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We present an automatized workflow which, starting from molecular dynamics simulations, identifies reaction events, filters them, and prepares them for accurate quantum chemical calculations using, for example, Density Functional Theory (DFT) or Coupled Cluster methods. The capabilities of the automatized workflow are demonstrated by the example of simulations for the combustion of some polycyclic aromatic hydrocarbons (PAHs). It is shown how key elementary reaction candidates are filtered out of a much larger set of redundant reactions and refined further. The molecular species in question are optimized using DFT and reaction energies, barrier heights, and reaction rates are calculated. The setup is general enough to include at this stage configurational sampling, which can be exploited in the future. Using the introduced machinery, we investigate how the observed reaction types depend on the gas atmosphere used in the molecular dynamics simulation. For the re-optimization on the DFT level, we show how the additional information needed to switch from reactive force-field to electronic structure calculations can be filled in and study how well ReaxFF and DFT agree with each other and shine light on the perspective of using more accurate semi-empirical methods in the MD simulation.

Recently the possibility of using electric fields as a further stimulus to trigger structural changes in metal–organic frameworks (MOFs) has been investigated. In general, rotatable groups or other types of mechanical motion can be driven by electric fields. In this study we demonstrate how the electric response of MOFs can be tuned by adding rotatable dipolar linkers, generating a material that exhibits paraelectric behavior in two dimensions and dielectric behavior in one dimension. The suitability of four different methods to compute the relative permittivity κ by means of molecular dynamics simulations was validated. The dependency of the permittivity on temperature T and dipole strength μ was determined. It was found that the herein investigated systems exhibit a high degree of tunability and substantially larger dielectric constants as expected for MOFs in general. The temperature dependency of κ obeys the Curie–Weiss law. In addition, the influence of dipolar linkers on the electric field induced breathing behavior was investigated. With increasing dipole moment, lower field strengths are required to trigger the contraction. These investigations set the stage for an application of such systems as dielectric sensors, order–disorder ferroelectrics, or any scenario where movable dipolar fragments respond to external electric fields., Rotatable dipolar groups, used as organic linkers in metal−organic frameworks (MOFs), can substantially alter their electric field response, in terms of both their dielectric and flexible properties.

Flexible metal–organic frameworks (MOFs) show large structural flexibility as a function of temperature or (gas)pressure variation, a fascinating property of high technological and scientific relevance. The targeted design of flexible MOFs demands control over the macroscopic thermodynamics as determined by microscopic chemical interactions and remains an open challenge. Herein we apply high‐pressure powder X‐ray diffraction and molecular dynamics simulations to gain insight into the microscopic chemical factors that determine the high‐pressure macroscopic thermodynamics of two flexible pillared‐layer MOFs. For the first time we identify configurational entropy that originates from side‐chain modifications of the linker as the key factor determining the thermodynamics in a flexible MOF. The study shows that configurational entropy is an important yet largely overlooked parameter, providing an intriguing perspective of how to chemically access the underlying free energy landscape in MOFs., By combining high‐pressure powder X‐ray diffraction and molecular dynamics simulation we gain insight into the microscopic chemical factors that determine the high‐pressure macroscopic thermodynamics of two flexible pillared‐layer MOFs, identifying configurational entropy as originating from side‐chain modifications as the determining factor of the macroscopic thermodynamics.

We present a computational multiscale study of a metal–organic framework (MOF)/polymer composite combining micro- and mesoscopic resolution, by coupling atomistic and coarse grained (CG) force field-based molecular dynamics simulations. As a proof of concept, we describe the copper paddlewheel-based HKUST-1 MOF/poly(vinyl alcohol) composite. Our newly developed CG model reproduces the salient features of the interface in excellent agreement with the atomistic model and allows the investigation of substantially larger systems. The polymer penetrates into the open pores of the MOF as a result of the interactions between its OH groups and the O and Cu atoms in the pores, suggesting an excellent MOF/polymer compatibility. Polymer structure is affected by the MOF surface up to a distance of ∼2.4 times its radius of gyration. This study paves the way toward understanding important interfacial phenomena such as aggregation and phase separation in these mixed matrix systems.

The prototypical pillared layer MOFs, formed by a square lattice of paddle-wheel units and connected by dinitrogen pillars, can undergo a breathing phasetransition by a “wine-rack” type motion of the square lattice. We studied this notyet fully understood behavior using an accurate first principles parameterized forcefield (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-cations for an interface between a closed and an open pore phase traveling throughthe system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. Inconventional simulations in small supercells this mechanism is prevented by periodicboundary conditions (PBC), enforcing a synchronous transformation of the entirecrystal. Here, we extend this investigation to pillared layer MOFs with flexibleside-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-tally known to have different properties with the side-chains acting as fixed guestmolecules. First, in order to extend the parameterization for such flexible groups,1a new parametrization strategy for MOF-FF had to be developed, using a multi-structure force based fit method. The resulting parametrization for a library offu-MOFs is then validated with respect to a set of reference systems and shows verygood accuracy. In the second step, a series of fu-MOFs with increasing side-chainlength is studied with respect to the influence of the side-chains on the breathingbehavior. For small supercells in PBC a systematic trend of the closed pore volumewith the chain length is observed. However, for a nanocrystallite model a distinctinterface between a closed and an open pore phase is visible only for the short chainlength, whereas for longer chains the interface broadens and a nearly concerted trans-formation is observed. Only by molecular dynamics simulations using accurate forcefields such complex phenomena can be studied on a molecular level.

One of the intriguing features of certain metal-organic frameworks (MOFs) is the large volume change upon external stimuli like pressure or guest molecule adsorption, referred to as “breathing”. This displacive phase transformation from an open to a closed pore has been investigated intensively by theoretical simulations within periodic boundary conditions (PBC). However, the actual free energy barriers for the transformation under real conditions and the impact of surface effects on it can only be studied beyond PBC for nanocrystallites. In this work, we used the first-principles parameterized forcefield MOF-FF to investigate the thermal- and pressure induced transformations for nanocrystallites of the pillared-layer DMOF-1 (Zn 2 (bdc) 2 (dabco); bdc: 1,4-benzenedicarboxylate; dabco: 1,4-diazabicyclo[2.2.2]octane) as a model system. By heating of prepared closed pore nanocrystallites of different size, a spontaneous opening is observed within a few tenth of picoseconds with an interface between the closed and open pore phase moving with a velocity of several 100 m/s through the system. The critical nucleation temperature for the opening transition raises with size. On the other hand, by forcing the closing transition with a distance restraint between paddle-wheel units placed on opposite edges of the crystallite, the free energy barrier can be determined by umbrella sampling. As expected, this barrier is substantially lower than the one determined for a concerted process under PBC. Interestingly, the barrier reduces with the size of the crystallite, indicating a hindering surface effect. The results demonstrate the need consider domain boundaries and surfaces, for example by simulations that go beyond PBC and to large system sizes in order to properly predict and describe first order phase transitions in MOFs.

In this paper we parameterized in a consistent way a new force field for a range of different zeolitic imidazolate framework systems (ZIF-8, ZIF-8(H), ZIF-8(Br) and ZIF- 8(Cl)), extending the MOF-FF parameterization methodology in two aspects. First, we implemented the possibility to use periodic reference data in order to prevent the difficulty of generating representative finite clusters. Second, a more efficient global optimizer based on the covariance matrix adaptation evolutionary strategy (CMA-ES) was employed during the parameterization process. We confirmed that CMA-ES, as a state-of-the-art black box optimizer for problems on continuous variables, is more suitable for force field optimization than the previous genetic algorithm. The obtained force field was then fully validated with respect to static and dynamic properties. Much effort was spent to ensure that the FF is able to describe the crucial linker swing effect in a large number of ZIF-8 derivatives. For this reason we compared our force field to ab initio molecular dynamic simulations and found an accuracy comparable to those obtained by different exchange–correlation functionals.

Atomistic simulations were performed in order to investigated the effect of pore dimension on the interaction of guest molecules with the inner surface of metal–organic frameworks (MOFs). In these systems, which only differ in the metric of their open structure, the chemical nature is conserved, and less impact on the host–guest interaction is expected compared to chemically funcionalized MOFs. However, by performing molecular dynamics simulations of benzene loaded MOF-5 derivatives (IRMOFs), which differ just in the length of the organic linker, it can be shown that impacts are present. The influence of the soft-modification can be explained only by a detailed analysis of the free energy topology and the diffusion mechanism. Note that the calculated self-diffusivity of benzene Dself shows no change with respect to the elongation of the linkers. The apparent contradiction between the macroscopic observable Dself and the microscopic free energy landscape could be resolved by introducing a hopping model for...

The temperature-responsive behavior of functionalized metal–organic frameworks (fu-MOF) with the general formula [Zn2(fu-L)2dabco]n has been investigated using molecular dynamics simulations (fu-L = alkoxy-functionalized 1,4-benzenedicarboxylate, dabco = 1,4-diazabicyclo[2.2.2]octane). The studied frameworks show a narrow pore (np) form at low temperatures, while at higher temperatures, large pore (lp) structures can be observed. The transition temperature is controlled by the chemical nature of the linker’s side chains as well as their length. In general, enhancing the side chain length decreases the transition temperature. On the other hand, more polar linkers shift the transition temperature to higher values. The so-called opening process of the narrow pores is caused by the thermally induced motion of the alkoxy side chains of the functionalized linkers. For qualitative comparison, the difference in internal energy as well as entropy between two forms (np and lp) was calculated for all studied linker ...

The dynamics of adsorbed CO 2 in the metal-organic framework Zn 2 (bdc) 2 dabco (DMOF-1) was investigated using molecular dynamics (MD) simulations and 13 C NMR spectroscopy. The statistical analysis of the MD trajectories suggest a preferred localization of the CO 2 molecules in the Zn 2 (bdc) 4 corners of the DMOF-1 lattice. The adsorbed molecules retain a high but anisotropic rotational and translational mobility in the channel system. Based on these MD-results, the residual chemical shift anisotropy 〈Δ δ 〉 MD = −114 ppm and the diffusion anisotropy ( D ∥ / D ⊥ ) MD = 9.8 ± 0.5 were calculated. They are found to be in reasonable agreement with the experimental NMR data of 〈Δ δ 〉 NMR =−(55 ± 2) ppm and ( D ∥ / D ⊥ ) NMR = 3 respectively.

The ab initio molecular dynamics simulations of metallic, charged, and electrochemical systems require, in principle, the inclusion of unequally occupied electronic states. In this contribution, the general approach to work with fixed but arbitrary occupations within the Car-Parrinello molecular dynamics scheme is revisited, focusing on the procedure which is required to maintain the orthonormality constraints in the commonly used position-Verlet integrator. Expressions to constrain also the orbital velocities, as it is demanded by a velocity-Verlet integrator, are then derived. The generalized unequal-occupation SHAKE algorithm is compared with the standard procedure for damped dynamics (energy optimization) of systems including fully unoccupied electronic states. In turn, the proposed unequal-occupation RATTLE algorithm is validated by the corresponding microcanonical ensemble simulations. It is shown that only with the proper orthogonalization method, a correct ordering of states and energy conserving dynamics can be achieved.

In this contribution, the diffusion of benzene in the porous metal organic framework MOF-5 is investigated by molecular dynamics simulations. Previously, we have shown that by using a first principles derived fully flexible force field the experimentally determined self-diffusion coefficients D self could be well reproduced [S. Amirjalayer, M. Tafipolsky, R. Schmid, Angew. Chem. Int. Ed. 46 (2007) 463]. Here, we use the same methodology to determine the loading dependence on the diffusion. It is found that diffusivity, which is in the range of liquid benzene, slightly increases up to a load of 32 molecules per unit cell and then falls off at higher load. Free energy maps reveal that additional sites appear at higher load due to attractive guest–guest interactions. The topology of these sites is very close to the experimentally determined locations of ferrocene molecules in MOF-5, which corroborates that attractive π – π interactions govern these systems. The site–site and site-phenylene distances are very similar to the first solvation radius of liquid benzene. For the very open MOF-5, the main barrier for diffusive transport is to overcome the attractive interaction in the binding pockets, which is in contrast to zeolitic microporous systems, where the barrier for diffusion is the hindrance of the pore window. Spatial free energy maps are used to investigate the diffusion pathway on a molecular level and the load dependence of the free energy barriers for these transport processes.

In this paper we present an application for a parallel multigrid solver in 3D to solve the Coulomb problem for the charge self interaction in a quantum-chemical program used to perform ab initio molecular dynamics. Techniques such as Mehrstellendiscretization and τ-extrapolation are used to improve the discretization error. The results show that the expected convergence rates and parallel performance of the multigrid solver are achieved. Within the applied Carr–Parrinello Molecular Dynamics scheme the quality of the solution also determines the accuracy in energy conservation. All forms of discretization employed lead to energy conserving dynamics. In order to test the applicability of our code to larger systems in a massively parallel environment, we investigated a 256 atom periodic supercell of bulk gallium nitride.

We report the synthesis of a tribenzotriquinacene-based (TBTQ) receptor (3) for C60 fullerene, which is extended by pentiptycene moieties to provide an almost enclosed concave ball bearing. The system serves as a model for a self-assembling molecular rotor with a flexible and adapting stator. Unexpectedly, nuclear magnetic resonance spectroscopic investigations reveal a surprisingly low complex stability constant of K1 =213±37 M(-1) for [C60 ⊂3], seemingly inconsistent with the previously reported TBTQ systems. Molecular dynamics (MD) simulations have been conducted for three different [C60 ⊂TBTQ] complexes to resolve this. Because of the dominating dispersive interactions, the binding energies increase with the contact area between guest and host, however, only for rigid host structures. By means of free-energy calculations with an explicit solvent model it can be shown that the novel flexible TBTQ receptor 3 binds weakly because of hampering entropic contributions.

The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (7) for C-60 fullerene, possessing C-3 point group symmetry, by threefold condensation of C-2-symmetric 1,2-diketone synthons (5) and a hexaaminotribenzotriquinacene core (6) is described. The chiral diketone was synthesized in a five-step reaction sequence starting from C-2h-symmetric 2,6-di-tert-butylanthracene. The highly diastereo-discriminating Diels-Alder reaction of 2,6-di-tertbutylanthracene with fumaric acid di(-)menthyl ester, catalyzed by aluminium chloride, is the relevant stereochemistry introducing step. The structure of the fullerene receptor was verified by H-1 and C-13 NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. VCD and ECD spectra were recorded, which were corroborated by ab initio DFT calculations, establishing the chiral nature of 7 with about 99.7% ee, based on the ee (99.9%) of the chiral synthon (1). The absolute configuration of 7 could thus be established as all-S [(2S,7S,16S,21S,30S,35S)-(7)]. Spectroscopic titration experiments reveal that the host forms 1: 1 complexes with either pure fullerene (C-60) or fullerene derivatives, such as rotor 1'-(4-nitrophenyl)-3'-(4-N,N-dimethylaminophenyl)-pyrazolino[4',5':1,2][60]fullerene (R). The complex stability constants of the complexes dissolved in CHCl3/CS2 (1:1 vol.%) are K([C-60 subset of 7])= 319(+/- 156) M-1 and K([R subset of 7])= 110(+/- 50) M-1. With molecular dynamics simulations using a first-principles parameterized force field the asymmetry of the rotational potential for [R subset of 7] was shown, demonstrating the potential suitability of receptor 7 to act as a stator in a unidirectionally operating nanoratchet.

A new valence force field has been developed and validated for a particular class of coordination polymers known as nanoporous metal-organic frameworks (MOFs), introduced recently by the group of Yaghi. The experimental, structural, and spectroscopic data in combination with density functional theory calculations on several model systems were used to parametrize the bonded terms of the force field, which explicitly treats the metal-oxygen interactions as partially covalent as well as distinguishes different types of oxygens in the framework. Both the experimental crystal structure of MOF-5 and vibrational infrared spectrum are reproduced reasonably well. The proposed force field is believed to be useful in atomistic simulations of adsorption/diffusion of guest molecules inside the flexible pores of this important class of MOF materials.

International audience; The concentration and temperature dependence of the self-diffusion of benzene adsorbed in the metal-organic framework MOF-5 (IRMOF-1) is studied by pulsed field gradient (PFG) NMR spectroscopy. When increasing the loading from 10 to 20 molecules per unit cell of MOF-5, the experimental diffusion data drop by a factor of about 3 while current molecular dynamic (MD) simulations predict slightly increasing diffusion coefficients for this range of loadings. The observation is rationalized using the recently predicted clustering of adsorbate molecules in microporous systems for temperatures well below the adsorbate critical temperature. Necessary improvements of molecular simulation models for predicting diffusivities under such conditions are discussed.