ChemInform Abstract: A MOLECULAR-MECHANICS STUDY OF 18-CROWN-6 AND ITS ALKALI COMPLEXES: AN ANALYSIS OF STRUCTURAL FLEXIBILITY, LIGAND SPECIFICITY, AND THE MACROCYCLIC EFFECT

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

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Revisiting the High-Pressure Properties of the Metal-Organic Frameworks ZIF-8 and ZIF-67

10.26434/chemrxiv.13146278.v1 ◽

2020 ◽

Author(s):

Pia Vervoorts ◽

Stefan Burger ◽

Karina Hemmer ◽

Gregor Kieslich

Keyword(s):

High Pressure ◽

State Of The Art ◽

Energy Landscape ◽

Structural Flexibility ◽

Zeolitic Imidazolate Frameworks ◽

Stimuli Responsive ◽

X Ray Diffraction ◽

X Ray ◽

Open Questions ◽

Metal Organic

The zeolitic imidazolate frameworks ZIF-8 and ZIF-67 harbour a series of fascinating stimuli responsive properties. Looking at their responsitivity to hydrostatic pressure as stimulus, open questions exist regarding the isotropic compression with non-penetrating pressure transmitting media. By applying a state-of-the-art high-pressure powder X-ray diffraction setup, we revisit the high-pressure behaviour of ZIF-8 and ZIF-67 up to p = 0.4 GPa in small pressure increments. We observe a drastic, reversible change of high-pressure powder X-ray diffraction data at p = 0.3 GPa, discovering large volume structural flexibility in ZIF-8 and ZIF-67. Our results imply a shallow underlying energy landscape in ZIF-8 and ZIF-67, an observation that might point at rich polymorphism of ZIF-8 and ZIF-67, similar to ZIF-4(Zn).

Download Full-text

Revisiting the High-Pressure Properties of the Metal-Organic Frameworks ZIF-8 and ZIF-67

10.26434/chemrxiv.13146278 ◽

2020 ◽

Author(s):

Pia Vervoorts ◽

Stefan Burger ◽

Karina Hemmer ◽

Gregor Kieslich

Keyword(s):

High Pressure ◽

State Of The Art ◽

Energy Landscape ◽

Structural Flexibility ◽

Zeolitic Imidazolate Frameworks ◽

Stimuli Responsive ◽

X Ray Diffraction ◽

X Ray ◽

Open Questions ◽

Metal Organic

The zeolitic imidazolate frameworks ZIF-8 and ZIF-67 harbour a series of fascinating stimuli responsive properties. Looking at their responsitivity to hydrostatic pressure as stimulus, open questions exist regarding the isotropic compression with non-penetrating pressure transmitting media. By applying a state-of-the-art high-pressure powder X-ray diffraction setup, we revisit the high-pressure behaviour of ZIF-8 and ZIF-67 up to p = 0.4 GPa in small pressure increments. We observe a drastic, reversible change of high-pressure powder X-ray diffraction data at p = 0.3 GPa, discovering large volume structural flexibility in ZIF-8 and ZIF-67. Our results imply a shallow underlying energy landscape in ZIF-8 and ZIF-67, an observation that might point at rich polymorphism of ZIF-8 and ZIF-67, similar to ZIF-4(Zn).

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A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

10.26434/chemrxiv.7019579.v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Walker M. Jones ◽

Aaron G. Davis ◽

R. Hunter Wilson ◽

Katherine L. Elliott ◽

Isaiah Sumner

Keyword(s):

Molecular Dynamics ◽

Quantum Mechanics ◽

Molecular Mechanics ◽

Reaction Rates ◽

Nucleophilic Attack ◽

Classical Molecular Dynamics ◽

Ubiquitin Conjugating Enzyme ◽

Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

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