Results 61 to 70 of about 9,026,292 (300)

Effect of Atomic Charges on Octanol–Water Partition Coefficient Using Alchemical Free Energy Calculation

Molecules, 2018
The octanol–water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field.
Koji Ogata, Makoto Hatakeyama, Shinichiro Nakamura   +2 more
doaj   +1 more source

Calculating Free Energy Changes in Continuum Solvation Models [PDF]

The Journal of Physical Chemistry B, 2016
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ].
Junming, Ho, Mehmed Z, Ertem
openaire   +2 more sources

Structures of mycobacterial 3‐methylcrotonyl‐CoA carboxylase reveal carrier‐domain translocation between catalytic sites

FEBS Letters, EarlyView.
Mycobacterial 3‐methylcrotonyl‐CoA carboxylase uses a mobile biotin‐carrying domain to shuttle a carboxyl group between two catalytic sites, enabling carboxylation of 3‐methylcrotonyl‐CoA during leucine breakdown. Cryo‐electron microscopy captures the carrier at both sites and reveals an inward loop movement that may prevent futile rebinding to the ...
Ajit Yadav, Bogdan I. Florea, Sebastian Geibel   +2 more
wiley   +1 more source

The changes of protein solvation free energy upon unfolding.

, 2012
For each state with a special d value, we compute the free energy of solvation for the state’s representative structure. The difference between this value and solvation free energy of native state (d = 0.0) is reported here in kcal/mol.
Bahram Goliaei (126827), Elizabeth A. Proctor (126824), Nikolay V. Dokholyan (84409), Ali A. Moosavi-Movahedi (126830), Hamid Hadi-Alijanvand (126821)   +4 more
core   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source

SOLVATION FREE ENERGY OF THIENO [3,2-b] PYRIMIDINE ANALOGS COMPRISING INTERMOLECULAR SOLVATION AND INTRAMOLECULAR SELF-SOLVATION [PDF]

, 2014
Objective: The aim was to estimate the various physiochemical properties of a molecule and the de-solvation cost for its binding to macromolecular receptors, the solvation free energy is a fundamental thermodynamics that has to be used.
K, Prabhu, Gopalakrishnan Vk, Mahto, Manoj Kumar, Prabhu K, VK, GOPALAKRISHNAN, Manoj Kumar Mahto   +5 more
core  

Chiral separation of chloroalkanes with the chromatographic column onboard Martian rovers

FEBS Letters, EarlyView.
Computer image of the Rosalind Franklin Rover of ESA's ExoMars mission. ExoMars is scheduled to land on planet Mars in Oxia Planum in 2029. This area represents an interesting spot to look for biosignatures. Investigations of ExoMars include measurement on molecular chirality. We show that chiral chloroalkanes, that have been identified on Mars, can be
Asma Merzougui, Agnes Banreti, Armelle L. Ernst, Guillaume Leseigneur, Uwe J. Meierhenrich   +4 more
wiley   +1 more source

An atomic radii set and Generalized Born implicit solvation model trained using explicit water solvation free energy data [PDF]

Compared with the other common implicit and explicit water models, Generalized Born (GB) models can provide a fast approximation of solvation free energy that is reasonably accurate but fast enough to use in molecular dynamics (MD) simulations.
Jorge, Pincay, Yuzhang, Wang, Chuan, Tian, Carlos, Simmerling   +3 more
core   +2 more sources

Roles of film-forming additives in diluted and concentrated electrolytes for lithium metal batteries: A density functional theory-based approach

Electrochemistry Communications, 2020
Electrolyte for lithium-ion batteries should facilitate Li+-ion transport and control solid electrolyte interface (SEI). To improve their performance, most of the researches focused more on the effect of the solvation structure of bulk electrolytes on ...
Hailemariam Kassa Bezabh, Meng-Che Tsai, Tesfaye Teka Hagos, Tamene Tadesse Beyene, Gebregziabher Brhane Berhe, Teklay Mezgebe Hagos, Ljalem Hadush Abrha, Shuo-Feng Chiu, Wei-Nien Su, Bing Joe Hwang   +9 more
doaj   +1 more source

Solvation free energies from neural thermodynamic integration

The Journal of Chemical Physics
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and the neural network potential is optimized to match the corresponding equilibrium potential at every intermediate ...
Mate, Balint, Fleuret, François Jean, Bereau, Tristan   +2 more
openaire   +3 more sources