scholarly journals Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

2018 ◽  
Vol 251 (3) ◽  
pp. 345-356 ◽  
Author(s):  
James C. Gumbart ◽  
Martin B. Ulmschneider ◽  
Anthony Hazel ◽  
Stephen H. White ◽  
Jakob P. Ulmschneider
Keyword(s):  
Computational Method ◽  
Free Energies ◽  
Peptide Insertion

scholarly journals Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

2018 ◽  
Vol 251 (3) ◽  
pp. 357-357
Author(s):  
James C. Gumbart ◽  
Martin B. Ulmschneider ◽  
Anthony Hazel ◽  
Stephen H. White ◽  
Jakob P. Ulmschneider
Keyword(s):  
Computational Method ◽  
Free Energies ◽  
Peptide Insertion

scholarly journals The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction

2021 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Linear Models ◽  
Theoretical Calculations ◽  
Computational Method ◽  
Basis Set ◽  
Free Energies ◽  
Nitrogen And Phosphorus ◽  
Atom Pairs ◽  
Leaving Groups ◽  
First Time ◽  
Nitrogen Phosphorus

AbstractThis communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.

Structural analogues of Hoveyda–Grubbs catalysts bearing the 1-benzofuran moiety or isopropoxy-1-benzofuran derivatives as olefin metathesis catalysts

RSC Advances ◽  
2016 ◽  
Vol 6 (26) ◽  
pp. 21423-21429 ◽  
Author(s):  
B. Trzaskowski ◽  
K. Ostrowska
Keyword(s):  
Olefin Metathesis ◽  
Computational Method ◽  
Free Energies ◽  
Grubbs Catalysts ◽  
Structural Analogues ◽  
Metathesis Catalysts ◽  
Derivatives Of

We have used the DFT/M06-D3 computational method to study structures and activation free energies for a series of Hoveyda–Grubbs-like catalysts with the isopropoxybenzene part replaced by 1-benzofuran and ten derivatives of isopropoxy-1-benzofuran.

scholarly journals Unlocking Phase Diagrams for Molybdenum and Tungsten Nanoclusters and Prediction of their Formation Constants

2021 ◽  
Author(s):  
Enric Petrus ◽  
Carles Bo
Keyword(s):  
Phase Diagrams ◽  
General Rule ◽  
Formation Constants ◽  
Computational Method ◽  
Reaction Networks ◽  
Free Energies ◽  
Computational Approaches ◽  
Chemical Equilibria ◽  
Gibbs Energies ◽  
And Tungsten

Understanding and controlling aqueous speciation of metal oxides are key for the discovery and development of novel materials, and challenge both experimental and computational approaches. Here we present a computational method, called POMSimulator, which is able to predict speciation phase diagrams (Conc. vs pH) for multi-species chemical equilibria in solution, and which we apply to molybdenum and tungsten isopolyoxoanions (IPAs). Starting from the MO4 monomers, and considering dimers, trimers, and larger species, the chemical reaction networks involved in the formation of [H32Mo36O128]8- and [W12O42]12- are sampled in an automatic manner. This information is used for setting up ~105 speciation models, and from there, we generate the speciation phase diagrams, which show an insightful picture of the behavior of IPAs in aqueous solution. Furthermore, we predict the values for 107 formation constants for a diversity of molybdenum and tungsten molecular oxides. Among these species, we could include several pentagonal shaped species and very reactive tungsten intermediates as well. Last but not least, the calibration employed for correcting the DFT Gibbs energies is remarkably similar for both metals, which suggests that a general rule might exist for correcting computed free energies for other metals.<br>

FINDING CONSERVED WELL-ORDERED RNA STRUCTURES IN GENOMIC SEQUENCES

2004 ◽  
Vol 04 (04) ◽  
pp. 417-430 ◽  
Author(s):  
SHU-YUN LE ◽  
JACOB V. MAIZEL ◽  
KAIZHONG ZHANG
Keyword(s):  
Statistical Significance ◽  
Quantitative Measure ◽  
Regulatory Elements ◽  
Similarity Score ◽  
Computational Method ◽  
Genomic Sequences ◽  
Rna Structures ◽  
Free Energies ◽  
High Statistical Significance ◽  
The Difference

Recent advances in RNA studies show that the well-ordered, structured RNAs perform a broad functions in various biological mechanisms. Included among these functions are regulations of gene expression at multiple levels by diversified ribozymes and various RNA regulatory elements. The discovered microRNAs (miRNAs) with a distinct stem-loops are a new class of RNA regulatory elements. The prediction of those well-ordered folding sequences (WFS) associated with the RNA regulatory elements in genomic sequences is very helpful for our understandings of RNA-based gene regulations. We present here a new computational method in searching for the conserved WFS in genomes. In the method, the WFS is assessed by a quantitative measure E diff that is defined as the difference of free energies between the computed optimal structure (OS) and its corresponding optimal restrained structure where all the previous base pairings in the OS are forbidden. From those WFS with high E diff scores, the conserved WFS is determined by computing the maximal similarity score (MSS) between the two compared structures. In practice, we first search for those distinct WFS with high statistical significance in genomic sequences and then seek for those conserved WFS with high MSS. The potential and implications of our discoveries in the genome of Caenorhabditis elegans are discussed.

scholarly journals Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

2020 ◽  
Author(s):  
Jinan Wang ◽  
Yinglong Miao
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Protein Interactions ◽  
Peptide Binding ◽  
Computational Method ◽  
Enhanced Sampling ◽  
Free Energies ◽  
Accelerated Molecular Dynamics ◽  
High Flexibility ◽  
Binding Free Energies

AbstractPeptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method “Pep-GaMD”, which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 μs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics.Significance StatementWe have developed a new computational method “Pep-GaMD” for enhanced sampling of peptide-protein interactions based on the Gaussian accelerated molecular dynamics (GaMD) technique. Pep-GaMD works by selectively boosting the essential potential energy of the peptide to effectively model its high flexibility. In addition, another boost potential can be applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Dual-boost Pep-GaMD has captured repetitive peptide dissociation and binding events within significantly shorter simulation time (microsecond) than conventional molecular dynamics. Compared with previous enhanced sampling methods, Pep-GaMD is easier to use and more efficient for unconstrained enhanced sampling of peptide binding and unbinding, which provides a novel physics-based approach to calculating peptide binding free energies and kinetics.

scholarly journals Unlocking Phase Diagrams for Molybdenum and Tungsten Nanoclusters and Prediction of their Formation Constants

2021 ◽  
Author(s):  
Enric Petrus ◽  
Carles Bo
Keyword(s):  
Phase Diagrams ◽  
General Rule ◽  
Formation Constants ◽  
Computational Method ◽  
Reaction Networks ◽  
Free Energies ◽  
Computational Approaches ◽  
Chemical Equilibria ◽  
Gibbs Energies ◽  
And Tungsten

Understanding and controlling aqueous speciation of metal oxides are key for the discovery and development of novel materials, and challenge both experimental and computational approaches. Here we present a computational method, called POMSimulator, which is able to predict speciation phase diagrams (Conc. vs pH) for multi-species chemical equilibria in solution, and which we apply to molybdenum and tungsten isopolyoxoanions (IPAs). Starting from the MO4 monomers, and considering dimers, trimers, and larger species, the chemical reaction networks involved in the formation of [H32Mo36O128]8- and [W12O42]12- are sampled in an automatic manner. This information is used for setting up ~105 speciation models, and from there, we generate the speciation phase diagrams, which show an insightful picture of the behavior of IPAs in aqueous solution. Furthermore, we predict the values for 107 formation constants for a diversity of molybdenum and tungsten molecular oxides. Among these species, we could include several pentagonal shaped species and very reactive tungsten intermediates as well. Last but not least, the calibration employed for correcting the DFT Gibbs energies is remarkably similar for both metals, which suggests that a general rule might exist for correcting computed free energies for other metals.<br>

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