A Framework for Modeling DNA Based Molecular Systems

The strategy of anchoring molecular catalysts on electrode surfaces combines the high selectivity and activity of molecular systems with the practicality of heterogeneous systems. The stability of molecular catalysts is, however, far less than that of traditional heterogeneous electrocatalysts, and therefore a method to easily replace anchored molecular catalysts that have degraded could make such electrosynthetic systems more attractive. Here, we apply a non-covalent “click” chemistry approach to reversibly bind molecular electrocatalysts to electrode surfaces via host-guest complexation with surface-anchored cyclodextrins. The host-guest interaction is remarkably strong and allows the flow of electrons between the electrode and the guest catalyst. Electrosynthesis in both organic and aqueous media was demonstrated on metal oxide electrodes, with stability on the order of hours. The catalytic surfaces can be recycled by controlled release of the guest from the host cavities and readsorption of fresh guest. This strategy represents a new approach to practical molecular-based catalytic systems.

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Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

10.26434/chemrxiv.11980119.v1 ◽

2020 ◽

Author(s):

Denis Artiukhin ◽

Patrick Eschenbach ◽

Johannes Neugebauer

Keyword(s):

Spin Density ◽

Reaction Center ◽

Density Functional ◽

Photosynthetic Reaction Center ◽

Chem Phys ◽

Molecular Structures ◽

Error Characteristic ◽

Molecular Systems ◽

Density Distributions ◽

The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

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Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

10.26434/chemrxiv.6015611.v1 ◽

2018 ◽

Author(s):

Maximiliano Riquelme ◽

Alejandro Lara ◽

David L. Mobley ◽

Toon Vestraelen ◽

Adelio R Matamala ◽

...

Keyword(s):

Force Field ◽

Functional Groups ◽

Electrostatic Interactions ◽

Organic Molecules ◽

Force Fields ◽

Chemical Elements ◽

Atomic Charges ◽

Free Energies ◽

Molecular Systems ◽

Solvent Model

<div>Computer simulations of bio-molecular 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 bio-molecular systems and are therein described by atomic point charges.</div><div>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 MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

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Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

10.26434/chemrxiv.7940810.v1 ◽

2019 ◽

Author(s):

Rebecca Lindsey ◽

Nir Goldman ◽

Laurence E. Fried ◽

Sorin Bastea

Keyword(s):

Carbon Monoxide ◽

Molecular System ◽

Interaction Model ◽

System Size ◽

Single Atom ◽

Reactive System ◽

Extreme Conditions ◽

Ambient Conditions ◽

Molecular Systems ◽

Three Body

<p>The interatomic Chebyshev Interaction Model for Efficient Simulation (ChIMES) is based on linear combinations of Chebyshev polynomials describing explicit two- and three-body interactions. Recently, the ChIMES model has been developed and applied to a molten metallic system of a single atom type (carbon), as well as a non-reactive molecular system of two atom types at ambient conditions (water). Here, we continue application of ChIMES to increasingly complex problems through extension to a reactive system. Specifically, we develop a ChIMES model for carbon monoxide under extreme conditions, with built-in transferability to nearby state points. We demonstrate that the resulting model recovers much of the accuracy of DFT while exhibiting a 10<sup>4</sup>increase in efficiency, linear system size scalability and the ability to overcome the significant system size effects exhibited by DFT.</p>

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