Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches.

Hydrated transition metal ions are prototypical systems that can be used to model properties of transition metals in complex chemical environments. These seemingly simple systems present challenges for computational chemistry and are thus crucial in evaluations of quantum chemical methods for spin-state and redox energetics. In this work, we explore the applicability of the domain-based pair natural orbital implementation of coupled cluster (DLPNO-CC) theory to the calculation of ionization energies and redox potentials for hydrated ions of all first transition row (3d) metals in the 2+/3+ oxidation states, in connection with various solvation approaches. In terms of model definition, we investigate the construction of a minimally explicitly hydrated quantum cluster with a first and second hydration layer. We report on the convergence with respect to the coupled cluster expansion and the PNO space, as well as on the role of perturbative triple excitations. A recent implementation of the conductor-like polarizable continuum model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent redox potentials at the coupled cluster level. Our results establish conditions for the convergence of DLPNO-CCSD(T) energetics and stress the absolute necessity to explicitly consider the second solvation sphere even when CPCM is used. The achievable accuracy for redox potentials of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore, multilayer approaches that combine a higher-level DLPNO-CCSD(T) description of the first solvation sphere with a lower-level description of the second solvation layer are investigated. The present work establishes optimal and transferable methodological choices for employing DLPNO-based coupled cluster theory, the associated CPCM implementation, and cost-efficient multilayer derivatives of the approach for open-shell transition metal systems in complex environments.

Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex.

Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.

Implicit solvation in domain based pair natural orbital coupled cluster (DLPNO-CCSD) theory.

A nearly linear scaling implementation of coupled-cluster with singles and doubles excitations (CCSD) can be achieved by means of the domain-based local pair natural orbital (DLPNO) method. The combination of DLPNO-CCSD with implicit solvation methods allows the calculation of accurate energies and chemical properties of solvated systems at an affordable computational cost. We have efficiently implemented different schemes within the conductor-like polarizable continuum model (C-PCM) for DLPNO-CCSD in the ORCA quantum chemistry suite. In our implementation, the overhead due to the additional solvent terms amounts to less than 5% of the time the equivalent gas phase job takes. Our results for organic neutrals and open-shell ions in water show that for most systems, adding solvation terms to the coupled-cluster amplitudes equations and to the energy leads to small changes in the total energy compared to only considering solvated orbitals and corrections to the reference energy. However, when the solute contains certain functional groups, such as carbonyl or nitrile groups, the changes in the energy are larger and estimated to be around 0.04 and 0.02 kcal/mol for each carbonyl and nitrile group in the solute, respectively. For solutes containing metals, the use of accurate CC/C-PCM schemes is crucial to account for correlation solvation effects. Simultaneously, we have calculated the electrostatic component of the solvation energy for neutrals and ions in water for the different DLPNO-CCSD/C-PCM schemes. We observe negligible changes in the deviation between DLPNO-CCSD and canonical-CCSD data. Here, DLPNO-CCSD results outperform those for Hartree-Fock and density functional theory calculations.

Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme.

The treatment of the solvation charges using Gaussian functions in the polarizable continuum model results in a smooth potential energy surface. These charges are placed on top of the surface of the solute cavity. In this article, we study the effect of the solute cavity (van der Waals-type or solvent-excluded surface-type) using the Gaussian charge scheme within the framework of the conductor-like polarizable continuum model on (a) the accuracy and computational cost of the self-consistent field (SCF) energy and its gradient and on (b) the calculation of free energies of solvation. For that purpose, we have considered a large set of systems ranging from few atoms to more than 200 atoms in different solvents. Our results at the DFT level using the B3LYP functional and the def2-TZVP basis set show that the choice of the solute cavity does neither affect the accuracy nor the cost of calculations for small systems (< 100 atoms). For larger systems, the use of a vdW-type cavity is recommended, as it prevents small oscillations in the gradient (present when using a SES-type cavity), which affect the convergence of the SCF energy gradient. Regarding the free energies of solvation, we consider a solvent-dependent probe sphere to construct the solvent-accessible surface area required to calculate the nonelectrostatic contribution to the free energy of solvation. For this part, our results for a large set of organic molecules in different solvents agree with available experimental data with an accuracy lower than 1 kcal/mol for both polar and nonpolar solvents.

Efficient implementation of the analytical second derivatives of hartree-fock and hybrid DFT energies within the framework of the conductor-like polarizable continuum model.

Calculation of vibrational frequencies for solvated systems is essential to study reactions in complex environments. In this paper, we report the implementation of the analytical self-consistent field Hessian at the Hartree-Fock and density functional theory levels in the framework of the conductor-like polarizable continuum model (C-PCM) into the ORCA quantum chemistry suite. The calculated vibrational frequencies agree very well with those computed through numerical differentiation of the analytical gradients. The deviation between both sets of data is smaller than 3 cm-1 for frequencies larger than 200 cm-1 and smaller than 5 cm-1 for the low-frequency regime (100 cm-1 < ω < 200 cm-1 ). The accuracy of the frequencies is not significantly affected by the size of the density functional theory (DFT) integration grid, with a deviation lower than 0.5 cm-1 between data computed with the smallest and that with the largest DFT grid size. The calculation of the analytical Hessian is between 3 and 12 times faster than its numerical counterpart. The C-PCM terms only add an overhead of 10-30% relative to the gas phase calculations. Finally, for acetone, the (B3LYP) values for the frequency shifts obtained in going from the gas phase to liquid acetone are in agreement with experiment. © 2019 Wiley Periodicals, Inc.

Shape control in concave metal nanoparticles by etching.

The shape control of nanoparticles constitutes one of the main challenges in today's nanotechnology. The synthetic procedures are based on trial-and-error methods and are difficult to rationalize as many ingredients are typically used. For instance, concave nanoparticles exhibiting high-index facets can be obtained from Pt with different HCl treatments. These structures present exceptional capacities when are employed as catalysts in electrochemical processes, as they maximize the activity per mass unit of the expensive material. Here we show how atomistic simulations based on density functional theory that take into account the environment can predict the morphology for the nanostructures and how it is even possible to address the appearance of concave structures. To describe the control by etching, we have reformulated the Wulff construction through the use of a geometric model that leads to concave polyhedra, which have a larger surface-to-volume ratio compared to that for nanocubes. Such an increase makes these sorts of nanoparticles excellent candidates to improve electrocatalytic performance.

Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT.

Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models.

Catalysis in a porous molecular capsule: activation by regulated access to sixty metal centers spanning a truncated icosahedron.

The 30 cationic {Mo(V)2O4(acetate)}(+) units linking 12 negatively charged pentagonal "ligands," {(Mo(VI))Mo(VI)5O21(H2O)6}(6-) of the porous metal-oxide capsule, [{Mo(VI)6O21(H2O)6}12{Mo(V)2O4(acetate)}30](42-) provide active sites for catalytic transformations of organic "guests". This is demonstrated using a well-behaved model reaction, the fully reversible cleavage and formation of methyl tert-butyl ether (MTBE) under mild conditions in water. Five independent lines of evidence demonstrate that reactions of the MTBE guests occur in the ca. 6 × 10(3) Å(3) interior of the spherical capsule. The Mo atoms of the {Mo(V)2O4(acetate)}(+) linkers--spanning an ca. 3-nm truncated icosahedron--are sterically accessible to substrate, and controlled removal of their internally bound acetate ligands generates catalytically active {Mo(V)2O4(H2O)2}(2+) units with labile water ligands, and Lewis- and Brønsted-acid properties. The activity of these units is demonstrating by kinetic data that reveal a first-order dependence of MTBE cleavage rates on the number of acetate-free {Mo(V)2O4(H2O)2}(2+) linkers. DFT calculations point to a pathway involving both Mo(V) centers, and the intermediacy of isobutene in both forward and reverse reactions. A plausible catalytic cycle--satisfying microscopic reversibility--is supported by activation parameters for MTBE cleavage, deuterium and oxygen-18 labeling studies, and by reactions of deliberately added isobutene and of a water-soluble isobutene analog. More generally, pore-restricted encapsulation, ligand-regulated access to multiple structurally integral metal-centers, and options for modifying the microenvironment within this new type of nanoreactor, suggest numerous additional transformations of organic substrates by this and related molybdenum-oxide based capsules.

Molecular modeling of diffusion coefficient and ionic conductivity of CO2 in aqueous ionic solutions.

Mass diffusion coefficients of CO(2)/brine mixtures under thermodynamic conditions of deep saline aquifers have been investigated by molecular simulation. The objective of this work is to provide estimates of the diffusion coefficient of CO(2) in salty water to compensate the lack of experimental data on this property. We analyzed the influence of temperature, CO(2) concentration,and salinity on the diffusion coefficient, the rotational diffusion, as well as the electrical conductivity. We observe an increase of the mass diffusion coefficient with the temperature, but no clear dependence is identified with the salinity or with the CO(2) mole fraction, if the system is overall dilute. In this case, we notice an important dispersion on the values of the diffusion coefficient which impairs any conclusive statement about the effect of the gas concentration on the mobility of CO(2) molecules. Rotational relaxation times for water and CO(2) increase by decreasing temperature or increasing the salt concentration. We propose a correlation for the self-diffusion coefficient of CO(2) in terms of the rotational relaxation time which can ultimately be used to estimate the mutual diffusion coefficient of CO(2) in brine. The electrical conductivity of the CO(2)-brine mixtures was also calculated under different thermodynamic conditions. Electrical conductivity tends to increase with the temperature and salt concentration. However, we do not observe any influence of this property with the CO(2) concentration at the studied regimes. Our results give a first evaluation of the variation of the CO(2)-brine mass diffusion coefficient, rotational relaxation times, and electrical conductivity under the thermodynamic conditions typically encountered in deep saline aquifers.

Dynamics of encapsulated water inside Mo132 cavities.

The structure and dynamics of water confined inside a polyoxomolybdate molecular cluster [{(Mo)Mo(5)O(21)(H(2)O)(6)}(12){Mo(2)O(4)(SO(4))}(30)](72-) metal oxide nanocapsule have been studied by means of molecular dynamics simulations under ambient conditions. Our results are compared to experimental data and theoretical analyses done in reverse micelles, for several properties. We observe that the characteristic three-dimensional hydrogen bond network present in bulk water is distorted inside the cavity where water organizes instead in concentric layered structures. Hydrogen bonding, tetrahedral order, and orientational distribution analyses indicate that these layers are formed by water molecules hydrogen bonded with three other molecules of the same structure. The remaining hydrogen bond donor/acceptor site bridges different layers as well as the whole structure with the hydrophilic inner side of the cavity. The most stable configuration of the layers is thus that of a buckyball with 12 pentagons and a variable number of hexagons. The geometrical constraints make it so that the bridges between the layers display a significant degree of frustration. The main modes of motion at short times are correlated fluctuations of the entire system with a characteristic frequency. Switches of water molecules between layers are rare events, due to the stability of the layers. At long times, the system shows a power law decay (pink noise) in properties like the fluctuations in the number of molecules in the structures and the total dipole moment. Such behavior has been attributed to the complex relaxation of the hydrogen bond network, and the exponents found are close to those encountered in bulk water for the relaxation of the potential energy. Our results reveal the importance of the competition between the confinement and the long-range structure induced in this system by the hydrogen bond network.