First Principles pKa Calculations on Carboxylic Acids Using the SMD Solvation Model: Effect of Thermodynamic Cycle, Model Chemistry, and Explicit Solvent Molecules

2012 ◽  
Vol 116 (39) ◽  
pp. 11999-12006 ◽  
Author(s):  
Catherine C. R. Sutton ◽  
George V. Franks ◽  
Gabriel da Silva
Keyword(s):  
Carboxylic Acids ◽  
First Principles ◽  
Thermodynamic Cycle ◽  
Cycle Model ◽  
Solvation Model ◽  
Pka Calculations ◽  
Explicit Solvent ◽  
Solvent Molecules

scholarly journals Multi-Fidelity Simulation of a Turbofan Engine With Results Zoomed Into Mini-Maps for a Zero-D Cycle Simulation

2004 ◽  
Author(s):  
Mark G. Turner ◽  
John A. Reed ◽  
Robert Ryder ◽  
Joseph P. Veres
Keyword(s):  
Boundary Conditions ◽  
Fluid Dynamic ◽  
Thermodynamic Cycle ◽  
High Fidelity ◽  
Operating Characteristics ◽  
Cycle Model ◽  
Turbofan Engine ◽  
Engine Model ◽  
Cycle Simulation ◽  
Component Models

A Zero-D cycle simulation of the GE90-94B high bypass turbofan engine has been achieved utilizing mini-maps generated from a high-fidelity simulation. The simulation utilizes the Numerical Propulsion System Simulation (NPSS) thermodynamic cycle modeling system coupled to a high-fidelity full-engine model represented by a set of coupled 3D computational fluid dynamic (CFD) component models. Boundary conditions from the balanced, steady-state cycle model are used to define component boundary conditions in the full-engine model. Operating characteristics of the 3D component models are integrated into the cycle model via partial performance maps generated from the CFD flow solutions using one-dimensional meanline turbomachinery programs. This paper high-lights the generation of the highpressure compressor, booster, and fan partial performance maps, as well as turbine maps for the high pressure and low pressure turbine. These are actually “mini-maps” in the sense that they are developed only for a narrow operating range of the component. Results are compared between actual cycle data at a take-off condition and the comparable condition utilizing these mini-maps. The mini-maps are also presented with comparison to actual component data where possible.

scholarly journals Machine Learning Guided Approach for Studying Solvation Environments

2019 ◽  
Author(s):  
Yasemin Basdogan ◽  
Mitchell C. Groenenboom ◽  
Ethan Henderson ◽  
Sandip De ◽  
Susan Rempe ◽  
...  
Keyword(s):  
A Priori ◽  
Optimization Procedure ◽  
Low Energy ◽  
Free Energies ◽  
Continuum Approach ◽  
Explicit Solvent ◽  
Linear Dimensionality Reduction ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Solvation Free Energies

<div><div><div><p>Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics based cluster-continuum approach for calculating single ion solvation free energies. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs the Smooth Overlap for Atomic Positions (SOAP) kernel to quantify the similarity between different low energy solute environments. From these data, we use sketch-map, a non-linear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies with errors within five percent of experimental measurements for most cases.</p></div></div></div>

scholarly journals Explicit solvent models in protein pKa calculations

1996 ◽  
Vol 71 (1) ◽  
pp. 138-147 ◽  
Author(s):  
C.J. Gibas ◽  
S. Subramaniam
Keyword(s):  
Pka Calculations ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Protein Pka

scholarly journals Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

2021 ◽  
Author(s):  
Gantulga Norjmaa ◽  
Gregori Ujaque ◽  
Agustí Lledós
Keyword(s):  
Homogeneous Catalysis ◽  
Solvent Effects ◽  
Solvent Polarity ◽  
Quantum Mechanical ◽  
Solvent Models ◽  
Quantum Mechanical Description ◽  
Explicit Solvent ◽  
Solvent Dynamics ◽  
Solvent Molecules ◽  
Continuum Solvent Models

AbstractIn homogeneous catalysis solvent is an inherent part of the catalytic system. As such, it must be considered in the computational modeling. The most common approach to include solvent effects in quantum mechanical calculations is by means of continuum solvent models. When they are properly used, average solvent effects are efficiently captured, mainly those related with solvent polarity. However, neglecting atomistic description of solvent molecules has its limitations, and continuum solvent models all alone cannot be applied to whatever situation. In many cases, inclusion of explicit solvent molecules in the quantum mechanical description of the system is mandatory. The purpose of this article is to highlight through selected examples what are the reasons that urge to go beyond the continuum models to the employment of micro-solvated (cluster-continuum) of fully explicit solvent models, in this way setting the limits of continuum solvent models in computational homogeneous catalysis. These examples showcase that inclusion of solvent molecules in the calculation not only can improve the description of already known mechanisms but can yield new mechanistic views of a reaction. With the aim of systematizing the use of explicit solvent models, after discussing the success and limitations of continuum solvent models, issues related with solvent coordination and solvent dynamics, solvent effects in reactions involving small, charged species, as well as reactions in protic solvents and the role of solvent as reagent itself are successively considered.

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