TURBOMOLE

Schafer A, Klamt A, Sattel D, Lohrenz JCW, Eckert F (2000) Cosmo implementation in turbomole Extension of an efficient quantum chemical code towards liquid systems. Phys Chem Chem Phys 2 2187-2193. 

Von Amim M, Ahlrichs R (1998) Performance of Parallel TURBOMOLE for Density Functional Calculations. J Comput Chem 19(15) 1746—1757. 

The CC2 method [74] is an approximation to coupled cluster with singles and doubles (CCSD), and the excited state energies calculated have MP2 quality. An implementation that employs the resolution of identity (RI) approximation for two-electron integrals to reduce the CPU time is also available, RI-CC2 [75], which is suitable for large scale integral-direct calculations. This method has been implemented in TURBOMOLE [76],... 

Ahlrichs R, Bar M, Haser M, Horn H, Kolmel C (1989) Electronic structure calculations on workstation computers The program system turbomole. Chem Phys Lett 162 165-169... 

The experimental peak energies of both fluorescence and absorption are in excellent agreement - Stokes shift in eV, 0.80 experimental and 0.83 (TD-DFT performed by package TURBOMOLE) (Ahlrichs et at. TURBOMOLE version 5.6 University of Karlsruhe Karlsruhe, Germany) with the theoretical values for compound 20 (Table 2) <2005PCB6004>. 

All quantum chemical calculations were performed with the TURBOMOLE suite of programs. 

Ahlrichs R, Bar M, Baron HP, Bauernschmitt R, Bocker S, Ehrig M, Eichkorn K, Elliott S, Furche F, Haase F, Haser M, Horn H, Huber C, Huniar U, Kattannek M, Kcilmel C, Kollwitz M, May K, Ochsenfeld C, Ohm H, Schafer A, Schneider U, Treut-ler O, von Arnim M, Weigend F, Weis F, Weiss H (2000) TURBOMOLE Version 5.3, Universitat Karlsruhe... 

Ahlrichs R, von Arnim M (1995) TURBOMOLE, parallel implementation of SCF, density functional, and chemical shift modules. In dementi E, Corongiu G (eds) Methods and techniques in computational chemistry. STEF, Cagliary Eichkorn K, Treutler O, Ohm H, Haser M, Ahlrichs R (1995) Chem Phys Lett 242 652 Becke AD (1988) Phys Rev A 38 3098 Perdew JP (1986) Phys Rev B 33 8822 Garrou PE (1985) Chem Rev 85 171 and references cited therein... 

M., Treutler, O., Unterreiner, B., von Arnim, M., Weigend, F., Weis, R, Weiss, H. turbomole, version 5.9. Universitat Karlsruhe, Karlsruhe, Germany, 2006. 

All of the systems were initially optimized using a much higher level of theory, in order to ensure that the OM2 method provides a realistic description of the structure. The method employed was the second-order Mpller-Plesset perturbation theory (MP2) [50] using the cc-pVDZ basis set [51]. The resolution-of-identity (RI) approximation for the evaluation of the electron-repulsion integrals implemented in Turbomole was utilized [52]. 

All electron calculations were carried out with the DFT program suite Turbomole (152,153). The clusters were treated as open-shell systems in the unrestricted Kohn-Sham framework. For the calculations we used the Becke-Perdew exchange-correlation functional dubbed BP86 (154,155) and the hybrid B3LYP functional (156,157). For BP86 we invoked the resolution-of-the-iden-tity (RI) approximation as implemented in Turbomole. For all atoms included in our models we employed Ahlrichs valence triple-C TZVP basis set with polarization functions on all atoms (158). If not noted otherwise, initial guess orbitals were obtained by extended Hiickel theory. Local spin analyses were performed with our local Turbomole version, where either Lowdin (131) or Mulliken (132) pseudo-projection operators were employed. Broken-symmetry determinants were obtained with our restrained optimization tool (136). Pictures of molecular structures were created with Pymol (159). 

Anyway, the first step toward any receptor-based COSMO-RS calculations is the calculation of qualitatively acceptable er-profiles of the receptor regions of enzymes. In a performance test of a highly parallel version of the TURBOMOLE program on the supercomputer at the Research Center Jiilich [141], we could show that TURBOMOLE presently can handle single point, i.e., fixed geometry, BP-SVP DFT-calculations of enzymes up to about 1,500 atoms. On the basis of preliminary data, an enzyme of 1,000 atoms requires about 6 CPU h on 32 CPUs of a supercomputer cluster with a minimum quadratic scaling of CPU-time with the number of atoms of the enzymes. Thus for medium-sized enzymes we would require a minimum of 600 h on such a supercomputer, which would be rather expensive, even if all the technical problems arising at these molecule sizes would be solved. Therefore, brute-force DFT calculations appear to be unfeasible at present, but they may be possible in the future. 

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