Molecular volumes

Gel permeation chromatography, exclusion chromatography. gel filtration chromatography. A technique for separating the components of a mixture according to molecular volume differences. A porous solid phase (a polymer, molecular sieve) is used which can physically entrap small molecules in the pores whilst large molecules pass down the column more rapidly. A solvent pressure up to 1000 psi may be used. 

A quite different means for the experimental determination of surface excess quantities is ellipsometry. The technique is discussed in Section IV-3D, and it is sufficient to note here that the method allows the calculation of the thickness of an adsorbed film from the ellipticity produced in light reflected from the film covered surface. If this thickness, t, is known, F may be calculated from the relationship F = t/V, where V is the molecular volume. This last may be estimated either from molecular models or from the bulk liquid density. 

This observation that the length of the hydrocarbon chain could be varied from 16 to 26 carbon atoms without affecting the limiting area could only mean that at this point the molecules were oriented vertically. From the molecular weight and density of palmitic acid, one computes a molecular volume of 495 A a molecule occupying only 21 A on the surface could then be about 4.5 A on the side but must be about 23 A long. In this way one begins to obtain information about the shape and orientation as well as the size of molecules. 

If the two constituting molecular volumes are identical in a two component system, we can obtain [37, 38]... 

Solvent-excluded surfaces correlate with the molecular or Connolly surfaces (there is some confusion in the literature). The definition simply proceeds from another point of view. In this c ase, one assumes to be inside a molecaile and examines how the molecule secs the surrounding solvent molecules. The surface where the probe sphere does not intersect the molecular volume is determined. Thus, the SES embodies the solvent-excluded volume, which is the sum of the van der Waals volume and the interstitial (re-entrant) volume (Figures 2-119. 2-120). 

The molecular electronic polarizability is one of the most important descriptors used in QSPR models. Paradoxically, although it is an electronic property, it is often easier to calculate the polarizability by an additive method (see Section 7.1) than quantum mechanically. Ah-initio and DFT methods need very large basis sets before they give accurate polarizabilities. Accurate molecular polarizabilities are available from semi-empirical MO calculations very easily using a modified version of a simple variational technique proposed by Rivail and co-workers [41]. The molecular electronic polarizability correlates quite strongly with the molecular volume, although there are many cases where both descriptors are useful in QSPR models. 

An extensive series of studies for the prediction of aqueous solubility has been reported in the literature, as summarized by Lipinski et al. [15] and jorgensen and Duffy [16]. These methods can be categorized into three types 1 correlation of solubility with experimentally determined physicochemical properties such as melting point and molecular volume 2) estimation of solubility by group contribution methods and 3) correlation of solubility with descriptors derived from the molecular structure by computational methods. The third approach has been proven to be particularly successful for the prediction of solubility because it does not need experimental descriptors and can therefore be applied to collections of virtual compounds also. 

A drawback of the SCRF method is its use of a spherical cavity molecules are rarely exac spherical in shape. However, a spherical representation can be a reasonable first apprc mation to the shape of many molecules. It is also possible to use an ellipsoidal cavity t may be a more appropriate shape for some molecules. For both the spherical and ellipsoi cavities analytical expressions for the first and second derivatives of the energy can derived, so enabling geometry optimisations to be performed efficiently. For these cavil it is necessary to define their size. In the case of a spherical cavity a value for the rad can be calculated from the molecular volume ... 

Tlie molecular volume Vm can in turn be obtained by dividing the molecular weight by density or from refractivity measurements is Avogadro s number. The cavity radius (... 

Molecular volume, surface area, polar surface 3D structure Polar surface area is the... 

Molecular volumes are usually computed by a nonquantum mechanical method, which integrates the area inside a van der Waals or Connolly surface of some sort. Alternatively, molecular volume can be determined by choosing an isosurface of the electron density and determining the volume inside of that surface. Thus, one could find the isosurface that contains a certain percentage of the electron density. These properties are important due to their relationship to certain applications, such as determining whether a molecule will fit in the active site of an enzyme, predicting liquid densities, and determining the cavity size for solvation calculations. 

The solvent-excluded volume is a molecular volume calculation that finds the volume of space which a given solvent cannot reach. This is done by determining the surface created by running a spherical probe over a hard sphere model of molecule. The size of the probe sphere is based on the size of the solvent molecule. 

The development of group additivity methods is very similar to the development of a QSPR method. Group additivity methods can be useful for properties that are additive by nature, such as the molecular volume. For most properties, QSPR is superior to group additivity techniques. 

Those involving solution nonideality. This is the most serious approximation in polymer applications. As we have already seen, the large differences in molecular volume between polymeric solutes and low molecular weight solvents is a source of nonideality even for athermal mixtures. 

Expressed in these units, a resembles a molecular volume hence a has units of length and is thus a length which characterizes the interaction between a molecule and the field. In view of this, it may be true that = f(a /X), since all we can say about Q is that it is dimensionless. 

In very small pores the molecules never escape from the force field of the pore wall even at the center of the pore. In this situation the concepts of monolayer and multilayer sorption become blurred and it is more useful to consider adsorption simply as pore filling. The molecular volume in the adsorbed phase is similar to that of the saturated Hquid sorbate, so a rough estimate of the saturation capacity can be obtained simply from the quotient of the specific micropore volume and the molar volume of the saturated Hquid. 

Steps 3 and 4, however, can be described as chemical plasticization since the rate at which these processes occur depends on the chemical properties of molecular polarity, molecular volume, and molecular weight. An overall mechanism of plasticizer action must give adequate explanations for this as weU as the physical plasticization steps. 

G. Le Bas, The Molecular Volumes of Liquid Chemical Compounds, Longmans, Gieen, New York, 1915. 

Subscript i identifies species, and J is a dummy index all summations are over all species. Note that Xp however, when i = J, then Xu = = 1. In these equations / (a relative molecular volume) and (a relative molecular surface area) are pure-species parameters. The influence of temperature on g enters through the interaction parameters Xp of Eq. (4-261), which are temperature dependent ... 

The interaction forces which account for the value of a in this equation arise from tire size, the molecular vibration frequencies and dipole moments of the molecules. The factor b is only related to the molecular volumes. The molar volume of a gas at one atmosphere pressure is 22.414 ImoD at 273 K, and this volume increases according to Gay-Lussac s law with increasing... 

Here Q is the charge delivered by the anode, V(H2) is the measured hydrogen volume and V(H2) its molecular volume under the same test conditions. 

Significant progress in the optimization of VDW parameters was associated with the development of the OPLS force field [53]. In those efforts the approach of using Monte Carlo calculations on pure solvents to compute heats of vaporization and molecular volumes and then using that information to refine the VDW parameters was first developed and applied. Subsequently, developers of other force fields have used this same approach for optimization of biomolecular force fields [20,21]. Van der Waals parameters may also be optimized based on calculated heats of sublimation of crystals [68], as has been done for the optimization of some of the VDW parameters in the nucleic acid bases [18]. Alternative approaches to optimizing VDW parameters have been based primarily on the use of QM data. Quantum mechanical data contains detailed information on the electron distribution around a molecule, which, in principle, should be useful for the optimization of VDW... 

Carbon Hydrogen Heat of vaporization Molecular volume... 

The essential feature of the AAA is a comparison of active and inactive molecules. A commonly accepted hypothesis to explain the lack of activity of inactive molecules that possess the pharmacophoric conformation is that their molecular volume, when presenting the pharmacophore, exceeds the receptor excluded volume. This additional volume apparently is filled by the receptor and is unavailable for ligand binding this volume is termed the receptor essential volume [3]. Following this approach, the density maps for each of the inactive compounds (in their pharm conformations superimposed with that of active compounds) were constructed the difference between the combined inactive compound density maps and the receptor excluded volume represents the receptor essential volume. These receptor-mapping techniques supplied detailed topographical data that allowed a steric model of the D[ receptor site to be proposed. 

Richards, EM. Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115 440-464, 1985. 

It is seen that if the diffusivity is to be correlated with the molecular weight, then a knowledge of the density of the solute is also necessary. The result of the correlation of the reciprocal of the diffusivity of the 69 different compounds to the product of the cube root of the molecular volume and the square root of the molecular weight is shown in Figure 1. A summary of the errors involved is shown in Figures 2 and 3... 

When values for the relative molecular volumes and areas are not available for the molecules of interest, they may be constructed from group contributions. 

F = Function of the molecular volume of the solute. Correlations for this parameter are given in Figure 7 as a function of the parameter (j), which is an empirical constant that depends on the solvent characteristics. As points of reference for water, (j) = 1.0 for methanol, (j) = 0.82 and for benzene, (j) = 0.70. The two-film theory is convenient for describing gas-liquid mass transfer where the pollutant solute is considered to be continuously diffusing through the gas and liquid films. 

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