Search

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.

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.

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., Advanced electronic structure methods provide a new insight into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of human DNA.

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.

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

Nanoparticles are applied in a variety of industrially relevant transformations as heterogeneous catalysts typically with the help of an external force (pressure, temperature, or voltage) to steer the chemistry. The modification of platinum nanoparticles by a phosphate–amino surfactant enables catalysis without external energy supply in the hydrogenation of nitrobenzene to aniline. This can be attributed to the complex surfactant/metal interface which is able to split hydrogen into protons and electrons. The subsequent hydrogenation process mimics the electrochemical reduction described by Haber. The surfactant decorated Pt catalyst is two orders of magnitude more active than the state-of-the-art Pb-poisoned Pt catalyst. Our study provides a new approach to understand the functionality of emerging catalytic systems and can be applied to design new materials with optimal interfaces.

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.

The dynamics of water encapsulated in the well-known polyoxomolybdate nanocapsules of the type Mo-132 is studied through molecular dynamics simulations. Two different ligands, namely, formate and sulfate ligands, are considered as decoration of the inner surface of the capsule. In both cases it is found that 172 water molecules are trapped inside, 72 of which are coordination water molecules, and the remaining 100 form a water nanodrop whose properties are studied. We find that the dynamic behavior of the nanodrop is significantly different between the two types of capsules considered as they have different interiors. We argue that the commensurability of the sulfate ligand nanocapsule imposes a high degree of tetrahedrality that confers rigidity to the three-dimensional water network affecting the whole water nanodrop in the cavity. The formate ligand capsule, instead, permits additional degrees of freedom that confer the water nanodrop a more liquid-like behavior. The overall size of the inner cavity is of the order of 1 nm which is comparable to the crossover length observed for effects related to the rigidity of water layers in contact with hydrophobic molecules.(1) The results could stimulate the investigation of encapsulated water in the presently used capsule, the interior of which can be widely tuned (even from hydrophilic to hydrophobic) in context with the fact that knowledge about water under confined conditions is of extreme importance.

The 30 cationic {(Mo2O4)-O-V(acetate)}(+) units linking 12 negatively charged pentagonal "ligands," {(Mo-VI)-(Mo5O21)-O-VI(H2O)(6)}(6-) of the porous metal-oxide capsule, [{(Mo6O21)-O-VI(H2O)(6)}(12){(Mo2O4)-O-V(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 x 10(3) angstrom(3) interior of the spherical capsule. The Mo atoms of the {(Mo2O4)-O-V(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 {(Mo2O4)-O-V(H2O)(2)}(2+) units with labile water ligands, and Lewis- and Bronsted-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 {(Mo2O4)-O-V(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.

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.

The relationship between the homogeneous and heterogeneous phases of a catalyst is widely neglected in part due to the inherent differences between the experimental and theoretical techniques employed to study them. It is well- known that, under reaction conditions, many homogeneous catalysts deactivate and generate black metals (i.e., nano- particles). Simultaneously, heterogeneous catalysts tend to suffer of leaching processes under harsh conditions, which produce the formation of species in the homogeneous phase (i.e., volatile or organometallic species). To unravel the links between these two types of catalytic species, we have taken PdAu catalysts in the oxidation of crotyl alcohol to crotonaldehyde and investigated the reaction process for both homogeneous and heterogeneous phases. We show that the process is possible in both phases and, essentially, contains the same elementary steps. The results indicate that the homogeneous catalyst is slightly more active; however, the enhanced stability of the heterogeneous phase provides a better performance under relevant reaction conditions. Both catalytic systems are connected through two simple steps that can be computed: oxidative leaching and deposition. The oxidative leaching of the PdAu nanoparticles in the presence of dioxygen can produce Pd(II) monomeric species able to catalyze the alcohol oxidation in homogeneous conditions. After the reaction the reduced Pd(0) homogeneous catalyst is reabsorbed onto the PdAu nanoparticles, preventing the aggregation process. The present work shows that the full homogeneous/heterogeneous catalytic cycle can be analyzed in a holistic manner with computational techniques.

Polyether polyols are used widely in the plastic and coating in- dustries in the form of polyurethanes. The polymerization of epoxides can be catalyzed by double metal cyanides (DMCs), Zn3[Co(CN)6]2. These catalysts were first reported in the 1960s by General Tire Inc. and provide products with excellent tech- nical features, which are better than those that result from tra- ditional alkaline polymerization as side reactions are alleviated. However, DMC-catalyzed polymerization is not free of draw- backs as high-molecular-weight side products (1–3 wt %) can form in the propylene process. These tails are detrimental to the subsequent use of these polymers, in particular to foam stability. Despite the wide industrial interest in DMCs, there are only a few experimental studies and a complete lack of theo- retical research of their structure, activity, and performance. The present work is thus the first attempt to describe the nature of the active site, the main polymerization mechanism, and two potential origins for the high-weight tails from a theo- retical standpoint by analyzing three crucial steps in the poly- merization process.

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.