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References and Theory

There are a number of different references that should be used when publishing data generated using DivCon's various functions and applications. These references also serve as excellent sources for a more theoretical explanation of the results. DivCon's primary output file includes a detailed rundown of the references required to adequately describe the parameters used in a simulation.

The primary references for all of DivCon include the following:

  • B. Wang, K. Raha, N. Liao, M. B. Peters, H. Kim, L. M. Westerhoff, A. M. Wollacott, A. van der Vaart, V. Gogonea, D. Suarez, S. L. Dixon, J. J. Vincent, E. N. Brothers and K. M. Merz Jr., DivCon, QuantumBio Inc., State College, PA 16803, 2005.
  • "Semiempirical Molecular Orbital Calculations with Linear System Size Scaling" S. L. Dixon; K. M. Merz, Jr. J. Chem. Phys. 1996, 104, 6643-6649.
  • "Fast, Accurate Semiempirical Molecular Orbital Calculations for Macromolecules" S. L. Dixon; K. M. Merz, Jr. J. Chem. Phys. 1997, 107, 879-893.
When using the solvation module, add the following reference:

  • "Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson-Boltzmann Equation" V. Gogonea; K. M. Merz, Jr. J. Phys. Chem. A. 1999, 103, 5171-5188.
When executing a pairwise energy decomposition calculation using the PWD module, add the following references:

  • A. van der Vaart, K. M. Merz, Jr., J. Phys. Chem. A. 103, 3321-3329 (1999)
  • K. Raha, A. Vaart, K. Riley, L. Westerhoff, H. Kim, and K. Merz, Jr., "Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction" J. Am. Chem. Soc. (2005) in press.
When using the NMR module, the following references are most pertinent:

  • B. Wang, E. N. Brothers, A. Vaart, and K. M. Merz Jr., J. Chem. Phys. 120, 11392-11400, (2004).
  • B. Wang, K. Raha, K. M. Merz Jr., J. Am. Chem. Soc., 126, 11430-11431 (2004).

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