A theoretical study of molecular conformations and gelation ability of N,N′-dipyridyl urea compounds in ethanol solution: DFT calculations and MD simulations

RSC Advances ◽  
2013 ◽  
Vol 3 (39) ◽  
pp. 18115 ◽  
Author(s):  
Suci Meng ◽  
Yaqun Tang ◽  
Yuan Yin ◽  
Xiulian Yin ◽  
Jimin Xie
Keyword(s):  
Dft Calculations ◽  
Theoretical Study ◽  
Md Simulations ◽  
Ethanol Solution ◽  
Molecular Conformations ◽  
Urea Compounds

Two-dimensional diamine-linked covalent organic frameworks for CO2/N2 capture and separation: theoretical modeling and simulations

2020 ◽  
Vol 22 (44) ◽  
pp. 25918-25929
Author(s):  
Yusuf Bramastya Apriliyanto ◽  
Noviyan Darmawan ◽  
Noelia Faginas-Lago ◽  
Andrea Lombardi
Keyword(s):  
Dft Calculations ◽  
Force Field ◽  
Theoretical Study ◽  
Gaseous Mixture ◽  
Md Simulations ◽  
Theoretical Modeling ◽  
Two Dimensional ◽  
Covalent Organic Frameworks ◽  
Modeling And Simulations ◽  
Mixture Adsorption

2D-COFs with diamine-based linkers have been designed and investigated for CO2/N2 gaseous mixture adsorption and separation via a systematic theoretical study by combining DFT calculations and force field-based MD simulations.

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>

Theoretical Study of Iron Heterogeneous Growth on the Surface of C60 Molecule

2014 ◽  
Vol 1081 ◽  
pp. 115-118
Author(s):  
Qi Cheng Liu ◽  
Yun Fang Li
Keyword(s):  
Crystallization Process ◽  
Theoretical Study ◽  
Covalent Bond ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Bond Forming ◽  
Regular Icosahedron ◽  
Molecule Dynamics ◽  
Molecule Surface ◽  
Regular Closed

Direct molecule dynamics (MD) simulations have also been performed to study heterogeneous nucleation and growth of iron on C60 molecule. The grown mechanism of this crystallization process was explored. The results indicate that 92 iron atoms attach to C60 molecule surface can form new covalent bond, forming a closed regular icosahedron. More atoms grow in layer to form bigger regular closed clathrate base on the structure of former one. As increase of atoms number, there will appear some crystal faces.

Theoretical Study of Octahedral Substitution Effect in Delaminated Pyrophyllite: Physicochemical Properties and Applications

2021 ◽  
Author(s):  
Carla Romina Luna ◽  
Walter Guillermo Reimers ◽  
Marcelo Avena ◽  
Alfredo Juan
Keyword(s):  
Dft Calculations ◽  
Physicochemical Properties ◽  
Electronic Properties ◽  
Theoretical Study ◽  
Substitution Effect ◽  
Isomorphic Substitution ◽  
Octahedral Sheet ◽  
Octahedral Substitution

We have studied, using DFT calculations, some geometrical and electronic properties of delaminated pyrophyllite (D-P) and the corresponding layers that resulted from three isomorphic substitution on the octahedral sheet (Mg2+,...

Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

2010 ◽  
Vol 66 (5) ◽  
pp. 527-543 ◽  
Author(s):  
Leonardo Lo Presti ◽  
Raffaella Soave ◽  
Mariangela Longhi ◽  
Emanuele Ortoleva
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Phase Ii ◽  
Density Functional ◽  
Organic Ligand ◽  
Stable Phase ◽  
Stable Form ◽  
Molecular Conformations

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.111,15.02,6.016,20)triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C24H30N6) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z′, density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z′ = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30–40 kJ mol−1. These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

Sign in / Sign up

Export Citation Format

Share Document