BOSS program

Born-Oppenheimer approximation, 1, 3, 54 Born-Oppenheimer (BO), 3, 156 BOSS program, 2, 264 boundary conditions, 1, 80... 

This work was supported by the National Science Foundation through grant CHE-0809199 to Auburn University. We thank Professor Jerzy Leszczynski of Jackson State University for optimized geometries of C96 and C144 and Professor Orlando Acevedo of Auburn University for advice on the use of the BOSS program. 

Results are presented here for halide ion - molecule complexes in the gas phase and for complexation of halide ions in solution by 1 and 2. The gas-phase interaction energies were obtained from energy minimizations and the relative binding affinities in solution were calculated with the free-energy perturbation (fep) method using Monte Carlo sampling. All calculations were carried out with the BOSS program. ... 

The calculations have been performed with version 3.1 of the BOSS program vhich permits sairpling for any designated bends, bond angles, and dihedral angles in the solutes. 0 The stretching and bending force... 

The focus in development of the OPLS-UA model was on the non-bonded parameters, which historically had been the most problematic, and the new approach was to perform large numbers of Monte Carlo statistical mechanics simulations of pure liquids for their refinement. This advance was made possible by increases in computer resources and the development of flexible, efficient software, namely, the BOSS program and its predecessors, that allowed rapid setup of simulations for new systems. The key point was that a principal application of such force fields was in condensed-phase simulations including protein dynamics, and testing of the force fields on prediction of well-characterized condensed-phase properties was needed. Minimally, reproduction of liquid densities and heats of vaporization provides some confidence in both the size of the molecules and the strengths of their intermolecular interactions. Furthermore, these quantities are obtained from both experiment and simulation with high precision. 

Command file for the BOSS program. Execute by entering the following ... 

The program can be used to generate time dependent displays of A, B and TR for input values of the effective proportional gain KC and set point temperature TSET, for initial conditions AO = BO = 0, T = TO at t = 0. 

Finally, the computer program EQUIL of Bos and Meershoek79 provides a rapid means of judging the accuracy of titrations in solvents with low e depending on estimated values of the equilibrium constants of the species possibly occurring in the solution80. 

The program of calculating the BO-level potentials from Schroedinger level cannot often be carried through with the accuracy required for the intermolecular forces in solution theory. (9.) Fortunately a great deal can be learned through the study of BO-level models in which the N-body potential is pairwise additive (as in Eq. (3)) and in which the pair potentials have very simple forms. (2, 3, 6) Thus for the hard sphere fluid we have, with a=sphere diameter,... 

Plot Bt/Bo vs t and calculate the maximal number of binding sites Bmax and the dissociation constant Kd using either a computer program (e.g., Prism) or a Scatchard plot (see Chap. 9.2). 

Real space algorithms (section 4) allow for mappings between present day computer programs and strict molecular quantum mechanics [10,11]. It is the separability of base molecular states that permits characterizing molecular states in electronic Hilbert space and molecular species in real space. This feature eliminates one of the shortcomings of the standard BO scheme [6,7,12]. Confining and asymptotic GED states are introduced. In section 5 the concept of conformation states in electronic Hilbert space is qualitatively presented. 

The organizing committee of the conference included W. M. Meier, general chairman J. B. Uytterhoeven, program chairman H. Sticher, P. K. Maher, and R. Peest. Mr. Peest resigned from the committee for professional reasons and was replaced by H. Berti. A committee of advisors assisted the program chairman and was composed of R. M. Barrer, V. Bos cek, D. W. Breck, L. Moscou, C. Naccache, L. V. C. Rees, J. V. Smith, P. B. Venuto, H. Villiger, and S. P. Zhdanov. The Swiss Federal Institute of Technology (ETH) in Zurich and the Swiss Chemical Society sponsored... 

Department of Health and Human Services (DHHS). 2001b. Program Memorandum Carriers, Transmittal B-01-40, Expanded Coverage of Diabetes Outpatient Self-Management Training June 15, 2001. Available at www.cms.hhs.gov/Transmittals/downloads/BO l40.pdf. 

The current composition of the AR TD program and its focus is summarized in Table 5. Here we indicate the various contractors and the study areas emphasized in the various projects. It can be seen that the principal focus of the program is on the major areas of concern related to synfuel combustion, viz NO emissions and soot formation. The program is balanced with bo h analytical and experimental studies, with the principal experimental activities taking place in bench-scale apparatus. Several of the studies will also include measurements performed in environments relative to industrial combustor and commercial-scale burners. 

Bos, M. and Meershoek, H. Q. J. A computer program for the calculation of equilibrium concentrations in complex systems, Anal. Chim. Acta 61, 185-194 Cl972). 

Another method of analysis makes use of a subtraction procedure and has been applied to investigate the oxidation state of a series of Ce-Zr mixed oxides during a temperature programmed process [195]. A difference spectrum between the sample at a defined state and the calcined, fully oxidized material displays a positive peak at the position of feature Bo, characteristic of Ce, and a negative peak at the position of feature C, characteristic of Ce. The overall peak-to-peak amplitude is then proportional to the average reduction degree of Ce in the sample. 

VDW VAN DER WAALS MODEL (S) + PRSV BOS VLE PROGRAM acetone-vrater temporary file at 100 C... 

Several programs have been written specifically for a very restricted class of equilibrium only problems. The Pit Method of Sillen and Warnquist has been widely used to solve for equilibrium constants in inorganic systems that have one or more simultaneous reversible reactions. DeLand uses goal-seeking routines to facilitate the matching of data, but free energy data for all reactants is required. Bos and Meershoek 24) have written a PL/1 program which uses the Newton-Raphson iteration to compute equilibrium constants in complex systems. 

However, let us revisit the plot of e, vs. x,- (Figure 3.3). There is reason to suspect that the linear regression model y = bo + biXi is not exact. Recall from Chapter 2 that we discussed both pure error and lack of fit in regression. Most statistical software programs have routines to compute these, or the computations can be done easily with the aid of a hand-held calculator. 

Eigen (A) values are connected to principal component analyses (found on most statistical software programs) and are derived fi-om the predictor x, variables in correlation matrix form. The bo parameter is usually ignored, because of centering and scaling the data. For example, the equation y = bo + biXi + b Xi + + b Xk is centered via the process of subtracting the mean from the actual values of each predictor variable, y, — y = f>i(x — Xi) + b ixi — X2) + + bkixi — Xjt), where bo = y The equation is next scaled, or standardized ... 

Studentized residuals usually are provided by standard statistical computer programs. As discussed earlier, these are termed Studentized residuals, because they approximate the Student s t distribution with n — k — 1 degrees of freedom, where k is the number of A,s in the data set, excluding bo- As noted in Equation 8.18 earlier, the Studentized residual value, S, , for multiple regression is ... 

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