We present RASPA3, a molecular simulation code for computing adsorption and diffusion in nanoporous materials and thermodynamic and transport properties of fluids. It implements force field based classical Monte Carlo/molecular dynamics in various ensembles. In this article, we introduce the new additions and changes compared to RASPA2. RASPA3 is rewritten from the ground up in C++23 with speed and code readability in mind. Transition-matrix Monte Carlo is added to compute the density of states and free energies. The Monte Carlo code for rigid molecules is based on quaternions, and the atomic positions needed in the energy evaluation are recreated from the center of mass position and quaternion orientation. The expanded ensemble methodology for fractional molecules, with a scaling parameter λ between 0 and 1, now also keeps track of analytic expressions of dU/dλ, allowing independent verification of the chemical potential using thermodynamic integration. The source code is freely available under the MIT license on GitHub. Using this code, we compare four Monte Carlo (MC) insertion/deletion techniques: unbiased Metropolis MC, Configurational-Bias Monte Carlo (CBMC), Continuous Fractional Component MC (CFCMC), and CB/CFCMC. We compare particle distribution shapes, acceptance ratios, accuracy and speed of isotherm computation, enthalpies of adsorption, and chemical potentials, over a wide range of loadings and systems, for the grand canonical ensemble and for the Gibbs ensemble.

Hydrogen peroxide plays a key role in many environmental and industrial chemical processes. We performed classical Molecular Dynamics and Continuous Fractional Component Monte Carlo simulations to calculate thermodynamic properties of H₂O₂ in aqueous solutions. The quality of the available force fields for H₂O₂ developed by Orabi and English (2018) [67], and by Cordeiro (2014) [69] was systematically evaluated. To assess which water force field is suitable for predicting properties of H₂O₂ in aqueous solutions, four widely used water force fields were used, namely the TIP3P, TIP4P/2005, TIP5P-E, and a modified TIP3P force field. While the computed densities of pure H₂O₂ in the temperature range of 253 - 353 K using the force field by Orabi & English are in excellent agreement with experimental results, the densities using the force field by Cordeiro are underestimated by 3%. The TIP4P/2005 force field in combination with the H₂O₂ force field developed by Orabi & English can predict the densities of H₂O₂ aqueous solution for the whole range of H₂O₂ mole fractions in very good agreement with experimental results. The TIP4P/2005 force field in combination with either of the H₂O₂ force fields can predict the viscosities of H₂O₂ aqueous solutions for the whole range of H₂O₂ mole fractions in reasonably good agreement with experimental results. The computed diffusion coefficients for H₂O₂ and water molecules using the TIP4P/2005 force field with either of the H₂O₂ force fields are almost constant for the whole range of H₂O₂ mole fractions. Hydrogen bond analysis showed a steady increase in the number of hydrogen bonds with the solute concentrations in H₂O₂ aqueous solutions for all combinations except for the Cordeiro-TIP5P-E and Orabi-TIP5P-E systems, which showed a minimum at intermediate concentrations. The Cordeiro force field for H₂O₂ in combination with either of the water force fields can predict the Henry coefficients of H₂O₂ in water in better agreement with experimental values than the force field by Orabi & English.

The confinement effect of porous materials on the thermodynamical equilibrium of the CO₂ hydrogenation reaction presents a cost-effective alternative to transition metal catalysts. In metal-organic frameworks, the type of metal center has a greater impact on the enhancement of formic acid production than the scale of confinement resulting from the pore size. The M-MOF-74 series enables a comprehensive study of how different metal centers affect HCOOH production, minimizing the effect of pore size. In this work, molecular simulations were used to analyze the adsorption of HCOOH and the CO₂ hydrogenation reaction in M-MOF-74, where M = Ni, Cu, Co, Fe, Mn, Zn. We combine classical simulations and density functional theory calculations to gain insights into the mechanisms that govern the low coverage adsorption of HCOOH in the surrounding of the metal centers of M-MOF-74. The impact of metal centers on the HCOOH yield was assessed by Monte Carlo simulations in the grand-canonical ensemble, using gas-phase compositions of CO₂, H₂, and HCOOH at chemical equilibrium at 298.15-800 K, 1-60 bar. The performance of M-MOF-74 in HCOOH production follows the same order as the uptake and the heat of HCOOH adsorption: Ni > Co > Fe > Mn > Zn > Cu. Ni-MOF-74 increases the mole fraction of HCOOH by ca. 10⁵ times compared to the gas phase at 298.15 K, 60 bar. Ni-MOF-74 has the potential to be more economically attractive for CO₂ conversion than transition metal catalysts, achieving HCOOH production at concentrations comparable to the highest formate levels reported for transition metal catalysts and offering a more valuable molecular form of the product.

The series of metal–organic frameworks M-MOF-74 gained popularity in the field of capture and separation of CO₂ due to the presence of numerous, highly reactive open-metal sites. The description of effective interactions between guest molecules and open-metal sites without accounting for polarization effects is challenging but it can significantly reduce the computational cost of simulations. In this study, we propose a non-polarizable force field for CO₂, and H₂ adsorption in M-MOF-74 (M = Ni, Cu, Co, Fe, Mn, Zn) by scaling the Coulombic interactions of M-MOF-74 atoms, and Lennard-Jones interaction potentials between the center of mass of H₂ and the open-metal centers. The presented force field is based on UFF and DREIDING parameters, characterized by high transferability and efficiency. The quantum behavior of H₂ at cryogenic temperatures is considered by incorporating Feynman–Hibbs quantum corrections. To validate the force field, the experimental isotherms of CO₂ at 298 K and 10⁻¹ – 10²kPa, the isotherms of H₂ at 77 K and 10⁻⁵ – 10²kPa, the corresponding enthalpy of adsorption, and the binding geometries in the M-MOF-74 series were reproduced using Monte Carlo simulations in the grand-canonical ensemble. The computed loadings, heats of CO₂ and H₂ adsorption, and binding geometries in M-MOF-74 are in very good agreement with the experimental values. The temperature transferability of the force field from 77 K to 87 K, and 298 K was shown for adsorption of H₂. The validated force field was used to study the adsorption and separation of CO₂/H₂ mixtures at 298 K. The adsorption of H₂ practically does not occur when CO₂ is present in the mixture. As indicated from simulated breakthrough curves, the breakthrough time of CO₂ in M-MOF-74 follows the same order as the uptake and the heat of CO₂ adsorption: Ni ¿ Co ¿ Fe ¿ Mn ¿ Zn ¿ Cu. Increasing the feed mole fraction of CO₂ in the breakthrough simulations from 0.1 to 0.9 speeds up the saturation of the adsorbent, leading to a faster exit of CO₂ with the column effluent. The application of the non-polarizable force field allows full investigation of the capture and separation of CO₂ in M-MOF-74, and can be expanded to study multi-component mixtures or industrial reactions in future research.

We present the RUPTURA code (https://github.com/iraspa/ruptura) as a free and open-source software package (MIT license) for (1) the simulation of gas adsorption breakthrough curves, (2) mixture prediction using methods like the Ideal Adsorption Solution Theory (IAST), segregated-IAST and explicit isotherm models, and (3) fitting of isotherm models on computed or measured adsorption isotherm data. The combination with the RASPA software enables computation of breakthrough curves directly from adsorption simulations in the grand-canonical ensemble. RUPTURA and RASPA have similar input styles. IAST is implemented near machine precision but we also provide several explicit mixture prediction methods that are non-iterative and potentially faster than IAST. The code supports a wide variety of isotherm models like Langmuir, Anti-Langmuir, BET, Henry, Freundlich, Sips, Langmuir-Freundlich, Redlich-Peterson, Toth, Unilan, O'Brian & Myers, Asymptotic Temkin, and Bingel & Walton. The isotherm model parameters can easily be obtained by the fitting module. Breakthrough plots and animations of the column properties are automatically generated. In addition to highlighting the code, we also review all the developed techniques from literature for mixture prediction, breakthrough simulations, and isotherm model fitting, and provide a tutorial discussing the workflows.

Formic acid production from CO₂ allows the reduction of carbon dioxide emissions while synthesizing a product with a wide range of applications. CO₂ hydrogenation is challenging due to the cost of transition metal catalysts and the toxicity of the transition elements. In this work, the thermodynamic confinement effects of the metal–organic framework UiO-66 on the CO₂ hydrogenation to formic acid were studied by force field-based molecular simulations. The confinement effects of UiO-66 and the metal–organic frameworks Cu-BTC, and IRMOF-1 were compared, to assess the impact of different pore size and metal centers on the production of HCOOH. Monte Carlo simulations in the grand-canonical ensemble were performed in the frameworks, using gas phase mole fractions of CO₂, H₂, and HCOOH at chemical equilibrium, obtained from Continuous Fractional Component Monte Carlo simulations in the Reaction Ensemble. The adsorption isobars of the components in metal–organic frameworks were computed at 298.15 – 800 K, 1 – 60 bar. The enhancement of HCOOH production due to preferential adsorption of HCOOH in metal–organic frameworks was calculated for all studied conditions. UiO-66, Cu-BTC, and IRMOF-1 affect CO₂ hydrogenation reaction, shifting the thermodynamical equilibrium toward HCOOH formation. The prevailing factor is the type of metal center in the metal–organic framework. The confinement effect of Cu-BTC turns out to exceed the enhancement caused by UiO-66, and IRMOF-1. The resulting mole fraction of HCOOH increased by ca. 2000 times compared to the gas phase at 298.15 K, 60 bar. Cu-BTC can be considered as an alternative to improve the production of HCOOH due to elimination of the high-cost temperature elevation, cost reduction of downstream processing methods, and comparable final concentration of HCOOH to the reported concentrations of formate obtained using transition metal catalysts.

Ideal Adsorbed Solution Theory (IAST) is a common method for modelling mixture adsorption isotherms based on pure component isotherms. When the adsorbent has distinct adsorption sites, the segregated version of IAST (SIAST) provides improved adsorbed loadings compared to IAST. We have adopted the concept of SIAST and applied it to an explicit isotherm model which takes into account the different sizes of the adsorbates: the so called Segregated Explicit Isotherm (SEI). The purpose of SEI is to have an explicit adsorption model that can consider both size-effects of the co-adsorbed molecules and surface heterogeneities. In sharp contrast to IAST and SIAST, no iterative scheme is required in case of SEI, which leads to much faster simulations. A comparative study has been performed to analyse the adsorption isotherms calculated using these three methods. The adsorbed loadings predicted by SEI and SIAST are in excellent agreement with the Grand-Canonical Monte Carlo (GCMC) simulation data. The loadings estimated by IAST show considerable deviations from the GCMC data at high pressures. Breakthrough curve modelling is used to compare the effects of these three models at dynamic conditions. The explicit model (SEI) leads to the fastest simulation run time, followed by SIAST.

There is a growing interest in the development of routes to produce formic acid from CO2, such as the electrochemical reduction of CO2 to formic acid. The solubility of CO2 in the electrolyte influences the production rate of formic acid. Here, the dependence of the CO2 solubility in aqueous HCOOH solutions with electrolytes on the composition and the NaCl concentration was studied by Continuous Fractional Component Monte Carlo simulations at 298.15 K and 1 bar. The chemical potentials of CO2, H2O, and HCOOH were obtained directly from single simulations, enabling the calculation of Henry coefficients and subsequently considering salting in or salting out effects. As the force fields for HCOOH and H2O may not be compatible due to the presence of strong hydrogen bonds, the Gibbs-Duhem integration test was used to test this compatibility. The combination of the OPLS/AA force field with a new set of parameters, in combination with the SPC/E force field for water, was selected. It was found that the solubility of CO2 decreases with increasing NaCl concentration in the solution and increases with the increase of HCOOH concentration. This continues up to a certain concentration of HCOOH in the solution, after which the CO2 solubility is high and the NaCl concentration has no significant effect.

We present several new major features added to the Monte Carlo (MC) simulation code Brick-CFCMC for phase- and reaction equilibria calculations (https://gitlab.com/ETh_TU_Delft/Brick-CFCMC). The first one is thermodynamic integration for the computation of excess chemical potentials (μex). For this purpose, we implemented the computation of the ensemble average of the derivative of the potential energy with respect to the scaling factor for intermolecular interactions (⟨∂U∂λ⟩). Efficient bookkeeping is implemented so that the quantity ∂U∂λ is updated after every MC trial move with negligible computational cost. We demonstrate the accuracy and reliability of the calculation of μex for sodium chloride in water. Second, we implemented hybrid MC/MD translation and rotation trial moves to increase the efficiency of sampling of the configuration space. In these trial moves, short Molecular Dynamics (MD) trajectories are performed to collectively displace or rotate all molecules in the system. These trajectories are accepted or rejected based on the total energy drift. The efficiency of these trial moves can be tuned by changing the time step and the trajectory length. The new trial moves are demonstrated using MC simulations of a viscous fluid (deep eutectic solvent).

According to the ISO 14687-2:2019 standard, the water content of H2 fuel for transportation and stationary applications should not exceed 5 ppm (molar). To achieve this water content, zeolites can be used as a selective adsorbent for water. In this work, a computational screening study is carried out for the first time to identify potential zeolite frameworks for the drying of high-pressure H2 gas using Monte Carlo (MC) simulations. We show that the Si/Al ratio and adsorption selectivity have a negative correlation. 218 zeolites available in the database of the International Zeolite Association are considered in the screening. We computed the adsorption selectivity of each zeolite for water from the high-pressure H2 gas having water content relevant to vehicular applications and near saturation. It is shown that due to the formation of water clusters, the water content in the H2 gas has a significant effect on the selectivity of zeolites with a helium void fraction larger than 0.1. Under each operating condition, five most promising zeolites are identified based on the adsorption selectivity, the pore limiting diameter, and the volume of H2 gas that can be dried by 1 dm3 of zeolite. It is shown that at 12.3 ppm (molar) water content, structures with helium void fractions smaller than 0.07 are preferred. The structures identified for 478 ppm (molar) water content have helium void fractions larger than 0.26. The proposed zeolites can be used to dry 400-8000 times their own volume of H2 gas depending on the operating conditions. Our findings strongly indicate that zeolites are potential candidates for the drying of high-pressure H2 gas.

Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and zeolitic imidazolate frameworks (ZIFs). The molecular confinement these materials offer has been exploited in adsorption and catalysis for almost 50 years. Molecular simulations have provided understanding of the underlying shape selectivity, and adsorption and diffusion effects. Much of the reliability of the modeling predictions depends on the accuracy and transferability of the force field. However, flexibility and the chemical and structural diversity of MOFs add significant challenges for engineering force fields that are able to reproduce experimentally observed structural and dynamic properties. Recent developments in design, parameterization, and implementation of force fields for MOFs and zeolites are reviewed.

Computational chemistry uses computer simulation to assist in solving chemical problems. Typical workflows of computational chemists include the use of dozens of utilities. 3D modeling programs are powerful tools that help researchers visualize their work and create illustrative graphics. In this review, we describe and highlight tools and visualization packages that are commonly used in the field of (bio-)chemistry and material science.

A new macOS software package, iRASPA, for visualisation and editing of materials is presented. iRASPA is a document-based app that manages multiple documents with each document containing a unique set of data that is stored in a file located either in the application sandbox or in iCloud drive. The latter allows collaboration on a shared document (on High Sierra). A document contains a gallery of projects that show off the main features, a CloudKit-based access to the CoRE MOF database (approximately 8000 structures), and local projects of the user. Each project contains a scene of one or more structures that can initially be read from CIF, PDB or XYZ-files, or made from scratch. Main features of iRASPA are: structure creation and editing, pictures and movies, ambient occlusion and high-dynamic range rendering, collage of structures, (transparent) adsorption surfaces, cell replicas and supercells, symmetry operations like space group and primitive cell detection, screening of structures using user-defined predicates, and GPU-computation of helium void fraction and surface areas in a matter of seconds. Leveraging the latest graphics technologies like Metal, iRASPA can render hundreds of thousands of atoms (including ambient occlusion) with stunning performance. The software is freely available from the Mac App Store.

The separation of light olefins from paraffins via cryogenic distillation is a very energy intensive process. Solid adsorbents and especially metal-organic frameworks with open metal sites have the potential to significantly lower the required energy. Specifically, M-MOF-74 has drawn considerable attention for application in olefin/paraffin separation. To investigate how the separation proceeds on a molecular level and to design better materials, molecular simulation can be a useful tool. Unfortunately, it is still a challenge to model the adsorption behavior of many adsorbates in metal-organic frameworks with open metal sites. Previously, the inclusion of explicit polarization has been suggested to improve the quality of classical force fields for such systems. Here, the potential of polarizable force fields for the description of olefins and paraffins in metal-organic frameworks with open metal sites is investigated. In particular, heats of adsorption, binding geometries, and adsorption isotherms are calculated for C2H4, C2H6, C3H6, and C3H8 in M-MOF-74 (with M = Co, Mn, Fe, and Ni). In this study, no force field parameters are adjusted to improve the model. The results show that including explicit polarization significantly improves the description of the adsorption in comparison to non-polarizable generic force fields which do not consider explicit polarization. The study also reveals that simulation predictions are sensitive to the assigned repulsive potential and framework charges. A fully re-parametrized polarizable force field may have the capability to improve the predictions even further.