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    Introduction

    In the olden days, before the light of dawn, there was a man named Krüger.

    (Fonzé 1995)

    references (Hansson 1998) (Kollman 2000) (Mikulskis 2011)

    Computational Details

    All calculations were done in the Dalton(Aidas 2013) program.

    Theory

    The transition density matrix between the groundstate \(i\) and the excited state \(a\) is \[\rho^T_{J,ia}(r) = \rho^g_{J,i}(r) - \rho^e_{J,a}(r)\]

    The coupling between the excited state \(i\) on molecule \(I\) and excited state \(j\) on molecule \(J\) is \[V_{IJ} = \iint \mathrm{d}r \, \mathrm{d}r' \frac{\rho^T_{I,ia}(r)\rho^T_{J,jb}(r')}{|r-r'|}\]

    Potential Derived Charges

    Surfaces

    PCM Surface

    This surface is generated in [GAMESS][1] using the [FIXPVA][1] scheme. The surface consist of a single layer.

    `r = range(1.2, 4.2, 0.2)`
    

    Tests were carried out for two point densities

    • low: 60
    • medium: 240

    Kollman surface

    Better known in [Gaussian][2] as an MK surface. The surface consists of

    • 1 or 4 layers. The default is 4.
    • The first layer is scaled as

      rscal = range(1.4, 4.2, 0.2)

    • subsequent layers (if included) are scaled by 0.2 as

      rinc = range(0.0, 0.8, 0.2)

    The filename convention is

    `ff_i_j_k.mep`
    

    where

    • ff: filename
    • i: nlayers
    • j: rscal
    • k: rinc

    Mixed mode

    Test the use of evaluating the charges on chromophore A with a surface around the target, i.e. chromophore B.

    References

    1. E. Fonzé, P. Charlier, Y. To, M. Vermeire, X. Raquet, A. Dubus, J.-M. Frère. TEM1 \(\upbeta\)-lactamase structure solved by molecular replacement and refined structure of the S235A mutant. Acta Crystallogr D Biol Cryst Struct Commun 51, 682–694 (1995). Link

    2. Tomas Hansson, John Marelius, Johan . Journal of Computer-Aided Molecular Design 12, 27–35 (1998). Link

    3. Peter A. Kollman, Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, Oreola Donini, Piotr Cieplak, Jaysharee Srinivasan, David A. Case, Thomas E. Cheatham. Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models. Acc. Chem. Res. 33, 889–897 (2000). Link

    4. Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde. Binding affinities in the SAMPL3 trypsin and hostguest blind tests estimated with the MM/PBSA and LIE methods. Journal of Computer-Aided Molecular Design 26, 527–541 (2011). Link

    5. Kestutis Aidas, Celestino Angeli, Keld L. Bak, VebjBakken, Radovan Bast, Linus Boman, Ove Christiansen, Renzo Cimiraglia, Sonia Coriani, PDahle, Erik K. Dalskov, Ulf Ekström, Thomas Enevoldsen, Janus J. Eriksen, Patrick Ettenhuber, Berta Fernández, Lara Ferrighi, Heike Fliegl, Luca Frediani, Kasper Hald, Asger Halkier, Christof Hättig, Hanne Heiberg, Trygve Helgaker, Alf Christian Hennum, Hinne Hettema, Eirik Hjertenaes, Stinne H, Ida-Marie H, Maria Francesca Iozzi, Branislav Jans', Hans JAa. Jensen, Dan Jonsson, Poul J, Joanna Kauczor, Sheela Kirpekar, Thomas Kjaergaard, Wim Klopper, Stefan Knecht, Rika Kobayashi, Henrik Koch, Jacob Kongsted, Andreas Krapp, Kasper Kristensen, Andr