scholarly journals Group Contribution Revisited: The Enthalpy of Formation of Organic Compounds with “Chemical Accuracy”

2021 ◽  
Vol 5 (2) ◽  
pp. 24
Author(s):  
Robert J. Meier
Keyword(s):  
Process Design ◽  
Organic Molecules ◽  
Optimal Parameter ◽  
Heat Of Formation ◽  
Group Contribution ◽  
Data Set ◽  
Additional Group ◽  
Chemical Knowledge ◽  
Parameter Values ◽  
The Enthalpy Of Formation

Group contribution (GC) methods to predict thermochemical properties are of eminent importance to process design. Compared to previous works, we present an improved group contribution parametrization for the heat of formation of organic molecules exhibiting chemical accuracy, i.e., a maximum 1 kcal/mol (4.2 kJ/mol) difference between the experiment and model, while, at the same time, minimizing the number of parameters. The latter is extremely important as too many parameters lead to overfitting and, therewith, to more or less serious incorrect predictions for molecules that were not within the data set used for parametrization. Moreover, it was found to be important to explicitly account for common chemical knowledge, e.g., geminal effects or ring strain. The group-related parameters were determined step-wise: first, alkanes only, and then only one additional group in the next class of molecules. This ensures unique and optimal parameter values for each chemical group. All data will be made available, enabling other researchers to extend the set to other classes of molecules.

scholarly journals Group Contribution Revisited: The Enthalpy of Formation of Organic Compounds with “Chemical Accuracy” Part II

AppliedChem ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 111-129
Author(s):  
Robert J. Meier
Keyword(s):  
Process Design ◽  
Organic Molecules ◽  
Contemporary Literature ◽  
Heat Of Formation ◽  
Group Contribution ◽  
Thermochemical Properties ◽  
High Quality ◽  
Flexible Part ◽  
Torsional Angles ◽  
The Enthalpy Of Formation

Group contribution (GC) methods to predict thermochemical properties are eminently important to process design. We present a group contribution parametrization for the heat of formation of organic molecules exhibiting chemical accuracy, maximum 1 kcal/mol (4.2 kJ/mol) difference between experiment and model values while minimizing the number of parameters avoiding overfitting and therewith avoiding reduced predictability. Compared to the contemporary literature, this was successfully achieved by employing available literature high-quality and consistent experimental data, optimizing parameters group by group, and introducing additional parameters when chemical understanding was obtained supporting these. A further important result is the observation that the applicability of the group contribution approach breaks down with increasing substitution levels, i.e., more heavily alkyl-substituted molecules, the reason being a serious influence of substitution on the conformation of the flexible part of the entire molecule within particular valence angles and torsional angles affected, which cannot be accounted for by additional GC parameters with fixed numerical values.

scholarly journals Selecting single cell clustering parameter values using subsampling-based robustness metrics

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ryan B. Patterson-Cross ◽  
Ariel J. Levine ◽  
Vilas Menon
Keyword(s):  
Single Cell ◽  
Optimal Parameter ◽  
Clustering Algorithms ◽  
Cell Types ◽  
Parameter Selection ◽  
Data Set ◽  
Biologically Relevant ◽  
Cell Clustering ◽  
Parameter Values ◽  
Robustness Metrics

Abstract Background Generating and analysing single-cell data has become a widespread approach to examine tissue heterogeneity, and numerous algorithms exist for clustering these datasets to identify putative cell types with shared transcriptomic signatures. However, many of these clustering workflows rely on user-tuned parameter values, tailored to each dataset, to identify a set of biologically relevant clusters. Whereas users often develop their own intuition as to the optimal range of parameters for clustering on each data set, the lack of systematic approaches to identify this range can be daunting to new users of any given workflow. In addition, an optimal parameter set does not guarantee that all clusters are equally well-resolved, given the heterogeneity in transcriptomic signatures in most biological systems. Results Here, we illustrate a subsampling-based approach (chooseR) that simultaneously guides parameter selection and characterizes cluster robustness. Through bootstrapped iterative clustering across a range of parameters, chooseR was used to select parameter values for two distinct clustering workflows (Seurat and scVI). In each case, chooseR identified parameters that produced biologically relevant clusters from both well-characterized (human PBMC) and complex (mouse spinal cord) datasets. Moreover, it provided a simple “robustness score” for each of these clusters, facilitating the assessment of cluster quality. Conclusion chooseR is a simple, conceptually understandable tool that can be used flexibly across clustering algorithms, workflows, and datasets to guide clustering parameter selection and characterize cluster robustness.

scholarly journals A Computational Protocol Combining DFT and Cheminformatics for Prediction of pH-Dependent Redox Potentials

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3978
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Organic Molecules ◽  
Ph Value ◽  
Computational Cost ◽  
Legendre Transform ◽  
Good Prediction ◽  
Redox Potentials ◽  
Free Energies ◽  
Hybrid Functional ◽  
Data Set ◽  
State Changes

Discovering new materials for energy storage requires reliable and efficient protocols for predicting key properties of unknown compounds. In the context of the search for new organic electrolytes for redox flow batteries, we present and validate a robust procedure to calculate the redox potentials of organic molecules at any pH value, using widely available quantum chemistry and cheminformatics methods. Using a consistent experimental data set for validation, we explore and compare a few different methods for calculating reaction free energies, the treatment of solvation, and the effect of pH on redox potentials. We find that the B3LYP hybrid functional with the COSMO solvation method, in conjunction with thermal contributions evaluated from BLYP gas-phase harmonic frequencies, yields a good prediction of pH = 0 redox potentials at a moderate computational cost. To predict how the potentials are affected by pH, we propose an improved version of the Alberty-Legendre transform that allows the construction of a more realistic Pourbaix diagram by taking into account how the protonation state changes with pH.

scholarly journals Differential Transform Method as an Effective Tool for Investigating Fractional Dynamical Systems

2021 ◽  
Vol 11 (15) ◽  
pp. 6955
Author(s):  
Andrzej Rysak ◽  
Magdalena Gregorczyk
Keyword(s):  
Optimal Parameter ◽  
Differential Transform Method ◽  
Bifurcation Diagrams ◽  
Transform Method ◽  
Rossler System ◽  
Differential Transform ◽  
Rössler System ◽  
Fractional System ◽  
Parameter Values

This study investigates the use of the differential transform method (DTM) for integrating the Rössler system of the fractional order. Preliminary studies of the integer-order Rössler system, with reference to other well-established integration methods, made it possible to assess the quality of the method and to determine optimal parameter values that should be used when integrating a system with different dynamic characteristics. Bifurcation diagrams obtained for the Rössler fractional system show that, compared to the RK4 scheme-based integration, the DTM results are more resistant to changes in the fractionality of the system.

scholarly journals Optimal parameter selection in Weeks’ method for numerical Laplace transform inversion based on machine learning

2021 ◽  
Vol 15 ◽  
pp. 174830262199962
Author(s):  
Patrick O Kano ◽  
Moysey Brio ◽  
Jacob Bailey
Keyword(s):  
Laplace Transform ◽  
Optimal Parameter ◽  
Large Data ◽  
Matrix Exponential ◽  
Resolvent Matrix ◽  
Data Set ◽  
Network Training ◽  
The Matrix ◽  
The Laplace Transform ◽  
Space Function

The Weeks method for the numerical inversion of the Laplace transform utilizes a Möbius transformation which is parameterized by two real quantities, σ and b. Proper selection of these parameters depends highly on the Laplace space function F( s) and is generally a nontrivial task. In this paper, a convolutional neural network is trained to determine optimal values for these parameters for the specific case of the matrix exponential. The matrix exponential eA is estimated by numerically inverting the corresponding resolvent matrix [Formula: see text] via the Weeks method at [Formula: see text] pairs provided by the network. For illustration, classes of square real matrices of size three to six are studied. For these small matrices, the Cayley-Hamilton theorem and rational approximations can be utilized to obtain values to compare with the results from the network derived estimates. The network learned by minimizing the error of the matrix exponentials from the Weeks method over a large data set spanning [Formula: see text] pairs. Network training using the Jacobi identity as a metric was found to yield a self-contained approach that does not require a truth matrix exponential for comparison.

scholarly journals A Cybernetic Approach to Modeling Lipid Metabolism in Mammalian Cells

Processes ◽  
2018 ◽  
Vol 6 (8) ◽  
pp. 126 ◽  
Author(s):  
Lina Aboulmouna ◽  
Shakti Gupta ◽  
Mano Maurya ◽  
Frank DeVilbiss ◽  
Shankar Subramaniam ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Metabolic Regulation ◽  
Metabolic Flux ◽  
Optimal Parameter ◽  
Gene Knockout ◽  
Model Parameters ◽  
Mouse Bone Marrow ◽  
Optimization Approach ◽  
Substrate Uptake ◽  
Data Set

The goal-oriented control policies of cybernetic models have been used to predict metabolic phenomena such as the behavior of gene knockout strains, complex substrate uptake patterns, and dynamic metabolic flux distributions. Cybernetic theory builds on the principle that metabolic regulation is driven towards attaining goals that correspond to an organism’s survival or displaying a specific phenotype in response to a stimulus. Here, we have modeled the prostaglandin (PG) metabolism in mouse bone marrow derived macrophage (BMDM) cells stimulated by Kdo2-Lipid A (KLA) and adenosine triphosphate (ATP), using cybernetic control variables. Prostaglandins are a well characterized set of inflammatory lipids derived from arachidonic acid. The transcriptomic and lipidomic data for prostaglandin biosynthesis and conversion were obtained from the LIPID MAPS database. The model parameters were estimated using a two-step hybrid optimization approach. A genetic algorithm was used to determine the population of near optimal parameter values, and a generalized constrained non-linear optimization employing a gradient search method was used to further refine the parameters. We validated our model by predicting an independent data set, the prostaglandin response of KLA primed ATP stimulated BMDM cells. We show that the cybernetic model captures the complex regulation of PG metabolism and provides a reliable description of PG formation.

scholarly journals Monitoring Robust Estimates for Compositional Data

2021 ◽  
Vol 50 (2) ◽  
pp. 16-37
Author(s):  
Valentin Todorov
Keyword(s):  
Compositional Data ◽  
Real Life ◽  
R Package ◽  
Diagnostic Tools ◽  
Data Set ◽  
Mahalanobis Distances ◽  
Robust Estimates ◽  
Real Life Data ◽  
Manufactured Exports ◽  
Parameter Values

In a number of recent articles Riani, Cerioli, Atkinson and others advocate the technique of monitoring robust estimates computed over a range of key parameter values. Through this approach the diagnostic tools of choice can be tuned in such a way that highly robust estimators which are as efficient as possible are obtained. This approach is applicable to various robust multivariate estimates like S- and MM-estimates, MVE and MCD as well as to the Forward Search in whichmonitoring is part of the robust method. Key tool for detection of multivariate outliers and for monitoring of robust estimates is the Mahalanobis distances and statistics related to these distances. However, the results obtained with thistool in case of compositional data might be unrealistic since compositional data contain relative rather than absolute information and need to be transformed to the usual Euclidean geometry before the standard statistical tools can be applied. Various data transformations of compositional data have been introduced in the literature and theoretical results on the equivalence of the additive, the centered, and the isometric logratio transformation in the context of outlier identification exist. To illustrate the problem of monitoring compositional data and to demonstrate the usefulness of monitoring in this case we start with a simple example and then analyze a real life data set presenting the technologicalstructure of manufactured exports. The analysis is conducted with the R package fsdaR, which makes the analytical and graphical tools provided in the MATLAB FSDA library available for R users.

A numerical method for determining optimal parameter values in forced periodic operation

1992 ◽  
Vol 47 (3) ◽  
pp. 605-613 ◽  
Author(s):  
Fatih Özgülşen ◽  
Raymond A. Adomaitis ◽  
Ali Çinar
Keyword(s):  
Numerical Method ◽  
Optimal Parameter ◽  
Periodic Operation ◽  
Parameter Values

scholarly journals Modelling temperature variations in polar snow using DAISY

1997 ◽  
Vol 43 (143) ◽  
pp. 180-191 ◽  
Author(s):  
Ε. M. Morris ◽  
H. -P. Bader ◽  
P. Weilenmann
Keyword(s):  
Field Experiments ◽  
A Priori ◽  
Model Parameters ◽  
Data Set ◽  
International Geophysical Year ◽  
Snow Model ◽  
Using Data ◽  
Polar Snow ◽  
Parameter Values ◽  
The Antarctic

AbstractA physics-based snow model has been calibrated using data collected at Halley Bay, Antarctica, during the International Geophysical Year. Variations in snow temperature and density are well-simulated using values for the model parameters within the range reported from other polar field experiments. The effect of uncertainty in the parameter values on the accuracy of the predictions is no greater than the effect of instrumental error in the input data. Thus, this model can be used with parameters determined a priori rather than by optimization. The model has been validated using an independent data set from Halley Bay and then used to estimate 10 m temperatures on the Antarctic Peninsula plateau over the last half-century.

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