scholarly journals Theoretical Insights into the Structure of the Aminotris(Methylenephosphonic Acid) (ATMP) Anion: A Possible Partner for Conducting Ionic Media

Symmetry ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 920
Author(s):  
Henry Adenusi ◽  
Gregory Chass ◽  
Enrico Bodo
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Md Simulations ◽  
Specific System ◽  
Symmetric Molecule ◽  
Variable Topology ◽  
Doubly Charged ◽  
High Degree ◽  
Transfer Mechanisms ◽  
Potential Use

We present a computational characterisation of Aminotris(methylenephosphonic acid) (ATMP) and its potential use as an anionic partner for conductive ionic liquids (ILs). We argue that for an IL to be a good candidate for a conducting medium, two conditions must be fulfilled: (i) the charge must be transported by light carriers; and (ii) the system must maintain a high degree of ionisation. The result trends presented herein show that there are molecular ion combinations that do comply with these two criteria, regardless of the specific system used. ATMP is a symmetric molecule with a total of six protons. In the bulk phase, breaking the symmetry of the fully protonated state and creating singly and doubly charged anions induces proton transfer mechanisms. To demonstrate this, we used molecular dynamics (MD) simulations employing a variable topology approach based on the reasonably reliable semiempirical density functional tight binding (DFTB) evaluation of the atomic forces. We show that, by choosing common and economical starting compounds, we can devise a viable prototype for a highly conductive medium where charge transfer is achieved by proton motion.

scholarly journals Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

2021 ◽  
Author(s):  
Bahaa Jawad ◽  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Density Functional ◽  
Vaccine Development ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Tight Binding ◽  
Md Simulations ◽  
Functional Theory ◽  
Generalized Born ◽  
The Density Functional Theory ◽  
Key Residues

<p>The spike protein of SARS-CoV-2 binds to ACE2 receptor <i>via</i> its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two <i>ab initio</i> quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q<sup>493</sup>, Y<sup>505</sup>, Q<sup>498</sup>, N<sup>501</sup>, T<sup>500</sup>, N<sup>487</sup>, Y<sup>449</sup>, F<sup>486</sup>, K<sup>417</sup>, Y<sup>489</sup>, F<sup>456</sup>, Y<sup>495</sup>, and L<sup>455</sup> have been identified as hotspots in RBD, while those in ACE2 are K<sup>353</sup>, K<sup>31</sup>, D<sup>30</sup>, D<sup>355</sup>, H<sup>34</sup>, D<sup>38</sup>, Q<sup>24</sup>, T<sup>27</sup>, Y<sup>83</sup>, Y<sup>41</sup>, E<sup>35</sup>, and E<sup>37</sup>. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q<sup>493</sup>, N<sup>501</sup>, F<sup>486</sup>, K<sup>417</sup>, and F<sup>456</sup> in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N<sup>487</sup>, Q<sup>493</sup>, Y<sup>449</sup>, T<sup>500</sup>, G<sup>496</sup>, G<sup>446</sup> and G<sup>502</sup> in RBD form pairs <i>via</i> specific hydrogen bonding with Q<sup>24</sup>, H<sup>34</sup>, E<sup>35</sup>, D<sup>38</sup>, Y<sup>41</sup>, Q<sup>42</sup> and K<sup>353</sup> in ACE2. </p>

scholarly journals Theoretical study of 2-phenylpyrrole molecule using various quantum-chemical approaches

2012 ◽  
Vol 5 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Lenka Rottmannová ◽  
Kraiwan Punyain ◽  
Ján Rimarčík ◽  
Vladimír Lukeš ◽  
Erik Klein ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Quantum Chemical ◽  
Density Functional ◽  
Theoretical Study ◽  
Tight Binding ◽  
Md Simulations ◽  
Am1 Method ◽  
Tight Binding Approximation ◽  
Neutral State ◽  
Moller Plesset

Theoretical study of 2-phenylpyrrole molecule using various quantum-chemical approaches A systematic theoretical study of 2-phenylpyrrole (PhPy) is presented for its neutral and monocharged states. The calculations were performed using the semiempirical Austin Model 1 (AM1) method, ab initio Møller-Plesset perturbation theory up to the second-order (MP2), density functional theory (DFT) and its tight-binding approximation (DFTB+). The comparison of the obtained equilibrium geometries showed that the C—C bond lengths in the phenylene ring are practically identical for the neutral state. Electric charging leads to significant changes in the geometry with respect to the neutral state. The C—N bonds in PhPy are elongated and the negative charging produces the out-of-plane distortion of N—H bond from the aromatic ring plane. The anionic state of the investigated molecule is connected with a higher perturbation of bond length alternation in both rings in comparison to the cationic state. The vibrationaly broadened absorption spectra, based on the on-the-fly molecular dynamics (MD) simulations, are also presented and compared with experimental spectra. Although the DFTB+ method has the tendency to planarize the investigated molecular structure, the agreement of simulated absorption spectra based on the MD DFTB+ geometries with TD-DFT calculations is acceptable.

scholarly journals Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

2021 ◽  
Author(s):  
Bahaa Jawad ◽  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Density Functional ◽  
Vaccine Development ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Tight Binding ◽  
Md Simulations ◽  
Functional Theory ◽  
Generalized Born ◽  
The Density Functional Theory ◽  
Key Residues

<p>The spike protein of SARS-CoV-2 binds to ACE2 receptor <i>via</i> its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two <i>ab initio</i> quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q<sup>493</sup>, Y<sup>505</sup>, Q<sup>498</sup>, N<sup>501</sup>, T<sup>500</sup>, N<sup>487</sup>, Y<sup>449</sup>, F<sup>486</sup>, K<sup>417</sup>, Y<sup>489</sup>, F<sup>456</sup>, Y<sup>495</sup>, and L<sup>455</sup> have been identified as hotspots in RBD, while those in ACE2 are K<sup>353</sup>, K<sup>31</sup>, D<sup>30</sup>, D<sup>355</sup>, H<sup>34</sup>, D<sup>38</sup>, Q<sup>24</sup>, T<sup>27</sup>, Y<sup>83</sup>, Y<sup>41</sup>, E<sup>35</sup>, and E<sup>37</sup>. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q<sup>493</sup>, N<sup>501</sup>, F<sup>486</sup>, K<sup>417</sup>, and F<sup>456</sup> in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N<sup>487</sup>, Q<sup>493</sup>, Y<sup>449</sup>, T<sup>500</sup>, G<sup>496</sup>, G<sup>446</sup> and G<sup>502</sup> in RBD form pairs <i>via</i> specific hydrogen bonding with Q<sup>24</sup>, H<sup>34</sup>, E<sup>35</sup>, D<sup>38</sup>, Y<sup>41</sup>, Q<sup>42</sup> and K<sup>353</sup> in ACE2. </p>

scholarly journals A DFTB-Based Molecular Dynamics Investigation of an Explicitly Solvated Anatase Nanoparticle

2022 ◽  
Vol 12 (2) ◽  
pp. 780
Author(s):  
Dáire O’Carroll ◽  
Niall English
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Tight Binding ◽  
Static Properties ◽  
Additional Information ◽  
Water Layers ◽  
Observed Behaviour ◽  
Large Systems ◽  
High Degree ◽  
Structure Calculations

We performed a self-consistent charge density functional tight-binding molecular dynamics (SCC DFTB-MD) simulation of an explicitly solvated anatase nanoparticle. From the 2 ps trajectory, we were able to calculate both dynamic and static properties, such as the energies of interaction and the formation of water layers at the surface, and compare them to the observed behaviour reported elsewhere. The high degree of agreement between our simulation and other sources, and the additional information gained from employing this methodology, highlights the oft-overlooked viability of DFTB-based methods for electronic structure calculations of large systems.

scholarly journals MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

2019 ◽  
Author(s):  
Jógvan Magnus Haugaard Olsen ◽  
Viacheslav Bolnykh ◽  
Simone Meloni ◽  
Emiliano Ippoliti ◽  
Martin P. Bircher ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
Multiscale Modeling ◽  
Density Functional ◽  
Data Exchange ◽  
Computational Cost ◽  
Coarse Graining ◽  
Md Simulations ◽  
Loosely Coupled ◽  
Multiple Data ◽  
High Degree

<div>We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a high degree of flexibility. MiMiC has been used in a new electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) implementation coupling the highly efficient CPMD and GROMACS programs but it can also be extended to use other programs. The framework can also be utilized to extend the partitioning of the system into several domains that can be treated using different models, such as models based on wavefunction or density functional theory as well as coarse-graining and continuum models. The new QM/MM implementation treats long-range electrostatic QM-MM interactions through the multipoles of the QM subsystem which substantially reduces the computational cost without loss of accuracy compared to an exact treatment. This enables QM/MM molecular dynamics (MD) simulations of very large systems.</div>

scholarly journals MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

2019 ◽  
Author(s):  
Jógvan Magnus Haugaard Olsen ◽  
Viacheslav Bolnykh ◽  
Simone Meloni ◽  
Emiliano Ippoliti ◽  
Martin P. Bircher ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
Multiscale Modeling ◽  
Density Functional ◽  
Data Exchange ◽  
Computational Cost ◽  
Coarse Graining ◽  
Md Simulations ◽  
Loosely Coupled ◽  
Multiple Data ◽  
High Degree

<div>We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a high degree of flexibility. MiMiC has been used in a new electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) implementation coupling the highly efficient CPMD and GROMACS programs but it can also be extended to use other programs. The framework can also be utilized to extend the partitioning of the system into several domains that can be treated using different models, such as models based on wavefunction or density functional theory as well as coarse-graining and continuum models. The new QM/MM implementation treats long-range electrostatic QM-MM interactions through the multipoles of the QM subsystem which substantially reduces the computational cost without loss of accuracy compared to an exact treatment. This enables QM/MM molecular dynamics (MD) simulations of very large systems.</div>

scholarly journals Dynamic versus Static Approach to Theoretical Anharmonic Vibrational Spectroscopy of Molecular Species Elevant to Atmospheric Chemistry: A Case Study of Formic Acid

2018 ◽  
Vol 19 (2) ◽  
pp. 119-130 ◽  
Author(s):  
Bojana Koteska ◽  
Verce Manevska ◽  
Anastas Mishev ◽  
Ljupco Pejov
Keyword(s):  
Formic Acid ◽  
Molecular Species ◽  
Atmospheric Chemistry ◽  
Density Functional ◽  
Tight Binding ◽  
Climate Science ◽  
Md Simulations ◽  
Covalently Bonded ◽  
Static Approach

Vibrational spectra of the two conformers of the free formic acid molecule are computed by two approaches, with a special emphasis on the region of O-H stretching modes. The first approach (referred to as a static one) is based on sequential computation of anharmonic O-H stretching vibrational potential and numerical solution of the vibrational Schr\"{o}dinger equation by the Numerov method. The second approach (referred to as a dynamic one) is based on molecular dynamics (MD) simulations performed within the atom-centered density matrix propagation scheme (ADMP) followed by spectral analysis of the velocity-velocity and dipole moment autocorrelation functions computed from the ADMP MD trajectories. All calculations are carried out within the density functional tight binding (DFTB) formalism. The computed properties are compared to the available experimental data and the advantages of the dynamic versus the static approach are outlined and analyzed in the context of detection of individual and non-covalently bonded molecular species relevant to climate science and atmospheric chemistry.

scholarly journals Topological and Energetic Conditions for Lithographic Production of Carbon Nanotubes from Graphene

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
D. Fülep ◽  
I. Zsoldos ◽  
I. László
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Linear Relationship ◽  
Systematic Study ◽  
Density Functional ◽  
Graphene Nanoribbons ◽  
Tight Binding ◽  
Md Simulations ◽  
Curvature Energy ◽  
Critical Curvature

Density Functional Based Tight-Binding (DFTB) molecular dynamics (MD) simulations were performed for producing carbon nanotubes from graphene nanoribbons. The constant temperature simulations were controlled with the help of Nosé-Hoover thermostat. In our systematic study we obtained critical curvature energies and determined topological conditions for nanotube production from two parallel graphene nanoribbons. We obtained linear relationship between the curvature energy and the square of the curvature.

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

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