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Reduction potentials of electrolyte molecules in the lithium–sulfur (Li/S) battery and their variations in several solvent environments are studied using the density functional theory method with D...

It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin (CaM), which adopts the most populated ternary structures determined from the MD simulations, followed by ab initio quantum mechanical (QM) calculations on all twelve amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential (ESP) in the context of a classical or polarizable force field (PFF). We discovered that the atomic radius of Ca2+ in conventional force fields is too large for the QM calculation to capture the variation in the coordination geometry of Ca2+ in its ionic form, leading to unphysical charges. Specifically, we found that the fitted atomic charges of Ca2+ in the context of PFF depend on the coordinating geometry of electronegative atoms from the amino acids in the loop. Although nearby water molecules do not influence the atomic charge of Ca2+, they are crucial for compensating for the coordination of Ca2+ due to the conformational flexibility in the EF-hand loop. Our method advances the development of force fields for metal ions and protein binding sites in dynamic environments., Comment: The following article has been accepted by Journal of Chemical Physics

Lithium-sulfur (Li/S) batteries are attractive substitutes for current lithium-ion batteries (LIBs) because of the lower cost and higher theoretical capacity of the cathode materials compared to the current transition metal oxide cathode materials in LIBs. However, the polysulfide (PS) redox shuttle causes severe capacity fading of Li/S batteries during cycling, and a strong self-discharge behavior. Although there can be a lot of efforts to reduce or prevent the PS redox shuttle, the development of additives to cover the surface of the cathode is the most efficient way to resolve the PS redox shuttle in the Li/S battery. The passivation film generated by electrolyte additives can not only reduce the oxidation of electrolyte solvents on the surface of the sulfur cathode but also inhibit the dissolution of PS from the cathode into the electrolyte. Few studies have been carried out for this purpose in Li/S batteries even when there have been a variety of studies in LIBs for high-voltage cathode materials. In order to understand how surface films are generated, oxidation potentials and oxidative decomposed products should be studied first. In this study, the oxidation potentials of electrolyte solvents, Li salts, and additives are calculated using the density functional theory (DFT) with a continuum solvation model. Together with electrolyte solvents and Li salts in Li/S batteries, the mostly employed cathode passivation additives in Li-ion batteries and in Li/S batteries are investigated for additives. In addition, it is also investigated how oxidation potentials of these electrolyte systems are varied by complexations with Li+, anions of Li salts, and S8 and pyrene as model systems to mimic the sulfur-carbon electrode materials in Li/S batteries.

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

The effects of solute-solvent interactions on solution structures of small peptides have been paid a great deal of attention. To study the effect of hydrogen-bonding interactions on peptide solution structures, we measured the amide I IR and VCD spectra of N-acetylproline amide (AP) in various protic solvents, i.e., D2O, MeOD, EtOD, and PrOD, and directly compared them with theoretically simulated ones. The numbers of protic solvent molecules hydrogen-bonded to the two peptide bonds in the AP were quantitatively determined by carrying out the molecular dynamics (MD) simulations and then compared with the spectral analyses of the experimentally measured amide I bands. The two peptides in the AP have different propensities of forming H-bonds with protic solvent molecules, and the H-bond population distribution is found to be strongly site-specific and solvent-dependent. However, it is found that adoption of the polyproline II (PII) conformation by AP in protic solvents does not strongly depend on the hydrogen bond network-forming ability of protic solvents nor on the solvent polarity. We present a brief discussion on the validity as well as limitation of the currently available force field parameters used for the present MD simulation study.

Carbon nanotubes (CNTs) were grown vertically aligned on silicon oxide substrates by pyrolyzing iron phthalocyanine (FePc), cobalt phthalocyanine (CoPc), and nickel phthalocyanine (NiPc) in the temperature range 700−1000 °C. As the temperature increases from 700 to 1000 °C, the growth rate of CNTs increases by a factor of approximately 45 and the average diameter increases from 30 to 80 nm. The CNTs grown using FePc exhibit about 2 times higher growth rate than those using CoPc and NiPc. The CNTs usually have a cylindrical structure, and a bamboo-like structure with a larger diameter at the higher temperature. The CNTs are doped with 2−6 at. % nitrogen atoms. The nitrogen content tends to decrease with the temperature increase. The CNTs grown using NiPc contain a higher nitrogen concentration compared to those grown using FePc and CoPc. The degree of crystalline perfection of the graphitic sheets increases with the temperature, but depends on the catalyst and the nitrogen content. The Arrhenius plot provi...

The explicit polarization (X-Pol) method is a self-consistent fragment-based electronic structure theory in which molecular orbitals are block-localized within fragments of a cluster, macromolecule, or condensed-phase system. To account for short-range exchange repulsion and long-range dispersion interactions, we have incorporated a pairwise, empirical potential, in the form of Lennard-Jones terms, into the X-Pol effective Hamiltonian. In the present study, the X-Pol potential is constructed using the B3LYP hybrid density functional with the 6-31G(d) basis set to treat interacting fragments, and the Lennard-Jones parameters have been optimized on a dataset consisting of 105 bimolecular complexes. It is shown that the X-Pol potential can be optimized to provide a good description of hydrogen bonding interactions; the root mean square deviation of the computed binding energies from full (i.e., nonfragmental) CCSD(T)/aug-cc-pVDZ results is 0.8 kcal/mol, and the calculated hydrogen bond distances have an average deviation of about 0.1 A from those obtained by full B3LYP/aug-cc-pVDZ optimizations.

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.