Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

Building Blocks ◽

Variable Number ◽

Polymer Chains ◽

Relaxation Processes ◽

Polymer Backbone ◽

Dynamics Simulations ◽

The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

10.26434/chemrxiv.12705695.v1 ◽

2020 ◽

Author(s):

Vivek Sundaram ◽

Alexey V. Lyulin ◽

Björn Baumeier

Keyword(s):

Force Field ◽

Density Functional ◽

Building Blocks ◽

Variable Number ◽

Polymer Chains ◽

Relaxation Processes ◽

Polymer Backbone ◽

Dynamics Simulations ◽

The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

Classical Polarizable Force Field to Study Hydrated Hectorite: Optimization on DFT Calculations and Validation against XRD Data

Minerals ◽

10.3390/min8050205 ◽

2018 ◽

Vol 8 (5) ◽

pp. 205 ◽

Cited By ~ 3

Author(s):

Ragnhild Hånde ◽

Vivien Ramothe ◽

Stéphane Tesson ◽

Baptiste Dazas ◽

Eric Ferrage ◽

...

Keyword(s):

Force Field ◽

Density Functional ◽

X Ray Diffraction ◽

Electronic Density ◽

Functional Theory ◽

Polarizable Force Field ◽

Xrd Patterns ◽

The One ◽

Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimental results. In the bihydrated state, the less structured electronic density profile obtained with PIM compared to the one from the state-of-the-art non-polarizable force field clayFF explains the slightly better agreement between the PIM results and experiments.

A New Phase of the Na+ Ion Conductor Na3PS4

10.26434/chemrxiv.8003717.v1 ◽

2019 ◽

Author(s):

Theodosios Famprikis ◽

James Dawson ◽

François Fauth ◽

Emmanuelle Suard ◽

Benoit Fleutot ◽

...

Keyword(s):

Solid Electrolytes ◽

Density Functional ◽

Orthorhombic Crystal ◽

Orthorhombic Crystal Structure ◽

Ion Conductor ◽

Solid State Batteries ◽

Density Analysis ◽

Two Phases ◽

<div> Solid electrolytes are crucial for next‑generation solid‑state batteries and Na3PS4 is one of the most promising Na+ conductors for such applications. At present, two phases of Na3PS4 have been identified and it had been thought to melt above 500 °C. In contrast, we show that it remains solid above this temperature and transforms into a third polymorph, γ, exhibiting superionic behavior. We propose an orthorhombic crystal structure for γ‑Na3PS4 based on scattering density analysis of diffraction data and density functional theory calculations. We show that the Na+ superionic behavior is associated with rotational motion of the thiophosphate polyanions pointing to a rotor phase, based on ab initio molecular dynamics simulations and supported by high‑temperature synchrotron and neutron diffraction, thermal analysis and impedance spectroscopy. These findings are of importance for the development of new polyanion‑based solid electrolytes. </div>

Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

Physical Chemistry Chemical Physics ◽

10.1039/d0cp04667a ◽

2020 ◽

Author(s):

Lijuan Meng ◽

Jinlian Lu ◽

Yujie Bai ◽

Lili Liu ◽

Tang Jingyi ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Chemical Vapor Deposition ◽

Molecular Dynamics Simulations ◽

Vapor Deposition ◽

Density Functional ◽

Chemical Vapor ◽

Functional Theory ◽

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

International Journal of Molecular Sciences ◽

10.3390/ijms22063244 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3244

Author(s):

Charuvaka Muvva ◽

Natarajan Arul Murugan ◽

Venkatesan Subramanian

Keyword(s):

Force Field ◽

Density Functional ◽

Amyloid Β ◽

Tau Proteins ◽

Functional Theory ◽

Energy Profiles ◽

Α Helix ◽

Semi Empirical ◽

Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Processes ◽

10.3390/pr7100699 ◽

2019 ◽

Vol 7 (10) ◽

pp. 699 ◽

Cited By ~ 2

Author(s):

Ma ◽

Zhong ◽

Liu ◽

Zhong ◽

Yan ◽

...

Keyword(s):

Molecular Dynamics ◽

Hydrogen Storage ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Storage Capacity ◽

Computational Study ◽

Hydrogen Storage Capacity ◽

Large Cage ◽

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

Microhydration of ionized building blocks of DNA/RNA: infrared spectra of pyrimidine$$^{+}$$-$$(\hbox {H}_{2}\hbox {O})_{\text {1-3}}$$ clusters

The European Physical Journal D ◽

10.1140/epjd/s10053-021-00065-z ◽

2021 ◽

Vol 75 (3) ◽

Author(s):

Kuntal Chatterjee ◽

Otto Dopfer

Keyword(s):

Density Functional ◽

Size Range ◽

Building Blocks ◽

Ion Solvation ◽

Structure Stability ◽

Consistent Picture ◽

Three Body ◽

And Function ◽

Stable Structures

Abstract Hydration of biomolecules is an important physiological process that governs their structure, stability, and function. Herein, we probe the microhydration structure of cationic pyrimidine (Pym), a common building block of DNA/RNA bases, by infrared photodissociation spectroscopy (IRPD) of mass-selected microhydrated clusters, $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n (W=$$\hbox {H}_{2}\hbox {O}$$ H 2 O ), in the size range $$n=1$$ n = 1 –3. The IRPD spectra recorded in the OH and CH stretch range are sensitive to the evolution of the hydration network. Analysis with density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level provides a consistent picture of the most stable structures and their energetic and vibrational properties. The global minima of $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n predicted by the calculations are characterized by H-bonded structures, in which the H-bonded $$\hbox {W}_{n}$$ W n solvent cluster is attached to the most acidic C4–H proton of $$\hbox {Pym}^{+}$$ Pym + via a single CH...O ionic H-bond. These isomers are identified as predominant carrier of the IRPD spectra, although less stable local minima provide minor contributions. In general, the formation of the H-bonded solvent network (exterior ion solvation) is energetically preferred to less stable structures with interior ion solvation because of cooperative nonadditive three-body polarization effects. Progressive hydration activates the C4–H bond, along with increasing charge transfer from $$\hbox {Pym}^{+}$$ Pym + to $$\hbox {W}_{n}$$ W n , although no proton transfer is observed in the size range $$n\leqslant $$ n ⩽ 3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic $$\hbox {N}_{2}$$ N 2 ligands, which strongly prefer interior ion solvation by $$\uppi $$ π stacking interactions. Comparison of $$\hbox {Pym}^{+}$$ Pym + -W with Pym-W and $$\hbox {H}^{+}$$ H + Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction. Graphic Abstract

First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

ASME/JSME 2011 8th Thermal Engineering Joint Conference ◽

10.1115/ajtec2011-44339 ◽

2011 ◽

Author(s):

Keivan Esfarjani ◽

Gang Chen ◽

Asegun Henry

Keyword(s):

Thermal Conductivity ◽

Molecular Dynamics ◽

Thermal Properties ◽

Force Field ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Density Functional ◽

Interatomic Potential ◽

Force Constants ◽

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.

Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

Physical Chemistry Chemical Physics ◽

10.1039/d0cp02919j ◽

2020 ◽

Vol 22 (30) ◽

pp. 17275-17290

Author(s):

Kuntal Chatterjee ◽

Otto Dopfer

Keyword(s):

Density Functional Theory ◽

Infrared Spectroscopy ◽

Density Functional ◽

Building Blocks ◽

Functional Theory ◽

Fragment Ions ◽

Sequential Loss ◽

Spectroscopic Identification

The structure of the predominant fragments of the fundamental pyrimidine cation arising from sequential loss of HCN are identified by infrared spectroscopy of tagged ions and dispersion-corrected density functional theory calculations.