Statistical Approaches to Estimating the Relative Contribution of Intermolecular Interactions in Aliphatic Alcohols: Application to QSPR/QSAR Modeling of Their Boiling Points

2009 ◽  
Vol 4 (1) ◽  
Author(s):  
Mohamed Nohair ◽  
Noura Mallouk ◽  
Marouane Benmarzouk ◽  
El Morrakchi Mohssine
Keyword(s):  
Boiling Point ◽  
Intermolecular Forces ◽  
Aliphatic Alcohols ◽  
General Description ◽  
Back Propagation Algorithm ◽  
Qsar Modeling ◽  
Data Set ◽  
Relative Contribution ◽  
Boiling Points ◽  
Autocorrelation Method

A three-layer feed forward neural network trained with a Levenberg–Marquardt batch error back propagation algorithm has been used to model the strong relationships between the boiling point of aliphatic alcohols and intermolecular forces consisting both in Van Der Waals forces and polar interactions, respectively. For that purpose, we use the multifunctional autocorrelation method to provide an appropriate topological description. Two types of descriptors are generated: the first is commonly used in QSARs and QSPRs modelling, it gives a general description of the whole of the molecule; the second is attributed to the local description of the group hydroxyl. In this we have turned our interests to the explanatory capacities of our methodology to explore the relative contribution and/or the contribution profile of the input factors compared to the size of the molecule. The initial data set is divided into different subsets in increasing order of values of boiling point. Then, we explore the good descriptive ability of the molecular descriptors calculated solely from the modified autocorrelation method to carry out a variable analysis and give information about features of the compounds responsible for their boiling points. This is made possible by comparing the regression coefficients for the established linear model, and by using the Garson weight portioning method for the ANN analysis.

scholarly journals The influence of pressure on the boiling points of metals

1910 ◽  
Vol 83 (565) ◽  
pp. 483-491 ◽  
Keyword(s):  
Atmospheric Pressure ◽  
Boiling Point ◽  
High Vacuum ◽  
Similar Type ◽  
Exact Relation ◽  
Reduced Pressure ◽  
Boiling Points ◽  
Experimental Values ◽  
Low Pressures ◽  
Very High

Part I. — Pressures below 760 mm . In a previous communication (‘Proc.’, A, vol. 82, 1909, p. 396) the approximate boiling points of a number of metals were determined at atmospheric pressure. Apart from the question of finding the exact relation between the boiling point and pressure, it is an important criterion of any method for fixing the temperatures of ebullition to demonstrate that the experimental values obtained are dependent on the pressure. It is specially desirable when dealing with substances boiling at temperatures above 2000° to have some evidence that the points indicated are true boiling points. Previous work on the vaporisation of metals at different pressures has been confined to experiments in a very high vacuum except for metals like bismuth, cadmium, and zinc, which boil at relatively low temperatures under atmospheric pressure. The observations were limited to very low pressures on account of the difficulty of obtaining any material capable of withstanding a vacuum at temperatures over 1400° and the consequent necessity for keeping the boiling point below this limit by using very low pressures. Moreover in the case of the majority of the metals, e. g. , copper, tin, ebullition under reduced pressure has never been observed. The difficulties indicated above were avoided by using a similar type of apparatus to that previously described, and arranging the whole furnace inside a vacuum enclosure, thus permitting of the use of graphite crucibles to contain the metal.

Replication of Data Analyses

2017 ◽  
Author(s):  
Emery R. Boose ◽  
Barbara S. Lerner
Keyword(s):  
Original Work ◽  
Statistical Tests ◽  
Scientific Paper ◽  
Scientific Data ◽  
Data Sources ◽  
Narrative Form ◽  
Data Provenance ◽  
General Description ◽  
Data Set ◽  
Data Analyses

The metadata that describe how scientific data are created and analyzed are typically limited to a general description of data sources, software used, and statistical tests applied and are presented in narrative form in the methods section of a scientific paper or a data set description. Recognizing that such narratives are usually inadequate to support reproduction of the analysis of the original work, a growing number of journals now require that authors also publish their data. However, finer-scale metadata that describe exactly how individual items of data were created and transformed and the processes by which this was done are rarely provided, even though such metadata have great potential to improve data set reliability. This chapter focuses on the detailed process metadata, called “data provenance,” required to ensure reproducibility of analyses and reliable re-use of the data.

scholarly journals Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2322 ◽  
Author(s):  
Saw Simeon ◽  
Nuttapat Anuwongcharoen ◽  
Watshara Shoombuatong ◽  
Aijaz Ahmad Malik ◽  
Virapong Prachayasittikul ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Docking ◽  
Binding Pocket ◽  
Binding Energies ◽  
Acetylcholinesterase Inhibition ◽  
Qsar Modeling ◽  
Qsar Study ◽  
Data Set ◽  
Ache Inhibitors ◽  
Redundant Data

Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds13,5and28exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding,π–πstacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors.

Ensemble-Based Modeling of Chemical Compounds with Antimalarial Activity

2019 ◽  
Vol 19 (11) ◽  
pp. 957-969 ◽  
Author(s):  
Ana Yisel Caballero-Alfonso ◽  
Maykel Cruz-Monteagudo ◽  
Eduardo Tejera ◽  
Emilio Benfenati ◽  
Fernanda Borges ◽  
...  
Keyword(s):  
Genetic Algorithms ◽  
Computational Models ◽  
Antimalarial Activity ◽  
Majority Vote ◽  
Chemical Compounds ◽  
Quantitative Structure Activity Relationship ◽  
Qsar Modeling ◽  
Design Work ◽  
Data Set ◽  
Selection Of

Background: Malaria or Paludism is a tropical disease caused by parasites of the Plasmodium genre and transmitted to humans through the bite of infected mosquitos of the Anopheles genre. This pathology is considered one of the first causes of death in tropical countries and, despite several existing therapies, they have a high toxicity. Computational methods based on Quantitative Structure- Activity Relationship studies have been widely used in drug design work flows. Objective: The main goal of the current research is to develop computational models for the identification of antimalarial hit compounds. Materials and Methods: For this, a data set suitable for the modeling of the antimalarial activity of chemical compounds was compiled from the literature and subjected to a thorough curation process. In addition, the performance of a diverse set of ensemble-based classification methodologies was evaluated and one of these ensembles was selected as the most suitable for the identification of antimalarial hits based on its virtual screening performance. Data curation was conducted to minimize noise. Among the explored ensemble-based methods, the one combining Genetic Algorithms for the selection of the base classifiers and Majority Vote for their aggregation showed the best performance. Results: Our results also show that ensemble modeling is an effective strategy for the QSAR modeling of highly heterogeneous datasets in the discovery of potential antimalarial compounds. Conclusion: It was determined that the best performing ensembles were those that use Genetic Algorithms as a method of selection of base models and Majority Vote as the aggregation method.

scholarly journals II. On the critical state of gases

1880 ◽  
Vol 30 (200-205) ◽  
pp. 323-329 ◽  
Keyword(s):  
Critical Point ◽  
Critical Points ◽  
Critical State ◽  
Atmospheric Pressure ◽  
Boiling Point ◽  
Chemical Society ◽  
Boiling Points ◽  
Intermediate Condition ◽  
Specific Volumes

In a paper read before the Chemical Society, in May, 1879, I gave an account of a method of determining what is termed by Kopp the “specific volumes” of liquids; that was shown to be the volume of liquid at its boiling-point, at ordinary atmospheric pressure, obtainable from 22,326 volumes of its gas, supposed to exist at 0°. Being desirous of extending these researches, with the view of ascertaining such relations at higher temperatures, since April, 1879, I have made numerous experiments, the results of, and deductions from which I hope to publish before long. The temperatures observed vary from the boiling-points of the liquids examined, to about 50° above their critical points; and in course of these experiments I have noticed some curious facts, which may not be unworthy of the attention of the Society. It is well known that at temperatures above that which produces what is termed by Dr. Andrews the “critical point” of a liquid, the substance is supposed to exist in a peculiar condition, and Dr Andrews purposely abstained from speculating on the nature of the matter, whether it be liquid or gaseous, or in an intermediate condition, to which no name has been given. As my observations bear directly on this point, it may be advisable first to describe the experiments I have made, and then to draw the deductions which appear to follow from them.

scholarly journals On the effect of temperature on the viscosity of air

1927 ◽  
Vol 117 (776) ◽  
pp. 245-257 ◽  
Keyword(s):  
Temperature Control ◽  
Boiling Point ◽  
Atmospheric Temperature ◽  
Imperial College ◽  
Electrical Heating ◽  
Effect Of Temperature ◽  
Normal Boiling Point ◽  
Saturated Vapour ◽  
Boiling Points ◽  
Cast Doubt

It appeared that further experiments on the viscosity of air were desirable in order to discriminate between the results of F. A. Williams* and those of most previous observers, and to test his conclusion respecting the validity of Sutherland’s law of the variation of viscosity with temperature. It happened that this could be done easily and expeditiously in the laboratories of the Imperial College. Mr. R. S. Edwards, the author of the following paper, was in the midst of preparations for determining the viscosity of neon at a number of temperatures ranging from atmospheric temperature to the normal boiling point of sulphur, and at my suggestion diverted his attention to the behaviour of air at the same temperatures. It is true that this range (about 430 centi­grade degrees) is not so extensive as the thousand degrees covered by Williams’ experiments, but it includes all that region in which, according to Williams, the value of Sutherland’s constant displays the large increase upon which I have cast doubt. Edwards’ method of temperature control and estimation involves heating by the saturated vapour of selected substances of well-established boiling points, and would appear to be more reliable than the electrical heating, and particularly the temperature measurement by a single thermocouple, as employed by Williams. In the present experiments also, considerable variations of the pressure conditions have been made, with consistent results, thus proving the validity of the transpiration formula assumed. No such internal evidence of accuracy was provided in Williams’ experiments.

scholarly journals XVI. On the relation between boiling-point and composition organic compounds

1860 ◽  
Vol 150 ◽  
pp. 257-276 ◽  
Keyword(s):  
Chemical Composition ◽  
Organic Compounds ◽  
Boiling Point ◽  
Royal Society ◽  
Chemical Compounds ◽  
Molecular Volume ◽  
Isomeric Compound ◽  
Boiling Points ◽  
Constituent Elements ◽  
Further Development

The researches which I beg, in the following pages, to submit to the Royal Society, embody the results obtained in the further development of an observation which I made a considerable number of years ago, and which, since that time, I had to defend against the objections of others, both by experimental inquiries of my own, and by the collection and discussion of facts elicited in the investigations of other observers. As far back as 1841* I pointed out that in analogous compounds the same difference of composition frequently involves the same difference in boiling-points. The assertion of the existence of this law-like relation between the chemical composition of substances and one of their most important physical properties, when first enunciated, met rather with the opposition than with the assent of chemists. In Germany especially it was contested by Schröder in his memoir “On the Molecular Volume of Chemical Compounds.” These objections led me to collect additional evidence in favour of my views, and to show more particularly that in very extensive series of compounds (alcohols C n H n+2 O 2 ; acids C n H n O 4 ; compound ethers C n H n O 4 , &c.) an elementary difference x C 2 H 2 is attended by a difference of x X 19°C. in the boiling-points, and how this fact is intimately connected with other regularities exhibited by the boiling-points of organic compounds. Almost at the same period Schröder § convinced himself that the relation I had pointed out obtains in most cases. He collected himself a considerable number of illustrations of the regularities I had traced, and showed that the relation in question is rendered more especially conspicuous if the compounds be expressed by formulæ representing equal vapour-volumes of the several substances. Some of the views, however, which were peculiar to Schröder have not gained the approbation of chemists. This physicist was inclined to consider the boiling-point of a substance as the most essential criterion of its proximate constituents, as the most trustworthy indicator of its molecular consti­tution. His views were chiefly based upon the assumption that the elementary difference C 2 H 2 , when occurring in alcohols C n H n+2 O 2 , involved a difference of boiling-points other than that occasioned by the same elementary difference obtaining in acids C n H n O 4 and that the isomeric compound ethers differed from one another in their boiling-points. An extensive series of boiling-point determinations* which I made of these isomeric ethers, proved that the latter assumption is not founded on facts. The exertions made by Schröder, Gerhardt, Löwig and others, in the hope of recognizing the influence of the constituent elements on the boiling-point of a compound, have also essentially remained without result.

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