Photochemical tuning of dynamic defects for high-performance atomically dispersed catalysts.

Developing active and stable atomically dispersed catalysts is challenging because of weak non-specific interactions between catalytically active metal atoms and supports. Here we demonstrate a general method for synthesizing atomically dispersed catalysts via photochemical defect tuning for controlling oxygen-vacancy dynamics, which can induce specific metal-support interactions. The developed synthesis method offers metal-dynamically stabilized atomic catalysts, and it can be applied to reducible metal oxides, including TiO2, ZnO and CeO2, containing various catalytically active transition metals, including Pt, Ir and Cu. The optimized Pt-DSA/TiO2 shows unprecedentedly high photocatalytic hydrogen evolution activity, producing 164 mmol g-1 h-1 with a turnover frequency of 1.27 s-1. Furthermore, it generates 42.2 mmol gsub-1 of hydrogen via a non-recyclable-plastic-photoreforming process, achieving a total conversion of 98%; this offers a promising solution for mitigating plastic waste and simultaneously producing valuable energy sources.

Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.

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 a wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin, which adopts the most populated ternary structures determined from the molecular dynamics simulations, followed by ab initio quantum mechanical (QM) calculations on all 12 amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential 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.

First-principles calculations of oxidation potentials of electrolytes in lithium-sulfur batteries and their variations with changes in environment.

Oxidation potentials of electrolyte molecules in Li-sulfur (Li/S) batteries and their variations in various solvent environments are investigated using first-principles calculations in order to understand oxidative decomposition reactions of electrolytes for cathode passivation. Electrolyte solvents, Li salts, and various additives in Li/S batteries along with some Li-ion battery additives are studied. Oxidation potentials of isolated electrolyte molecules are found to be out of the operating range of typical Li/S batteries. The complexation of electrolyte molecules with Li+, salt anion, salt, S8, and pyrene alters oxidation potentials compared to those of the isolated systems. The salt anion lowers oxidation potentials of electrolyte molecules by at least 4.7% while the complexes with Li+ have higher oxidation potentials than the isolated molecules by at least 10.4%. S8 and pyrene, used as model compounds for sulfur and sulfur/carbon composite cathode materials, also affect oxidation potentials of electrolyte molecules, but their influence is negligible and the oxidation trends differ from those of the Li+ and salt anion. Although complexations change the oxidation potentials of electrolyte molecules, they are still higher than the operating voltage range of Li/S batteries, which indicates that oxidation of the studied electrolytes in Li/S batteries is not expected under ambient conditions.

Quantum mechanical force field for water with explicit electronic polarization.

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.

Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional.

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 Å from those obtained by full B3LYP/aug-cc-pVDZ optimizations.

On the Interplay between Electronic Structure and Polarizable Force Fields When Calculating Solution-Phase Charge-Transfer Rates.

We present a comprehensive analysis of the interplay between the choice of an electronic structure method and the effect of using polarizable force fields vs. nonpolarizable force fields when calculating solution-phase charge-transfer (CT) rates. The analysis is based on an integrative approach that combines inputs from electronic structure calculations and molecular dynamics simulations and is performed in the context of the carotenoid-porphyrin-C60 molecular triad dissolved in an explicit tetrahydrofuran (THF) liquid solvent. Marcus theory rate constants are calculated for the multiple CT processes that occur in this system based on either polarizable or nonpolarizable force fields, parameterized using density functional theory (DFT) with either the B3LYP or the Baer-Neuhauser-Livshits (BNL) density functionals. We find that the effect of switching from nonpolarizable to polarizable force fields on the CT rates is strongly dependent on the choice of the density functional. More specifically, the rate constants obtained using polarizable and nonpolarizable force fields differ significantly when B3LYP is used, while much smaller changes are observed when BNL is used. It is shown that this behavior can be traced back to the tendency of B3LYP to overstabilize CT states, thereby pushing the underlying electronic transitions to the deep inverted region, where even small changes in the force fields can lead to significant changes in the CT rate constants. Our results demonstrate the importance of combining polarizable force fields with an electronic structure method that can accurately capture the energies of excited CT states when calculating charge-transfer rates.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

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.

Nitrile and thiocyanate IR probes: molecular dynamics simulation studies.

Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

Site-specific hydrogen-bonding interaction between N-acetylproline amide and protic solvent molecules: comparisons of IR and VCD measurements with MD simulations.

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.

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.