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Density functional theory in classical explicit solvents: Mean‐field QM / MM method for simulating solid–liquid interfaces
Abstract
Solid–liquid interfaces are ubiquitous in scientifically and technologically important systems, and they govern complex chemophysical processes such as those in electrochemistry and heterogeneous catalysis. Atomic-level elucidation of interfacial structures has been extensively pursued; however, related research is still limited. A major obstacle lies in the intrinsic character of interfaces: they are located between two bulk phases that make the application of spectroscopic or surface-science techniques be difficult. Although this suggests the possibility of employing computational approaches to explore interfacial structures, modern molecular simulation methods suffer from an inability to simulate large interfacial systems in a sufficient time scale at the all-atom resolution. To develop a method capable of simulating solid–liquid interfaces, we have been developing a mean-field quantum mechanics/molecular mechanics (QM/MM) method. This Review briefly summarizes the theoretical background of mean-field QM/MM, as well as recent efforts to advance it. Furthermore, we summarize several studies performed based on this method.
... Assuming that the solvation effect's presence is a major distinction between the inter-residue interactions of folded proteins and IDPs, we explored aromatic π-π interactions in aqueous environments. We examined how water solvation modifies the π-π interaction of benzene and phenol dimers by combining two modern computational chemistry methods: (1) the van der Waals (vdW)-corrected density functional theory (DFT) for an accurate description of direct monomer-monomer interaction energy; (2) DFT in classical explicit solvents (DFT-CES), which is a mean-field quantum mechanics/molecular mechanics (QM/MM) method [26][27][28] enabling an explicit treatment of solvent molecules for a reliable description of solvation free energy. We found that the solvation effect renormalizes the interaction energies between benzene and phenol molecules, the conformational dependence of which can be understood in terms of the changes in the number of hydrogen bonds (HB) before and after dimer formation: water-benzene HB for benzene dimers and water-hydroxyl HB for phenol dimers. ...
... DFT-CES is a grid-based mean-field QM/MM method that was recently developed by the Kim group [26][27][28]. The mean-field QM/MM method iteratively solves QM optimizations and molecular dynamics (MD) simulations until a self-consistent solution is obtained [29][30][31]. ...
The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.
... 9−12 It is noteworthy that these iterations can be understood as optimizing the QM subsystem on the Helmholtz free energy surface. 13 As an interaction communication channel, DFT-CES utilizes a 3D rectangular grid to provide an accurate and seamless description of E Coul between nuclei charge/electron density in the QM region and point charges in the MM region. E vdW relies on a typical pairwise description, with parameters currently adopted from the OPLS-AA force fields 14 for organic systems, which demonstrate notable accuracy in predicting the hydration free energies of small molecules. ...
The solid–liquid interface plays a crucial role in governing complex chemical phenomena, such as heterogeneous catalysis and (photo)electrochemical processes. Despite its importance, acquiring atom-scale information about these buried interfaces remains highly challenging, which has led to an increasing demand for reliable atomic simulations of solid–liquid interfaces. Here, we introduce an innovative first-principles-based multiscale simulation approach called DFT-CES2, a mean-field QM/MM method. To accurately model interactions at the interface, we developed a quantum-mechanics-based embedding scheme that partitions complex noncovalent interactions into Pauli repulsion, Coulomb (including polarization), and London dispersion energies, which are described using atom-dependent transferable parameters. As validated by comparison with high-level quantum mechanical energies, DFT-CES2 demonstrates chemical accuracy in describing interfacial interactions. DFT-CES2 enables the investigation of complex solid–liquid interfaces while avoiding extensive parametrization. Therefore, we expect DFT-CES2 to be broadly applicable for elucidating atom-scale details of large scale solid–liquid interfaces for multicomponent systems.
... To identify the chemical role of M + during CO 2 RR, we first investigate atomic details of the catalyst-electrolyte interface using density functional theory in classical explicit solvent (DFT-CES) simulation 36 . This method offers an accurate description of the electrified interface at a balanced computational cost, by mean-field coupling of a quantum mechanical description on the catalyst surface with a molecular dynamics description on the liquid structure of the electrolyte phase 37 . Recent advances in computational simulations enable a direct investigation of the electrode-electrolyte structure, highlighting the importance of the atomic arrangement of EDL constituents (e.g. ...
Electrocatalysis, whose reaction venue locates at the catalyst–electrolyte interface, is controlled by the electron transfer across the electric double layer, envisaging a mechanistic link between the electron transfer rate and the electric double layer structure. A fine example is in the CO2 reduction reaction, of which rate shows a strong dependence on the alkali metal cation (M⁺) identity, but there is yet to be a unified molecular picture for that. Using quantum-mechanics-based atom-scale simulation, we herein scrutinize the M⁺-coupling capability to possible intermediates, and establish H⁺- and M⁺-associated ET mechanisms for CH4 and CO/C2H4 formations, respectively. These theoretical scenarios are successfully underpinned by Nernstian shifts of polarization curves with the H⁺ or M⁺ concentrations and the first-order kinetics of CO/C2H4 formation on the electrode surface charge density. Our finding further rationalizes the merit of using Nafion-coated electrode for enhanced C2 production in terms of enhanced surface charge density.
... In this section, a brief discussion is presented on the various features of the biosensors and drug delivery systems, that can be predicted using quantum chemical methods. Density functional theory (DFT) ranks as the most widely used quantum mechanical method and plays an increasingly larger role in a number of disciplines besides chemistry, such as physics, materials, biology, and pharmacy [94][95][96][97][98][99][100][101][102][103]. While DFT computations have long been used to complement experimental investigations, the approach has emerged as an indispensable and powerful tool for predictions of different fields. ...
In this chapter, we presented an analysis of the recent advances in the applications of boron clusters in biomedical fields such as the development of biosensors and drug delivery systems on the basis of quantum chemical calculations. Biosensors play an essential role in many sectors, e.g., law enforcement agencies for sensing illicit drugs, medical communities for detecting overdosed medications from human and animal bodies, etc. The drug delivery systems have theoretically been proposed for many years and subsequently implemented by experiments to deliver the drug to the targeted sites by reducing the harmful side effects significantly. Boron clusters form a rich and colorful family of atomic clusters due to their unconventional structures and bonding phenomena. Boron clusters and their complexes have various biological activities such as the drug delivery, imaging for diagnosis, treatment of cancer, and probe of protein-biomolecular interactions. For all of these reactivities, the interaction mechanisms and the corresponding energetics between biomaterials and boron clusters are of essential importance as a basic step in the understanding, and thereby design of relevant materials. During the past few years, attempts have been made to probe the nature of these interactions using quantum chemical calculations mainly with density functional theory (DFT) methods. This chapter provides a summary of the theoretical viewpoint on this issue.
Lithium–sulfur batteries (LSBs) have gained remarkable attention over the past several years, however, their inherent limitations, such as the poor interfacial stability of their Li anodes and the severe dissolution of polysulfide, are regarded as bottlenecks that prevent these batteries from entering commercial markets. In this study, a 1,1‐diethoxyethane (DEE), which has been functionalized with acetal groups, is proposed as an electrolyte cosolvent to complement the limitations of the electrode materials of LSBs. In Li/Li symmetric cells, the DEE cosolvent exhibited stable cycling behavior, whereas the cell with the baseline electrolyte exhibited rapidly increasing polarization, even after 650 h. In LSB cells, the electrolyte that contains 50% DEE exhibits the highest cycling retention (65.0%) compared to the baseline electrolyte (49.8%) because it effectively protects the interface of the Li anode, but also suppresses the dissolution of polysulfide species.
New materials for electrochemical energy storage and conversion are the key to the electrification and sustainable development of our modern societies. Molecular modelling based on the principles of quantum mechanics and statistical mechanics as well as empowered by machine learning techniques can help us to understand, control and design electrochemical energy materials at atomistic precision. Therefore, this roadmap, which is a collection of authoritative opinions, serves as a gateway for both the experts and the beginners to have a quick overview of the current status and corresponding challenges in molecular modelling of electrochemical energy materials for batteries, supercapacitors, CO2RR, and fuel cell applications.
Incorporating solvent-adsorbate interactions is paramount in models of aqueous (electro)catalytic reactions. Although a number of techniques exist, they are either highly demanding in computational terms or inaccurate. Microsolvation offers a trade-off between accuracy and computational expenses. Here, we dissect a method to swiftly outline the first solvation shell of species adsorbed on transition-metal surfaces and assess their corresponding solvation energy. Interestingly, dispersion corrections are generally not needed in the model, but caution is to be exercised when water-water and water-adsorbate interactions are of similar magnitude.
Colloidal photocatalysts can utilize solar light for the conversion of CO2 to carbon-based fuels, but controlling the product selectivity for CO2 reduction remains challenging, in particular in aqueous solution. Here, we present an organic surface modification strategy to tune the product selectivity of colloidal ZnSe quantum dots (QDs) towards photocatalytic CO2 reduction even in the absence of transition metal co-catalysts. Besides H2, imidazolium-modified ZnSe QDs evolve up to 2.4 mmolCO gZnSe -1 (TONQD > 370) after 10 h of visible light irradiation (AM 1.5G, λ > 400 nm) in aqueous ascorbate solution with a CO-selectivity of up to 20%. This represents a four-fold increase in CO-formation yield and 13-fold increase in CO-selectivity compared to non-functionalized ZnSe QDs. The binding of the thiolated imidazolium ligand to the QD surface is characterized quantitatively using 1H-NMR spectroscopy and isothermal titration calorimetry, revealing that a subset of 12 to 17 ligands interacts strongly with the QDs. Transient absorption spectroscopy reveals an influence of the ligand on the intrinsic charge carrier dynamics through passivating Zn surface sites. Density functional theory calculations indicate that the imidazolium capping ligand plays a key role in stabilizing the surface-bound *CO2 - intermediate, increasing the yield and selectivity toward CO production. Overall, this work unveils a powerful tool of using organic capping ligands to modify the chemical environment on colloids, thus enabling control over the product selectivity within photocatalyzed CO2 reduction.
Experiments have shown that graphene-supported Ni-single atom catalysts (Ni-SACs) provide a promising strategy for the electrochemical reduction of CO2 to CO, but the nature of the Ni sites (Ni-N2C2, Ni-N3C1, Ni-N4) in Ni-SACs has not been determined experimentally. Here, we apply the recently developed grand canonical potential kinetics (GCP-K) formulation of quantum mechanics to predict the kinetics as a function of applied potential (U) to determine faradic efficiency, turn over frequency, and Tafel slope for CO and H2 production for all three sites. We predict an onset potential (at 10 mA cm−2) Uonset = −0.84 V (vs. RHE) for Ni-N2C2 site and Uonset = −0.92 V for Ni-N3C1 site in agreement with experiments, and Uonset = −1.03 V for Ni-N4. We predict that the highest current is for Ni-N4, leading to 700 mA cm−2 at U = −1.12 V. To help determine the actual sites in the experiments, we predict the XPS binding energy shift and CO vibrational frequency for each site. Single atom catalysts (SACs) are promising in electrocatalysis but challenging to characterize. Here, the authors apply a recently developed quantum mechanical grand canonical potential kinetics method to predict reaction mechanisms and rates for CO2 reduction at different sites of graphene-supported Ni-SACs.
The water/metal interface often governs important chemophysical processes in various technologies. Therefore, from scientific and engineering perspectives, the detailed molecular-level elucidation of the water/metal interface is of high priority, but the related research is limited. In experiments, the surface-science techniques, which can provide full structural details of the surface, are not easy to directly apply to the interfacial systems under ambient conditions, and the well-defined facets cannot be entirely free from contamination at the contact with water. To answer long-standing debates regarding the wettability, structure, and dynamics of water at metal interfaces, we here develop reliable first-principles-based multiscale simulations. Using the state-of-the-art simulations, we find that the clean metal surfaces are actually superhydrophilic and yield zero contact angles. Furthermore, we disclose an inadequacy of widespread ice-like bilayer model of the water adlayers on metal surfaces from both averaged structural and dynamic points of view. Our findings on the nature of water on metal surfaces provide new molecular level perspectives on the tuning and design of water/metal interfaces that are at the heart of many energy applications.
The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar aromatic compounds. To investigate a cause of error, we employed a novel systematic framework of quantum-mechanical/molecular-mechanical (QM/MM) coupling protocol in explicit solvation manner, termed DFT-CES, based on the grid-based mean-field treatment. With the aid of DFT-CES, we delved into multiple energy parts, thereby comparing DFT-CES and PB models component-by-component. By applying the modified PB model to estimate the hydration free energies of non-polar solutes, we find a possibility to improve the predictability of PB models. We expect that this study could shed light on providing an accurate route to study the hydration thermodynamics for various solute compounds.
Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
Electrochemical CO2 conversion technology is becoming indispensable in the development of a sustainable carbon-based economy. While various types of electrocatalytic systems have been designed, those based on room-temperature ionic liquids (RTILs) have attracted considerable attention because of their high efficiencies and selectivities. Furthermore, it should be possible to develop more advanced electrocatalytic systems for commercial use because target-specific characteristics can be fine-tuned using various combinations of RTIL ions. To achieve this goal, we require a systematic understanding of the role of the RTIL components in electrocatalytic systems, however, their role has not yet been clarified by experiment or theory. Thus, the purpose of this short review is to summarize recent experimental and theoretical mechanistic studies to provide insight into and to develop guidelines for the successful development of new CO2 conversion systems. The results discussed here can be summarized as follows. Complex physical and chemical interactions between the RTIL components and the reaction intermediates, in particular at the electrode surface, are critical for determining the activity and selectivity of the electrocatalytic system, although no single factor dominates. Therefore, more fundamental research is required to understand the physical, chemical, and thermodynamic characteristics of complex RTIL-based electrocatalytic systems.
The corrosion properties of copper in ultrapure water have been studied experimentally by submerging copper samples (99.9999%) in pure water for up to 29 months. The surface was first electropolished at ambient temperature, then exposed to hydrogen gas treatment at 300–400 °C, thereby reducing the bulk hydrogen content to 0.03 ppm. These copper samples, the water and the glassware were all then subjected to precise chemical analysis. Great care was taken to avoid contamination. After exposure, only ∼6 μg/L copper had accumulated in the water phase. Electron spectroscopy could not detect Cu2O or any other oxidation products containing copper.
Young's construction for a contact angle at a three-phase intersection forms the basis of all fields of science that involve wetting and capillary action. We find compelling evidence from recent experimental results on the deformation of a soft solid at the contact line, and displacement of an elastic wire immersed in a liquid, that Young's equation can only be interpreted by surface energies, and not as a balance of surface tensions. It follows that the a priori variable in finding equilibrium is not the position of the contact line, but the contact angle. This finding provides the explanation for the pinning of a contact line.
The impact of phosphorous (P)-doping on the electrochemical performance and surface chemistry of soft carbon is investigated by means of galvanostatic cycling and ex situ X-ray photoelectron spectroscopy (XPS). P-doping plays an important role in storing more Li ions and discernibly improves reversible capacity. However, the discharge capacity retention of P-doped soft carbon electrodes deteriorated at compared to non-doped soft carbon. This poor capacity retention could be improved by vinylene carbonate (VC) participating in forming a protective interfacial chemistry on soft carbon. In addition, the effect of P-doping on exothermic thermal reactions of lithiated soft carbon with electrolyte solution is discussed on the basis of differential scanning calorimetry (DSC) results.
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.
The structure of water on metal electrodes is addressed based on first-principles calculations. Special emphasis is placed on the competition between water-metal and water-water interaction as the structure determining factors. Thus the question will be discussed whether water at metal surfaces is ice- or rather liquid-like. The proper description of liquid phases requires to perform thermal averages. This has been done by combining first-principles electronic structure calculations with molecular dynamics simulations. After reviewing recent studies about water on flat, stepped and pre-covered metal electrodes, some new results will be presented.
The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
Density functional theory (DFT) was used to determine the ground state geometries of indigo and new design
dyes (IM-Dye-1 IM-Dye-2 and IM-Dye-3). The time dependant density functional theory (TDDFT) was used
to calculate the excitation energies. All the calculations were performed in both gas and solvent phase. The
LUMO energies of all the dyes were above the conduction band of TiO2, while the HOMOs were below the
redox couple (except IM-Dye-3). The HOMO-LUMO energy gaps of new design dyes were smaller as
compared to indigo. All new design dyes were strongly red shifted as compared to indigo. The improved light
harvesting efficiency (LHE) and free energy change of electron injection ΔGinject
of new designed sensitizers
revealed that these materials would be excellent sensitizers. The broken coplanarity between the benzene near
anchoring group having LUMO and the last benzene attached to TPA unit in all new design dyes consequently
would hamper the recombination reaction. This theoretical designing will the pave way for experimentalists to
synthesize the efficient sensitizers for solar cells.
It is generally accepted that supported graphene is hydrophobic and that its water contact angle is similar to that of graphite. Here, we show that the water contact angles of freshly prepared supported graphene and graphite surfaces increase when they are exposed to ambient air. By using infrared spectroscopy and X-ray photoelectron spectroscopy we demonstrate that airborne hydrocarbons adsorb on graphitic surfaces, and that a concurrent decrease in the water contact angle occurs when these contaminants are partially removed by both thermal annealing and controlled ultraviolet-O3 treatment. Our findings indicate that graphitic surfaces are more hydrophilic than previously believed, and suggest that previously reported data on the wettability of graphitic surfaces may have been affected by unintentional hydrocarbon contamination from ambient air.
QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical
(QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom
methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider
methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state
chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We
also discuss some available software. Finally, we present a few comments about future directions of research in this exciting
area, where we focus on more intimate blends of QM with MM.
The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent. Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multigrid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system. Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum surface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)] of the solute. The resulting self-consistent continuum solvation model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the polarizable continuum model with a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes. Two parameters allow to fit experimental solvation energies on the same set with a mean absolute error of 1.3 kcal/mol. A detailed analysis of these results, broken down along different classes of chemical compounds, shows that several classes of organic compounds display very high accuracy, with solvation energies in error of 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond-forming compounds.
Band gaps and band alignments for AlN, GaN, InN, and InGaN alloys are investigated using density functional theory with the with the Heyd-Scuseria-Ernzerhof {HSE06 [J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 134, 8207 (2003); 124, 219906 (2006)]} XC functional. The band gap of InGaN alloys as a function of In content is calculated and a strong bowing at low In content is found, described by bowing parameters 2.29 eV at 6.25% and 1.79 eV at 12.5%, indicating the band gap cannot be described by a single composition-independent bowing parameter. Valence-band maxima (VBM) and conduction-band minima (CBM) are aligned by combining bulk calculations with surface calculations for nonpolar surfaces. The influence of surface termination [(1100) m-plane or (1120) a-plane] is thoroughly investigated. We find that for the relaxed surfaces of the binary nitrides the difference in electron affinities between m- and a-plane is less than 0.1 eV. The absolute electron affinities are found to strongly depend on the choice of XC functional. However, we find that relative alignments are less sensitive to the choice of XC functional. In particular, we find that relative alignments may be calculated based on Perdew-Becke-Ernzerhof [J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 134, 3865 (1996)] surface calculations with the HSE06 lattice parameters. For InGaN we find that the VBM is a linear function of In content and that the majority of the band-gap bowing is located in the CBM. Based on the calculated electron affinities we predict that InGaN will be suited for water splitting up to 50% In content.
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
While fluid flow on solid-liquid interfaces has been of great interest, studying its behavior is challenging because it requires a comprehensive understanding of the complex interactions that exist at various realistic solid-liquid interfaces. In particular, the slip phenomenon had been a debated subject for decades before the phenomenon was proven on a molecular level. Since the slip behavior is widely acknowledged, its fundamental relationships with other measurable physical properties have been studied intensively. Here we present a first-principles-based multiscale simulation study on various solid-water interfacial systems to understand how the physical quantities influence the slip length. Based on the simulation results, we propose an extended quasi-universal relationship between the slip length and the work of adhesion by considering surface packing density. Furthermore, we scrutinize the effects of the electron density tail from the solid wall on both slip length and work of adhesion. We also investigate the relationship between the self-diffusivity of the fluid at the interface and the slip length. Our present study underlines the impact of atomic-level details of solid-liquid interfaces, such as surface packing structure and electrostatic interactions, in determining hydrodynamic boundary conditions.
The electrodeposited-film electrode CFeCoNiP was fabricated to serve as bifunctional electrocatalyst for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Kinetic Tafel slope analysis suggests that HER catalytic process is involved in Volmer-Tafel mechanism (29 mV/dec), indicating the recombination of two adsorbed hydrogen atoms as rate-determining step. In comparison with FeCoNi-based thick film (thickness 168.3 m) showing metallic state favorable for electron transfer, in operando XAS investigation on FeCoNi-based thin film (thickness 389.2 nm) unravels that Fe3+-assisted water dissociation promotes the formation of Co2+--H-Ni3+ (catalyst-Had) species, which subsequently undergoes reductive elimination to furnish H2 gas under HER process. During OER, CoNi-oxide matrix acts as a chemical and electroconductive host to build/stabilize the key intermediate [Fe4+=O/Fe3+-O˙] motifs that subsequently triggers catalytic O-O bond formation (30 mV/dec) through radical-radical coupling of the adjacent [Fe4+=O/Fe3+-O˙] motifs or/and OH– attack on Fe4+-induced electrophilic oxygen center leading to O2 release. The mechanistic experiments advance insight into catalytic kinetics/intermediates and demonstrate the electronically cooperative interplay among Fe/Co/Ni offers the enhanced alkaline water electrolysis. The CFeCoNiP catalyst exhibits excellent HER activity (specific activity js = 0.227 mA/cm2) with low charge transfer resistance (3.9 ) and overpotential of 37 mV achieving current density of 10 mA/cm2, and also shows good OER activity (js = 1.798 mA/cm2) with low charge transfer resistance (2.1 ) and 250 mV overpotential approaching a current density of 10 mA/cm2 in 1 M NaOH aqueous solution. The CFeCoNiP/NF (electrodeposition on Ni foam) electrode-pair device reaches a current density of 100 and 500 mA/cm2 at a voltage of 1.65 and 1.86 V, respectively, under alkaline condition.
A structural analysis of solvating water layers on a Pt(111) electrode has been performed based on extensive ab initio molecular dynamics simulations. We have emulated different electrochemical conditions by varying...
The ab initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of degrees of freedom involved. In this work, we develop a computationally efficient model where the electrode part of the interface is described at the density-functional theory (DFT) level, and the electrolyte part is represented through an implicit solvation model based on the Poisson-Boltzmann equation. We describe the implementation of the linearized Poisson-Boltzmann equation into the Vienna Ab initio Simulation Package, a widely used DFT code, followed by validation and benchmarking of the method. To demonstrate the utility of the implicit electrolyte model, we apply it to study the surface energy of Cu crystal facets in an aqueous electrolyte as a function of applied electric potential. We show that the applied potential enables the control of the shape of nanocrystals from an octahedral to a truncated octahedral morphology with increasing potential.
To date, copper is the only heterogeneous catalyst that has shown a propensity to produce valuable hydrocarbons and alcohols, such as ethylene and ethanol, from electrochemical CO2 reduction (CO2R). There are variety of factors that impact CO2R activity and selectivity, including the catalyst surface structure, morphology, composition, the choice of electrolyte ions and pH, and the electrochemical cell design. Many of these factors are often intertwined, which can complicate catalyst discovery and design efforts. Here we take a broad and historical view of these different aspects and their complex interplay in CO2R catalysis on Cu, with the purpose of providing new insights, critical evaluations, and guidance to the field with regard to research directions and best practices. First, we describe the various experimental probes and complementary theoretical methods that have been used to discern the mechanisms by which products are formed, and next we present our current understanding of the complex reaction networks for CO2R on Cu. We then analyze two key methods that have been used in attempts to alter the activity and selectivity of Cu: nanostructuring and the formation of bimetallic electrodes. Finally, we offer some perspectives on the future outlook for electrochemical CO2R.
Conversion of CO2 to value-added products is the favorable route both for the greenhouse gas mitigation and carbon-resource utilization. It is still a huge challenge to efficiently, selectively, and economically convert CO2 to highly valuable products. Many reviews focus on the catalysts and the products of CO2 utilization have been published. However, no comprehensively review on ionic liquids (ILs)-mediated CO2 valorization had published. Here, we gave a review on the ILs-mediated conversion of CO2. During the conversion of CO2, ILs could play the role of solvent, electrolyte, CO2 absorbent, CO2 activating agent, catalyst or co-catalyst. The effects of the cation, the anion, the alkyl chain length, and functional group of ILs, as long as the temperature, pressure, other solvent, or co-catalyst on the catalytic efficiency and selectivity are discussed. We intend to provide a comprehensive understanding on recent experimental and theoretical progresses of thermal, electrochemical and photochemical conversion of CO2 mediated by ionic liquids, and make clear the role of ILs in the process of CO2 conversion.
The solid-liquid interface is of great interest because of its highly heterogeneous character and its ubiquity in various applications. The most fundamental physical variable determining the strength of the solid-liquid interface is the solid-liquid interfacial tension, which is usually measured according to the contact angle. However, an accurate experimental measurement and a reliable theoretical prediction of the contact angle remain lacking because of many practical issues. Here, we propose a first principles-based simulation approach to quantitatively predict the contact angle of an ideally clean surface using our recently developed multiscale simulation method of density functional theory in classical explicit solvents (DFT-CES). Using this approach, we simulate the surface wettability of a graphene and graphite surface, resulting in a reliable contact angle value that is comparable to the experimental data. From our simulation results, we find that the surface wettability is dominantly affected by the strength of the solid-liquid van der Waal’s interaction. However, we further elucidate that there exists a secondary contribution from the change of water-water interaction, which is manifested by the change of liquid structure and dynamics of interfacial water layer. We expect that our proposed method can be used to quantitatively predict and understand the intriguing wetting phenomena at an atomistic level and can eventually be utilized to design a surface with a controlled hydrophobic(philic)ity.
Recently, many experimental and theoretical efforts are being intensified to develop high-performance catalysts for electrochemical CO2 conversion. Beyond the catalyst materials screening, it is also critical to optimize surrounding reaction medium. From vast experiments, inclusion of room-temperature ionic liquid (RTIL) in the electrolyte is found to be beneficial for CO2 conversion; however, there is yet no unified picture of the role of RTIL, prohibiting further optimization of the reaction medium. Using a state-of-the-art multiscale simulation, we here unveil the atomic origin of catalytic promotion effect of RTIL during CO2 conversion. Unlike the conventional belief, which assumes a specific intermolecular coordination by the RTIL component, we find that the promotion effect is collectively manifested by tuning the reaction microenvironment. This mechanism suggests the critical importance of the bulk properties (e.g., resistance, gas solubility and diffusivity, viscosity, etc.) over the detailed chemical variations of the RTIL components in designing the optimal electrolyte components, which is further supported by our experiments. This fundamental understanding of complex electrochemical interfaces will help to develop more advanced electrochemical CO2 conversion catalytic systems in the future.
While the surface atomic structure of RuO2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) was used to determine the surface structural changes on single-crystal RuO2 (110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of -H2O on the coordinatively unsaturated Ru sites (CUS) and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring -OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the -OH group used to stabilize –OO was found to be rate-limiting.
The use of ionic liquids as reaction media can confer many advantages upon catalytic reactions over reactions in organic solvents. In ionic liquids, catalysts having polar or ionic character can easily be immobilized without additional structural modification and thus the ionic solutions containing the catalyst can easily be separated from the reagents and reaction products, and then, be reused. More interestingly, switching from an organic solvent to an ionic liquid often results in a significant improvement in catalytic performance (e.g., rate acceleration, (enantio)selectivity improvement and an increase in catalyst stability). In this review, some recent interesting results which can nicely demonstrate these positive ?ionic liquid effect? on catalysis are discussed.
Among various models that incorporate solvation effects into first-principles based electronic structure theory, such as density functional theory (DFT), the average solvent electrostatic potential/molecular dynamics (ASEP/MD) method is particularly advantageous. This method explicitly includes the nature of complicated solvent structures that is absent in implicit solvation methods, while retaining computational cost that is less significant than that with conventional QM/MM approaches including full dynamics of solute and solvent molecules. Herein, we present a real-space rectangular grid-based method to implement the mean-field QM/MM idea of ASEP/MD to plane-wave DFT, which is named as "DFT in classical explicit solvents", or DFT-CES. By employing a three dimensional real-space grid as a communication medium, we can treat the electrostatic interactions between the DFT solute and the ASEP sampled from MD simulations, in a seamless and straightforward manner. Moreover, we couple a fast and efficient free energy calculation method based on the two-phase thermodynamic (2PT) model with our DFT-CES method, which enables direct and simultaneous computations of the solvation free energies as well as the geometric and electronic response of a solute of interest under the solvation effect. With the aid of DFT-CES/2PT, we investigate the solvation free energies and detailed solvation thermodynamics for 17 types of organic molecules, which show good agreement with the experimental data. We further compare our simulation results with previous theoretical models and assumptions made for the development of implicit solvation models. We anticipate that our proposed method, DFT-CES/2PT, enables the vast utilization of the ASEP/MD method for investigations of solvation properties of materials by using periodic DFT calculations in the future.
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory (KSDFT) based polarizable Poisson model for modeling polar solvation free energies. For the nonpolar component, either the standard model of surface area, molecular volume, and van der Waals interactions, or a model with atomic surface areas and molecular volume is employed. Based on the assumption that similar molecules have similar parametrizations, we develop scoring and ranking algorithms to classify solute molecules. Four sets of radius parameters are combined with four sets of charge force fields to arrive at a total of 16 different parametrizations for the Poisson model. A large database with 668 experimental data is utilized to validate the proposed protocol. The lowest leave-one-out root mean square (RMS) error for the database is 1.33k cal/mol. Additionally, five subsets of the database, i.e., SAMPL0-SAMPL4, are employed to further demonstrate that the proposed protocol offers some of the best solvation predictions. The optimal RMS errors are 0.93, 2.82, 1.90, 0.78, and 1.03 kcal/mol, respectively for SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 test sets. These results are some of the best, to our best knowledge.
CO2 conversion is an essential technology to develop a sustainable carbon economy for the present and the future. Many studies have focused extensively on the electrochemical conversion of CO2 into various useful chemicals. However, there is not yet a solution of sufficiently high enough efficiency and stability to demonstrate practical applicability. In this work, we use first-principles-based high-throughput screening to propose silver-based catalysts for efficient electrochemical reduction of CO2 to CO while decreasing the overpotential by 0.4-0.5 V. We discovered the covalency-aided electrochemical reaction (CAER) mechanism in which p-block dopants have a major effect on the modulating reaction energetics by imposing partial covalency into the metal catalysts, thereby enhancing their catalytic activity well beyond modulations arising from d-block dopants. In particular, sulfur or arsenic doping can effectively minimize the overpotential with good structural and electrochemical stability. We expect this work to provide useful insights to guide the development of a feasible strategy to overcome the limitations of current technology for electrochemical CO2 conversion.
The high cost of proton exchange membrane fuel cells (PEMFCs) comes largely from the use of platinum-containing electrocatalysts. Despite significant progress made the past decade on reducing the platinum catalyst loading in the PEMFC electrodes, further substantial cost reductions require the replacement of platinum with less expensive nonplatinum electrocatalytic materials. In this study, PdCu alloys have computationally been investigated as possible non-Pt catalysts for oxygen reduction reaction (ORR) in PEMFCs. We used density functional theory (DFT) calculations to determine the structural preference and ORR activity as a function of the composition and structure. Five PdCu alloy surface structures, B2, L12, L10, L11-nonlayered, and L11-layered, were considered, and the layered L11 surface structure was found to exhibit significantly improved ORR kinetics compared to that of pure Pd.
ASEP/MD is a computer program designed to implement the Averaged Solvent Electrostatic Potential/Molecular Dynamics (ASEP/MD) method developed by our group. It can be used for the study of solvent effects and properties of molecules in their liquid state or in solution. It is written in the FORTRAN90 programming language, and should be easy to follow, understand, maintain and modify. Given the nature of the ASEP/MD method, external programs are needed for the quantum calculations and molecular dynamics simulations. The present version of ASEP/MD includes interface routines for the GAUSSIAN package, HONDO, and MOLDY, but adding support for other programs is straightforward. This article describes the program and its usage.
Experimental and theoretical investigations bearing on the question of the wettability, by water, of clean oxygen-free metal surfaces are reviewed. Results on gold, silver, and copper are discussed in terms of surface cleanliness, surface structure, and extent of dispersion (London) force interaction. It is concluded that clean solid metal surfaces are hydrophilic. They will yield a zero degree contact angle when prepared in the amorphous state and possibly in the perfect crystalline state as well. These results do not necessarily preclude the possibility that physical interaction at the metal-water interface consists solely of dispersion forces.
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The structure and dynamics of liquid water at the interface with three solid surfaces has been investigated via molecular dynamics simulation. The three surfaces include a flat hydrophobic surface, an atomically rough hydrophobic surface, and a contrasting, hydrophilic, fully hydroxylated silica surface. The results of analysis show that, as expected, the solvent near each of the two hydrophobic surfaces behaves essentially equivalently, with loss of hydrogen bonding at the interface. For the hydroxylated surface, surface–solvent hydrogen bonding is stronger than interactions in the bulk solvent, with the nearest solvent layer interacting specifically with up to three surface hydroxyl groups. Nevertheless, distinct structural perturbation of the solvent extends in every case no more than about 10 Å from the surface, and the perturbation is only strong in the immediate solvation layer. Furthermore, the corresponding dynamical perturbation of the solvent, as measured by the diffusion rates and reorientation times in comparison to the bulk, is always relatively small. For the hydrophilic case, it is largest, but even here it is less than a factor of 5 at the immediate interface and less than a factor of 2 in the second hydration layer. The residence time for solvent at the interface is found to be insensitive to the hydrophilicity of the surface. Calculated nuclear magnetic resonance (NMR) order parameters for the solvent are found to reflect solvent orientational ordering, but are shown not to be distinctive of the nature of that order.
We have developed a three-dimensional (3D) extension of the reference interaction site model-self-consistent field (RISM-SCF) method to treat the electronic structure of a solvated molecule. The site–site treatment of the solute–solvent correlations involving the approximation of radial averaging constitutes a bottleneck of the RISM-SCF method, and thus lacks a 3D picture of the solvation structure for complex solutes. To resolve this problem, we devised out a 3D generalization of the RISM integral equations which yields the 3D correlation functions of interaction sites of solvent molecules around a solute of arbitrary shape. In the present article, we propose a SCF combination of the ab initio molecular orbital (MO) methods and 3D-RISM approach. A benchmark result for carbon monoxide in ambient water is also presented. © 2000 American Institute of Physics.
We have developed a self-consistent description of an interface between a metal and a molecular liquid by combination of the density functional theory in the Kohn–Sham formulation (KS DFT) for the electronic structure, and the three-dimensional generalization of the reference interaction site model (3D RISM) for the classical site distribution profiles of liquid. The electron and classical subsystems are coupled in the mean field approximation. The procedure takes account of many-body effects of dense fluid on the metal–liquid interactions by averaging the pseudopotentials of liquid molecules over the classical distributions of the liquid. The proposed approach is substantially less time-consuming as compared to a Car–Parrinello-type simulation since it replaces molecular dynamics with the integral equation theory of molecular liquids. The calculation has been performed for pure water at normal conditions in contact with the (100) face cubic centered (fcc) surface of a metal roughly modeled after copper. The results are in good agreement with the Car–Parrinello simulation for the same metal model. The shift of the Fermi level due to the presence of water conforms with experiment. The electron distribution near an adsorbed water molecule is affected by dense water, and so the metal–water attraction follows the shapes of the metal effective electrostatic potential. For the metal model employed, it is strongest at the hollow site adsorption positions, and water molecules are adsorbed mainly at the hollow and bridge site positions rather than over metal atoms. Layering of water molecules near the metal surface is found. In the first hydration layer, adsorbed water molecules are oriented in parallel to the surface or tilted with hydrogens mainly outwards the metal. This orientation at the potential of zero charge agrees with experiment. © 1999 American Institute of Physics.
The Young-Dupre equation for the work of adhesion of a liquid drop to a solid surface, where the solid surface is in equilibrium with the vapor of the liquid, is given as W = (gamma L)(1 + cos theta), where (gamma L) is the surface tension of the liquid and theta the contact angle. This work (W) has generally been identified with the free energy of adhesion. It is shown here that it constitutes the total work of adhesion only under the artificial condition that the sessile drop retains its shape after detaching from the solid surface. Under ''real conditions, W represents only one component of the total free-energy change taking place when a drop is separated from, or attached to, a vapor-equilibrated smooth solid surface. In the present work, a Net Free Energy of Adhesion, Delta F-N, is derived which gives the total free energy necessary to separate a sessile drop from a smooth solid surface to form a free sphere (its negative, of course, is the free energy of attachment of the sphere). It is given by Delta F-N = pi r(2) (gamma L)[(2a/sin theta)(2/3) - alpha], where r is the radius of the solid-liquid interface and a, called the ''effective area'', is [2/(1 + cos theta)] - cos theta. The Net Free Energy of Adhesion and Young-Dupre work of adhesion are compared as functions of the contact angle. This is done for systems of constant solid-liquid interfacial area and for systems of constant drop volume.
It was previously found that bakeout and ultrahigh evacuation of the (0001) plane of oriented graphite produced a clean surface (as determined by AES) which yielded a water contact angle of ∼35°. Ion bombardment of that evacuated surface reduced the water contact angle to 0°. The present work seeks to determine whether the ion bombardment removed undetectable (to AES) residual contamination or merely disordered an already clean surface. The (0001) plane of ZYB oriented graphite was examined by LEED after vacuum heating to ∼800°C, and the water contact angle measured in situ. The surface was then put through several cycles of ion bombardment, LEED analysis, and water contact angle measurement. The original heated surface showed LEED patterns characteristic of clean graphite (0001) and yielded water contact angles of 38 ± 3°. The LEED patterns gradually disappeared with increasing ion bombardment, accompanied by decreasing water contact angles. The water contact angle did not reach zero before the LEED pattern had completely disappeared. It is concluded that the contact angle of 38 ± 3° represents a clean (0001) surface of ZYB oriented graphite while the 0° contact angle results from formation on the surface of a disordered (amorphous) layer. The value of 38 ± 3° found on ordered ZYB is not necessarily that for a perfect (0001) surface. The contact angle of the latter is estimated to be in the range of 42 ± 7°. The results are discussed in terms of values reported in the literature for the surface energy of graphite (0001), and the wettability of surface carbon in general.
Quantum chemical solvent effect theories deal with the description of the electronic structure of a molecular subsystem embedded in a solvent or other molecular environment. The average reaction field theories, which describe electrostatic and polarization interactions between solute and solvent, can be formulated in terms of a nonlinear reaction potential operator. This operator depends on the one hand on the reaction potential function of the solvent, and on the other hand on the charge density operators, which appear in the solute-solvent interaction. The former quantity is determined by the physical model of the solvent (e.g. dielectric continuum, discrete model, crystal lattice, etc.). The charge density operator can be approximated at different levels, like exact, one-centered and multicentered multipolar forms. These two ingredients of the theory, the reaction potential response function and the specific charge density operator, define unequivocally different solvent effect models. Various versions of average reaction field models are critically reviewed on the basis of this common theoretical framework.
The microscopic process of the formation of oxides on metal surfaces is barely known or understood. Using density-functional theory we studied the oxidation of : from the initial oxygen adsorption, subsequent O incorporation into the metal, aggregation of sub-surface islands, to the transition to the oxide film. Along the atomistic pathway several metastable precursor configurations are identified. It is argued that their properties and the metastabilities in the surface-oxide formation process will have important consequences for the discernment and molecular modeling of catalysis.
Electroreduction of carbon dioxide (CO(2))--a key component of artificial photosynthesis--has largely been stymied by the impractically high overpotentials necessary to drive the process. We report an electrocatalytic system that reduces CO(2) to carbon monoxide (CO) at overpotentials below 0.2 volt. The system relies on an ionic liquid electrolyte to lower the energy of the (CO(2))(-) intermediate, most likely by complexation, and thereby lower the initial reduction barrier. The silver cathode then catalyzes formation of the final products. Formation of gaseous CO is first observed at an applied voltage of 1.5 volts, just slightly above the minimum (i.e., equilibrium) voltage of 1.33 volts. The system continued producing CO for at least 7 hours at Faradaic efficiencies greater than 96%.
Structural and energetic changes are two important characteristic properties of a chemical reaction process. In the condensed phase, studying these two properties is very challenging because of the great computational cost associated with the quantum mechanical calculations and phase space sampling. Although the combined quantum mechanics/molecular mechanics (QM/MM) approach significantly reduces the amount of the quantum mechanical calculations and facilitates the simulation of solution phase and enzyme catalyzed reactions, the required quantum mechanical calculations remain quite expensive and extensive sampling can be achieved routinely only with semiempirical quantum mechanical methods. QM/MM simulations with ab initio QM methods, therefore, are often restricted to narrow regions of the potential energy surface such as the reactant, product and transition state, or the minimum energy path. Such ab initio QM/MM calculations have previously been performed with the QM/MM-Free Energy (QM/MM-FE) method of Zhang et al.1 to generate the free energy profile along the reaction coordinate using free energy perturbation calculations at fixed structures of the QM subsystems. Results obtained with the QM/MM-FE method depend on the determination of the minimum energy reaction path, which is based on local conformations of the protein/solvent environment and can be difficult to obtain in practice. To overcome the difficulties associated with the QM/MM-FE method and to further enhance the sampling of the MM environment conformations, we develop here a new method to determine the QM/MM minimum free energy path (QM/MM-MFEP) for chemical reaction processes in solution and in enzymes. Within the QM/MM framework, we express the free energy of the system as a function of the QM conformation, thus leading to a simplified potential of mean force (PMF) description for the thermodynamics of the system. The free energy difference between two QM conformations is evaluated by the QM/MM free energy perturbation method. The free energy gradients with respect to the QM degrees of freedom are calculated from molecular dynamics simulations at given QM conformations. With the free energy and free energy gradients in hand, we further implement chain-of-conformation optimization algorithms in the search for the reaction path on the free energy surface without specifying a reaction coordinate. This method thus efficiently provides a unique minimum free energy path for solution and enzyme reactions, with structural and energetic properties being determined simultaneously. To further incorporate the dynamic contributions of the QM subsystem into the simulations, we develop the reaction path potential of Lu, et al.2 for the minimum free energy path. The combination of the methods developed here presents a comprehensive and accurate treatment for the simulation of reaction processes in solution and in enzymes with ab initio QM/MM methods. The method has been demonstrated on the first step of the reaction of the enzyme triosephosphate isomerase with good agreement with previous studies.
A general method for detailed study of enzymic reactions is presented. The method considers the complete enzyme-substrate complex together with the surrounding solvent and evaluates all the different quantum mechanical and classical energy factors that can affect the reaction pathway. These factors include the quantum mechanical energies associated with bond cleavage and charge redistribution of the substrate and the classical energies of steric and electrostatic interactions between the substrate and the enzyme. The electrostatic polarization of the enzyme atoms and the orientation of the dipoles of the surrounding water molecules is simulated by a microscopic dielectric model. The solvation energy resulting from this polarization is considerable and must be included in any realistic calculation of chemical reactions involving anything more than an isolated molecule in vacuo. Without it, acidic groups can never become ionized and the charge distribution on the substrate will not be reasonable. The same dielectric model can also be used to study the reaction of the substrate in solution. In this way the reaction in solution can be compared with the enzymic reaction.In this paper we study the stability of the carbonium ion intermediate formed in the cleavage of a glycosidic bond by lysozyme. It is found that electrostatic stabilization is an important factor in increasing the rate of the reaction step that leads to the formation of the carbonium ion intermediate. Steric factors, such as the strain of the substrate on binding to lysozyme, do not seem to contribute significantly.
Hamaker constants of systems involving liquid water are evaluated, within the full Lifshitz theory, by means of a recently proposed model of the dielectric function of this substance [Dingfelder et al., Radiat. Phys. Chem. 53, 1 (1998)], which has been extended in the present work by including terms corresponding to infrared excitations and microwave relaxation. An important feature of the complete model is that, besides a good fit to experimental data, it satisfies the physical constraint provided by the f sum rule. For symmetrical systems interacting across water, calculated Hamaker constants are generally in good agreement with results obtained using the Ninham-Parsegian representation with the Roth and Lenhoff parameters for water. Copyright 2000 Academic Press.
After introducing a new form of density-functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment, we present the first detailed study of the impact of a solvent on the surface chemistry of Cr(2)O(3), the passivating layer of stainless steel alloys. In comparison to a vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but has a dramatic effect on the binding of hydrogen to that surface. These results indicate that the dielectric screening properties of water are important to the passivating effects of the oxygen-terminated surface.
The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.