Due to solvation, excess charge carriers on 1d semiconductor nanostructures immersed in polar solvents undergo self-localization into polaronic states. Using a simplified theoretical model for small-diameter structures, we study low-frequency properties of resulting 1d adiabatic polarons. The combined microscopic dynamics of the electronic charge density and the solvent leads to macroscopic Langevin dynamics of a polaron and to the appearance of local dielectric relaxation modes. Polaron mobility is evaluated as a function of system parameters. Numerical estimates indicate that the solvated carriers can have mobilities orders of magnitude lower than the intrinsic values.
Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energ…
Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a c…
The time-dependent fluorescence Stokes shifts monitors the relaxation of the polarization of a polar solvent in the surroundings of a photoexcited solute molecule, but also the structural variation of the solute following photoexcitation and the subsequent molecular charge redistribution. Here, we formulate a simple nonequilibrium quantum theory of solvation for an explicitly time-dependent continuous solvent. The time-dependent solvent induces nonequilibrium fluctuations on the solvent dynamics which are directly reflected in different time components in the time-dependent Stokes shift. We il…
We present a multiwavelet-based implementation of a quantum/classical polarizable continuum model. The solvent model uses a diffuse solute-solvent boundary and a position-dependent permittivity, lifting the sharp-boundary assumption underlying many existing continuum solvation models. We are able to include both surface and volume polarization effects in the quantum/classical coupling, with guaranteed precision, due to the adaptive refinement strategies of our multiwavelet implementation. The model can account for complex solvent environments and does not need a posteriori corrections for volu…
We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in water--co-solvent mixtures. The first modification involves perturbing the macroscopic dielectric-flux interface condition at the solute--solvent interface with a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is a simple treatment of the microscopic interface potential (sta…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity. The new model approximates the cavity-formation energy as that of a shell capacitor: the inner, solute-shaped conductor is held at the static potential, and the outer conductor (at the first solvation shell) is held at zero potential. Compared to cavity energies computed using free-energy pertubation with explicit-solvent molecular dynamics, the new model ex…
We propose a predictive Density Functional Theory (DFT) for the calculation of solvation free energies. Our approach is based on a Helmholtz free-energy functional that is consistent with the perturbed-chain SAFT (PC-SAFT) equation of state. This allows a coarse-grained description of the solvent, based on an inhomogeneous density of PC-SAFT segments. The solute, on the other hand, is described in full detail by atomistic Lennard-Jones interaction sites. The approach is entirely predictive, as it only takes the PC-SAFT parameters of the solvent and the force-field parameters of the solute as i…
The solvation dynamics and isomerization process of an organic dye, IR-140, in polar solvents and nonpolar solvents have been investigated using pump supercontinuum-probing (PSCP) technique. In all solvents, the dynamics exhibits solvent-dependent. Solvent induced spectral shifts of the absorption and emission spectra of IR-140 have also been studied in a variety of solvents. At the same time, the photoisomerization process has been examined. The approximate energy-band structure of IR-140 was also supposed firstly.
We present a brief review of the classical density functional theory of atomic and molecular fluids. We focus on the application of the theory to the determination of the solvation properties of arbitrary molecular solutes in arbitrary molecular solvent. This includes the prediction of the solvation free energies, as well as the characterization of the microscopic, three-dimensional solvent structure.
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it…
We develop a linear response theory of solvation of ionic and dipolar solutes in anisotropic, axially symmetric polar solvents. The theory is applied to solvation in polar nematic liquid crystals. The formal theory constructs the solvation response function from projections of the solvent dipolar susceptibility on rotational invariants. These projections are obtained from Monte Carlo simulations of a fluid of dipolar spherocylinders which can exist both in the isotropic and nematic phase. Based on the properties of the solvent susceptibility from simulations and the formal solution, we have ob…
Recent atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in several solvents. The force curve is thought as the solvation structure in some cases, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is just only a mean force between the probe and sample surface. Since theoretical relation between the mean force and the solvation structure had not been clearly known, we have recently derived a relational expression within a simple liquid. Alth…
In the given paper we describe methods finding analytical gradients (derivatives) of solvation energy over atomic coordinates. It is made both for not polar energy and for the polar energy found by methods PCM, COSMO and SGB. These gradients are searched with use of analytical gradients of parameters (coordinates, normal vectors and squares) the surface meshes. The surface meshes are located on both the optimal smooth molecular surfaces: solvent excluded surface (SES) and surface solvent accessible surface (SAS) received from SES. These surfaces are found by methods of primary and secondary ro…
For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and …
We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This …
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy de…
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the…
The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption measurements published in the companion paper revealed an influence of hydrophobic sidechain alterations on the observed solvation dynamics of a chromophore in water. As the influence of shape, size and structure of chromophores on the time-dependent Stokes shift was so far thought to play a role only in slowly rotating solvents compared to the solute or if …
An iterative method for calculating the polar component of the solvation Gibbs energy under a smooth change in dielectric permittivity, both between a substrate and a solvent and in a solvent is formulated on the basis of a previously developed model. The method is developed in the approximation of the local relationship D = \eps (r) E between the displacement vectors D and the electric field intensity E.
Water, the ubiquitous solvent, is also prominent in forming liquid solid interfaces with catalytically active surfaces, in particular with promoted oxides. We study the complex interface of a gold nanocatalyst, pinned by an F center on titania support, and water. The ab initio simulations uncover the microscopic details of solvent-induced charge rearrangements at the metal particle. Water is found to stabilize charge states differently from the gas phase as a result of structure specific charge transfer from to the solvent, thus altering surface reactivity. The metal cluster is shown to featur…
We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere, and, (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general en…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is analyzed by numerically solving the Poisson equation using the DelPhi program. The resulting solvation properties depend sensitively on the shape and size of the cavity. In the second method, the solvent and solute molecules are treated explicitly in molecular dynamics simulations using Ewald boundary conditions. We find a 2 kcal/mole difference in solvation f…
Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally developed to handle non-polar solutes in the TIP3P water model but can be extended to accurately treat polar solutes in other polar solvents. In this manuscript, we demonstrate how to adapt IS-SPA to include the treatment of solvent orientation and long ranged electrostatics in a…
The excess electron in liquid ammonia ("ammoniated electron") is commonly viewed as a cavity electron in which the s-type wave function fills the interstitial void between 6-9 ammonia molecules. Here we examine an alternative model in which the ammoniated electron is regarded as a solvent stabilized multimer radical anion, as was originally suggested by Symons [Chem. Soc. Rev. 1976, 5, 337]. In this model, most of the excess electron density resides in the frontier orbitals of N atoms in the ammonia molecules forming the solvation cavity; a fraction of this spin density is transferred to the m…
Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in J. Phys. Chem. Lett. 5 (2014), 1845, where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to…
Lithium based deep eutectic solvents (DESs) are excellent candidates for eco-friendly electrolytes in lithium ion batteries. While some of these DES have shown promising results, a clear mechanism of lithium ion transport in DESs is not yet established. This work reports the study on the solvation and transport of lithium in a DES made from lithium perchlorate and acetamide using Molecular Dynamics (MD) simulation and neutron scattering techniques. Based on hydrogen bonding (H-bonding) of acetamide with neighbouring molecules/ions, two states are largely prevalent: 1) acetamide molecules which…
Competitive solvation of an ion by two or more solvents is one of the key phenomena determining the identity of our world. Solvation in polar solvents frequently originates from non-additive non-covalent interactions. Pre-parametrized potentials poorly capture these interactions, unless the force field derivation is repeated for every new system. Development cost increases drastically as new chemical species are supplied. This work represents an alternative simulation approach, PM7-MD, by coupling the latest semiempirical parametrization, PM7, with equation-of-motion propagation scheme and tem…
Na is known to deliver very low energy capacity for sodium intercalation compared to Lithium. In this study, we use quantum mechanics based metadynamics simulations to obtain the free energy landscape for sodium ion intercalation from Dimethyl sulfoxide (DMSO) solvent into graphite. We find that the lowest free energy minima from the metadynamics are associated with sodium solvated by 3 or 4 DMSO. The free energy minima of these states are activated by a free energy of solvation computed to be 0.17 eV, which in turn are the most thermodynamically stable. We observe weak interactions of sodium …
The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric response still solves the electrostatic problem inefficiently or not at all for solutes larger than $\approx 10$ non-hydrogen atoms. In existing MPE parameterizations, the resulting systematic underestimation of the electrostatic solute-solvent interaction is presently compensated for by a systematic overestimation of non-electrostatic attractive interactions. Ev…
We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent struc…
For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising …
Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich（工程物理与计算系，TUM工程与设计学院，慕尼黑技术大学）；Atomistic Modeling Center (AMC), Munich Data Science Institute (MDSI), Technical University of Munich（原子建模中心（AMC），慕尼黑数据科学研究所（MDSI），慕尼黑技术大学）
Solvation effect might have a tremendous influence on chemical reactions. However, precise quantum chemistry calculations are most often done either in vacuum neglecting the role of the solvent or using continuum solvent model ignoring its molecular nature. We propose a new method coupling a quantum description of the solute using electronic density functional theory with a classical grand-canonical treatment of the solvent using molecular density functional theory. Unlike previous work, both densities are minimized self consistently, accounting for mutual polarization of the molecular solvent…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent in a mean-field fashion with implicit solvent models. However, a challenge with existing implicit solvent models is that they often lack accuracy or certain physical properties compared to explicit solvent models, as the many-body effects of the neglected solvent molecules is difficult to model as a mean field. Here, we leverage machine learning (ML…
We study accommodation of an excess charge carrier on long even-N polyynic oligomers C_{N}H_{2} due to displacements of the underlying carbon lattice and polarization of the surrounding solvent in the context of carrier self-localization into a polaronic state. Spatial patterns of bond-length alternation, excess charge and spin densities are compared as derived with Hartree-Fock and two hybrid-DFT methods (BHandHLYP and B3LYP) in conjunction with the polarizable continuum model. Quite distinct resulting pictures of carrier accommodation are found when contributions from different interactions …
Computational Study of Li+ Solvation Structures in Fluorinated Ether, Non-Fluorinated Ether, and Organic Carbonate-Based Electrolytes at Low and High Salt Concentrations
When a one-dimensional (1D) semiconductor nanostructure is immersed in a sluggish polar solvent, fluctuations of the medium may result in the appearance of localized electronic levels inside the band gap. An excess charge carrier can occupy such a level and undergo self-localization into a large-radius adiabatic polaron surrounded by a self-consistent medium polarization pattern. Within an appropriately adapted framework of the Marcus theory, we explore the description and qualitative picture of thermally activated electron transfer involving solvation-induced polaronic-like states by consider…
This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has b…
Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders …
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to smal…
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from firstprinciples quantum mechanics. However, despite much recent interest in such models, to date the applicability of such models in the plane-wave context to non-aqueous solvents has been limited because the determination of the model parameters requires fitting to a large database of experimental solvation energies for each new solvent considered. This work presents an alternate approach …
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous extrapolation schemes by including additionally new techniques such as an exponential scaling transformation of coordinate space with weights complemented by a dynamically adjusted balancing between the least square minimization of force deviations and the norm of expansion coefficients in the approximation. The expensive mean potential forces are treated in terms of t…
In this work, we investigate the excited-state solute and solvation structure of $\mathrm{[Ru(bpy)_3]^{2+}}$, $\mathrm{[Fe(bpy)_3]^{2+}}$, $\mathrm{[Fe(bmip)_2]^{2+}}$ and $\mathrm{[Cu(phen)_2]^{+}}$ (bpy=2,2'-pyridine; bmip=2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine; phen=1,10-phenanthroline) transition metal complexes (TMCs) in terms of solute-solvent radial distribution functions (RDFs) and evaluate the performance of some of the most popular partial atomic charge (PAC) methods for obtaining these RDFs by molecular dynamics (MD) simulations. To this end, we compare classical MD of a fro…
We introduce a multimodel approach to the simulation of the optical properties of molecular dyes in solution, whereby the effects of thermal fluctuations and of dielectric screening on the absorption spectra are accounted for by explicit and implicit solvation models, respectively. Thermal effects are treated by averaging the spectra of molecular configurations generated by an ab initio molecular-dynamics simulation where solvent molecules are treated explicitly. Dielectric effects are then dealt with implicitly by computing the spectra upon removal of the solvent molecules and their replaceme…
Predicting solvation free energies with an implicit solvent machine learning potential
Faculty of Physics and Center for NanoScience, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München（物理系和纳米科学中心、兽医学系，路德维希-马克西米利安大学慕尼黑）；Atomistic Modeling Center, Munich Data Science Institute, Technical University of Munich（原子模型中心、慕尼黑数据科学研究所，慕尼黑技术大学）；Multiscale Modeling of Fluid Materials, Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich（多尺度流体材料建模，工程物理与计算系，TUM工程与设计学院，慕尼黑技术大学）
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (19…
Recent surface force apparatus (SFA) and atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in solvent. The force curve is thought as the solvation structure in some articles, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is only the force between the probe and the sample surface. Therefore, this brief paper presents a method for calculating the solvation structure from the force curve. The method is constructed by using integral equatio…
Downsizing microswimmers to the nanoscale, and using light as an externally controlled fuel, are two important goals within the field of active matter. Here we demonstrate using all-atom molecular dynamics simulations that solvation relaxation, the solvent dynamics induced after visible light electronic excitation of a fluorophore, can be used to propel nanoparticles immersed in polar solvents. We show that fullerenes functionalized with fluorophore molecules in liquid water exhibit substantial enhanced mobility under external excitation, with a propulsion speed proportional to the power dissi…
