A discrete solvent reaction field model for calculating frequency-dependent hyperpolarizabilities of molecules in solution

We present a discrete solvent reaction field (DRF) model for the calculation of frequency-dependent hyperpolarizabilities of molecules in solution. In this model the solute is described using density functional theory (DFT) and the discrete solvent molecules are described with a classical polarizable model. The first hyperpolarizability is obtained in an efficient way using time-dependent DFT and the (2n+1) rule. The method was tested for liquid water using a model in which a water molecule is embedded in a cluster of 127 classical water molecules. The frequency-dependent first and second hyperpolarizabilities related to the electric field induced second harmonic generation (EFISH) experiment, were calculated both in the gas phase and in the liquid phase. For water in the gas phase, results are obtained in good agreement with correlated wave function methods and experiments by using the so-called shape-corrected exchange correlation (xc)-potentials. In the liquid phase the effect of using asymptotically correct functionals is discussed. The model reproduced the experimentally observed sign change in the first hyperpolarizaibility when going from the gas phase to the liquid phase. Furthermore, it is shown that the first hyperpolarizability is more sensitive to damping of the solvent-solute interactions at short range than the second hyperpolarizability. (C) 2003 American Institute of Physics

Understanding Trends in Molecular Bond Angles

Trends in bond angle are identified in a systematic study of more than a thousand symmetric A(2)B triatomic molecules. We show that, in series where atoms A and B are each varied within a group, the following trends hold: (1) the A-B-A bond angle decreases for more polarizable central atoms B, and (2) the A-B-A angle increases for more polarizable outer atoms A. The physical underpinning is provided by the extended Debye polarizability model for the chemical bond angle, hence our present findings also serve as validation of this simple classical model. We use experimental bond angles from the literature and, where not available, we optimize molecular geometries with quantum chemical methods, with an open mind with regards to the stability of these molecules. We consider main group elements up to and including the sixth period of the periodic table

Structure and stability of complexes of agmatine with some functional receptor residues of proteins

The paper reports the results of a theoretical study of the conformational behavior and basicity of biogenic amine agmatine. The complexes modelling of agmatine - protein interaction are also under scrutiny of our investigation using the Becke3LYP and B97D levels of the density functional theory. The relative stabilities (Gibbs energies) of individual complexes are by both DFT methods described equally. Hydration has a dramatic effect on the hydrogen bonded complexes studied. The pairing acidic carboxylate group with different agmatine species resulted in charged hydrogen bond complexes containing negatively charged acetate species acting as proton acceptors. (C) 2017 Elsevier B.V. All rights reserved

Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

This study reports in detail the results of systematic large-scale theoretical investigations of the acidic dimeric structural units (D-E, E-F, F-G, and G-H) and pentamer D-E-F-G-H (fondaparinux) of the glycosaminoglycan heparin, and their anionic forms. The geometries and energies of these oligomers have been computed using HF/6-31G(d), Becke3LYP/6-31G(d), and Becke3LYP/6-311+G(d,p) methods. The optimized geometries indicate that the most stable structure of these units in the neutral state is stabilized via a system of intramolecular hydrogen bonds. The equilibrium structure of these species changed appreciably upon dissociation. Water has a remarkable effect on the geometry of the anions studied. Because of high negative charge, the solvent effect also resulted in an appreciable energetic stabilization of biologically active anionic forms of these glycosaminoglycans. The stable energy conformations around glycosidic bonds found for dimers and pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals with proteins

Microscopic and macroscopic polarization within a combined quantum mechanics and molecular mechanics model

A polarizable quantum mechanics and molecular mechanics model has been extended to account for the difference between the macroscopic electric field and the actual electric field felt by the solute molecule. This enables the calculation of effective microscopic properties which can be related to macroscopic susceptibilities directly comparable with experimental results. By seperating the discrete local field into two distinct contribution we define two different microscopic properties, the so-called solute and effective properties. The solute properties account for the pure solvent effects, i.e.. effects even when the macroscopic electric field is zero, and the effective properties account for both the pure solvent effects and the effect from the induced dipoles in the solvent due to the macroscopic electric field. We present results for the linear and nonlinear polarizabilities of water and acetonitrile both in the gas phase and in the liquid phase. For all the properties we find that the pure solvent effect increases the properties whereas the induced electric field decreases the properties. Furthermore, we present results for the refractive index, third-harmonic generation (THG), and electric field induced second-harmonic generation (EFISH) for liquid water and acetonitrile. We find in general good agreement between the calculated and experimental results for the refractive index and the THG susceptibility. For the EFISH susceptibility, however, the difference between experiment and theory is larger since the orientational effect arising from the static electric field is not accurately described. (C) 2005 American Institute of Physics

The behaviour of charge distributions in dielectric media

Screened Coulomb interaction in dielectrics is often used as an argument for a lower exciton binding energy and easier exciton dissociation in a high dielectric material. In this paper, we show that at length scales of excitons (10-20 angstrom), the screened Coulomb law is invalid and a microscopic (quantum chemical) description is necessary to describe the medium effect on exciton dissociation. The exciton dissociation energy decreases with increasing dielectric constant, albeit deviating from the inversely proportional relationship. The electron-hole interaction energy, approximated with a point charge model, is apparently not affected by the dielectric constant of the environment. (C) 2014 Elsevier B.V. All rights reserved

A discrete solvent reaction field model within density functional theory

In this work we present theory and implementation for a discrete reaction field model within Density Functional Theory (DFT) for studying solvent effects on molecules. The model combines a quantum mechanical (QM) description of the solute and a classical description of the solvent molecules (MM). The solvent molecules are modeled by point charges representing the permanent electronic charge distribution, and distributed polarizabilities for describing the solvent polarization arising from many-body interactions. The QM/MM interactions are introduced into the Kohn-Sham equations, thereby allowing for the solute to be polarized by the solvent and vice versa. Here we present some initial results for water in aqueous solution. It is found that the inclusion of solvent polarization is essential for an accurate description of dipole and quadrupole moments in the liquid phase. We find a very good agreement between the liquid phase dipole and quadrupole moments obtained using the Local Density Approximation and results obtained with a similar model at the Coupled Cluster Singles and Doubles level of theory using the same water cluster structure. The influence of basis set and exchange correlation functional on the liquid phase properties was investigated and indicates that for an accurate description of the liquid phase properties using DFT a good description of the gas phase dipole moment and molecular polarizability are also needed. (C) 2003 American Institute of Physics

Medium perturbations on the molecular polarizability calculated within a localized dipole interaction model

We have studied the medium effects on the frequency-dependent polarizability of water by separating the total polarizability of water clusters into polarizabilities of the individual water molecules. A classical frequency-dependent dipole–dipole interaction model based on classical electrostatics and an Unsöld dispersion formula has been used. It is shown that the model reproduces the polarizabilities of small water clusters calculated with time-dependent density functional theory. A comparison between supermolecular calculations and the localized interaction model illustrate the problems arising from using supermolecular calculations to predict the medium perturbations on the solute polarizability. It is also noted that the solute polarizability is more dependent on the local geometry of the cluster than on the size of the cluster

Polarizabilities in the condensed phase and the local fields problem: A direct reaction field formulation

A consistent derivation is given for local field factors to be used for correcting measured or calculated static (hyper)polarizabilities in the condensed phases. We show how local fields should be used in the coupled perturbative Hartree–Fock or finite field methods for calculating these properties, specifically for the direct reaction field (DRF) approach, in which a quantum chemically treated “solute” is embedded in a classical “solvent” mainly containing discrete molecules. The derivation of the local fields is based on a strictly linear response of the classical parts and they are independent of any quantum mechanical method to be used. In applications to two water dimers in two basis sets it is shown that DRF matches fully quantum mechanical results quite well. For acetone in eleven different solvents we find that if the solvent is modeled by only a dielectric continuum (hyper)polarizabilities increase with respect to their vacuum values, while with the discrete model they decrease. We show that the use of the Lorentz field factor for extracting (hyper)polarizabilities from experimental susceptibilities may lead to serious errors

Time-dependent density functional theory/discrete reaction field spectra of open shell systems:The visual spectrum of [Fe-III(PyPepS)(2)](-) in aqueous solution

We report the calculated visible spectrum of [Fe-III(PyPepS)(2)](-) in aqueous solution. From all-classical molecular dynamics simulations on the solute and 200 water molecules with a polarizable force field, 25 solute/solvent configurations were chosen at random from a 50 ps production run and subjected the systems to calculations using time-dependent density functional theory (TD-DFT) for the solute, combined with a solvation model in which the water molecules carry charges and polarizabilities. In each calculation the first 60 excited states were collected in order to span the experimental spectrum. Since the solute has a doublet ground state several excitations to states are of type "three electrons in three orbitals," each of which gives rise to a manifold of a quartet and two doublet states which cannot properly be represented by single Slater determinants. We applied a tentative scheme to analyze this type of spin contamination in terms of Delta and Delta transitions between the same orbital pairs. Assuming the associated states as pure single determinants obtained from restricted calculations, we construct conformation state functions (CFSs), i.e., eigenfunctions of the Hamiltonian (S) over cap (z) and (S) over cap (2), for the two doublets and the quartet for each Delta,Delta pair, the necessary parameters coming from regular and spin-flip calculations. It appears that the lower final states remain where they were originally calculated, while the higher states move up by some tenths of an eV. In this case filtering out these higher states gives a spectrum that compares very well with experiment, but nevertheless we suggest investigating a possible (re)formulation of TD-DFT in terms of CFSs rather than determinants