Supporting Information s67

SUPPORTING INFORMATION

Journal of Molecular Modeling

Conformational Analysis of Piperazine and Piperidine Analogs of GBR 12909: Stochastic Approach to Evaluation of the Effect of Force Field and Solvent

Deepangi Pandit1,2, William Roosma3, Milind Misra1,4, Kathleen M. Gilbert1, William J. Skawinski1, and Carol A. Venanzi1, *

1Department of Chemistry and Environmental Science, New Jersey Institute of Technology, 323 King Blvd., Newark, NJ 07102

2BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, NJ

3Department of Computer Science, New Jersey Institute of Technology, 323 King Blvd., Newark, NJ 07102

4Present address: Multiscale Dynamic Materials Modeling Department, Sandia National Laboratories, Albuquerque, NM 87185-1413

*Corresponding author: Carol A. Venanzi, Department of Chemistry and Environmental Science, New Jersey Institute of Technology, 323 King Blvd., Newark, NJ 07102

Phone: (973) 596-3596; Fax: (973) 596-3596; E-mail:

Analog 2 (Tripos, vacuum) / Analog 2 (Tripos, solvent)
Analog 3 (Tripos, vacuum) / Analog 3 (Tripos, solvent)
Analog 2 (MMFF94, vacuum) / Analog 2 (MMFF94, solvent)
Analog 3 (MMFF94, vacuum) / Analog 3 (MMFF94, solvent)

Fig. S1 Local minima of 2 and 3 in (B2, B3) space. Torsional angles are given in degrees. Minima are color coded by energy in units of kcal/mol. GEM marked by circle. Plot symbols: pink diamond: 0 – 4, green box: 4 – 8, blue triangle: 8 – 12, yellow box: 12 – 16, red box: 16 – 20.

Fig. S2 Local minima of 2 and 3 in (B3, B4) space. Torsional angles are given in degrees. Minima are color coded by energy in units of kcal/mol. GEM marked by circle. Plot symbols: pink diamond: 0 – 4, green box: 4 – 8, blue triangle: 8 – 12, yellow box: 12 – 16, red box: 16 – 20.

Fig. S3 Local minima of 2 and 3 in (B4, B6) space. Torsional angles are given in degrees. Minima are color coded by energy in units of kcal/mol. GEM marked by circle. Plot symbols: pink diamond: 0 – 4, green box: 4 – 8, blue triangle: 8 – 12, yellow box: 12 – 16, red box: 16 – 20. The GEM structure appears twice due to the symmetry of the molecule to rotation of the phenyl ring around the B6 torsional angle.

Fig. S4 Local minima of 2 and 3 in (B5, B6) space. Torsional angles are given in degrees. Minima are color coded by energy in units of kcal/mol. GEM marked by circle. Plot symbols: pink diamond: 0 – 4, green box: 4 – 8, blue triangle: 8 – 12, yellow box: 12 – 16, red box: 16 – 20. The GEM structure appears four times due to the symmetry of the molecule to rotation of the phenyl ring around the B5 and B6 torsional angle.