Molecule builder

Jaguar comes with a graphic user interface, but it is not a molecule builder. The interface can be used to set the program options. The user must input the geometry by typing in Cartesian coordinates or a Z-matrix. The interface may... 

Our reviewer felt the molecule builder was easy to use. It is set up for organic molecules. Specialized building modes are available for peptides, nucleotides, and carbohydrates. It is also possible to impose constraints on the molecular geometry. Functions are accessed via a separate window with buttons labeled with abbreviated names. This layout is convenient to use, but not completely self-explanatory. The program is capable of good-quality rendering. At the time of this book s publication, a new three-dimensional graphic user interface called Maestro was under development. 

The graphic interface is a multitasking environment that works well. The protein and carbohydrate builders are particularly convenient to use. The small-molecule builder has a selection of common organic functional groups as well as individual atoms for organics and common heteroatoms. There are a... 

GaussView (we used Version 2.08) is a graphic interface for use with the Gaussian ah initio program. It can be used to build molecules, set up the options in the input hie, run a calculation, and display results. GaussView uses the molecule builder that was written by SemiChem, but has screens for setting up calculations that are different from those in the AMPAC GUI sold by SemiChem. 

The program has a Z-matrix editor, which is not the same as a graphic molecule builder. This allows the user to display the Z-matrix and then define... 

The program was made somewhat less convenient to use by the fact that it does not have a molecule builder. In order to predict chemical shifts, the molecular structure must be built with some other software package and then im-... 

The central routine UTAH is a modification of the Fortran MOLECULE BUILDER program written by Boyd The input consists of the Cartesian coordinates of the trial model plus a set of interactions, describing the structural parameters and the constants for the chosen potential functions. The trial model is obtained from guessed internal coordinates which are transformed to Cartesians by the routine FIXAT ). 

To obtain Cartesian coordinates for complicated molecules, one can use a molecule builder, as discussed in the next paragraph and in the subsection at the end of this section. 

Semiempirical methods are widely available in many programs. Gaussian 09 (Section 15.14) includes the MNDO, AMI, PM3, PPDG, PM6, MINDO/3, INDO, and CNDO methods. Spartan includes the MNDO, MNDO/d, AMI, PM3, PM6, and RMl methods. HyperChem has the MNDO, MNDO/d, AMI, PM3, RMl, MINDO/3, CNDO, INDO, INDO/S and extended Hiickel methods. MOPAC2012 (openmopac.net/homeJitml) has the MNDO, AMI, PM3, PM6, PM6-DH2, PM6-DH-H, PM7, and RMl methods. It is available in Linux, Macintosh, and Windows versions and is free to academic researchers. An older version is MOPAC2009 (openmopac.net/MOPAC2009.htmI). AMPAC 9 (www. semichem.com) has the SAMI, AMI, PM3, RMl, PM6, MNDO, and MNDO/d methods and a molecule builder, and is available for Windows, Linux, and Macintosh operating systems. 

One very practical use of molecular mechanics is to refine the structure produced by a molecule builder (Sec. 15.15). After one draws onscreen the molecule to be studied by an ab initio, density functional, or semiempirical method, molecule builders in most programs allow you to refine the structure by doing a quick molecular mechanics calculation to locate the local MM energy minimum nearest the structure drawn. By starting from the MM structure, the geometry optimization will take less time. 

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