interphase Formation Processes in Lithium-Ion Batteries.

The solid electrolyte interphase (SEI) film, which consists of the products of reduction reaction of the electrolyte, has a strong influence on the lifetime and safety of Li-ion batteries. Of particular importance when designing SEI films is its strong dependence on the electrolyte solvent. In this study, we focused on geometric isomers cis- and trans-2,3-butylene carbonates ( c/ t-BC) as model electrolytes. Despite their similar structures and chemical properties, t-BC-based electrolytes have been reported to enable the reversible reaction of graphite anodes [as in ethylene carbonate (EC)], whereas c-BC-based electrolytes cause the exfoliation of graphite [as in propylene carbonate (PC)]. To understand the microscopic origin of the different electrochemical behaviors of t-BC and c-BC, we applied Red Moon simulation to elucidate the microscopic SEI film formation processes. The results revealed that the SEI film formed in c-BC-based electrolytes contains fewer dimerized products, which are primary components of a good SEI film; this lower number of dimerized products can cause reduced film stability. As one of the origins of the decreased dimerization in c-BC, we identified the larger solvation energy of c-BC for the intermediate species and its smaller diffusion constant, which largely diminishes the dimerization. Moreover, the correlation among the Li+ intercalation behavior, nature of the SEI film, and strength of solvation was found to be common for EC/PC and t-BC/ c-BC electrolytes, confirming the importance of solvation of the intermediates in the stability of the SEI film. These results suggest that weakening the solvation of the intermediates is one possible way to stabilize the SEI film for better charge-discharge performance.

Microscopic Elucidation of Solid-Electrolyte Interphase (SEI) Film Formation via Atomistic Reaction Simulations: Importance of Functional Groups of Electrolyte and Intact Additive Molecules.

Secondary batteries such as Li-ion battery are expected to be utilized as not only ubiquitous electric power sources such as mobile phones but also large-scale electricity storage devices. Therefore, it is urgent to develop the higher performance secondary batteries. Their lifetime and stability are found to be strongly dependent on the nature of passivation film called solid electrolyte interphase (SEI) film formed on the anode surface in the initial charge-discharge cycle. However, since it is difficult to directly observe the film formation processes in experiment, its microscopic mechanism is still not found. On the other hand, although the theoretical methods are useful complement to the experiment, some new methodologies are necessary to understand the long-term processes of SEI film, which is produced as a result of that a lot of chemical reactions proceed simultaneously. Under the circumstances, we have developed Red Moon method that can simulate such complex chemical reaction systems, and were able to analyze for the first time the SEI film formation processes on the anode surface at the atomistic level. Then, we clarified theoretically the microscopic mechanism of the additive effect which is essential to improve the Na-ion battery performance so as to enhance the SEI film formation. This new microscopic insight must provide an important guiding principle for use in designing the most suitable electrolytes for developing high-performance secondary batteries.

Atomistic chemical computation of Olefin polymerization reaction catalyzed by (pyridylamido)hafnium(IV) complex: Application of Red Moon simulation.

We have realized the microscopic simulation of olefin polymerization, that is, the simulation of the catalytic polymerization (CP) reaction system composed of (pyridylamido)hafnium(IV) complex as the catalyst. For this purpose, we adopted Red Moon (RM) method, a novel molecular simulation method to simulate the complex reaction system. First, according to the previous research, with the help of the QM calculation, we proposed a model system and elementary processes and explained the theoretical treatment of the simulation by the RM method (the RM simulation). In addition, we also proposed a macroscopic simulation based on chemical kinetics simulation. Then, we performed two simulations and compared them in terms of the effective time evolution of the three macroscopic physical quantities, the number-average molecular weight Mn , the mass-average molecular weight Mw , and the molar-mass dispersity DM . The comparison showed that the two simulations are in quantitative or partially qualitative agreement with each other. Therefore, it is concluded that the RM simulation could not only simulate the CP reaction process microscopically, but also it is connected essentially to reproduce the time evolution of the macroscopic physical quantities on the basis of its microscopic simulation data. © 2018 Wiley Periodicals, Inc.

The crucial role of electron transfer from interfacial molecules in the negative potential shift of Au electrode immersed in ionic liquids.

Potential of zero charge (PZC) is essential in electrochemistry to understand physical and chemical phenomena at the interface between an electrode and a solution. A negative potential shift from the work function to the PZC has been experimentally observed in a metal/ionic liquid (IL) system, but the mechanism remains unclear and controversial. In this paper we provide valuable insight into the mechanism on the potential shift in the Au/IL (1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide: [BMIM][TFSA]) system using a computational approach combining classical molecular dynamics simulations and first-principles calculations. By separately estimating some contributions to the potential shift, the shift is calculated in an easy-to-understand manner. The resultant PZC is shown to be in good agreement with the experimental one. Among the contributions, the electron redistribution at the Au/IL interface is found to provide the largest negative potential change. This indicates that the redistribution plays a crucial role in determining the potential shift of the Au electrode immersed in the IL. Detailed analyses suggest that the redistribution corresponds to the electron transfer not only from the anionic TFSA but also from the cationic BMIM molecules to the Au electrode surface. This unique observation is understood to originate from the interfacial structure where the IL molecules are in very close proximity to the electrode surface via dispersion interaction.