Molecular mechanics (MM3) study of organogermanes

Chen, Kuohsiang; Allinger, Norman L.

doi:10.1002/(sici)1099-1395(199907)12:7<528::aid-poc114>3.0.co;2-#

Cited by 11 publications

(2 citation statements)

References 65 publications

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“…68 The MOF-FF force field was used to treat a 2 × 2 × 2 supercell of MOF-5 and TNBG, the primary component of DAPHNE-7575. 69 Parameters associated with the Ge site used the MM3 force field, 70 which is itself the basis of MOF-FF. Simulations presented for N,N-dimethylformamide also used the MM3 force field and partial charges identified by Caleman et al 71 Trajectories consisted of 500 ps stages with increasing pressure, where the final 250 ps was used for analysis.…”

Section: Methodsmentioning

confidence: 99%

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

et al. 2022

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Mechanisms underlying the mechanically induced amorphization of metal–organic frameworks (MOFs) are of current interest, and both high-pressure experimentation and molecular dynamics simulations have been used to reveal the fundamentals of load bearing, deformation, and pressure-induced amorphization (PIA) in these highly porous materials. Unfortunately, MOFs are typically highly susceptible to amorphization, which limits the conditions under which they can be processed and used. However, their flexible structures can be stabilized at high pressures by incorporating guest species into the framework matrix. In this study, a large-molecule pressure transmitting medium (DAPHNE 7575) is used as a structure-fortifying guest species to stabilize the prototypical MOF-5 at high pressures (>9 GPa) and enable the recovery of crystalline material upon decompression. Structural changes associated with the penetration of the pressure transmitting medium on compression are examined using a combination of high-pressure synchrotron powder diffraction and molecular dynamics simulations. This work enhances the understanding of PIA in MOFs while showcasing a potential route for the stabilization of MOFs at surprisingly high pressures.

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Section: Methodsmentioning

confidence: 99%

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

et al. 2022

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“…First a test set of molecules was created and MM3 atoms types were assigned to each species. This test set primarily included molecules that were used to parametrize the existing MM3 parameters as described in various publications; − however, it was necessary to add a substantial number of additional molecules in order to cover a larger selection of the MM3 bonding types. This test set is listed in the online Supporting Information.…”

Section: Morse Fittingmentioning

confidence: 99%

Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field

et al. 2019

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Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and non-equilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parameterized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is amongst the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, this data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches, and (2) enable more accurate treatments of energy transfer. 23.Hattig, C.; Tew, D. P.; Kohn, A., Communications: Accurate and efficient approximations to explicitly correlated coupled-cluster singles and doubles, CCSD-F12.

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Calculation of Vibrational Frequencies by Molecular Mechanics

Hotokka¹

2001

Handbook of Vibrational Spectroscopy

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The molecular mechanics (MM) method is a purely classical ball‐and‐spring model as opposed to the quantum chemical computational methods. The MM energy is formed as a sum of terms based on parameters such as the stiffness and equilibrium value of the chemical bonds, bond angles, torsions etc. Therefore, the success of the MM method depends on the flexibility of the parameterization or the force field. The basic principles of the MM method and a few examples of the available force fields are presented. The MM method is shown to offer a cost‐effective way of calculating the vibrational frequencies quite accurately. The band intensities may also be estimated.

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Molecular mechanics (MM3) study of organogermanes

Abstract: The MM3 force field has been extended to permit the treatment of organogermanes. The vibrational spectra, molecular structures, moments of inertia, dipole moments and conformational energies of 21 compounds were studied. The available experimental data are mostly well reproduced.

Cited by 11 publications

References 65 publications

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field

Calculation of Vibrational Frequencies by Molecular Mechanics

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