ChemPen3D© 3D Molecular Modeling for Windows®

Introduction Features Building 3D Molecules Reaction Energetics Measurements 2D Drawings C-13 NMR Shift Prediction Requirements Organic Reactions Purchase ChemPen 3D

Introduction

Do you need 3D molecular structures? to analyze molecular geometry? to explore molecular mechanics? to analyze reaction energetics? If yes, ChemPen3D is the tool for you. ChemPen includes all the features of ChemPen+ and more. Create 3D drawings using the same easy mouse and menu driven methods of ChemPen. ChemPen3D uses a modified version of the popular modified DREIDING molecular mechanics force field to optimize molecular geometry. ChemPen3D's force field has been extended to cover the entire periodic table thus allowing you to create metal complexes along with organic molecules.

ChemPen3D Features

• Mouse and Menu Driven Drawing Interface
• Group, bond, atom, symbol and text editors
• Extended DREIDING molecular mechanics force field for geometries
• Hydrogen-bonding potentials
• Fast geometry optimization
• Estimate reaction enthalpy, entropy, free energy and equilibrium constant.
• Calculate molecular weight, formula and composition.
• Calculate strain energy, internal energy, dipole moment
• New C-13 NMR Shift Prediction
• Fourteen display modes for 3D structures
• Pivot structure around atom or bond.
• Visualize with spinning, tumbling, wagging and rocking.
• Parallax stereo view
• Display inter-atomic distance, bond angle, Bond length, and torsion angles.
• Save separate atomic coordinate and bond table file
• Paste Drawings to Windows Word Processors
• Online Help and Tutorial 

Building Molecules with ChemPen3D

This animation illustrates creating a ChemPen3D molecular model at about the same speed as an experienced user. The process occurs as follows. A cobalt atom is added and charged to +2. Three five member rings are joined to the metal cation. Single keystrokes change then cobalt bonded carbonds to NHs. These are similarly changed to NH2s. A quick optimization(3 to 5 seconds on a 75MHz pentium) and a change is display gives the structure shown. If you don't have animation click the image to see an alternate display.

CHEMPEN3D Measurement Tool

The measurement tool displays bond lengths, bond angles, torsion dihedral angles or interatomic distances.

Analyzing Reaction Energetics With ChemPen3D

Reaction energetics can be analyzed using ChemPen3D. An example of a ChemPen3D style reaction constructed with geometry-optimized molecules appears to the left. The Reaction Tool, below, is used to balance the reaction and set its conditions. While certainly no substitute for calorimetry, ChemPen3D can usually predict whether a reaction will be endothermic or exothermic, spontaneous or non spontaneous.

Creating Conventional Drawings with ChemPen3D

Because it builds upon ChemPen+, ChemPen3D easily creates conventional drawings like the one below.

C-13 NMR Shift Prediction

One of ChemPen3D's newest and most attractive additions is C-13 NMR chemical shift prediction. ChemPen3D includes NMRPenLite© the light version of NMRPen© . NMRPenLite combines a database of assigned C-13 NMR shifts with empirical shift prediction methods to estimate C-13 NMR shifts.

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ChemPen3D -The DREIDING Generic Molecular Mechanics Force Field

Molecular mechanics, developed by N. Allinger Ref.1 , et al,is a simplified molecular modeling method that simplifies molecular geometry and energy calculations. Calculations are atomistic, classical and semi empirical.

Some force fields developed for making molecular mechanics calculations include MM2 and MMP2 force fields of Allinger, et al Ref.1, the AMBER force field of Kollman, et al Ref.2 and the CHARMM force field of Karplus, et al Ref.3 . These force fields are optimized for specific classes of molecules.

A more general force field, the DREIDING generic, was introduced by S.L. Mayo, B.D. Olafson and W. A. Goddard III in 1990 Ref 4. DREIDING, while slightly less accurate than its specialized counterparts, is sufficient for most situations.

The ChemPen3D DREIDING molecular mechanics force field has been extended to cover the entire periodic table. ChemPen3D can handle metal complexes.

References

a) Allinger, N. L. J. Am. Chem. Soc., 1977, 99, 8127
b) Sprague, J. T.; Tai, J. C.; Yuh, Y.; Allinger, N.L.; J. Comput. Chem. 1987, 8, 581
c) Burkert, U.; Allinger, N. L. Molecular Mechanics, ACS; Washington D.C., 1982.
a) Weiner, S. J.; Kollman, P.A., Case, D. A.; Singh, U. C.; Ghio, C.; Algona, G; Profeta Jr., S.; Weiner, P. J.; J. Am. Chem. Soc., 1984, 106, 765
b) Weiner, S.J; Kollman, P.A., et al; J. Comput. Chem., 1986, 7, 230
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M., J. Comput. Chem., 1983, 4, 1987,Nillson, L; Karplus, M. , ibid., 1983, 4, 1987
Mayo, S. L.; Olafson, B. D.; Goddard III, W. A. J. Phys. Chem., 1990, 94, 8897

ChemPen3D System Requirements

Despite it power and features ChemPen3D is a small program with small system requirements. The minimum recommended system is a 33MHz 486DX, Windows 95,98, or NT 16MB RAM and 2MB free HDD space. ChemPen3D can run on 486SX systems but a math coprocessor is highly recommended For email delivered versions: Microsoft Installer Engine installed(It's usually present).

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