Continuous and smooth potential energy surface for conductorlike screening solvation model using fixed points with variable areas

Single-Hydroxide Bridged Dimers of U and Np Actinyls: A Density Functional Study on Their Existence and Structure in Aqueous Solution

With quantum chemical calculations at the density functional theory level, we examined the structure and the stability of diactinyl monohydroxo complexes [(AnO₂)₂(OH)]^3+/+ in aqueous solution for An = U(VI), Np(VI), and Np(V). In particular, this study contributes to understanding the hydrolysis of Np(VI) and Np(V), which is less well characterized than for U(VI). [(UO₂)₂(OH)]³⁺ is a known hydrolysis complex of U(VI) at low pH. Although not yet found in experiments, [(NpO₂)₂(OH)]³⁺ is suggested to exist due to the similarity between Np(VI) and U(VI) complexes, while [(NpO₂)₂(OH)]⁺ is a hypothetical species thus far. Our calculations suggest that the An(VI) complexes favor the parallel orientation of actinyls, whereas for the Np(V) complex a perpendicular arrangement is stabilized by hydrogen bonds between aqua ligands and the actinyl oxygen atoms. The Np(VI) complex [(NpO₂)₂(OH)]³⁺ features a structure and stability similar to its U(VI) analogue. From calculated formation constants for An(VI) diactinyl monohydroxo complexes, we find qualitative agreement with the experiment for U(VI). Both An(VI) complexes are only slightly less stable than the separate mononuclear constituents, the actinyl aqua and the monohydroxo complex. For the Np(V) species [(NpO₂)₂(OH)]⁺, we calculated a considerably lower complexation constant than for its An(VI) analogues, but it is more stable against decay into its constituents. Thus, this complex may exist at about the pH where Np(V) hydrolysis starts at not too low Np(V) concentrations.

Theoretical free energy profile and benchmarking of functionals for amino-thiourea organocatalyzed nitro-Michael addition reaction

Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate addition reactions. The interaction of the reactants with the catalyst has a substantial effect of dispersion forces and is a challenge for a reliable description when applying density functional theory. In this report, the classical addition of acetylacetone to β-nitro-styrene catalyzed by Takemoto's catalyst in toluene was studied using the PBE functional for geometry optimization and the DLPNO-CCSD(T) benchmark method for single point energy. The complete free energy profile calculated for the reaction was able to explain all experimental observations, including the fact that the carbon-carbon bond formation step is rate-determining. The overall barrier was calculated to be 22.8 kcal mol^-1 (experimental value approximately 20 kcal mol^-1), and the enantiomeric excess was calculated to be 88% (experimental value in the range of 84 to 92%). Some functionals were tested for single point energy. The hybrid B3LYP presented a high mean absolute deviation (MAD) from the DLPNO-CCSD(T) benchmark method by approximately 20 kcal mol^-1. The inclusion of empirical dispersion correction in the B3LYP method decreased the MAD to 6 kcal mol^-1. Even the double-hybrid mPW2-PLYP and B2GP-PLYP methods had MAD values of approximately 5 kcal mol^-1. The inclusion of the dispersion correction decreased the MAD to 3.6 kcal mol^-1. M06-2X and ωB97X-D3 were the most accurate among the tested functionals, with MADs of 2.5 kcal mol^-1 and 1.8 kcal mol^-1, respectively. Additivity approximation of the correlation energy was also tested and presented a MAD of only 0.6 kcal mol^-1.

Hydration Structure and Hydrolysis of U(IV) and Np(IV) Ions: A Comparative Density Functional Study Using a Modified Continuum Solvation Approach

We studied the hydration and the first hydrolysis reaction of U(IV) and Np(IV) ions in an aqueous environment, applying a relativistic density functional method together with a recently proposed variant of a continuum solvation model where the solute cavities are constructed with effective atomic radii, based on charge-dependent scaling factors. In this way, one obtains improved solvation energies of charged species. We demonstrate that solute cavities, constructed with scaled atomic radii as described, permit one to calculate hydrolysis constants of acceptable accuracy. As a consequence, one is also able to estimate free hydration energies of U(IV) and Np(IV) in adequate agreement with empirical data. According to the model calculations, U(IV) is coordinated by eight to nine water molecules, while the preferred coordination number of Np(IV) is 8. For the highly charged ions under study, the modified solvation model simultaneously yields improved geometries, hydration energies, and hydrolysis constants.

Energy decomposition analysis based on broken symmetry unrestricted density functional theory

In this paper, the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme is extended to molecular interactions in open shell singlet states, which is a challenge for many popular EDA methods due to the multireference character. Based on broken symmetry (BS) unrestricted density functional theory with a spin projection approximation, the extension scheme, named GKS-EDA(BS) in this paper, divides the total interaction energy into electrostatic, exchange-repulsion, polarization, correlation, and dispersion terms. Test examples include the pancake bond in the phenalenyl dimer, the ligand interactions in the Fe(ii)-porphyrin complexes, and the radical interactions in dehydrogenated guanine-cytosine base pairs and show that GKS-EDA(BS) is a practical EDA tool for open shell singlet systems.

Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method

Based on induced solvent charges, a new model of solvent screening is developed in the framework of the fragment molecular orbital combined with the polarizable continuum model. The developed model is applied to analyze interactions in a prototypical zwitterionic system, sodium chloride in water, and it is shown that the large underestimation of the interaction in the original solvent screening based on local charges is successfully corrected. The model is also applied to a complex of the Trp-cage (PDB: 1L2Y ) miniprotein with an anionic ligand, and the physical factors determined protein-ligand binding in solution are unraveled.

Simulations of infrared and Raman spectra in solution using the fragment molecular orbital method

Calculation of IR and Raman spectra in solution for large molecular systems made possible with analytic FMO/PCM Hessians.

What kind of neutral halogen bonds can be modulated by solvent effects?

Halogen bonds with a large portion of polarization can be modulated by solvent effects.

Computational study of the interaction between NO, NO+, and NO- with H2O

In this computational study the interaction of NO^., NO⁺, and NO^- with H₂O: [NO--H₂O]^., 1 ^., [NO--H₂O]⁺, 1 ⁺ , and [NO--H₂O]^-, 1 ^- was analysed. The optimized geometries indicate that the relative position of NO and H₂O depends on the total charge: (ON^.--H-OH), (NO^---H-OH), and (ON⁺--OH₂). Moreover, atomic spin density along with frontier molecular orbitals help to identify the preferred reduction or oxidation sites on the nitric oxide. Thus, quantum theory of atoms in molecules (QTAIM), electron localization function (ELF), and natural bond-bond polarizability (NBBP) methods aid to quantify the electron delocalization level between NO and H₂O, 1 ⁺ > 1 ^. > 1 ^- , and show the predominantly ionic, and covalent character to inter-molecular, and intra-molecular chemical bonds, respectively. Furthermore, the natural bond orbital (NBO) and localized molecular orbital energy decomposition analysis (LMO-EDA) methods enable energy analyses of the interaction between NO and H₂O in the complexes 1 ^., 1 ⁺ , and 1 ^- . Where, the first method showed that the interaction between the natural bond orbitals in 1 ^- is more favorable, than in 1 ⁺ , and less in 1 ^., however, the second method designates that the total interaction energy is lower for 1 ⁺ in relation to 1 ^- and 1 ^., due mainly to the electrostatic component. As a final point, analysis of the electrostatic potential surfaces provides a clear and direct explanation for the relative position of the monomers. It also shows that the predominant Coulombic attraction between H₂O and the charged NO⁺, and NO^- compounds will be stronger in relation to the neutral NO^.. Graphical abstract ᅟ.

Electrochemical Electron Transfer and Proton-Coupled Electron Transfer: Effects of Double Layer and Ionic Environment on Solvent Reorganization Energies

Electron transfer and proton coupled electron transfer (PCET) reactions at electrochemical interfaces play an essential role in a broad range of energy conversion processes. The reorganization energy, which is a measure of the free-energy change associated with solute and solvent rearrangements, is a key quantity for calculating rate constants for these reactions. We present a computational method for including the effects of the double layer and ionic environment of the diffuse layer in calculations of electrochemical solvent reorganization energies. This approach incorporates an accurate electronic charge distribution of the solute within a molecular-shaped cavity in conjunction with a dielectric continuum treatment of the solvent, ions, and electrode using the integral equations formalism polarizable continuum model. The molecule-solvent boundary is treated explicitly, but the effects of the electrode-double layer and double layer-diffuse layer boundaries, as well as the effects of the ionic strength of the solvent, are included through an external Green's function. The calculated total reorganization energies agree well with experimentally measured values for a series of electrochemical systems, and the effects of including both the double layer and ionic environment are found to be very small. This general approach was also extended to electrochemical PCET and produced total reorganization energies in close agreement with experimental values for two experimentally studied PCET systems.

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.

On the Calculation of Vibrational Frequencies for Molecules in Solution Beyond the Harmonic Approximation

We report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent interactions, the latter being described by means of the polarizable continuum model (PCM). Density functional theory force fields are employed as well as a new implementation of the PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide prototypes show that our approach is able to yield a quantitative agreement with experiments for vacuo-to-solvent harmonic and anharmonic frequency shifts.

Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model

We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates.

Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale

A solvation free energy scale excluding the net electrostatic potential inside the solute cavity is presented.

Hydrogen bonding motifs in a hydroxy-bisphosphonate moiety: revisiting the problem of hydrogen bond identification

Relative energy of conformers are highly correlated with their sum of local density of potential energy at H-bond critical points.

A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+

We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.

Energy decomposition scheme based on the generalized Kohn-Sham scheme

In this paper, a new energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS) and the localized molecular orbital energy decomposition analysis (LMO-EDA) scheme, named GKS-EDA, is proposed. The GKS-EDA scheme has a wide range of DFT functional adaptability compared to LMO-EDA. In the GKS-EDA scheme, the exchange, repulsion, and polarization terms are determined by DFT orbitals; the correlation term is defined as the difference of the GKS correlation energy from monomers to supermolecule. Using the new definition, the GKS-EDA scheme avoids the error of LMO-EDA which comes from the separated treatment of EX and EC functionals. The scheme can perform analysis both in the gas and in the condensed phases with most of the popular DFT functionals, including LDA, GGA, meta-GGA, hybrid GGA/meta-GGA, double hybrid, range-separated (long-range correction), and dispersion correction. By the GKS-EDA scheme, the DFT functionals assessment for hydrogen bonding, vdW interaction, symmetric radical cation, charge-transfer, and metal-ligand interaction is performed.

Structure and electronic spectra of purine-methyl viologen charge transfer complexes

The structure and properties of the electron donor-acceptor complexes formed between methyl viologen and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and (1)H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT). Energy decomposition analysis indicates that dispersion and induction (charge-transfer) interactions dominate the total binding energy, whereas electrostatic interactions are largely repulsive. The appearance of charge transfer bands in the absorption spectra of the complexes are well-described by time-dependent DFT and are further explained in terms of the redox properties of purine monomers and solvation effects. Crystal structures are reported for complexes of methyl viologen with the purines 2'-deoxyguanosine 3'-monophosphate (DAD'DAD' type) and 7-deazaguanosine (DAD'ADAD' type). Comparison of the structures determined in the solid state and by theoretical methods in solution provides valuable insights into the nature of charge-transfer interactions involving purine bases as electron donors.

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase.

Revisiting the mechanism of neutral hydrolysis of esters: water autoionization mechanisms with acid or base initiation pathways

The mechanism of neutral hydrolysis of ester has long been explored by theoretical studies. However, reliable theoretical calculations show that the usual bifunctional catalysis mechanism reported by different authors cannot explain the experimental kinetics. An important advance was recently reported by Gunaydin and Houk, suggesting that ions are involved in the mechanism and the process initiates by water autoionization followed by protonation of the ester (W(AI)A mechanism). However, this mechanism does not explain the hydrolysis of activated esters. In this work, we have used ab initio calculations, continuum solvation models, and intrinsic reaction coordinate method to support the W(AI)A mechanism for normal ester. In the case of activated esters, the process can also be viewed as water autoionization with formation of hydroxide ion aided by a second water molecule acting as a general base (W(AI)B mechanism). This is the mechanism that was proposed by Jencks and Carriuolo 50 years ago. Our analysis point out that the usual method for exploring mechanisms, searching for saddle points, may not work for problems like the present one, since there are no saddle points on the reaction pathway. Rather, the formation of a pair of ions from a neutral species may have an asymptotic barrier. The approach used in this paper allows the calculation of the free energy profile and enable us to explain the mechanism and kinetics of the neutral hydrolysis of normal (methyl acetate) and activated (methyl trifluoroacetate) esters. In addition, the present study suggests that formation of a pair of ions should always be considered in reactions in aqueous solution.

Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation

The analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculations are derived and implemented for spin-restricted closed shell (RMP2), Z-averaged spin-restricted open shell (ZAPT2), and spin-unrestricted open shell (UMP2) cases. Using these methods, the geometries of the S(0) ground state and the T(1) state of three nucleobase pairs (guanine-cytosine, adenine-thymine, and adenine-uracil) in the gas phase and aqueous solution phase are optimized. It is found that in both the gas phase and the aqueous solution phase the hydrogen bonds in the T(1) state pairs are weakened by ~1 kcal/mol as compared to those in the S(0) state pairs.