Descriptors environment

Perminova I, Grechishcheva N, Peterosyan V (1999) Relationships between structure and binding affinity of humic substances for polycyclic aromatic hydrocarbons relevance of molecular descriptors. Environ Sci Technol 33 3781-3787... 

Basak, S. C., Mills, D., El-Masri, H. A., Mumtaz, M. M., Hawkins, D. M. Predicting blood air partition coefficients using theoretical molecular descriptors. Environ. Toxicol. Pharmacol. 2004, 16, 45-55. 

Berger, B. and N.L. Wolfe. 1996. Hydrolysis and biodegradation of sulfonylurea herbicides in aqueous buffers and anaerobic water-sediment systems Assessing fate pathways using molecular descriptors. Environ. Toxicol Chem. 15 1599-1507. 

Schuurmann, G., QSAR analysis of the acute toxicity of organic phosphorothionates using theoretically derived molecular descriptors, Environ. Toxicol. Chem., 9, 417-428, 1990. 

Berger, B.M. and Wolfe, N.L. (1996). Hydrolysis and Biodegradation of Sulfonylurea Herbicides in Aqueous Buffers and Anaerobic Water-Sediment Systems. Assessing Fate Pathways Using Molecular Descriptors. Environ.Toxicol.Chem., 15,1500-1507. 

A particularly good selection of physical properties may be spectra, because they are known to depend strongly on the chemical structure. In fact, different types of spectra carry different kinds of structural information, NMR spectra characterize individual carbon atoms in their molecular environment. They therefore correspond quite closely to fragment-based descriptors, as underlined by the success of approaches to predict NMR spectra by fragment codes (see Section 10.2.3). 

An enhancement of the simple substructure approach is the Fragment Reduced to an Environment that is Limited (FREL) method introduced by Dubois et al. [7] With the FREL method several centers of the molecule are described, including their chemical environment. By taking the elements H, C, N, O, and halogens into account and combining all bond types (single, double, triple, aromatic), the authors found descriptors for 43 different FREL centers that can be used to characterize a molecule. 

A combination of physicochemical, topological, and geometric information is used to encode the environment of a proton, The geometric information is based on (local) proton radial distribution function (RDF) descriptors and characterizes the 3D environment of the proton. Counterpropagation neural networks established the relationship between protons and their h NMR chemical shifts (for details of neural networks, see Section 9,5). Four different types of protons were... 

The water-vapor transmission rate (WVTR) is another descriptor of barrier polymers. Strictly, it is not a permeabihty coefficient. The dimensions are quantity times thickness in the numerator and area times a time interval in the denominator. These dimensions do not have a pressure dimension in the denominator as does the permeabihty. Common commercial units for WVTR are (gmil)/(100 in. d). Table 2 contains conversion factors for several common units for WVTR. This text uses the preferred nmol/(m-s). The WVTR describes the rate that water molecules move through a film when one side has a humid environment and the other side is dry. The WVTR is a strong function of temperature because both the water content of the air and the permeabihty are direcdy related to temperature. Eor the WVTR to be useful, the water-vapor pressure difference for the value must be reported. Both these facts are recognized by specifying the relative humidity and temperature for the WVTR value. This enables the user to calculate the water-vapor pressure difference. Eor example, the common conditions are 90% relative humidity (rh) at 37.8°C, which means the pressure difference is 5.89 kPa (44 mm Hg). 

Kovatdieva A, Golbraikh A, Oloff S, Feng J, Zheng W, Tropsha A. QSAR modeling of datasets with enantioselective compounds using chirality sensitive molecular descriptors. SAR QSAR Environ Re. 2005 16(l-2) 93-102. 

Raevsky, O. A., Dearden, J. C. Creation of predictive models of aquatic toxicity of environmental pollutants with different mechanisms of action on the basis of molecular similarity and HYBOT descriptors. SAR QSAR Environ. Res. 2004, 15, 433-448. 

Lipophilicity represents the affinity of a molecule or a moiety for a lipophilic (= fat-loving) environment and is commonly measured by the partition coefficient, (where aaa represent a generic biphasic system, e.g. oct indicates the standard octanol-water). P is valid for a single electrical species, to be specified (P for neutral forms and P for ionized species). The distribution coefficient, expressed as is a pH-dependent descriptor (Eq. 3) for ionizable solutes and results from the weighted contributions of all electrical forms present at this pH ... 

Lipophilicity is intuitively felt to be a key parameter in predicting and interpreting permeability and thus the number of types of lipophilicity systems under study has grown enormously over the years to increase the chances of finding good mimics of biomembrane models. However, the relationship between lipophilicity descriptors and the membrane permeation process is not clear. Membrane permeation is due to two main components the partition rate constant between the lipid leaflet and the aqueous environment and the flip-flop rate constant between the two lipid leaflets in the bilayer [13]. Since the flip-flop is supposed to be rate limiting in the permeation process, permeation is determined by the partition coefficient between the lipid and the aqueous phase (which can easily be determined by log D) and the flip-flop rate constant, which may or may not depend on lipophilicity and if it does so depend, on which lipophilicity scale should it be based ... 

The major differences between behavior profiles of organic chemicals in the environment are attributable to their physical-chemical properties. The key properties are recognized as solubility in water, vapor pressure, the three partition coefficients between air, water and octanol, dissociation constant in water (when relevant) and susceptibility to degradation or transformation reactions. Other essential molecular descriptors are molar mass and molar volume, with properties such as critical temperature and pressure and molecular area being occasionally useful for specific purposes. A useful source of information and estimation methods on these properties is the handbook by Boethling and Mackay (2000). 

As required by (36), the variational parameter k is calculated to vary between k = 2 at R = 0 and k = 1 at R > 5ao- The parameter k is routinely interpreted as either a screening constant or an effective nuclear charge, as if it had real physical meaning. In fact, it is no more than a mathematical artefact, deliberately introduced to remedy the inadequacy of hydrogenic wave functions as descriptors of electrons in molecular environments. No such parameter occurs within the Burrau [84] scheme. 

Pollutants with high VP tend to concentrate more in the vapor phase as compared to soil or water. Therefore, VP is a key physicochemical property essential for the assessment of chemical distribution in the environment. This property is also used in the design of various chemical engineering processes [49]. Additionally, VP can be used for the estimation of other important physicochemical properties. For example, one can calculate Henry s law constant, soil sorption coefficient, and partition coefficient from VP and aqueous solubility. We were therefore interested to model this important physicochemical property using quantitative structure-property relationships (QSPRs) based on calculated molecular descriptors [27]. 

Gute, B. D., Basak, S. C. Predicting acute toxicity of benzene derivatives using theoretical molecular descriptors A hierarchical QSAR approach. SAR QSAR Environ. Res. 1997, 7, 117-131. 

The overall procedure is called MetaSite (site of metabolism prediction) [32]. The M IF calculations, pharmacophoric recognition, descriptor handling, similarity computation, reactivity computation, inhibition and subselectivity are calculated automatically once the ligand compound(s) is(are) provided. The complete calculation is performed in few seconds in IRIX Linux or Windows environments. 

Dubois et al. developed the Description, Acquisition, Retrieval, Computer-aided design-Elucidation by Progressive Intersection of Ordered Structures (DARC-EPIOS) system for structural elucidation.Their approach was based on C spectra. These were predicted using an additive method, but based on their DARC descriptor of environment, as opposed to the more common HOSE code. The EPIOS system was designed to take account of the diagnostic (or not) nature of the C spectrum with respect to environment, i.e., depending on the specific sub-structures. 

Geometry-based approach from a geometrical point of view, a cavity is a concave empty space that can be described using 2D (surface) or 3D shape descriptors (19-21). We consider three regions in the protein environment the protein bulk, the bulk solvent and the cavity space. The protein bulk is the space filled by the protein atoms. The bulk solvent is the space outside the protein which differentiates from the space inside the protein which defines the cavity where the drug-like molecule is supposed to bind. The identification of protein pockets by numerical methods suppose the capacity to discriminate first the protein bulk from the rest... 

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