Lattice density functional theory of molecular diffusion

A density functional theory of diffusion is developed for lattice fluids with molecular flux as a functional of the density distribution. The formalism coincides exactly with the generalized Ono-Kondo density functional theory when there is no gradient of chemical potential, i.e., at equilibrium. Away from equilibrium, it gives Fick's first law in the absence of a potential energy gradient, and it departs from Fickian behavior consistently with the Maxwell-Stefan formulation. The theory is applied to model a nanopore, predicting nonequilibrium phase transitions and the role of surface diffusion in the transport of capillary condensate.     

The adsorption of CO on charged and neutral Au and Au2: a comparison between wave-function based and density functional theory

Quantum theoretical calculations are presented for CO attached to charged and neutral Au and Au(2) with the aim to test the performance of currently applied density functional theory (DFT) by comparison with accurate wave-function based results. For this, we developed a compact sized correlation-consistent valence basis set which accompanies a small-core energy-consistent scalar relativistic pseudopotential for gold. The properties analyzed are geometries, dissociation energies, vibrational frequencies, ionization potentials, and electron affinities. The important role of the basis-set superposition error is addressed which can be substantial for the negatively charged systems. The dissociation energies decrease along the series Au(+)-CO, Au-CO, and Au(-)-CO and as well as along the series Au(2)(+)-CO, Au(2)-CO, and Au(2)(-)-CO. As one expects, a negative charge on gold weakens the carbon oxygen bond considerably, with a consequent redshift in the CO stretching frequency when moving from the positively charged to the neutral and the negatively charged gold atom or dimer. We find that the different density functional approximations applied are not able to correctly describe the rather weak interaction between CO and gold, thus questioning the application of DFT to CO adsorption on larger gold clusters or surfaces.     

The onset of calcium carbonate nucleation: a density functional theory molecular dynamics and hybrid microsolvation/continuum study

Density functional theory (Perdew-Burke-Ernzerhof) based methods have been used to study the structure and hydration environment of the building blocks of CaCO 3 in aqueous solutions of calcium bicarbonate and calcium carbonate. Car-Parrinello molecular dynamics simulations of Ca(2+)/CO3(2-) and Ca (2+)/HCO3(-) in explicit water were performed to investigate the formation of CaCO3 and the hydration shell of the solvated hetero-ion pair. Our simulations show that the formation of the monomer of CaCO3 occurs with an associative mechanism and that the dominant building block of calcium (bi)carbonate in aqueous solution is Ca[eta(1)-(H)CO3](H2O)5, i.e., the preferred hydration number is five, while the (bi)carbonate is coordinated to the calcium in a monodentate mode. This result agrees with static calculations, where a hybrid approach using a combination of explicit solvent molecules and a polarizable continuum model has been applied to compute the solvation free energies of calcium bicarbonate species. Furthermore, the discrete-continuum calculations predict that the Ca(HCO3)2 and Ca(HCO3)3(-) species are stable in an aqueous environment preferentially as Ca(HCO3)2(H2O)4 and Ca(HCO3)3(H2O)2(-), respectively.     

Modeling of adsorption and nucleation in infinite cylindrical pores by two-dimensional density functional theory

In this paper, we present an analysis of argon adsorption in cylindrical pores having amorphous silica structure by means of a nonlocal density functional theory (NLDFT). In the modeling, we account for the radial and longitudinal density distributions, which allow us to consider the interface between the liquidlike and vaporlike fluids separated by a hemispherical meniscus in the canonical ensemble. The Helmholtz free energy of the meniscus was determined as a function of pore diameter. The canonical NLDFT simulations show the details of density rearrangement at the vaporlike and liquidlike spinodal points. The limits of stability of the smallest bridge and the smallest bubble were also determined with the canonical NLDFT. The energy of nucleation as a function of the bulk pressure and the pore diameter was determined with the grand canonical NLDFT using an additional external potential field. It was shown that the experimentally observed reversibility of argon adsorption isotherms at its boiling point up to the pore diameter of 4 nm is possible if the potential barrier of 22kT is overcome due to density fluctuations.     

Projected gradient algorithms for Hartree-Fock and density matrix functional theory calculations

We present projected gradient algorithms designed for optimizing various functionals defined on the set of N-representable one-electron reduced density matrices. We show that projected gradient algorithms are efficient in minimizing the Hartree-Fock or the Muller-Buijse-Baerends functional. On the other hand, they converge very slowly when applied to the recently proposed BBk (k=1,2,3) functionals [O. Gritsenko et al., J. Chem. Phys. 122, 204102 (2005)]. This is due to the fact that the BBk functionals are not proper functionals of the density matrix.     

Gadolinium ion bonding on the surface of carboxylated detonation nanodiamond in terms of magnetochemistry and density functional theory

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Atomic and electronic structures of neutral and charged Pbn clusters (n=2-15): theoretical investigation based on density functional theory

The geometric and electronic structures of the Pbn+ clusters (n=2-15) have been investigated and compared with neutral clusters. The search for several low-lying isomers was carried out under the framework of the density functional theory formalism using the generalized gradient approximation for the exchange correlation energy. The wave functions were expanded using a plane wave basis set and the electron-ion interactions have been described by the projector augmented wave method. The ground state geometries of the singly positively charged Pbn+ clusters showed compact growth pattern as those observed for neutrals with small local distortions. Based on the total energy of the lowest energy isomers, a systematic analysis was carried out to obtain the physicochemical properties, viz., binding energy, second order difference in energy, and fragmentation behavior. It is found that n=4, 7, 10, and 13 clusters are more stable than their neighbors, reflecting good agreement with experimental observation. The chemical stability of these clusters was analyzed by evaluating their energy gap between the highest occupied and lowest unoccupied molecular orbitals and adiabatic ionization potentials. The results revealed that, although Pb13 showed higher stability from the total energy analysis, its energy gap and ionization potential do not follow the trend. Albeit of higher stability in terms of binding energy, the lower ionization potential of Pb13 is interesting which has been explained based on its electronic structure through the density of states and electron shell filling model of spherical clusters.     

白花丹素分子结构和红外光谱的密度泛函理论研究

白花丹素(5-羟基-2-甲基-1,4-萘醌)是中药白花丹的主要成分之一,是一种具有抗肿瘤活性的萘醌类化合物.采用密度泛函(DFT)B3LYP/6-31+G(d)方法对白花丹素分子的几何构型进行全优化,得到其几何构型参数,进一步计算得到白花丹素的红外振动光谱.对计算得到的振动频率进行归属和解析并与文献值比较,发现理论计算...     

Time-dependent density functional theory based upon the fragment molecular orbital method

Time-dependent density functional theory (TDDFT) was combined with the two-body fragment molecular orbital method (FMO2). In this FMO2-TDDFT scheme, the system is divided into fragments, and the electron density for fragments is determined self-consistently. Consequently, only one main fragment of interest and several fragment pairs including it are calculated by TDDFT. To demonstrate the accuracy of FMO2-TDDFT, we computed several low-lying singlet and triplet excited states of solvated phenol and polyalanine using our method and the standard TDDFT for the full system. The BLYP functional with the long-range correction (LC-BLYP) was employed with the 6-31G(*) basis set (some tests were also performed with 6-311G(*), as well as with B3LYP and time-dependent Hartree-Fock). Typically, FMO2-TDDFT reproduced the full TDDFT excitation energies within 0.1 eV, and for one excited state the error was about 0.2 eV. Beside the accurate reproduction of the TDDFT excitation energies, we also automatically get an excitation energy decomposition analysis, which provides the contributions of individual fragments. Finally, the efficiency of our approach was exemplified on the LC-BLYP6-31G(*) calculation of the lowest singlet excitation of the photoactive yellow protein which consists of 1931 atoms, and the obtained value of 3.1 eV is in agreement with the experimental value of 2.8 eV.     

Homogeneous nucleation in vapor-liquid phase transition of Lennard-Jones fluids: a density functional theory approach

Density functional theory (DFT) with square gradient approximation for the free energy functional and a model density profile are used to obtain an analytical expression for the size-dependent free energy of formation of a liquid drop from the vapor through the process of homogeneous nucleation, without invoking the approximations used in classical nucleation theory (CNT). The density of the liquid drop in this work is not the same as the bulk liquid density but it corresponds to minimum free energy of formation of the liquid drop. The theory is applied to study the nucleation phenomena from supersaturated vapor of Lennard-Jones fluid. The barrier height predicted by this theory is significantly lower than the same in CNT which is rather high. The density at the center of the small liquid drop as obtained through optimization is less than the bulk density which is in agreement with other earlier works. Also proposed is a sharp interface limit of the proposed DFT of nucleation, which is as simple as CNT but with a modified barrier height and this modified classical nucleation theory, as we call it, is shown to lead to improved results.     

Determination of extremely localized molecular orbitals in the framework of density functional theory

Extremely localized molecular orbitals are rigorously localized on only a preselected set of atoms and do not have any tails outside the localization region. The importance of these orbitals lies in their ability to be transferred from one molecule to another one. A new algorithm to determine extremely localized molecular orbitals in the framework of the density functional theory method is presented. This could also be a valuable tool in the quantum mechanics/molecular mechanics methodology where localized molecular orbitals are used to describe covalent bonds across the frontier region. The present approach is used to build up the electron density of thymopentin, a polypeptide constituted by five residues, starting from extremely localized molecular orbitals determined on a set of model molecules. The results obtained confirm good transferability properties for these orbitals.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Analytic energy gradient in combined time-dependent density functional theory and polarizable force field calculation

Formulas for evaluating analytic energy gradient are derived for combined time-dependent density functional theory (TDDFT) and polarizable force field methods that incorporate dipole polarizability tensors and linearly induced point dipoles. The Z-vector method for determining relaxed one-particle difference density matrix in regular TDDFT methods is extended to include induced dipoles. The analytic gradient of the mutual polarization energy of the force field and the TDDFT excited state can be formulated by using the TDDFT difference density-induced dipoles and the transition state density-induced dipoles. All the forces and torques involving induced dipoles can be efficiently evaluated using standard electrostatic formulas as if the induced dipoles were permanent dipoles. The formulas are given in the most general form and are applicable to various flavors of polarizable force fields. Implementation and tests with a polarizable five-point water model show that the formulas are rigorous. The carbonyl vibration modes and infrared spectrum intensities of a cluster formed by acetone and two water molecules are studied.     

Adsorption of CO on oxygen preadsorbed neutral and charged gas phase Pd4 clusters: A density functional study

We present the results of a density functional calculation on adsorption of O₂, CO, and their coadsorption at various sites of neutral, cationic, and anionic Pd₄ clusters. For all the clusters, the dissociative adsorption of oxygen sitting on Pd bridge sites is found to be preferable. Both O₂ and CO binding energies are found to be higher for the anionic Pd₄ cluster followed by cationic and neutral cluster. However, binding energies of O₂ or CO in the coadsorption complexes follow the trend: anionic > neutral > cationic. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Vapor phase nucleation on neutral and charged nanoparticles: condensation of supersaturated trifluoroethanol on Mg nanoparticles

A new technique is described to study the condensation of supersaturated vapors on nanoparticles under well-defined conditions of vapor supersaturation, temperature, and carrier gas pressure. The method is applied to the condensation of supersaturated trifluoroethanol (TFE) vapor on Mg nanoparticles. The nanoparticles can be activated to act as condensation nuclei at supersaturations significantly lower than those required for homogeneous nucleation. The number of activated nanoparticles increases with increasing the vapor supersaturation. The small difference observed in the number of droplets formed on positively and negatively charged nanoparticles is attributed to the difference in the mobilities of these nanoparticles. Therefore, no significant charge preference is observed for the condensation of TFE vapor on the Mg nanoparticles.     

On the evaluation of molecular electron affinities by approximate density functional theory

The ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH₃, NH₂, OH, and HC₂ as well as the multibonded species CN, BO, N₃, OCN, and NO₂. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EA_ad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EA_ad by 0.2 eV. It is concluded that the LDA/NL method affords EA_ad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.     

Utilization of deformations in molecular quantum chemistry and application to density functional theory

The aim of this article is to present in a way accessible to most quantum chemists a general mathematical method which consists in deforming wave functions and density functions (in the spirit of the local scaling transformation). This deformation method allows us to obtain several new results, including a characterization of the set of wave functions that have the same given density function (which gives a new insight on a result of G. Zumbach and K. Maschke, Phys. Rev. A 28 , 544 (1983)) and an N-representability result where symmetry is taken into account. We also propose new theoretical ways to generate approximations of the exact density functional and give a numerical example. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 221–231, 1998     

Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory

The polarizable continuum model (PCM) for describing the solvent effect was combined with the fragment molecular orbital-based time-dependent density functional theory (TDDFT). Several levels of the many-body expansion were implemented, and the importance of the many-body contributions to the singlet-excited states was discussed. To calibrate the accuracy, we performed a number of the model calculations using our method and the regular TDDFT in solution, applying them to phenol and polypeptides at the long-range corrected BLYP/6-31G* level. It was found that for systems up to 192 atoms the largest error in the excitation energy was 0.006 eV (vs. the regular TDDFT/PCM of the full system). The solvent shifts and the conformer effects were discussed, and the scaling was found to be nearly linear. Finally, we applied our method to the lowest singlet excitation of the photoactive yellow protein (PYP) in aqueous solution and determined the excitation energy to be in reasonable agreement with experiment. The excitation energy analysis provided the contributions of individual residues, and the main factors as well as their solvent shifts were determined.