Atomic and Molecular Systems
Computational Methods
Molecular Properties

A variety of computational and visual tools for different atomic and molecular systems are presented here. This work is based on introductory chemistry classes and other training on the methods of computational approaches for atomic and molecular systems.

• Methods of Computational Chemistry
  A discussion of the foundations of the methods used to solve Schrödinger's equation for the properties of atomic and molecular systems. Commonly called Computational Chemistry.
  
  
• Electron Shells of a neutral copper atom.
  The s, p and d electron shells are discussed.
  
  
• Minimum Energy Geometric Structure of planer and non-planer molecules determined via DFT calculations.
  The optimization of the structure and the calulation of the molecular properties were done using DMol³ and displayed using the STM[1] suite of AVS/Express[2] modules written by Dr. Ken Flurchick and Dr. Lee Bartolotti.
  
  
• Distribution of electric charge around some example molecules.
  The computation of the charge density and the optimized geometric structure were done using DMol³ and displayed using the STM[1] suite of AVS/Express[2] modules written by Dr. Ken Flurchick and Dr. Lee Bartolotti.
  
  
• Vibrational motion of atoms in molecules.
  A web based lecture about vibrational motion of atoms in molecules.
  
  
• The Octane molecule
  This shows the differences in the distribution of eletric charge for an octane molecules with several different atomic substitutions. The displays show both the geometric structure, the eletron density and the electrostatic potential.
  
  
• Hydrogen Bonding
  A hydrogen bond is formed as a water molecule is brought toward the acid end of the hexanoic molecule. The electronic shape of the molecule (spatial distribution of the charge density) is displayed with data values from the electrostatic potential. The images are displayed using the STM[1] suite of AVS/Express[2] modules written by Dr. Ken Flurchick and Dr. Lee Bartolotti.
  
  
• OH and H bonding to form water.
  As a hydrogen atom approaches an OH molecule, a bond is formed between the oxygen and the approaching hydrogen thereby making water. The display shows the distortion of the electron density as the bond is formed.
  
  
• Hellman-Feynman forces on the atoms in a molecule during a geometry optimization.
  During the SCF minimization, the forces on the atoms are computed and displayed using the STM[1] suite of AVS/Express[2] modules written by Dr. Ken Flurchick and Dr. Lee Bartolotti.
  STM reads the forces and energies for each step in a geometry optization using the GAUSSIAN 2003 program[3].
  
  
• Butantoxin
  Butantoxin is a derivative of Scorpion venom is shown as a single molecule and 'docked' to inhibit the flow of calcium ions through a cell receptor.
  
  
• Napthalene Timer.
  A molecular dynamics simulation of three napthalene molcules, initially in a random configuration settle into a stacked configuration.

References

1. K.M. Flurchick and Lee Bartolotti, Visualizing Properties of Atomic and Molecular Systems, Journal of Molecular Graphics, 13, 10, (1995). And K. Flurchick, Lee Bartolotti and Mark Reed, Visualizing Properties of Atomic and Molecular Systems in AVS, AVS'94 Proceedings. Viewing Gaussian© Cube Files Using AVS and AVS Express, AVS'97 Proceedings.
   
   
2. Advanced Visual Systems, Inc.
   
   
3. Gaussian 03, Revision A.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2003.
   
   
4. Accelrys Software Inc., http://www.accelrys.com.
   
   
5. DMOL³ B. Delley, J. Chem. Phys. A 92, 508 (1990).

Atomic and Molecular Systems

©Ken Flurchick 2006