QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

2020 ◽  
Vol 41 (16) ◽  
pp. 1509-1520
Author(s):  
Filip Šebesta ◽  
Jakub Šebera ◽  
Vladimír Sychrovský ◽  
Yoshiyuki Tanaka ◽  
Jaroslav V. Burda
Keyword(s):  
Umbrella Sampling ◽  
Reaction Energy ◽  
Bond Model ◽  
Energy Profiles ◽  
Constant Ph

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations

2015 ◽  
Vol 17 (19) ◽  
pp. 12857-12869 ◽  
Author(s):  
Jia-Kai Zhou ◽  
Dah-Yen Yang ◽  
Sheh-Yi Sheu
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Mechanism ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
G Quadruplex ◽  
Free Energy Profiles

The mechanical properties and kinetic pathways of the ligand BMVC unbinding from the G-quadruplex were investigated via the computation of free energy profiles.

scholarly journals autodE: Automated Calculation of Reaction Energy Profiles – Application to Organic and Organometallic Reactions

2020 ◽  
Author(s):  
Tom Young ◽  
Joseph Silcock ◽  
Alistair Sterling ◽  
Fernanda Duarte
Keyword(s):  
Claisen Rearrangement ◽  
Reductive Elimination ◽  
Conformational Sampling ◽  
Reaction Energy ◽  
General Applicability ◽  
Organometallic Reactions ◽  
Energy Profiles ◽  
Migratory Insertion ◽  
Human Effort ◽  
Metal Catalyzed

Calculating reaction profiles to aid in mechanistic elucidation has long been the domain of the expert computational chemist. We introduce autodE, an open-source tool capable of locating transition states and minima and delivering a full reaction energy profile with minimal human effort (https://github.com/duartegroup/autodE). autodE is broadly applicable to study organic and organometallic reaction classes, including addition, substitution, elimination, migratory insertion, oxidative addition and reductive elimination; it accounts for conformational sampling of both minima and TSs, and is compatible with many electronic structure packages. The general applicability of autodE is demonstrated in complex multi-step reactions, including metal-catalyzed cobalt- and rhodium-catalyzed hydroformylation, and an Ireland-Claisen rearrangement.

scholarly journals Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase

2021 ◽  
Vol 118 (40) ◽  
pp. e2105507118
Author(s):  
Chigusa Kobayashi ◽  
Yasuhiro Matsunaga ◽  
Jaewoon Jung ◽  
Yuji Sugita
Keyword(s):  
Free Energy ◽  
Structural Changes ◽  
Umbrella Sampling ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Energy Profiles ◽  
Intermediate States ◽  
Before And After ◽  
Energetic Analysis ◽  
Dynamics Simulations

Sarcoplasmic reticulum (SR) Ca2+-ATPase transports two Ca2+ ions from the cytoplasm to the SR lumen against a large concentration gradient. X-ray crystallography has revealed the atomic structures of the protein before and after the dissociation of Ca2+, while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca2+ and E2P. Here, we explore the pathway and free energy profile of the transition using atomistic molecular dynamics simulations with the mean-force string method and umbrella sampling. The simulations suggest that a series of structural changes accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca2+ ions toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization. Free energy profiles of the transition assuming different protonation states suggest rapid exchanges between Ca2+ ions and protons when the Ca2+ ions are released toward the SR lumen.

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS

2005 ◽  
Vol 04 (02) ◽  
pp. 433-448 ◽  
Author(s):  
KATSUMI MURATA ◽  
YUJI SUGITA ◽  
YUKO OKAMOTO
Keyword(s):  
Free Energy ◽  
Energy Analysis ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Sequence Dependence ◽  
Reaction Coordinates ◽  
Energy Profiles ◽  
Dynamics Simulations ◽  
Free Energy Analysis ◽  
Good Agreement

The free energy change of the stacking process of DNA dimers has been investigated by potential of mean force (PMF) calculations. Two reaction coordinates were considered. One is the distance R between the glycosidic nitrogen atoms of the bases. The other is the pseudo dihedral angle X (N–Cl′–Cl′–N) . All 16 possible DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in 5′ and 3′ positions were considered. From the free energy profiles, we observed good stacking for all DNA dimers and sequence-dependent stacking stability. This sequence dependence of the stacking free energy is in good agreement with the experimental results. We also observed that the PMF is the lowest at R = 4.0~4.4 Å and X = 20~40° for all the DNA dimers except for the dGpdA dimer. These values are close to those of the canonical B-DNA (4.4 Å and 29°).

scholarly journals Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Toluene Molecules through Phospholipid Bilayers

2019 ◽  
Author(s):  
Sang Noh ◽  
Rebecca Notman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Computational Efficiency ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
Toluene Molecule ◽  
Molecular Dynamics Methods ◽  
Viable Approach ◽  
The Cost

In this study, we use Molecular Dynamics (MD) to analyze three different corrections of the Steered Molecular Dynamics (SMD) implementation of Jarzynski's Equality (JE) to calculate the FE change for the translocation of a toluene molecule across a lipid bilayer, and compare the accuracy and computational efficiency of these approaches to the results obtained using Umbrella Sampling (US). We show that when computing the free energy profile of a small molecule across a model membrane, the SMD approach suffers from sampling issues that may be alleviated through the use of a slower pulling velocity, but at the cost of computational efficiency. We deduce that, despite its drawbacks, US remains the more viable approach of the two for computing the free energy (FE) profile.

Sign in / Sign up

Export Citation Format

Share Document