Application of reference‐modified density functional theory: Temperature and pressure dependences of solvation free energy

Recently, we proposed a reference‐modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard‐sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard‐sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard‐sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high‐temperature and high‐pressure unfolding of the protein. © 2017 Wiley Periodicals, Inc.     

受限于纳米狭缝中的四缔合Lennard-Lones流体的相平衡和界面张力研究

分别用改进的基础测量理论和平均球近似理论表达短程作用和长程作用对四缔合Lennard-Jones流体的过剩自由能的贡献. 在密度函泛理论的框架下, 研究了平均密度等温线, 密度分布, 未缔合分子在平衡汽相和液相中的分布, 相平衡以及平衡时的界面张力等热力学性质. 分析了缔合能量, 流体-固体作用和孔宽对受限于纳米狭缝中的四缔合Lennard-Jones流体相行为的影响.     

Photo absorption of ‐coumaric acid in aqueous solution: RISM‐SCF‐SEDD theory approach

Photo absorption properties of p‐coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated by means of reference interaction site model self‐consistent field with spatial electron density distribution (RISM‐SCF‐SEDD) method. RISM‐SCF‐SEDD is a combination methodology of electronic structure theory and statistical mechanics for molecular liquids. Here, time‐dependent density functional theory was coupled with RISM equation to study the electronic structure of p‐coumaric acid in aqueous system. Excitation energies of the chromophore in its neutral, two monoanionic and dianionic forms were computed to elucidate the effect of the deprotonation and solvation on the spectroscopic properties. We found that solvation strongly affects the excitation character of the chromophore, especially for phenolate anion and dianion. The free energy difference among the four protonation states is also discussed. © 2017 Wiley Periodicals, Inc.     

Microstructure of inhomogeneous polyatomic mixtures from a density functional formalism for atomic mixtures

A free energy density functional theory (DFT) for inhomogeneous polymeric mixtures is developed by treating the polyatomic system as a strongly associating atomic fluid mixture. The theory, derived in terms of segment density, retains the simple form of the DFTs for atomic fluids. Invoking the complete bonding limit of a stoichiometric mixture in the association free energy functional yields a computationally simple and accurate functional for the polyatomic system. Comparisons of theory calculations with molecular simulations are presented for inhomogeneous solutions and blends of linear and branched chains, demonstrating the capability of the theory to accurately capture the entropic and enthalpic effects governing the microstructure.     

Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach

Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.     

Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package

The three-dimensional reference interaction site model with the closure relation by Kovalenko and Hirata (3D-RISM-KH) in combination with the density functional theory (DFT) method has been implemented in the Amsterdam density functional (ADF) software package. The analytical first derivatives of the free energy with respect to displacements of the solute nuclear coordinates have also been developed. This enables study of chemical reactions, including reaction coordinates and transition state search, with the molecular solvation described from the first principles. The method yields all of the features available by using other solvation approaches, for instance infrared spectra of solvated molecules. To evaluate the accuracy of the present method, test calculations have been carried out for a number of small molecules, including four glycine conformers, a set of small organic compounds, and carbon nanotubes of various lengths in aqueous solution. Our predictions for the solvation free energy agree well with other approaches as well as experiment. This new development makes it possible to calculate at modest computational cost the electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture from the first principles.     

Analytical gradients for subsystem density functional theory within the slater‐function‐based amsterdam density functional program

We present a new implementation of analytical gradients for subsystem density‐functional theory (sDFT) and frozen‐density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT‐LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave‐function theory results. However, sDFT‐PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN‐trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc.     

Grid‐based density functional calculations of many‐electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many‐electron systems in the 3D cartesian coordinate grid (CCG). The atom‐centered localized gaussian basis set, electronic density, and the two‐body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange‐correlation potential, while Hay‐Wadt‐type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, and atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom‐centered grid as well as the grid‐free calculation. Results for three atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many‐electron systems. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Alternative Representations of the Correlation Energy in Density‐Functional Theory: A Kinetic‐Energy Based Adiabatic Connection

The adiabatic‐connection framework has been widely used to explore the properties of the correlation energy in density‐functional theory. The integrand in this formula may be expressed in terms of the electron–electron interactions directly, involving intrinsically two‐particle expectation values. Alternatively, it may be expressed in terms of the kinetic energy, involving only one‐particle quantities. In this work, we explore this alternative representation for the correlation energy and highlight some of its potential for the construction of new density functional approximations. The kinetic‐energy based integrand is effective in concentrating static correlation effects to the low interaction strength regime and approaches zero asymptotically, offering interesting new possibilities for modeling the correlation energy in density‐functional theory     

1,2,3-三氮杂苯－(水)3复合物多体相互作用

The interaction between 1,2,3-triazine and three water molecules was studied using density functional theory B3LYP method at 6-31-t＋＋G^＊＊ basis set. Various structures for 1,2,3-triazine-（water）n （n= 1, 2, 3） complex were investigated and the different lower energy structures were reported. Many-body analysis was also carded out to obtain relaxation energy and many-body interaction energy （two, three, and four-body）, and the most stable conformer has the basis set superposition error corrected interaction energy of -- 102.61 kJ/mol. The relaxation energy, two- and three-body interactions have significant contribution to the total interaction energy whereas four-body interaction was very small for 1,2,3-triazine-（water）3 complex.     

Solvatochromism and preferential solvation of Brooker's merocyanine in water–methanol mixtures

The excitation energy of Brooker's merocyanine in water–methanol mixtures shows nonlinear behavior with respect to the mole fraction of methanol, and it was suggested that this behavior is related to preferential solvation by methanol. We investigated the origin of this behavior and its relation to preferential solvation using the three‐dimensional reference interaction site model self‐consistent field method and time‐dependent density functional theory. The calculated excitation energies were in good agreement with the experimental behavior. Analysis of the coordination numbers revealed preferential solvation by methanol. The free energy component analysis implied that solvent reorganization and solvation entropy drive the preferential solvation by methanol, while the direct solute–solvent interaction promotes solvation by water. The difference in the preferential solvation effect on the ground and excited states causes the nonlinear excitation energy shift. © 2017 Wiley Periodicals, Inc.     

Density functional theory of solvation and its relation to implicit solvent models

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.     

Highly efficient implementation of pseudospectral time‐dependent density‐functional theory for the calculation of excitation energies of large molecules

We have developed and implemented pseudospectral time‐dependent density‐functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm–Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time‐dependent density‐functional theory with full linear response (PS‐FLR‐TDDFT) and within the Tamm–Dancoff approximation (PS‐TDA‐TDDFT) for G2 set molecules using B3LYP/6‐31G*^* show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS‐FLR‐TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS‐FLR‐TDDFT and best estimations demonstrate that the accuracy of both PS‐FLR‐TDDFT and PS‐TDA‐TDDFT. Calculations for a set of medium‐sized molecules, including C_n fullerenes and nanotubes, using the B3LYP functional and 6‐31G^** basis set show PS‐TDA‐TDDFT provides 19‐ to 34‐fold speedups for C_n fullerenes with 450–1470 basis functions, 11‐ to 32‐fold speedups for nanotubes with 660–3180 basis functions, and 9‐ to 16‐fold speedups for organic molecules with 540–1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46‐residue crambin protein, fullerenes up to C₅₄₀ and nanotubes up to 14×(6,6), using the B3LYP functional and 6‐31G^** basis set with up to 8100 basis functions show that PS‐FLR‐TDDFT CPU time scales as N^2.05 with the number of basis functions. © 2016 Wiley Periodicals, Inc.     

On the choice of a reference state for one‐step perturbation calculations between polar and nonpolar molecules in a polar environment

One‐step perturbation is an efficient method to estimate free energy differences in molecular dynamics (MD) simulations, but its accuracy depends critically on the choice of an appropriate, possibly unphysical, reference state that optimizes the sampling of the physical end states. In particular, the perturbation from a polar moiety to a nonpolar one and vice versa in a polar environment such as water poses a challenge which is of importance when estimating free energy differences that involve entropy changes and the hydrophobic effect. In this work, we systematically study the performance of the one‐step perturbation method in the calculation of the free enthalpy difference between a polar water solute and a nonpolar “water” solute molecule solvated in a box of 999 polar water molecules. Both these polar and nonpolar physical reference states fail to predict the free enthalpy difference as obtained by thermodynamic integration, but the result is worse using the nonpolar physical reference state, because both a properly sized cavity and a favorable orientation of the polar solute in a polar environment are rarely, if ever, sampled in a simulation of the nonpolar solute in such an environment. Use of nonphysical soft‐core reference states helps to sample properly sized cavities, and post‐MD simulation rotational and translational sampling of the solute to be perturbed leads to much improved free enthalpy estimates from one‐step perturbation. © 2012 Wiley Periodicals, Inc.     

Novel method of self‐interaction corrections in density functional calculations

It is demonstrated that the commonly applied self‐interaction correction (SIC) used in density functional theory does not remove all self‐interaction. We present as an alternative a novel method that, by construction, is totally free from self‐interaction. The method has the correct asymptotic 1/r dependence. We apply the new theory to localized f electrons in praseodymium and compare with the old version of SIC, the local density approximation (LDA) and with an atomic Hartree–Fock calculation. The results show a lowering of the f level, a contraction of the f electron cloud and a lowering of the total energy by 13 eV per 4 f electron compared to LDA. The equilibrium volume of the new SIC method is close to the ones given by LDA and the older SIC method and is in good agreement with experiment. The experimental cohesive energy is in better agreement using the new SIC method, both compared to LDA and another SIC method. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 247–252, 2001     

Effect of attractions on the structure of polymer solutions confined between surfaces: a density functional approach

A density functional theory is presented to study the effect of attractions on the structure of polymer solutions confined between surfaces. The polymer molecules have been modeled as a pearl necklace of freely jointed hard spheres and the solvent as hard spheres, both having Yukawa-type attractions and the mixture being confined between attractive Yukawa-type surfaces. The present theory treats the ideal gas free energy functional exactly and uses weighted density approximation for the hard chain and hard sphere contributions to the excess free energy functional. The attractive interactions are calculated using the direct correlation function obtained from the polymer reference interaction site model theory along with the mean spherical approximation closure. The theoretical predictions on the density profiles of the polymer and the solvent molecules are found to agree quite well with the Monte Carlo simulation results for varying densities, chain lengths, wall separations, and different sets of interaction potentials.     

Structure of inhomogeneous polymer solutions: a density functional approach

The structure of polymer solutions confined between surfaces is studied using a density functional theory where the polymer molecules have been modeled as a pearl necklace of freely jointed hard spheres and the solvent as hard spheres. The present theory uses the concept of universality of the free energy density functional to obtain the first-order direct correlation function of the nonuniform system from that of the corresponding uniform system, calculated through the Verlet-modified type bridge function. The uniform bulk fluid direct correlation function required as input has been calculated from the reference interaction site model integral equation theory using the Percus-Yevick closure relation. The calculated results on the density profiles of the polymer as well as the solvent are shown to compare well with computer simulation results.