scholarly journals Structural Features of Triethylammonium Acetate through Molecular Dynamics

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1432 ◽  
Author(s):  
Enrico Bodo
Keyword(s):  
Complex System ◽  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Density Functional ◽  
Tight Binding ◽  
Structural Features ◽  
Triethylammonium Acetate ◽  
Empirical Density ◽  
Semi Empirical ◽  
Partial Process

I have explored the structural features and the dynamics of triethylammonium acetate by means of semi-empirical (density functional tight binding, DFTB) molecular dynamics. I find that the results from the present simulations agree with recent experimental determinations with only few minor differences in the structural interpretation. A mixture of triethylamine and acetic acid does not form an ionic liquid, but gives rise to a very complex system where ionization is only a partial process affecting only few molecules (1 over 4 experimentally). I have also found that the few ionic couples are stable and remain mainly embedded inside the AcOH neutral moiety.

scholarly journals Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides

2020 ◽  
Vol 7 (2) ◽  
pp. 191562
Author(s):  
James A. Platts
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
A Priori ◽  
Tight Binding ◽  
Amyloid Β ◽  
Model Systems ◽  
Binding Modes ◽  
Biologically Relevant ◽  
Dynamics Simulations ◽  
Semi Empirical

We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal–peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.

scholarly journals A quantitative evaluation of computational methods to accelerate the study of alloxazine-derived electroactive compounds for energy storage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qi Zhang ◽  
Abhishek Khetan ◽  
Süleyman Er
Keyword(s):  
Energy Storage ◽  
Density Functional ◽  
Tight Binding ◽  
Computational Cost ◽  
Redox Potentials ◽  
Storage Compounds ◽  
Computational Screening ◽  
Chemical Descriptor ◽  
Lowest Unoccupied Molecular Orbital ◽  
Semi Empirical

AbstractAlloxazines are a promising class of organic electroactive compounds for application in aqueous redox flow batteries (ARFBs), whose redox properties need to be tuned further for higher performance. High-throughput computational screening (HTCS) enables rational and time-efficient study of energy storage compounds. We compared the performance of computational chemistry methods, including the force field based molecular mechanics, semi-empirical quantum mechanics, density functional tight binding, and density functional theory, on the basis of their accuracy and computational cost in predicting the redox potentials of alloxazines. Various energy-based descriptors, including the redox reaction energies and the frontier orbital energies of the reactant and product molecules, were considered. We found that the lowest unoccupied molecular orbital (LUMO) energy of the reactant molecules is the best performing chemical descriptor for alloxazines, which is in contrast to other classes of energy storage compounds, such as quinones that we reported earlier. Notably, we present a flexible in silico approach to accelerate both the singly and the HTCS studies, therewithal considering the level of accuracy versus measured electrochemical data, which is readily applicable for the discovery of alloxazine-derived organic compounds for energy storage in ARFBs.

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

Thermal Properties of Divalent Metal Oxides: CaO as a Prototype

2013 ◽  
Vol 209 ◽  
pp. 190-193
Author(s):  
Nisarg K. Bhatt ◽  
Brijmohan Y. Thakore ◽  
P.R. Vyas ◽  
A.Y. Vahora ◽  
Asvin R. Jani
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Mean Field ◽  
Field Potential ◽  
Theoretical Data ◽  
Test Case ◽  
Generalized Gradient ◽  
Core Electrons ◽  
Vibrational Free Energy ◽  
Semi Empirical

Commonly employed quasiharmonic approximation (QHA) is inadequate to account for intrinsic anharmonism such as phonon-phonon interaction, vacancy contribution, etc. Though anharmonic contributions are important at high temperatures and low pressure, complete ab initio calculations are scanty due largely to laborious computational requirements. Nevertheless, some simple semi-empirical schemes can be used effectively to incorporate the anharmonism. In this regards, in the present study we have proposed a simple computational scheme to include the effect of vacancy directly into the description within the mean-field potential approach, which calculates vibrational free energy of ions. Validity of the scheme is verified by taking calcium oxide as a test case. Equilibrium properties at (T,P) = (0,0) condition is obtained within the tight-binding second-moment approximation (TB-SMA), whose parameters were determined through first principles density functional theory. Kohn-Sham equations for core electrons were solved using ultrasoft plane-wave pseudopotential employing the generalized gradient approximation for exchange and correlation. Present findings for thermal expansion and high-T EOS clearly show perceptible improvement over the case when vacancy contribution was not included. Some related thermodynamic properties are also calculated and compared with the available experimental and theoretical data.

Diamond {111} Surface: Graphitization or Reconstruction?

1995 ◽  
Vol 383 ◽  
Author(s):  
G. Jungnickel ◽  
D. Porezag ◽  
Th. Frauenheim ◽  
W. R. L. Lambrecht ◽  
B. Segall ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Density Functional ◽  
Tight Binding ◽  
Diamond Growth ◽  
Functional Theory ◽  
Surface Phases ◽  
Surface Graphitization

ABSTRACTThe reconstruction of the diamond {1111} surface is re-examined by means of density functional theory based tight-binding molecular dynamics. Evidence is found for competition between a graphitizing tendency leading to an unreconstructed but relaxed 1 × 1 surface and a π-bonded chain-like 2 × 1 reconstruction. The implications of the possible co-existence of these two distinct surface phases for diamond growth are discussed.

Cluster, Surface and Bulk Properties of ZnCd Binary Alloys: Molecular-Dynamics Simulations

2005 ◽  
Vol 502 ◽  
pp. 51-56 ◽  
Author(s):  
Sakir Erkoc
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Structural Features ◽  
Bulk Materials ◽  
Bulk Properties ◽  
Atom Clusters ◽  
Dynamics Simulations ◽  
Mixed Clusters ◽  
Stable Structures

The structural and electronic properties of isolated neutral ZnmCdn clusters for m+n £ 3 have been investigated by performing density functional theory calculations at B3LYP level. The optimum geometries, vibrational frequencies, electronic structures, and the possible dissosiation channels of the clusters considered have been obtained. An empirical many-body potential energy function (PEF), which comprices two- and three-body atomic interactions, has been developed to investigate the structural features and energetics of ZnmCdn (m+n=3,4) microclusters. The most stable structures were found to be triangular for the three-atom clusters and tetrahedral for the four-atom clusters. On the other hand, the structural features and energetics of Znn-mCdm (n=7,8) microclusters, and Zn50, Cd50, Zn25Cd25, Zn12Cd38, and Zn38Cd12 nanoparticles have been investigated by performing molecular-dynamics computer simulations using the developed PEF. The most stable structures were found to be compact and three-dimensional for all elemental and mixed clusters. An interesting structural feature of the mixed clusters is that Zn and Cd atoms do not mix in mixed clusters, they come together almost without mixing. Surface and bulk properties of Zn, Cd, and ZnCd systems have been investigated too by performing molecular-dynamics simulations using the developed PEF. Surface reconstruction and multilayer relaxation on clean surfaces, adatom on surface, substitutional atom on surface and bulk materials, and vacancy on surface and bulk materials have been studied extensively.

Mechanisms and kinetics of initial pyrolysis and combustion reactions of 1,1-diamino-2,2-dinitroethylene from density functional tight-binding molecular dynamics simulations

2019 ◽  
Vol 97 (11) ◽  
pp. 795-804 ◽  
Author(s):  
Dong Xiang ◽  
Weihua Zhu
Keyword(s):  
Activation Energy ◽  
Molecular Dynamics ◽  
Density Functional ◽  
Tight Binding ◽  
Combustion Process ◽  
Exponential Factor ◽  
Three Stages ◽  
Dynamics Simulations ◽  
Combustion Processes ◽  
Kinetics Of

The density functional tight-binding molecular dynamics approach was used to study the mechanisms and kinetics of initial pyrolysis and combustion reactions of isolated and multi-molecular FOX-7. Based on the thermal cleavage of bridge bonds, the pyrolysis process of FOX-7 can be divided into three stages. However, the combustion process can be divided into five decomposition stages, which is much more complex than the pyrolysis reactions. The vibrations in the mean temperature contain nodes signifying the formation of new products and thereby the transitions between the various stages in the pyrolysis and combustion processes. Activation energy and pre-exponential factor for the pyrolysis and combustion reactions of FOX-7 were obtained from the kinetic analysis. It is found that the activation energy of its pyrolysis and combustion reactions are very low, making both take place fast. Our simulations provide the first atomic-level look at the full dynamics of the complicated pyrolysis and combustion process of FOX-7.

scholarly journals Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II

2021 ◽  
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chlorophyll A ◽  
Density Functional ◽  
Light Harvesting ◽  
Higher Plants ◽  
Tight Binding ◽  
Spectral Densities ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born–Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.

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