Prediction of Henry's law constant of benzene derivatives using quantum chemical continuum‐solvation models

Semiempirical (SM2, SM5.4A, MST‐AM1, COSMO‐AM1) and ab inito (HF/PCM‐vdW, MP2//PCM‐vdW, COSMO‐DFT) dielectric continuum‐solvation models as well as the surface‐tension model SM5.0R are analyzed with respect to predicting Henry's law constant at 25°C using a compound set of benzene and 39 benzene derivatives. Both hydrophilic and hydrophobic compounds are covered with a total variation in Henry's law constant of almost eight orders of magnitude corresponding to 44 kJ/mol, and the data set is selected such that there are cases where subtle changes in the molecular structure result in substantial changes of the free energy of solvation. The calculations with SM2, COSMO‐AM1, and COSMO‐DFT include solution‐phase geometry optimization, and the ab initio results refer to polarized basis sets of double‐zeta quality, with two gradient‐corrected functionals (BPW and BLYP) being used for the DFT‐based models. The results show considerable differences in performance between the different continuum‐solvation models, and among the methods yielding solvation free energies the systematic error ranges from −0.9 kJ/mol (SM5.0R) to 12.1 kJ/mol (MP2//PCM‐vdW). In particular, the nonelectrostatic solvation energy contributions of SM2, SM5.4A, MST‐AM1, and PCM‐vdW do not correlate with each other, and with PCM‐vdW omission of the nonelectrostatic component significantly improves the relative trend. The best statistics after scaling through linear regression are achieved with the electrostatic component of MP2//PCM‐vdW (r=0.94) and with COSMO‐DFT (r=0.93). The discussion includes detailed analyses of pecularities associated with certain functional groups, deviations from the expected relationship between dipole moment and solvation energy, and a simple approach to model dispersion interaction and cavitation energy by surface area terms that differentiate between individual atom types. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 17–34, 2000     

Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics

Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Water solvent effects using continuum and discrete models: The nitromethane molecule,CH3NO2

The first three valence transitions of the two nitromethane conformers (CH₃NO₂) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas‐phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor‐like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S‐QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry‐adapted‐cluster CI (SAC‐CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic‐diagrammatic construction (ADC(2)) electronic structure methods were used. Gas‐phase CASPT2, SAC‐CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC‐CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S‐QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S‐QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S‐QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.     

Predicting hydration energies for multivalent ions

We have predicted the free energy of hydration for 40 monovalent and multivalent cations and anions using density functional theory and the implicit solvent model COnductor like Screening MOdel for Real Solvents (COSMO‐RS) at the Becke‐Perdew (BP)/Triple zeta valence with polarization functions (TZVP) level. Agreement with experimental data for monovalent and divalent ions is good and shows no significant systematic errors. Predictions are noticeably better than with standard COSMO. The agreement with experimental data for trivalent and tetravalent ions is slightly worse and shows systematic errors. Our results indicate that quantum chemical calculations combined with COSMO‐RS solvent treatment is a reliable method for treating multivalent ions in solution, provided one hydration shell of explicit water molecules is included for metal cations. The accuracy is not high enough to allow absolute predictions of hydration energies but could be used to investigate trends for several ions, thanks to the low computational cost, in particular for ligand exchange reactions. © 2014 Wiley Periodicals, Inc.     

A study on orientation and absorption spectrum of interfacial molecules by using continuum model

In this work, a numerical procedure based on the continuum model is developed and applied to the solvation energy for ground state and the spectral shift against the position and the orientation of the interfacial molecule. The interface is described as a sharp boundary separating two bulk media. The polarizable continuum model (PCM) allows us to account for both electrostatic and nonelectrostatic solute-solvent interactions when we calculate the solvation energy. In this work we extend PCM to the interfacial system and the information about the position and orientation of the interfacial molecule can be obtained. Based on the developed expression of the electrostatic free energy of a nonequilibrium state, the numerical procedure has been implemented and used to deal with a series of test molecules. The time-dependent density functional theory (TDDFT) associated with PCM is used for the electron structure and the spectroscopy calculations of the test molecules in homogeneous solvents. With the charge distribution of the ground and excited states, the position- and orientation-dependencies of the solvation energy and the spectrum have been investigated for the interfacial systems, taking the electrostatic interaction, the cavitation energy, and the dispersion-repulsion interaction into account. The cavitation energy is paid particular attention, since the interface portion cut off by the occupation of the interfacial molecule contributes an extra part to the stabilization for the interfacial system. The embedding depth, the favorable orientational angle, and the spectral shift for the interfacial molecule have been investigated in detail. From the solvation energy calculations, an explanation has been given on why the interfacial molecule, even if symmetrical in structure, tends to take a tilting manner, rather than perpendicular to the interface.     

Building cavities in a fluid of spherical or rod-like particles: a contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model

A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod-like molecules in spherical or rod-like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results.     

The hydration of the uranyl dication: Incorporation of solvent effects in parallel density functional calculations with the program PARAGAUSS

The parallel density functional program PARA GAUSS has been extended by a tool for computing solvent effects based on the conductor‐like screening model (COSMO). The molecular cavity in the solvent is constructed as a set of overlapping spheres according to the GEPOL algorithm. The cavity tessellation scheme and the resulting set of point charges on the cavity surface comply with the point group symmetry of the solute. Symmetry is exploited to reduce the computational effort of the solvent model. To allow an automatic geometry optimization including solvent effects, care has been taken to avoid discontinuities due to the discretization (weights of tesserae, number of spheres created by GEPOL). In this context, an alternative definition for the grid points representing the tesserae is introduced. In addition to the COSMO model, short‐range solvent effects are taken into account via a force field. We apply the solvent module to all‐electron scalar‐relativistic density functional calculations on uranyl, UO₂²⁺, and its aquo complexes in aqueous solution. Solvent effects on the geometry are very small. Based on the model [UO₂(H₂O)₅]²⁺, the solvation energy of uranyl is estimated to be about ?400 kcal/mol, in agreement with the range of experimental data. The major part of the solvation energy, about ?250 kcal/mol, is due to a donor–acceptor interaction associated with a coordination shell of five water ligands. One can interpret this large solvation energy also as a compounded effect of an effective reduction of the uranyl moiety plus a solvent polarization. The energetic effect of the structure relaxation in the solution is only about 8 kcal/mol. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution

The absolute pKa values of 24 representative amine compounds, including cocaine, nicotine, 10 neurotransmitters, and 12 anilines, in aqueous solution were calculated by performing first-principles electronic structure calculations that account for the solvent effects using four different solvation models, i.e., the surface and volume polarization for electrostatic interaction (SVPE) model, the standard polarizable continuum model (PCM), the integral equation formalism for the polarizable continuum model (IEFPCM), and the conductor-like screening solvation model (COSMO). Within the examined computational methods, the calculations using the SVPE model lead to the absolute pKa values with the smallest root-mean-square-deviation (rmsd) value (1.18). When the SVPE model was replaced by the PCM, IEFPCM, and COSMO, the rmsd value of the calculated absolute pKa values became 3.21, 2.72, and 3.08, respectively. All types of calculated pKa values linearly correlate with the experimental pKa values very well. With the empirical corrections using the linear correlation relationships, the theoretical pKa values are much closer to the corresponding experimental data and the rmsd values become 0.51-0.83. The smallest rmsd value (0.51) is also associated with the SVPE model. All of the results suggest that the first-principles electronic structure calculations using the SVPE model are a reliable approach to the pKa prediction for the amine compounds.     

Molecular orientations at interfaces by extended polarizable continuum model

This study presents an investigation into orientation of molecular solutes at the interface of liquid water and other media. The calculation of electrostatic free energy of molecular solute is based on an extension of the polarizable continuum model (PCM) to interfacial system. The extended PCM computational scheme is incorporated with the self‐consistent field procedure which is necessary to obtain more accurate electrostatic free energy and charge density distribution. The computation of non‐electrostatic energy for interfacial system is also realized. Applying the numerical procedure to molecular systems, N,N′‐diethyl‐p‐nitroaniline (DEPNA) at air/water interface and p‐nitrophenol (PNP) at cyclohexane/water interface, the average orientational angles are in reasonable agreement with the experimental results. Taking both the electrostatic and the non‐electrostatic energies into account, the analysis on the energy profiles shows that the electrostatic solvation energy is the dominant factor in determining the orientation angle for PNP, whereas for DEPNA, the orientation angle mainly depends on the cavitation energy. This suggests that, in addition to the electrostatic energy, taking the cavitation energy into account may provide a more complete view when we survey the molecular orientation at interface. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Incorporation of solvent effects into density functional predictions of molecular polarizabilities and hyperpolarizabilities

A study of the effect of the field, the basis set, the functional, and the cavity size on molecular polarizabilities and hyperpolarizabilities of substituted benzenes in liquid or solution is reported. The calculations have been performed using the density functional theory (DFT) within the conductor‐like screening model (COSMO). The optimized computational parameters are adopted to calculate molecular polarizabilities and hyperpolarizabilities of substituted benzenes in liquid or solution. The results show good agreement with the experimental values. From comparison of the different theoretical results, it is found that at the same theoretical level, the selection of the different solvation models may play an important role in the calculations of molecular solvation polarizability, and using the same solvation model, the effects of the different theoretical methods are relatively small. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A “vertex‐based” approach, where a computing thread is started per particle, is compared to an “edge‐based” approach, where a thread is started per each potentially non‐zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores—as opposed to their computing power—remains, the “edge‐based” approach will gradually become the most efficient choice in an increasing number of cases. © 2014 Wiley Periodicals, Inc.     

DFT plus PCM calculation for pairing specificity of Watson–Crick‐type bases in aqueous solutions

This study is aimed at explaining the preference for AT and CG pairings and the possible insertion of other tautomeric DNA base pairs such as G_enolT, that respect energetic and steric requirements including at least two hydrogen bonds and 11 ± 0.5Å distance between the 9‐CH₃ of purine and 5‐CH₃ of pyrimidine. The calculated free energy of formation ΔΔG at the DFT B3LYP/6‐31G*‐PCM/BEM level pointed out the CG and AT pairs as the most favored, followed closely by G_enolT, in good agreement with Michaelis–Menten first order kinetics (CG ≈ AT > G_enolT). Unusual DNA base pairs complexes such as AG (BEM) and CT (PCM) resulted to be stable, but it is very difficult to assume that they are likely to be included in the double strand DNA. The calculated enthalpy and dipole moments of isolated DNA bases agree well with experiment. The free energy of hydration, ΔG_hyd, was found to depend on the electrostatic term, while cavitation‐dispersion components are almost constant. The stability of DNA complexes in water resulted from PCM calculations is markedly influenced by the free energy of hydration. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A general,most basic rule for ion dissociation: Protonated molecules

Contrary to the common but potentially misleading belief that when a protonated molecule is excited, it is its most stable protomer that will mandatorily dissociate, we demonstrate herein that, when rationalizing or predicting the chemistry of such ions, we should always search for the most labile protomer. This “most labile protomer” rule, based on the mobile proton model, states therefore that when a protonated molecule is heated, during ionization or by collisions for instance, the loosely bonded proton (H⁺) can acquire enough energy to detach itself from the most basic site of the molecule and then freely “walk through” the molecular framework to eventually find, if available, another protonation site, forming other less stable but more labile protomers, that is, protomers that may display lower dissociation thresholds. To demonstrate the validity of the “most labile protomer” rule as well as the misleading nature of the “most stable protomer” rule, we have selected several illustrative molecules and have collected their ESI(+)-MS/MS. To compare energies of precursors and products, we have also performed PM7 calculations and elaborated potential energy surface diagrams for their possible protomers and dissociation thresholds. We have also applied the “most labile protomer” rule to reinterpret—exclusively via classical charge-induced dissociation cleavages—several dissociation processes proposed for protonated molecules. In an accompanying letter, we have also applied a similar “most labile electromer” rule to ionized molecules.     

An investigation of a separation process involving liquid—water—coal systems

A liquid—liquid—solid separation procedure wherein a water—oil—coal—mineral matter slurry is allowed to come to equilibrium through mechanical agitation has for many years been applied to the separation of coal from mineral matter. The product is a black “cottage cheese”-like mass of agglomerated coal particles and oil suspended in the excess water which supports the dispersed mineral matter particles. A liquid “bridge” model was proposed by earlier investigators which is reviewed critically and used to estimate the free energy per unit area of the separation of coals of different ranks. Observations of the kinetics of the process suggest that the simple liquid “bridge” model is insufficient, probably due to the heterogeneous surfaces of the coal. An alternative model is proposed.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

An improved interface for inductively coupled plasma-mass spectrometry (ICP-MS)

Adiabatic sampling of the plasma from an inductively coupled plasma (ICP) torch is a crucial first step for inductively coupled plasma-mass spectrometry (ICP-MS) to reach its full potential as a trace multi-element analysis system. Previous results in the literature are reviewed, and a series of experiments reported, which indicate that a discharge, previously called a “pinch” effect, can be present in which the plasma properties are strongly altered by a constricted current flowing between the plasma and the sampling orifices, i.e. a secondary discharge. Measurements and calculations indicate that this mechanism is consistent with previously reported deleterious effects—abnormal production of doubly ionized species, a wide kinetic energy distribution for the ions sampled into vacuum, formation of ions from metal eroded from the sampling orifices, and a decreased orifice life-time. The mechanism producing the effect was found to be an unwanted capacitive coupling between the voltage on the induction coil and the plasma. Results are included which show that by centre-grounding the coil, the “pinch” effect can be reduced to negligible proportions. The resulting improvements for ICP-MS operation are described.