Erratum: “Note: Smooth torsional potentials for degenerate dihedral angles” [J. Chem. Phys. 146, 226101 (2017)]

Michael P. Howard; Antonia Statt; Athanassios Z. Panagiotopoulos

doi:10.1063/5.0046594

Note: Smooth torsional potentials for degenerate dihedral angles

The Journal of Chemical Physics ◽

10.1063/1.4985251 ◽

2017 ◽

Vol 146 (22) ◽

pp. 226101 ◽

Cited By ~ 6

Author(s):

Michael P. Howard ◽

Antonia Statt ◽

Athanassios Z. Panagiotopoulos

Keyword(s):

Dihedral Angles ◽

Torsional Potentials

Download Full-text

Transferability of first principles derived torsional potentials for mesogenic molecules and fragments

Molecular Physics ◽

10.1080/00268979809482281 ◽

1998 ◽

Vol 93 (6) ◽

pp. 947-954 ◽

Cited By ~ 12

Author(s):

C.J. ADAM ◽

S.J. CLARK ◽

M.R. WILSON ◽

G.J. ACKLAND ◽

J. CRAIN

Keyword(s):

First Principles ◽

Torsional Potentials

Download Full-text

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 Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, 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.

Download Full-text

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

10.26434/chemrxiv.12000132 ◽

2020 ◽

Author(s):

Michele Larocca

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Theoretical Approach ◽

Polypeptide Chain ◽

Hydrophobic Effect ◽

Side Chain ◽

Dihedral Angles ◽

Mechanical Forces ◽

Specific Chemical

Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.

Download Full-text

`Diet GMKTN55' Offers Accelerated Benchmarking Through a Representative Subset Approach

10.26434/chemrxiv.7038428.v2 ◽

2018 ◽

Author(s):

Tim Gould

Keyword(s):

Density Functional ◽

Chem Phys ◽

Comprehensive Analysis ◽

Genetic Approach ◽

Representative Subset ◽

Phys Chem Chem Phys

The GMTKN55 benchmarking protocol introduced by [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] allows comprehensive analysis and ranking of density functional approximations with diverse chemical behaviours. But this comprehensiveness comes at a cost: GMTKN55's 1500 benchmarking values require energies for around 2500 systems to be calculated, making it a costly exercise. This manuscript introduces three subsets of GMTKN55, consisting of 30, 100 and 150 systems, as `diet' substitutes for the full database. The subsets are chosen via a stochastic genetic approach, and consequently can reproduce key results of the full GMTKN55 database, including ranking of approximations.

Download Full-text

Porous Aluminophosphates as Adsorbents for the Separation of CO2/CH4 and CH4/N2 Mixtures – a Monte Carlo Simulation Study

10.26434/chemrxiv.6133346.v2 ◽

2018 ◽

Author(s):

Michael Fischer

Keyword(s):

Monte Carlo ◽

Landfill Gas ◽

Experimental Studies ◽

Chem Phys ◽

Monte Carlo Simulation Study ◽

Mixture Adsorption ◽

Vacuum Swing Adsorption ◽

Separation Of Co2 ◽

Pressure Swing ◽

Gcmc Simulations

<div>Aluminophosphates with zeolite-like topologies (AlPOs) have received considerable attention as potential adsorbents for use in the separation of methane-containing gas mixtures. Such separations, especially the removal of carbon dioxide and nitrogen from methane, are of great technological relevance in the context of the “upgrade” of natural gas, landfill gas, and biogas. While more than 50 zeolite frameworks have been synthesised in aluminophosphate composition or as heteroatom substituted AlPO derivatives, only a few of them have been characterised experimentally with regard to their adsorption and separation behaviour. In order to predict the potential of a variety of AlPO frameworks for applications in CO2/CH4 and CH4/N2 separations, atomistic grand-canonical Monte Carlo (GCMC) simulations were performed for 53 different structures. Building on previous work, which studied CO2/N2 mixture adsorption in AlPOs (M. Fischer, Phys. Chem. Chem. Phys., 2017, 19, 22801–22812), force field parameters for methane adsorption in AlPOs were validated through a comparison to available experimental adsorption data. Afterwards, CO2/CH4 and CH4/N2 mixture isotherms were computed for all 53 frameworks for room temperature and total pressures up to 1000 kPa (10 bar), allowing the prediction of selectivities and working capacities for conditions that are relevant for pressure swing adsorption (PSA) and vacuum swing adsorption (VSA). For CO2/CH4 mixtures, the GIS, SIV, and ATT frameworks were found to have the highest selectivities and CO2 working capacities under VSA conditions, whereas several frameworks, among them AFY, KFI, AEI, and LTA, show higher working capacities under PSA conditions. For CH4/N2 mixtures, all frameworks are moderately selective for methane over nitrogen, with ATV exhibiting a significantly higher selectivity than all other frameworks. While some of the most promising topologies are either not available in pure-AlPO4 composition or collapse upon calcination, others can be synthesised and activated, rendering them interesting candidates for future experimental studies. In addition to predictions of mixture adsorption isotherms, further simulations were performed for four selected systems in order to investigate the microscopic origins of the macroscopic adsorption behaviour, e.g. with regard to the very high CH4/N2 selectivity of ATV and the loading-dependent evolution of the heat of CO2 adsorption and CO2/CH4 selectivity of AEI and GME.</div>

Download Full-text