Conformational analysis of methylphenidate: Comparison of molecular orbital and molecular mechanics methods

Kathleen M. Gilbert, William J. Skawinski, Milind Misra, Kristina A. Paris, Neelam H. Naik, Ronald A. Buono, Howard M. Deutsch, Carol A. Venanzi

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte > MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.

Original languageEnglish (US)
Pages (from-to)719-738
Number of pages20
JournalJournal of Computer-Aided Molecular Design
Issue number11
StatePublished - Nov 2004

All Science Journal Classification (ASJC) codes

  • Drug Discovery
  • Computer Science Applications
  • Physical and Theoretical Chemistry


  • AM1/SM5.4
  • Ab initio
  • Cocaine
  • Conformation alanalysis
  • Dopamine
  • Grid search
  • Hartree-Fock,Methylphenidate
  • Molecular mechanics
  • Molecular orbital
  • Random search
  • Solvation
  • Tripos force field


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