1.     Introduction

1.1     What is ACD/3D Viewer?

ACD/3D Viewer is a program that converts two-dimensional structures from ACD/ChemSketch into their three-dimensional counterparts and calculates bond angles and atom-to-atom distances.  ACD/3D Viewer is fully integrated with the ChemSketch structure drawing program.    It provides a wide range of features:

·         Import:  Read in structures in the MDL molfile format, which is highly compatible with other computational chemistry software.

·         Export:  ACD/3D Viewer provides additional file-saving options—from the 3D interface as 3D OLE server files, or from the ChemSketch interface as sketch, bitmap or MDL molfiles.

·         Display:  Specify the representation of the structure displayed: molecule’s color and “view–type” .  Structural display options range from using sticks, balls-and-sticks, to the more sophisticated opaque space-filling technique or transparent dots-on-a-sphere.

·         Move:  The position of the molecule can be changed through mouse control.  Or, a structure can be set to auto-rotate, with or without changing the display styles.

·         Measure:  Perform atom-to-atom measurements, and 3- and 4-vertex (torsion) angle measurement.

·         Customize:  You can modify individual atomic radii and colors, as well as background color.

·         Integration:  Copy the contents from the workspace to the Clipboard and paste it into other OLE-supported Microsoft Windows applications, such as word processors or graphics applications.

1.2     3D Optimization Algorithm

The 3D optimization algorithm rapidly transforms the planar (2D) structure from ChemSketch into a realistic 3-dimensional structure.  It is based on modified molecular mechanics which take into account bond stretching, angle bending, internal rotation and van der Waals non-bonded interactions.  Modifications include minor simplification of potential functions and enforcement of the minimization scheme by additional heuristic algorithms for dealing with "bad" starting conformations.

The 3D optimization algorithm is a proprietary version of molecular mechanics with the force field initially based on CHARMM parametrization.[1] The modifications involve some simplification and were intended to increase the stability and speed of computation.  Note that 3D-optimizer is NOT a full-scale molecular mechanics engine.  Its design aims to reliably reproduce reasonable conformations from (possibly very unreasonable) 2D drawings, rather than to precisely optimize 3D structures.

Occasionally an R-conformation input will change to an S-conformation in the process of optimization.  This is because the algorithm does not restrict conformations.  If ACD/3D Viewer produces a molecular conformation different from what you have expected, do not be surprised.  It is the very essence of conformational analysis that molecules typically have many conformations.  The optimizer finds only one, and it is not necessarily the one you expected.  For example, you probably expect a cyclohexane fragment to be a chair, but the optimizer may generate twist-boat, which is also one of its suitable conformations (indeed, in many structures this fragment exists in a twisted form).  In some cases, for example, if you want to obtain desired enantiomers for structures with a chiral center, you can use the Up and Down Stereo Bonds tools in the ChemSketch Window to define the required direction of bonds.

1.2.1     Limitations of ACD/3D Optimizer

ACD/3D Viewer can only optimize structures containing C (IV), H (I), F (I), Cl (I), Br (I), I (I), N (III, IV), O (II) and S (II, IV, VI).  It cannot optimize organometallic compounds or structures with charged atoms (except azide and nitro groups).  Also, it does not take into account hydrogen bonding.

1.3     What’s New in 5.0?

1.3.1     General ACD/Labs Functions

·       All ACD software programs run as 32-bit applications on PCs with Windows 95/98/NT/ME/2000 operating systems, except for ACD/I-Lab for Intranets, Batch for the SGI and Batch for Sun Solaris products.

·       All ACD software programs running on PCs are controlled by ACD/Host which allows you to set loading, timeout and auto-reload parameters.