Equilibrium files

The data files are ascii text files arranged in columns separated by space, tabs, or commas with header lines. Equilibrium files contain total ligand concentrations in the first column and free ligand concentrations in the second column. Initial velocity files contain substrate concentrations in the first column and initial velocities of duplicate assays in the subsequent columns. Progress curve files contain time in the first column and the measured experimental signal in the second column. 

Using MOPAC and the MNDO Hamiltonian, calculate the energy and equilibrium bond length of N2 to 4 significant figures. The input file is... 

Two Tq values are given for each MM+ bond, and rg . If rg is available (has a non-zero value in the parameter file) then it is used in preference to the normal for bonds where atom i and atom j have at least two hydrogen atoms directly attached to them. For example, CH2-CH2, CH2-CH3, or CH3-CH3 bonds may have their own equilibrium distance differentiated from the average single bond between carbon atoms. 

Red phosphorus is formed by heating white phosphorus. Calculate file temperature at which the two forms are at equilibrium, given... 

Chapter 5 introduces the equations that describe equilibrium between dissolved species of carbon in the ocean. The carbon system is central to so many aspects of ocean, atmosphere, and sedimentary rocks that I wish to make available a general method of solution. This chapter also introduces several housekeeping routines that I have found useful. Examples are routines to read files of specifications, including initial values, to write... 

Such information has been stored within a database in the ECES system. Then, using user input in the form of equation (1), ECES writes the expression for computing the thermodynamic equilibrium constant as a function of temperature to a file where it will eventually become part of a program to solve the many equilibria that might describe a complex system. 

CHEMRev The Comparison of Detailed Chemical Kinetic Mechanisms Forward Versus Reverse Rates with CHEMRev, Rolland, S. and Simmie, J. M. Int. J. Chem. Kinet. 37(3), 119-125 (2005). This program makes use of CHEMKIN input files and computes the reverse rate constant, kit), from the forward rate constant and the equilibrium constant at a specific temperature and the corresponding Arrhenius equation is statistically fitted, either over a user-supplied temperature range or, else over temperatures defined by the range of temperatures in the thermodynamic database for the relevant species. Refer to the website http //www.nuigalway.ie/chem/c3/software.htm for more information. 

EQUIL A.E. Lutz and F. Rupley, Sandia National Laboratories, Livermore, CA. A Fortran computer program (eqlib.f) for calculating chemical equilibrium using a modified solution procedure of STANJAN (stanlib.f, W.C. Reynolds, Stanford U.) and CHEMK1N data files for input. For the most recent versions, refer to the Reaction Design website http //www.reactiondesign.com/lobby/ open/index.html. 

There seems no doubt that Paracelsus discovered many facts which became of great importance in chemistry he prepared the inflammable gas we now call hydrogen, by the reaction between iron filings and oil of vitriol he distinguished metals from substances which had been classed with metals but lacked the essential metalline character of ductility he made medicinal preparations of mercury, lead and iron, and introduced many new and powerful drugs, notably laudanum. Paracelsus insisted that medicine is a branch of chemistry, and that the restoration of the body of a patient to a condition of chemical equilibrium is the restoration to health. 

We state, however, that at about COP a 2.0 Special Dirac sea hole current phenomena are encountered in close-looping, as a new kind of decay mechanism from the disequilibrium state back to the Lorentz equilibrium. Bedini and Bearden have filed a patent application for energy transduction processes to overcome this effect and allow close-looping. 

Besides the text output the postscript file marry dp. ps is generated (if the input file contained no line with the sequence name the filename defaults to dot. ps). The dot plot shows the pair probabilities within the equilibrium ensemble as an n x n matrix and is an excellent way to visualize structural alternatives (Figure 12.1). A square at row i and column j indicates a base pair. The area of a square in the upper right half of the matrix is proportional to the probability of the base pair (i, j) within the equilibrium ensemble. The lower left half shows all pairs belonging to the mfe structure. The matrix of a sequence with well-defined MFE structure should show only a few very small additional squares in the upper right half compared to the lower left half. 

PPDS2 National Engineering Laboratory (NEL, U.K.) thermodynamic and phase equilibrium data, provides a modeling system based on several groups of physical properties data (six files)... 

These considerable solvent-dependent shifts demonstrate that for molecules with such pronounced conformational ambiguity, the equilibration of conformations has to be taken into account in the calculation of thermodynamic phase-equilibrium data. In order to enable a consistent treatment, we have implemented an automated conformation equilibration scheme in COSMO therm. A compound X can be represented by a set of COSMO-files for the conformers, and a multiplicity ojx(i) can be assigned to each con-former based on geometrical degeneration aspects. Then the population of a conformer, i, in a solvent S is calculated as... 

The following example shows how this can be modeled in PHREEQC. First of all, a master- ami a solution species tritium T or T1 have to be defined. Since the input of data for log k und -gamma within the key word SOLUTION SPECIES is required, but unknown, any value can be entered here as a free parameter ( dummy , e g. 0.0). This value is not used for kinetic calculations and thus, does not cause any problems. However, all results based on equilibrium calculations (e.g. the calculation of the saturation index) are nonsense for this species . The tritium values have to be entered in tritium units. However, in order not to have to define or convert them in an extra step, they are entered fictitiously with the unit umol/kgw instead of TU in PHREEQC. As no interactions of tritium with any other species are defined, the unit is eventually irrelevant. After modeling, remember that the result is displayed in mol/kgw as always in PHREEQC and has to be recalculated to the fictitious tritium unit umol/kgw. Entering mol/kgw in the input file, the solution algorithm quits due to problems with too high total ionic strengths. 

The existing input file is extended by setting up equilibrium not only with pyrite but also with calcite. 2.621 mmol of calcite dissolve. The amount of pyrite dissolved is the same as in the absence of calcite (1.347 mmol). The pH value of 7.58 is in the neutral range. Thus, to neutralize the pH approximately 2 moles of calcite must be added for every mol of pyrite. The saturation index of gypsum is still clearly undersaturated (SI = -1.09), i.e. that gypsum is not a limiting mineral phase and hence the sulfate contents stay more or less invariable. 

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