Structural Classification of Complex Molecules by Artificial Intelligence Techniques

Algorithms for classification and taxonomy bases on criteria, e.g., information entropy. The feasibility of replacing a given molecule by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using structural properties. In taxonomy the detailed comparison of the sequences of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree. The method is applied to the classifications of (1) indazolols (against Trichomonas vaginalis), (2) fullerenes and fullerite, (3) living and heat-inactivated lactic acid bacteria against cytokines, (4) phylogenesis of avian birds and 1918 influenza virus, (…

Fullerite crystal thermodynamic characteristics and the law of corresponding states.

The existence of single-wall carbon nanotubes in organic solvents in the form of clusters is discussed. A theory is developed based on a bundlet model, which enables describing the cluster-size distribution function. Comparison of calculated solubilities with experiments would permit obtaining energetic parameters, characterizing the interaction of a nanotube with its surrounding. Fullerenes and nanotubes are objects whose behaviour in many physical situations is characterized by peculiarities, which show up in that these systems represent the only soluble forms of carbon, what is related to their molecular structures. The fullerene molecule is a virtually uniform closed spherical-spheroida…

Effect of packing on the cluster nature of C nanotubes: An information entropy analysis

The possibility of the existence of single-wall carbon nanotubes (SWNTs) in organic solvents in the form of clusters is discussed. A theory is developed based on a bundlet model for clusters, which enables describing the distribution function of clusters by size. Comparison of the calculated values of solubility with experiments would permit obtaining energetic parameters characterizing the interaction of an SWNT with its surrounding, in a solid or solution. Fullerenes and SWNTs are unique objects, whose behaviour in many physical situations is characterized by remarkable peculiarities. Peculiarities in solutions show up first in that fullerenes and SWNTs represent the only soluble forms of…

Experimental Studies for Modelling the Phase Behaviour of Monomer/Polymer/Disc Composites

Nanoparticles do not stabilize the mixtures of epoxy monomer (prepolymer)/thermoplastic modifier (PS) and the ones of thermoplastic modifier dispersed within cured epoxy matrix. A small amount of thermoplastic co-polymer poly(styrene-b-methyl methacrylate) [P(S-b-MMA)] of MMA 4-22 wt.%, mixed with PS, makes compatible the mixtures with monomer epoxy precursor and cured epoxy matrix. The mixtures of cured epoxy matrix with thermoplastic consisting of PS and P(S-b-MMA), with nanofil 1%, are stable: the instability produced by the nanofil is overcome by the stability provided by the co-polymer. A model by Balazs' group to explain the phase behaviour of polymer/clay composites is extended.

Comparative analysis of the electrostatics of the binding of cationic proteins to vesicles: Asymmetric location of anionic phospholipids

The role of electrostatics is studied in the adsorption of cationic proteins to zwitterionic phosphatidylcholine (PC) and anionic PC/phosphatidylglycerol (PG) mixed small unilamellarvesicles (SUVs). For model proteins the interaction is monitored vs. PG content at low ionic strength. The adsorption of lysozyme and myoglobin (isoelectric point, pl 7-11) is investigated in SUVs, along with changes of the fluorescence emission spectra of the cationic proteins, via their adsorption on SUVs. In the Gouy-Chapman formalism, the activity coefficient goes with the square of charge number. Deviations from the ideal model could indicate the asymmetric location of the anionic phospholipid in the bilaye…

Molecular Classification of Pesticides Including Persistent Organic Pollutants, Phenylurea and Sulphonylurea Herbicides

Pesticide residues in wine were analyzed by liquid chromatography–tandem mass spectrometry. Retentions are modelled by structure–property relationships. Bioplastic evolution is an evolutionary perspective conjugating effect of acquired characters and evolutionary indeterminacy–morphological determination–natural selection principles; its application to design co-ordination index barely improves correlations. Fractal dimensions and partition coefficient differentiate pesticides. Classification algorithms are based on information entropy and its production. Pesticides allow a structural classification by nonplanarity, and number of O, S, N and Cl atoms and cycles; different behaviours depend …

Ideas in the History of Nano/Miniaturization and (Quantum) Simulators: Feynman, Education and Research Reorientation in Translational Science

Cultural history of nanominiaturization, computing, quantum computing and simulating is necessary to comprehend human character and place it in the whole of living beings. Ideas in the history of physics by Feynman, etc. are valued by the questions that generate. A series of questions, answers and hypothesis introduces the nature of the history of nanominiaturization, providing facts. Nanotechnology adds a third dimension to the periodic table of the elements. Thinking about computers was useful. It must do with learning computers possibilities and physics potential. Provisional conclusions follow. (1) Nature (space–time) is not classical but discrete; quantization is a different kind of ma…

Graphene and Fullenene Clusters

Interacting induced-dipoles polarization in code POLAR permits calculating molecular polarizability, which is tested with endohedral metallofullerenes Scn@Cm and clusters Cn (fullerene, graphene, GR). Polarizability identifies aggregates with dissimilar numbers of atoms and separates isomers. Results are of the same order of magnitude as reference computations performed with code PAPID. Polarizability bulk limit is estimated from Clausius–Mossotti relationship. Polarizability trend for clusters vs. size is unexpected: they are more polarizable than bulk. Theory yielded the same for small Sin, Gen and GanAsm; however, experiment oppositely deferred for larger Sin, GanAsm and GenTem. Smaller …

Information entropy-based classification of triterpenoids and steroids from Ganoderma

Abstract A set of 71 triterpenoid and steroid compounds from Ganoderma were periodically classified using a procedure based on information entropy with artificial intelligence. Six features were used in hierarchical order to classify the triterpenoids and steroids structurally. The phytochemicals belonging to the same group in the periodic table present similar antioxidant activity, and those compounds belonging to the same period exhibit maximum resemblance. The periodic classification is related to the experimental bioactivity and antioxidant potency data that are available in the literature: a steroid with a three-ketone group conjugated with two carbon–carbon double bonds in the right s…

Polyphenolic Phytochemicals in Cancer Prevention and Therapy: Bioavailability versus Bioefficacy

Natural polyphenols are organic chemicals which contain phenol units in their structures. They show antitumor properties. However, a key problem is their short half-life and low bioavailability under in vivo conditions. Still, definitively demonstrating the human benefits of isolated polyphenolic compounds (alone or in combination) using modern scientific methodology has proved challenging. The most common discrepancy between experimental and clinical observations is the use of nonphysiologically relevant concentrations of polyphenols in mechanistic studies. Thus, it remains highly controversial how applicable underlying mechanisms are with bioavailable concentrations and biological half-li…

QSPR Prediction of Retention Times of Methylxanthines and Cotinine by Bioplastic Evolution

High-performance liquid-chromatographic retention times of methylxanthines and cotinine in human plasma and urine are modelled by structure–property relationships. Bioplastic evolution is an evolutionary perspective conjugating the effect of acquired characters, and relations that emerge among the principles of evolutionary indeterminacy, morphological determination and natural selection. It is applied to design co-ordination index, which is used to characterize retentions of methylxanthines, etc. Parameters used to calculate co-ordination index are formation enthalpy, molecular weight and surface area. Morphological and co-ordination indices provide strong correlations. Effect of different…

Sesquiterpene lactones from Artemisia herba-alba

Abstract The aerial parts of Artemisia herba-alba subsp. valentine yielded, in addition to known compounds, a new germacranolide, six new eudesmanolides and ilicic acid methyl ester.

Molecular Classification of 5-Amino-2-Aroylquinolines and 4-Aroyl-6,7,8-Trimethoxyquinolines as Highly Potent Tubulin Polymerization Inhibitors

Algorithms for classification and taxonomy are proposed based on criteria as information entropy and its production. It is classified a series of 5-amino-2-aroylquinolines (AAQs) and 4-aroyl-6,7,8-trimethoxyquinolines (TMQs) combretastatin analogues for anti-cancer activity. 5-Amino-6-methoxy-2-aroylquinoline AAQ showed anti-proliferative activity more potent as compared to combretastatin A-4 (CA4), against various human cancer cell lines and a multidrug resistance (MDR) cancer cell line. On the basis of AAQ/TMQ structure–activity relationship new derivatives are designed. The AAQs/TMQs are classified using nine characteristic chemical properties in molecules. Many classification algorithms…

Classification of flavonoid compounds by using entropy of information theory

A total of 74 flavonoid compounds are classified into a periodic table by using an algorithm based on the entropy of information theory. Seven features in hierarchical order are used to classify structurally the flavonoids. From these features, the first three mark the group or column, while the last four are used to indicate the row or period in a table of periodic classification. Those flavonoids in the same group and period are suggested to show maximum similarity in properties. Furthermore, those with only the same group will present moderate similarity. In this report, the flavonoid compounds in the table, whose experimental data in bioactivity and antioxidant properties have been prev…

Computational Study of Nanosized Drug Delivery from Cyclodextrins, Crown Ethers and Hyaluronan in Pharmaceutical Formulations

Abstract The problem in this work is the computational characterization of cyclodextrins, crown ethers and hyaluronan (HA) as hosts of inclusion complexes for nanosized drug delivery vehicles in pharmaceutical formulations. The difficulty is addressed through a computational study of some thermodynamic, geometric and topological properties of the hosts. The calculated properties of oligosaccharides of D-glucopyranoses allow these to act as co-solvents of polyanions in water. In crown ethers, the central channel is computed. Mucoadhesive polymer HA in formulations releases drugs in mucosas. Geometric, topological and fractal analyses are carried out with code TOPO. Reference calculations are…

QSPR prediction of retention times of phenylurea herbicides by biological plastic evolution.

A simple/sensitive high-performance liquid chromatographic method, with ultraviolet (UV) detection, was developed for phenylurea-herbicide analysis, which involves preconcentration using solid-phase extraction. Mobile phase was acetonitrile/water at flow-rate of 1 mL.min-1 with direct UV absorbance detection at 210 nm. Analyte separation studied on a C18 column was applied successfully to herbicide analysis in soft drink's brands and tap water. Good linearity/repeatability was observed for all pesticides. Retention times increase as: metoxuron < monuron < diuron < matazachlor < linuron. They are modelled by structure-property relations. The effect of different types of features is analyzed:…

Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors

Algorithms for classification and taxonomy are proposed in this chapter based information entropy (IE) and its production. The 38  N- aryloxazolidinone-5-carboxamides (NCAs), for human immunodeficiency virus (HIV) protease (PR) inhibition, are classified using seven characteristic chemical properties of different moieties: R 1/2 , R 3–6 on different phenyls and R 7 . Many classification algorithms are based on IE. When applying some procedures to moderate-sized sets, excessive number of results appear compatible with the data and suffer combinatorial explosion. However, after the equipartition conjecture (EC), one has a selection criterion among different variants that results from classifi…

A NEW TOOL FOR THE STUDY OF RESONANCE IN CHEMICAL EDUCATION

The objective of this study is to present a computer-based project, for which our program POLAR and our version of PAPID were written for the study of the subject of resonance in chemistry. Both algorithms allow a better didactic strategy and methodological adaptation for the study of molecular properties in chemical education. Teachers will find the options of POLAR and PAPID useful for demonstrations. It is still to be explored the methodological application of these computational programs enriching the present teaching techniques. Implementing new algorithms in learning situations is technically simple, but checking their usefulness in teaching practice is extraordinarily complex and req…

Using Chemical Structural Indicators for Periodic Classification of Local Anaesthetics

Algorithms for classification and taxonomy based on criteria as information entropy and its production are proposed. Some local anaesthetics, currently in use, are classified using five characteristic chemical properties of different portions of their molecules. Many classification algorithms are based on information entropy. When applying the procedures to sets of moderate size, an excessive number of results appear compatible with data and the number suffers a combinatorial explosion. However, after the equipartition conjecture one has a selection criterion between different variants resulting from classification between hierarchical trees. Information entropy and principal component anal…

Revealing the relationship between vegetable oil composition and oxidative stability: A multifactorial approach

Abstract A detailed composition analysis was performed for 22 diverse oils and fats and included determination of tocopherols (α, γ and δ), β-carotene, chlorophyll, total phenolic compounds (TPC) and fatty acid (FA) composition, as well as the determination of their oxidative stability (Rancimat test). Principal components analysis was applied to obtain an overview of the sample variations and to identify behavioural patterns. Linear regression correlations and a multiple linear regression model were performed to quantify the relationship between the composition of oils and fats and their oxidative stability. The TPC and saturated FA were the main individual factors that correlated positive…

Cooperativity of Protein Binding to Vesicles

Electrostatics role is studied in protein adsorption to phosphatidylcholine (PC) and PC/phosphatidylglycerol (PG) small unilamellar vesicles (SUVs). Protein interaction is monitored vs. PG content at low ionic strength. Adsorption of lysozyme, myoglobin and bovine serum albumin (BSA) isoelectric point (pI) is investigated in SUVs, along with changes in protein fluorescence emission spectra. Partition coefficients and cooperativity parameters are calculated. At pI, binding is maximum while at lower/higher pHs binding drops. In Gouy–Chapman model activity coefficient goes with square charge number, which deviations indicate asymmetric location of anionic lipid in the bilayer inner leaflet, in…

Nanostructures Cluster Models in Solution

The existence of Single-Wall C-Nanocones (SWNCs), especially nanohorns (SWNHs), and BC2N/Boron Nitride (BN) analogues in cluster form is discussed in solution in this chapter. Theories are developed based on models bundlet and droplet describing size-distribution function. The phenomena present unified explanation in bundlet in which free energy of (BC2N/BN-)SWNCs involved in cluster is combined from two parts: volume one proportional to the number of molecules n in cluster and surface one, to n1/2. Bundlet enables describing distribution function of (BC2N/BN-)SWNC clusters by size. From geometrical differences bundlet [(BC2N/BN-)SWNCs] and droplet (C60/B15C30N15/B30N30) predict dissimilar …

Hyperconjugative Control by Remote Substituents of Diastereoselectivity in the Oxygenation of Hydrocarbons.

The oxidation of 2-substituted adamantanes (2) with TFDO (1) is reported. The data show a stereodifferentiation of the chemical environments induced by remote electron-withdrawing substituents which produces remarkable Z/E diastereoselectivity in the oxidation of the tertiary C(5)-H and C(7)-H bonds. The results show a bell-shaped correlation between the Z/E stereoselectivity and the substituent constant sigma(I), which is interpreted in terms of hyperconjugative stabilization of the diastereomeric transition states.

Multiple Linear Regression to predict larvicidal activity against &lt;em&gt;Aedes aegypti &lt;/em&gt;mosquito

Vector-borne diseases are one of the important health problems in most tropical countries. Aedes aegypti is an important vector for transmission of dengue, yellow fever, chikungunya, arthritis, and Zika fever. According to the World Health Organization, it is estimated that Ae. aegypti causes 50 million infections and 25,000 deaths per year. The emerging scenario highlights that the eco-friendly and effective control measures for mosquito vectors is of crucial importance. One of the most effective vector control measures has been the use of larvicidal compounds however; this success was short lived due to development of resistance against them in many mosquito strains, ecological imbalance …

Complexity, Emergence and Molecular Diversity via Information Theory

Numerous definitions for complexity have been proposed with little consensus. The definition here is related to Kolmogorov complexity and Shannon entropy measures. However, the price is to introduce context dependence into the definition of complexity. Such context dependence is an inherent property of complexity. Scientists are uncomfortable with such context dependence that smacks of subjectivity, which is the reason why little agreement is found on the meaning of the terms. In an article published in Molecules, Lin presented a novel approach for assessing molecular diversity based on Shannon information theory. A set of compounds is viewed as a static collection of microstates that can r…

Oxyfunctionalization of Aliphatic Esters by Methyl(trifluoromethyl)dioxirane

The oxidation of lineal, cyclic, and bicyclic aliphatic p-chlorobenzoic and p-chorobenzenesulfonic acid esters 2 with methyl(trifluoromethyl)dioxirane (TFDO) (1) occurs at positions in the hydrocarbon chain distant from the directing group with a significant degree of selectivity to give the corresponding keto or hydroxy esters. Compounds 2 are relatively deactivated with respect to this oxidation due to the electron-withdrawing nature of the ester moiety. Methylene Cα−H and Cβ−H bonds remain unchanged in all cases, but tertiary Cβ−H bonds undergo oxidation with TFDO (1). Stereoelectronic factors are used to explain the faster reaction rate in competition experiments for the oxidation of en…

Cluster Origin of Solvent Features of Fullerenes, Single-Wall Carbon Nanotubes, Nanocones, and Nanohorns

This chapter discusses the existence of single-wall carbon nanocones (SWNCs), especially nanohorns (SWNHs) in organic solvents in the form of clusters. A theory is developed based on a bundlet model describing their distribution function by size. Phenomena have a unified explanation in bundlet model in which free energy of an SWNC, involved in a cluster, is combined from two components: a volume one, proportional to number of molecules n in a cluster, and a surface one proportional to n1/2. A bundlet model enables describing distribution function of SWNC clusters by size. From purely geometrical differences, bundlet (SWNCs) and droplet (fullerene) models predict different behaviours. The SW…

Eine allgemeine und effiziente Methode zur Monohydroxylierung von Alkanen

Negatively cooperative binding of melittin to neutral phospholipid vesicles

Abstract The association of basic amphipathic peptides to neutral phospholipid membranes is investigated in terms of binding and partition models. The binding of native and modified melittin to egg-yolk phosphatidylcholine vesicles is studied by steady-state fluorescence spectroscopy. The effect of the ionic strength shows an enhancement of the association as the ionic strength increases. After correction for electrostatic effects by the Gouy–Chapman theory, the melittin binding isotherms could be described by a partition model. In terms of conventional binding mechanisms, which do not take into account electrostatic effects, this would correspond to a negative cooperativity. A plausible wa…

Bundlet Model of Single- Wall Carbon, BC2N and BN Nanotubes, Cones and Horns in Organic Solvents

Bundlet Model of Single- Wall Carbon, BC2N and BN Nanotubes, Cones and Horns in Organic Solvents The existence of Single-wall C-nanocones (SWNCs), especially nanohorns (SWNHs) and BC2N/Boron Nitride (BN) analogues is discussed in organic solvents in cluster form. A theory is developed based on the bundlet model, describing distribution function by size. The phenomena present unified explanation in the model, in which free energy of (BC2N/BN )SWNCs involved in cluster, is combined from two components: volume one proportional to the number of molecules n in cluster and surface one, to n1/2. The model enables describing distribution function of (BC2N/BN )SWNC clusters by size. From geometrical…

Information Theoretic Entropy for Molecular Classification: Oxadiazolamines as Potential Therapeutic Agents

In this review we present algorithms for classification and taxonomy based on information entropy, followed by structure-activity relationship (SAR) models for the inhibition of human prostate carcinoma cell line DU-145 by 26 derivatives of N-aryl-N-(3-aryl-1,2,4-oxadiazol-5-yl)amines (NNAs). The NNAs are classified using two characteristic chemical properties based on different regions of the molecules. A table of periodic properties of inhibitors of DU-145 human prostate carcinoma cell line is obtained based on structural features from the amine moiety and from the oxadiazole ring. Inhibitors in the same group and period of the periodic table are predicted to have highly similar propertie…

Quantitative Structure-Antioxidant Activity Models of Isoflavonoids: A Theoretical Study

Seventeen isoflavonoids from isoflavone, isoflavanone and isoflavan classes are selected from Dalbergia parviflora. The ChEMBL database is representative from these molecules, most of which result highly drug-like. Binary rules appear risky for the selection of compounds with high antioxidant capacity in complementary xanthine/xanthine oxidase, ORAC, and DPPH model assays. Isoflavonoid structure-activity analysis shows the most important properties (log P, log D, pKa, QED, PSA, NH + OH ≈ HBD, N + O ≈ HBA). Some descriptors (PSA, HBD) are detected as more important than others (size measure Mw, HBA). Linear and nonlinear models of antioxidant potency are obtained. Weak nonlinear relationship…

Cluster nature of the solvent features of single-wall carbon nanohorns

The existence of single-wall carbon nanotubes (SWNTs) in organic solvents, in the form of clusters, is discussed. A theory is developed based on a bundlet model for clusters, describing the distribution function of clusters by size. The phenomena have a unified explanation in the bundlet model of clusters, in accordance with which the free energy of an SWNT, involved in a cluster, is combined from two components: a volume one, proportional to the number of molecules n in a cluster, and a surface one proportional to n1/2. The bundlet model for clusters enables describing the distribution function of SWNT clusters by size. The droplet model is formally analogous to the one for fullerene clust…

QSAR of Natural Sesquiterpene Lactones as Inhibitors of Myb-dependent Gene Expression

Background Protein c-Myb is a therapeutic target. Some sesquiterpene lactones suppress Myb-dependent gene expression, which results in their potential anti-cancer activity. Material & methods Database ChEMBL is a representative of lactones for physicochemical and physiochemical properties. Data presented for 31 natural lactones are discussed in terms of quantitative structureactivity relationships with the objective to predict inhibitors of Myb-induced gene expression. Several constitutional descriptors are related to structure-activity. α-Methylene-γ-lactone groups enhance while OH functions worsen potency. The latter feature is in agreement with the fact that the more lipophilic the lacto…

Fractal Dimension of Transdermal-Delivery Drug Models: 4-Alkylanilines

Abstract The pathways that exist in porous membranes used to deliver drugs form fractal percolating paths. For a homologous series of 4-alkylanilines, the fractal dimension D is calculated as a model for transdermal-delivery drugs. Program TOPO is used for the calculation of the solvent-accessible surface AS, which is denoted by the centre of a probe, which is allowed to roll on the outside while maintaining contact with the bare molecular surface S. AS depends on the probe radius R. For 4-alkylanilines, the quadrupole moment Θ is doubled. The hydrophobic contribution to AS is doubled while its hydrophilic part remains constant. D increases 11%. Geometric descriptor and topological index re…

Elementary Polarizability of Sc/Fullerene/Graphene Aggregates and Di/Graphene–Cation Interactions

Elementary Polarizability of Sc/Fullerene/Graphene Aggregates and Di/Graphene–Cation Interactions Interacting induced-dipoles polarization in code POLAR allows molecular polarizability, which is tested with Scn/Cn [fullerene/ graphene (GR)]/Scn@Cm clusters. Polarizability sees clusters of unlike sizes, parting isomers. Bulk limit is estimated from Clausius– Mossotti relation. Clusters are more polarizable than the bulk. Theory yielded this for small Sin/Gen/GanAsm; however, experiment, reversely for larger Sin/GanAsm/GenTem. Smaller clusters need not act like middle: surface dangling bonds cause small-clusters polarizability that resembles metallic. Code AMYR models GR(2)– Mz+. A 24-atom pl…

(Co-)solvent selection for single-wall carbon nanotubes: best solvents, acids, superacids and guest-host inclusion complexes.

Analysis of 1-octanol-water, cyclohexane-water and chloroform (CHCl(3))-water partition coefficients P(o-ch-cf) allows calculation of molecular lipophilicity patterns, which show that for a given atom log P(o-ch-cf) is sensitive to the presence of functional groups. Program CDHI does not properly differentiate between non-equivalent atoms. The most abundant single-wall carbon nanotube (SWNT), (10,10), presents a relatively small aqueous solubility and large elementary polarizability, P(o-ch-cf) and kinetic stability. The SWNT solubility is studied in various solvents, finding a class of non-hydrogen-bonding Lewis bases with good solubility. Solvents group into three classes. The SWNTs in so…

Table of periodic properties of human immunodeficiency virus inhibitors

Classification algorithms are proposed based on information entropy. The feasibility of mixing a given human immunodeficiency virus (HIV) inhibitor with dissimilar ones is studied. The 31 inhibitors are classified by their structural chemical properties. Many classification algorithms are based on information entropy. An excessive number of results appear compatible with the data and suffer combinatorial explosion. However, after the equipartition conjecture one has a selection criterion. According to this conjecture, the best configuration is that in which entropy production is most uniformly distributed. The structural elements of an inhibitor can be ranked according to their inhibitory a…

Classification of stilbenoid compounds by entropy of artificial intelligence

A set of 66 stilbenoid compounds is classified into a system of periodic properties by using a procedure based on artificial intelligence, information entropy theory. Eight characteristics in hierarchical order are used to classify structurally the stilbenoids. The former five features mark the group or column while the latter three are used to indicate the row or period in the table of periodic classification. Those stilbenoids in the same group are suggested to present similar properties. Furthermore, compounds also in the same period will show maximum resemblance. In this report, the stilbenoids in the table are related to experimental data of bioactivity and antioxidant properties avail…

Cluster Origin of Solvation Features of C-Nanostructures in Organic Solvents

The existence of fullerenes, Single-Wall Carbon Nanocones (SWNCs), especially Nanohorns (SWNHs), Single-Wall Carbon Nanotube (SWNT) (CNT) (NT), NT-Fullerene Bud (NT-BUD), Nanographene (GR) and GR-Fullerene Bud (GR-BUD) in cluster form is discussed in organic solvents. Theories are developed based on columnlet, bundlet and droplet models describing size-distribution functions. The phenomena present a unified explanation in the columnlet model in which free energy of cluster-involved GR comes from its volume, proportional to number of molecules n in cluster. Columnlet model enables describing distribution function of GR stacks by size. From geometrical considerations, columnlet (GR/GR-BUD), b…

&lt;strong&gt;Artemisinin: Tentative Mechanism of Action and Resistance&lt;/strong&gt;

The sesquiterpene lactones constitute a large class of secondary plant metabolites, which carry a‑methylene‑g‑lactone groups as common structural element and display a number of bioactivities. Every year, 1–2 million people living in the tropics and subtropics die of malaria. Lactone artemisinin is the most effective treatment vs. malaria, the most infectious disease in the world today. Artemisinins are derived from extracts of sweet wormwood (Artemisia annua) and are well established for the treatment of malaria, e.g., highly drug-resistant strains. They resulted in one of the most significant advances in the treatment of malaria since the discovery and first use of quinine over 300 years …

Reflections on the Nature of the Periodic Table of the Elements: Implications in Chemical Education

The periodic table of the elements (PTE) results essential to understand our nature and place in the whole of beings. The same happens with our food, drugs, materials, etc. A series of questions were asked to introduce PTE and provide answers. The ideas in PTE should be valued by the number of questions that they generate. The PTE was related to electron configurations. The emergence of elements (nucleosynthesis) in physics was explained. The PTE results essential to understand our nature and place in the whole of beings. The same happens with our food, drugs, materials, etc. Schwarz and Rich asked a series of questions (Qs) to introduce PTE and provided answers. The ideas on PTE should be …

A General and Efficient Method for the Monohydroxylation of Alkanes

Structure-Activity Relationships of Cytotoxic Lactones as Inhibitors and Mechanisms of Action.

Background: Some lactones prevent protein Myb-dependent gene expression. Objective: The object is to calculate inhibitors of Myb-brought genetic manifestation. Methods: Linear quantitative structure–potency relations result expanded, among sesquiterpene lactones of a variety of macrocycles (pseudoguaianolides, guaianolides, eudesmanolides and germacranolides), to establish which part of the molecule constitutes their pharmacophore, and predict their inhibitory potency on Myb-reliant genetic manifestation, which may result helpful as leads for antileukaemic therapies with a new mechanism of action. Results: Several count indices are connected with structure–activity. The α-methylene-γ-lacto…

Bundlet Model for Single-Wall Carbon Nanotubes, Nanocones and Nanohorns

This paper discusses the existence of single-wall carbon nanocones (SWNCs), especially nanohorns (SWNHs), in organic solvents in the form of clusters. A theory is developed based on a bundlet model describing their distribution function by size. Phenomena have a unified explanation in bundlet model in which free energy of an SWNC, involved in a cluster, is combined from two components: a volume one, proportional to number of molecules n in a cluster, and a surface one proportional to n1/2. Bundlet model enables describing distribution function of SWNC clusters by size. From purely geometrical differences, bundlet (SWNCs) and droplet (fullerene) models predict different behaviours. The SWNCs…

Corrigendum to: “Solvent features of cluster single-wall C, BC2N and BN nanotubes, cones and horns” [Microelectron. Eng. 108 (2013) 127–133]

Periodic Classification of Local Anaesthetics (Procaine Analogues)

Algorithms for classification are proposed based on criteria (information entropyand its production). The feasibility of replacing a given anaesthetic by similar ones in thecomposition of a complex drug is studied. Some local anaesthetics currently in use areclassified using characteristic chemical properties of different portions of their molecules.Many classification algorithms are based on information entropy. When applying theseprocedures to sets of moderate size, an excessive number of results appear compatible withdata, and this number suffers a combinatorial explosion. However, after the equipartitionconjecture, one has a selection criterion between different variants resulting fromc…

Mucoadhesive Polymer Hyaluronan as Biodegradable Cationic/Zwitterionic-Drug Delivery Vehicle

Mucoadhesive polymers in pharmaceutical formulations release drugs in mucosal areas. They interact and fix to mucus via molecular interpenetration, etc ., which increase drug bioavailability. Polymers physicochemical properties affect formulation mucoadhesion, rheological behaviour and drug absorption. Hyaluronan (HA) is selected as a mucoadhesive and biodegradable polymer. Geometric, topological and fractal analyses are carried out with program TOPO. Reference calculations are performed with algorithm GEPOL. Procedure TOPO underestimates molecular volume by 0.7%. Error results 5% in surface area and derived topological indices. Solvent-accessible surface is undercalculated by 3%: from hexa…

QSPR prediction of chromatographic retention times of pesticides: Partition and fractal indices

The high-performance liquid-chromatographic retentions of red-wine pesticide residues are modeled by structure-property relationships. The effect of different types of features is analyzed: geometric, lipophilic, etc. The properties are fractal dimensions, partition coefficient, etc., in linear and nonlinear correlation models. Biological plastic evolution is an evolutionary perspective conjugating the effect of acquired characters and relations that emerge among the principles of evolutionary indeterminacy, morphological determination and natural selection. It is applied to design the co-ordination index that is used to characterize pesticide retentions. The parameters used to calculate th…

Cluster Origin of the Solubility of Single-Wall Carbon Nanotubes

The possibility of the existence of single-wall carbon nanotubes (SWNT) in organic solvents, in the form of clusters containing a number of SWNTs, is discussed. A theory is developed based on a bundletmodel for clusters, which enables describing the distribution function of clusters by size. Comparison of the calculated values of solubility with experimental data would permit obtaining energetic parameters characterizing the interaction of an SWNT with its surrounding in a solid phase or solution. Fullerenes and SWNTs are unique objects, whose behavior in many physical situations is characterized by remarkable peculiarities. Peculiarities in solutions show up in that fullerenes and SWNTs re…

USEDAT: USA-Europe Data Analysis Training Worldwide Program, 2019 ed.

USA-Europe Data Analysis Training School (USEDAT) is a Multi-center Trans-Atlantic initiative offering hands-on training focused in both Introduction to Experimental Data Recording (NMR, MS, IR, 2DGE, EEG, etc.) and/or posterior Computational Data Analysis (Machine Learning, Complex Networks, etc.). We made emphasis on applications in for Cheminformatics, Bioinformatics, Medicinal Chemistry, Nanotechnology, Systems Biology, Biomedical Engineering, etc. The school also promotes training and knowledge of ethical and legal regulatory issues (GDPR, REACH, OECD, FDA, etc.) about data use and data protection in chemistry and biomedical research. The school is directed to researchers and students …

Influence of Remote Substituents on the Equatorial/Axial Selectivity in the Monooxygenation of Methylene C−H Bonds of Substituted Cyclohexanes

The reactivity of individual C--H bonds in the methyl(trifluoromethyl)dioxirane TFDO oxygenation of stereogenic methylene groups in conformationally homogeneous monosubstituted cyclohexanes (2) has been determined. The unexpectedly high occurrence of O-atom insertion into C--H(ax) bonds suggests an in plane trajectory attack in the oxygenation while the diastereoselectivity of the reaction is qualitatively interpreted on the basis of the distinct hyperconjugative stabilization by the substituent of diastereomeric transition states due to long-range through bond interactions.

Improvement of charge-transfer indices for multifunctional amino acids: Application to lysozyme

Valence topological Charge-Transfer (CT) indices are applied to the calculation of pH at the isoelectric point (pI). The model is generalized for molecules with heteroatoms. The ability of the indices for the description of molecular charge distribution is established by comparing them with the pI of 21 amino acids. Linear correlation models are obtained. The CT indices improve multivariable regression equations for pI. The variance decreases by 95%. No superimposition of the corresponding G(k)-J(k) and G(k)(V)-J(k)(V) pairs is observed in most fits, which diminishes the risk of collinearity. The inclusion of heteroatoms in pi-electron system is beneficial for the description of pI, the bec…

Molecular Clustering of Phenylurea Herbicides: Comparison with Sulphonylureas, Pesticides and Persistent Organic Pollutants

Chromatographic retention times of phenylurea herbicides are modelled by structure–property relationships. Properties are hydration free energy and dipole. Bioplastic evolution is an evolutionary perspective conjugating the effect of acquired characters and relations that emerge among evolutionary indeterminacy, morphological determination and natural selection principles. Classification algorithms are proposed based on information entropy and production. Phenylureas are classified by Cl2, O2 and N2 presence; their different behaviour depends on the number of Cl atoms. When applying procedures to moderate-sized sets, excessive results appear compatible with data and suffer a combinatorial e…

Classification of Complex Molecules

Algorithms for classification and taxonomy based on criteria, e.g., information entropy and its production are proposed. In molecular classification, the feasibility of replacing a given molecule (e.g, anaesthetic) by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using characteristic chemical properties of different portions of their molecules. In taxonomy, the detailed comparison of the sequences (primary structures) of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree for some species, e.g. the 1918 influenza virus. The method is applied to the classifications of: (1) …

Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives

The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative.

Binding of water-soluble, globular proteins to anionic model membranes

Abstract The role of electrostatics is studied in the adsorption of proteins to negatively charged (phosphatidylcholine/phosphatidylglycerol, PC/PG) and neutral (PC) small unilamellar vesicles (SUVs). For model proteins the interaction is monitored vs . pH at low ionic strength. The adsorption behaviour of lysozyme, myoglobin and albumin (isoelectronic point, p I 5–11) is investigated in SUVs, along with changes of the fluorescence emission spectra of the charged proteins, via their adsorption on SUVs. Significant adsorption of the proteins to negatively charged SUVs is found only at pH values, where the number of positive charge moieties exceeds the number of negative charge moieties on th…

Classification of Congeneric and QSAR of Homologous Antileukemic S–Alkylcysteine Ketones

Based on a set of six vector properties, the partial correlation diagram is calculated for a set of 28 S-alkylcysteine diazomethyl- and chloromethyl-ketone derivatives. Those with the greatest antileukemic activity in the same class correspond to high partial correlations. A periodic classification is performed based on information entropy. The first four characteristics denote the group, and the last two indicate the period. Compounds in the same period and, especially, group present similar properties. The most active substances are situated at the bottom right. Nine classes are distinguished. The principal component analysis of the homologous compounds shows five subclasses included in t…