Connolly method

Whereas the contact region is the basis in the Connolly method, the center of the solvent-sphere determines the shape of the molecular. surface in the SAS method. In this case, the resulting surface is larger and the transition between the different atoms is more significant. 

Feldmann and others have developed a series of teaching tools for macromolecular structure using color-coded molecular graphics-derived images 24 28). Connolly and others have improved upon this approach by clearly showing which portions of the protein surface are indeed accessible to a water molecule, as opposed to those portions which are inaccessible, such as in clefts, etc 27). Images based on the Connolly methods directly show those regions of the protein surface which can be expected to interact with other molecules. It provides immediate, comprehensible information about steric complimentarity. 

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 molecular HF-Xa method has been reviewed by Connolly, and you might like to see how it works for the H2O example. 

LA. Abrikosov, A.V. Ruban, B. Johansson, and H.L. Skriver, Total energy calculations of random alloys Connolly-Wiliams and CPA methods, in Stability of Materials , Series E Applied Sciences, A. Gonis, P.E.A. Turchi, and J. Kudrnovsky, ed., Kluwer Academic Publishers, the Netherlands (1996). 

Ab-initio studies of surface segregation in alloys are based on the Ising-type Hamiltonian, whose parameters are the effective cluster interactions (ECI). The ECIs for alloy surfaces can be determined by various methods, e.g., by the Connolly-Williams inversion scheme , or by the generalized perturbation method (GPM) . The GPM relies on the force theorem , according to which only the band term is mapped onto the Ising Hamiltonian in the bulk case. The case of macroscopically inhomogeneous systems, like disordered surfaces is more complex. The ECIs can be determined on two levels of sophistication ... 

Milnes, T. A., Connolly, J. S., Inman, R. E., Reed, T. B., and Seibert, M. Research Overview of Biological and Chemical Methods and Identification of Key Research Areas. SERI/TR-33-067, Solar Energy and Research Institute, Golden, CO. 1978. 61 p. 

I do not recall when I first heard of the Hohenberg-Kohn-Sham papers, but I do know that the quantum chemistry community at first paid little attention to them. In June of 1966 Lu Sham spoke about DFT at a Gordon Conference. But in those days, there was more discussion about another prescription that had been on the scene since 1951, the Slater Xa method. The Xa method was a well-defined, substantial improvement over the Thomas-Fermi method, a sensible approximation to exact Kohn-Sham. Debate over Xa went on for a number of years. Slater may never have recognized DFT as the major contribution to physics that it was. [When I asked John Connolly five or six years ago how he thought Slater had viewed DFT, he replied that he felt that Slater regarded it as obvious. ]... 

The Molecular Surface (MS) first introduced by Richards (19) was chosen as the 3D space where the MLP will be calculated. MS specifically refers to a molecular envelope accessible by a solvent molecule. Unlike the solvent accessible surface (20), which is defined by the center of a spherical probe as it is rolled over a molecule, the MS (19), or Connolly surface (21) is traced by the inwardfacing surface of the spherical probe (Fig. 2). The MS consists of three types of faces, namely contact, saddle, and concave reentrant, where the spherical probe touches molecule atoms at one, two, or three points, simultaneously. Calculation of molecular properties on the MS and integration of a function over the MS require a numerical representation of the MS as a manifold S(Mk, nk, dsk), where Mk, nk, dsk are, respectively, the coordinates, the normal vector, and the area of a small element of the MS. Among the published computational methods for a triangulated MS (22,23), the method proposed by Connolly (21,24) was used because it provides a numerical presentation of the MS as a collection of dot coordinates and outward normal vectors. In order to build the 3D-logP descriptor independent from the calculation parameters of the MS, the precision of the MS area computation was first estimated as a function of the point density and the probe radius parameters. When varying... 

J. W. D. Connolly, in Semiempirical Methods of Electronic Structure Calculation, Part A Techniques, edited by G. A. Segal (Plenum, New York, 1977),p. 105. 

McNeill, G. P. and Connolly, J. F. (1989). A method for quantification of individual free fatty acids in cheese Application to ripening of Cheddar type cheeses. Irish ]. Food Sci. Technol. 13, 119-128. 

Reviews (a) Connolly JWD (1977). In Segal GA (ed) Semiempirical methods of electronic structure calculations part A techniques. Plenum, New York, (b) Johnson KH (1973) Adv Quantum Chem 7 143... 

The package of Connolly, named MSDOT, is widely used in molecular modeling for visualization of molecules (especially in the field of biochemistry and molecular biology), ESP fitting, and docking but it has been rarely used in combination with continuum solvation methods [10]. In its modern formulation, the Connolly surface presents a full analytical tessellation [11] but the reliability of it and of its differentiability has never been tested with PCM-like calculations. 

Most of the methods discussed above have been used with milk but the majority can be applied to other products. Some minor variations in extraction procedures, such as the inclusion of anhydrous sodium sulphate to remove water (Deeth et al., 1983) or inclusion of an aqueous acid wash step to remove lactic acid (Chilliard et al., 1983) may be necessary. Collomb and Spahni (1995) suggested that the above International Dairy Federation reference method could be a universal method if the adaptations made by McNeill et al. (1986) for butter and McNeill and Connolly (1989) for cheese were incorporated. 

Bills et al. (1963) used pre-treated Amberlite resin dispersed in hexane to isolate FFAs from milk. Fat was removed from the resin using hexane, absolute ethanol and methanol and the FFAs were esterified prior to analysis by GC. Needs et al. (1983) extracted lipids from milk by using ether and the FFAs were isolated using a strong basic anion exchange resin (Amberlyst 26, BDH Ltd, Poole Dorset, UK). The FFAs were methylated and resolved by GC. McNeill et al. (1986) also used Amberlyst resin to isolate FFAs in conjunction with silicic acid to remove phospholipids. Extracted FFAs were then analyzed by GC. This method was used by McNeill and Connolly (1989) to quantify FFAs in a number of semi-hard cheeses. 

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