Atomic Point Charges Research Articles

Plasma-Assisted Dinitrogen Activation via Dual Platinum Cluster Catalysis: A Strategy for Ammonia Synthesis under Mild Conditions

Plasma-Assisted Dinitrogen Activation via Dual Platinum Cluster Catalysis: A Strategy for Ammonia Synthesis under Mild Conditions

Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles.

The ground state intermolecular potential of bimolecular complexes of N‐heterocycles is analyzed for the impact of individual terms in the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, and dispersion contributions are tested at both short‐ and long‐distance sides of the potential energy surface, for various alignments of the pyrrole dimer as well as the cytosine–uracil complex. The integration of a DFT/CCSD density embedding scheme, with dispersion terms from the effective fragment potential (EFP) method is found to provide good agreement with a reference CCSD(T) potential overall; simultaneously, a quantum mechanics/molecular mechanics approach using CHELPG atomic point charges for the electrostatic interaction, augmented by EFP dispersion and Pauli repulsion, comes also close to the reference result. Both schemes have the advantage of not relying on predefined force fields; rather, the interaction parameters can be determined for the system under study, thus being excellent candidates for ab initio modeling.

Probing computational methodologies in predicting mid-infrared spectra for large polycyclic aromatic hydrocarbons

ABSTRACT We extend the prediction of vibrational spectra to large sized polycyclic aromatic hydrocarbon (PAH) molecules comprising up to ∼1500 carbon atoms by evaluating the efficiency of several computational chemistry methodologies. We employ classical mechanics methods (Amber and Gaff) with improved atomic point charges, semi-empirical (PM3, and density functional tight binding), and density functional theory (B3LYP) and conduct global optimizations and frequency calculations in order to investigate the impact of PAH size on the vibrational band positions. We primarily focus on the following mid-infrared emission bands 3.3, 6.2, 7.7, 8.6, 11.3, 12.7, and 17.0 μm. We developed a general Frequency Scaling Function ($\mathcal {FSF}$) to shift the bands and to provide a systematic comparison versus the three methods for each PAH. We first validate this procedure on IR scaled spectra from the NASA Ames PAH Database, and extend it to new large PAHs. We show that when the $\mathcal {FSF}$ is applied to the Amber and Gaff IR spectra, an agreement between the normal mode peak positions with those inferred from the B3LYP/4-31G model chemistry is achieved. As calculations become time intensive for large sized molecules Nc > 450, this proposed methodology has advantages. The $\mathcal {FSF}$ has enabled extending the investigations to large PAHs where we clearly see the emergence of the 17.0 μm feature, and the weakening of the 3.3 μm one. We finally investigate the trends in the 3.3 μm/17.0 μm PAH band ratio as a function of PAH size and its response following the exposure to fields of varying radiation intensities.

Quantifying Fluctuations of Average Solvent Environments for Embedding Calculations.

The viability and effectiveness of replacing an ensemble of embedded solute calculations by a single calculation using an average description of the solvent environment are evaluated. This work explores the fluctuations of the average description of the system obtained in two ways: from calculations on an ensemble of geometries and from an average environment constructed from the same ensemble. To this end, classical molecular dynamics simulations of a rigid acetone solute in SPCE water are performed in order to generate an ensemble of solvent environments. From this ensemble of solvent configurations, a number of different approaches for constructing an average solvent environment are employed. We perform a thorough numerical analysis of the fluctuations of the electrostatic potential experienced by the solute, as well as the resulting fluctuations of the solute's electronic density, measured through its dipole moment and fitted atomic point charges. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed method for generating the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum confinement effects, which may be important in certain cases, the fluctuations in the shift due to the interaction with the solvent are evaluated using frozen-density-embedding theory. Our results demonstrate that, for normally distributed environments, the constructed average environment is a reasonably good representation of a fluctuating molecular solvent environment. We then provide guidance for future comparisons between these theoretical treatments of solute/solvent systems to experimental measurements.

Classical electronic and molecular dynamics simulation for optical response of metal system.

An extended molecular dynamics simulation that incorporates classical free electron dynamics in the framework of the force-field model has been developed to enable us to describe the optical response of metal materials under the visible light electric field. In the simulation, dynamical atomic pointcharges follow equations of motion of classical free electrons that include Coulomb interactions with the oscillating field and surrounding atomic sites and collision effects from nearby electrons and ions. This scheme allows us to simulate an interacting system of metals with molecules using an ordinary polarizable force-field and preserves energy conservation in the case without applying an external electric field. As the first applications, we show that the presented simulation accurately reproduces (i) the classical image potential in a metal-charge interaction system and (ii) the dielectric function of bulk metal. We also demonstrate (iii) calculations of absorption spectra of metal nano-particles with and without a water solvent at room temperature, showing reasonable red-shift by the solvent effect, and (iv) plasmon resonant excitation of the metal nano-particle in solution under the visible light pulse and succeeding energy relaxation of the absorbed light energy from electrons to atoms on the metal and to the water solvent. Our attempt thus opens the possibility to expand the force-field based molecular dynamics simulation to an alternative tool for optical-related fields.

Evaluating equilibrium and kinetics of CO2 and N2 adsorption into amine-functionalized metal-substituted MIL-101 frameworks using molecular simulation

The primary objective of the present research is to evaluate the equilibrium and kinetics of CO2 and N2 adsorption into different varieties of MIL-101 including Cr-, Al-, and Fe-based amine-functionalized MIL-101 metal organic frameworks (MOF) using grand canonical Monte-Carlo (GCMC) and molecular dynamics (MD) simulation methods. In the present study, an attempt is also made to clarify the adsorption mechanisms. To achieve this goal, the adsorption isotherms and self-diffusion coefficients of CO2 and N2 in these MIL-101 MOF adsorbents are computed at different temperatures using the universal force field (UFF). Isosteric heat of adsorption and the selectivity values of the CO2/N2 mixture are also calculated. Among the three computed atomic point charge models, including the QM-based Mulliken population analysis, electrostatic potential (ESP) derived, and semi-empirical charge equilibration (QEq) methods, the latter produces more accurate results compared to the others. The results show that molecular simulation using GCMC and MD methods with UFF and QEq can be an appropriate alternative to experiment for predicting equilibrium and kinetic data of the CO2 and N2 adsorption into different varieties of MIL-101. The radial distribution functions (RDF) indicate that the metal centers are dominant active sites compared to the amine groups in the amine-functionalized Cr-based MIL-101. However, it is not the case for the amine-functionalized Al- and Fe- based MIL-101 frameworks, for which the amine groups are more capable than metal sites to capture CO2 molecules.

Molecular dynamics of fluoromethane type I hydrates

Fluorinated methane derivatives are small size molecules susceptible to be enclathrated inside type I water hydrate structure. These hydrates present a great interest due to the very high global warming potential of fluoromethanes. Nevertheless, their properties at microscopic scale have not been sufficiently investigated yet. In fact, there are scarce, if any, molecular dynamics simulations studies available in the literature. In the present work we have performed atomistic molecular dynamics simulations of fluoromethanes and their hydrates. OPLS-AA and TIP4P/ICE force fields were employed to model fluoromethanes and water, respectively. Liquid–vapor equilibrium simulations were performed to test OPLS-AA force field for fluorinated compounds. As results were not satisfactory, the molecular models were refined through the recalculation of atomic electric point charges. Then, molecular simulations were performed to study the three phase equilibrium of their hydrates, comparing with available experimental information.

Correction to: The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

Recently, we presented a detailed and systematic molecular simulation study of the effect of point charges on adsorption of carbon dioxide and water in a series of typical MOF materials [1]. Unfortunately, we have since detected a mistake in one of the input files pertaining to water adsorption isotherm simulations—concretely, the structure of the water molecule was modelled as linear instead of obeying the correct H-O-H angle of 109.47o for the SPC/E model [2]. As we later found out, this led to a significant underestimation of the amount adsorbed in all water isotherms reported in our original paper, although the relative differences between isotherms obtained using different charge sets are qualitatively the same. We have repeated all the water adsorption simulations, and report the new results here in graphical format. With the exception of a few minor statements, which we also correct below, the conclusions of the original work remain unchanged.

The role of distributed atomic point charges and polarizabilities of solvent molecules on one‐ and two‐photon absorption spectra of aqueous p‐nitroaniline

AbstractIn this work, we demonstrated the electrostatic and polarization effects created from distributed atomic point charges and polarizabilities of solvent molecules, respectively, when calculating optical response properties of solution‐phase molecule within the context of the discrete solvent reaction field. Aqueous p‐nitroaniline molecule was selected as the model system for our research purpose. One‐ and two‐photon absorption spectra were constructed by carrying out the damped response theory calculations within time‐dependent density functional theory. As compared to the full treatment, we investigated different effects of electrostatics and polarizations on spectral parameters of interest. Our calculations showed that the larger contributions to the calculated red shift in excitation energy was from electrostatic term, but polarization contribution was comparable in magnitude. On the other hand, electrostatic term was the principal feature for absorption strength and spectral width.

Computing Protein pKas Using the TABI Poisson–Boltzmann Solver

A common approach to computing protein pKas uses a continuum dielectric model in which the protein is a low dielectric medium with embedded atomic point charges, the solvent is a high dielectric medium with a Boltzmann distribution of ionic charges, and the pKa is related to the electrostatic free energy which is obtained by solving the Poisson–Boltzmann equation. Starting from the model pKa for a titrating residue, the method obtains the intrinsic pKa and then computes the protonation probability for a given pH including site–site interactions. This approach assumes that acid dissociation does not affect protein conformation aside from adding or deleting charges at titratable sites. In this work, we demonstrate our treecode-accelerated boundary integral (TABI) solver for the relevant electrostatic calculations. The pKa computing procedure is enclosed in a convenient Python wrapper which is publicly available at the corresponding author’s website. Predicted results are compared with experimental pKas for several proteins. Among ongoing efforts to improve protein pKa calculations, the advantage of TABI is that it reduces the numerical errors in the electrostatic calculations so that attention can be focused on modeling assumptions.

Comparison of Electrostatic Potential Obtained From Different Atomic Point Charges Calculation Methods for a Large Set of Molecules

The Electrostatic Potential is of great importance in chemical reactivity since it is closely related to many of molecular properties. Despite the fact that there are significant improvements in the quantum mechanical calculation methods, the atom centered partial charge approximation keeps hold of its importance in the field of estimating electrostatic potential as an inexpensive alternative to the ab initio method. However, even today, there is no universally accepted the best method for computing a partial atomic charge. Here, we compared the electrostatic potential obtained from different atomic point charges calculation methods for a large set of molecules. To this end, the large Grimme set of molecules was used. Some of the molecules in the set naturally failed in estimating the electrostatic potential. This failure, therefore, was investigated in depth. The Iterative Hirshfeld method can be preferable for electrostatic potential field generation.

Comparison of Electrostatic Potential obtained from different atomic point charges calculation methods for a large set of molecules

The Electrostatic Potential is of great importance in chemical reactivity since it is closely related to many of molecular properties. Despite the fact that there are significant improvements in th...

Mining the Cambridge Database for theoretical chemistry. Mi-LJC: a new set of Lennard-Jones–Coulomb atom–atom potentials for the computer simulation of organic condensed matter

A novel, universal Lennard-Jones–Coulomb (LJC) atom–atom force field parametrization reproduces the experimental sublimation enthalpies of 377 molecular crystals drawn from the CSD.

The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

The interactions between metal–organic frameworks (MOFs) and adsorbates have been increasingly predicted and studied by computer simulations, particularly by Grand-Canonical Monte Carlo (GCMC), as this method enables comparing the results with experimental data and also provides a degree of molecular level detail that is difficult to obtain in experiments. The assignment of atomic point charges to each atom of the framework is essential for modelling Coulombic interactions between the MOF and the adsorbate. Such interactions are important in adsorption of polar gases like water or carbon dioxide, both of which are central in carbon capture processes. The aim of this work is to systematically investigate the effect of varying atomic point charges on adsorption isotherm predictions, identify the underlying trends, and based on this knowledge to improve existing models in order to increase the accuracy of gas adsorption prediction in MOFs. Adsorption isotherms for CO2 and water in several MOFs were generated with GCMC, using the same computational parameters for each material except framework point charge sets that were obtained through a wide range of computational approaches. We carried out this work for 6 widely studied MOFs; IRMOF-1, MIL-47, UiO-66, CuBTC, Co-MOF-74 and SIFSIX-2-Cu-I. We included both MOFs with and without open metal sites (OMS), specifically to investigate whether this property affects the predicted adsorption behaviour. Our results show that point charges obtained from quantum mechanical calculations on fully periodic structures are generally more consistent and reliable than those obtained from either cluster-based QM calculations or semi-empirical approaches. Furthermore, adsorption in MOFs that contain OMS is much more sensitive to the point charge values, with particularly large variability being observed for water adsorption in such MOFs. This suggests that particular care must be taken when simulating adsorption of polar molecules in MOFs with open metal sites to ensure that accurate results are obtained.

Building a Consistent and Reproducible Database for Adsorption Evaluation in Covalent-Organic Frameworks.

We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal’s postcombustion flue gases. This workflow is applied to a database of 324 covalent–organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps: (1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory, (2) fitting atomic point charges based on the electron density, (3) characterizing the pore geometry of the structures before and after optimization, (4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally, (5) assessing the CO2 parasitic energy via process modeling. The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.

Classical Electrostatic Interaction Is the Origin for Blue-Shifting Halogen Bonds.

Studies have shown that, on the one hand, charge transfer (CT) plays a key role in halogen bonds (D···X-A) (D = donor; X = halogen atom; A = acceptor), suggesting considerable covalent character of halogen bonding. But, on the other hand, it has been proposed that halogen bonding is dominated by the electrostatic attraction between the electropositive σ-hole at the halogen atom X and the electronegative donor D. It has also been well-recognized that the CT from the donor D to the antibonding σ*(X-A) would weaken and lengthen the X-A bond. Yet, intriguingly, there is a blue-shifting phenomenon in halogen bonding, where the X-A bond contracts with an enhanced stretching vibrational frequency. Here we explored the nature of blue-shifting halogen bonds with the iconic case of H3N···ClNO2, which exhibits the blue-shifting phenomenon along with a strong CT interaction and its analogous H3N···XNY2 (X = Cl, Br, and I; Y = O, S). By decomposing the binding energy to a number of energy components and exploring their energy profiles along with the halogen-bonding distances with the block-localized wave function (BLW) method, we showed that the classical electrostatic interaction is the governing factor for the blue-shifting of the X-N bonds. This is further supported by the similar magnitudes of blue-shifting obtained when NH3 is replaced with atomic point charges in the complexes. Alternatively, by applying external electric field (E-field) along the X-N bond direction, the blue-to-red shifting transition can be identified. This is because both polarization and CT interactions tend to stretch the X-N bond, and both are enhanced simultaneously under the external E-field. Finally, roles of individual energy components are reconfirmed using the force analysis based on the BLW energy decomposition approach.

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.

Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol-1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.

A molecular dynamics framework to explore the structure and dynamics of layered double hydroxides

Abstract It is presented a straightforward procedure based on the CLAYFF force field to perform molecular dynamics (MD) computer simulations with the GROMACS open source package of layered double hydroxide (LDH) materials with different intercalated anions. This procedure enables running very long simulations of systems where all atomic positions are allowed to move freely, while maintaining the integrity of the LDH structure intact. Therefore, it has the potential to model different important applications of LDH involving ion-exchange and interlayer equilibrium processes in diverse areas as drug delivery, water purification, and corrosion protection. The magnesium-aluminium based LDH with a metallic ratio 2:1 (Mg2Al) was chosen to validate our computer simulation framework, because of the comprehensive experimental and computational studies reported in the literature devoted to the understanding of the structure of Mg2Al LDH. Potential parameters from the literature were used to model the Mg2Al LDH with different intercalated anions using a new set of atomic point charges calculated with the DDEC6 formalism. Once the model was validated through careful comparisons of the simulated and experimental structures, the procedure was adapted to the Zn2Al LDH materials. Lennard-Jones parameters had to be developed for zinc (II) cations and calibrated using the experimental structural data found in the literature for Zn2Al LDH and the height of the galleries determined experimentally in this work for Zn2Al with intercalated nitrate anions. The consistency of the model is proved by carrying out MD simulations to reproduce in the computer the typical experimental conditions in which the Zn2Al LDH is immersed in a sodium chloride water solution to act as a nanotrap for aggressive anions in corrosion protection applications. The LDH structure is maintained in the MD simulation in which the LDH is free to move alongside the solution and allowing a natural anion exchange between the LDH and the solution as well as dehydration/hydration of the basal space.

Creation of models and parametrization of a classical force field for amorphous Al2O3/water interfaces based on Density Functional Theory

We present realistic models of amorphous alumina/water interfaces taking into account the chemical termination with hydroxyl groups and chemisorbed water molecules, as predicted by DFT-based MD simulations. On the basis of these models we parametrize a fixed-charges force field to describe the interactions within alumina and across the alumina/water interface, which can be seamlessly combined with biomolecular force fields via straightforward combination rules. The potential parameters are fitted to DFT reference calculations of water/surface interactions and are shown to be very well transferable to organic molecules adsorbing on alumina, in particular amino acid analogues. The correct protonation/deprotonation equilibria of the surface sites in contact with water solutions at different pH values is taken into account and implemented in the surface models and force field parameters via adjustments of the atomic point charges. The ability of our models and force field to predict experimental observables is demonstrated by unbiased calculations of the heat of immersion of alumina powders and of the adsorption free energy of glutathione disulfide on alumina in comparison with experimental data.

Absorption Spectra for Disordered Aggregates of Chromophores Using the Exciton Model.

Optimizing the optical properties of large chromophore aggregates and molecular solids for applications in photovoltaics and nonlinear optics is an outstanding challenge. It requires efficient and reliable computational models that must be validated against accurate theoretical methods. We show that linear absorption spectra calculated using the molecular exciton model agree well with spectra calculated using time-dependent density functional theory and configuration interaction singles for aggregates of strongly polar chromophores. Similar agreement is obtained for a hybrid functional (B3LYP), a long-range corrected hybrid functional (ωB97X), and configuration interaction singles. Accounting for the electrostatic environment of individual chromophores in the parametrization of the exciton model with the inclusion of atomic point charges significantly improves the agreement of the resulting spectra with those calculated using all-electron methods; different charge definitions (Mulliken and ChelpG) yield similar results. We find that there is a size-dependent error in the exciton model compared with all-electron methods, but for aggregates with more than six chromophores, the errors change slowly with the number of chromophores in the aggregate. Our results validate the use of the molecular exciton model for predicting the absorption spectra of bulk molecular solids; its formalism also allows straightforward extension to calculations of nonlinear optical response.