Molecule command

NMR-SIM uses the predefined command molecule and endmol to set up the individual spin systems or molecules within the spin system definition file. All statements relating to nuclei, interactions and initial spin states are defined in a block that begins with the command molecule and ends with the command endmol. All the statements that occur in this block only relate to that particular spin system. Each spin system defined in this way has to be named, the name appearing on the same line as the molecule command separated by a space. Finally the relative concentration of the individual spin systems is added, separated from the name by a space. 

The spin system file should contain six molecule statements, each starting with the command molecule and concluding with the command endmol as shown in the result file. The approximate natural abundance of each isotopomer should be added to the same line as the molecule command. Start the simulation using the Go I Run Experiment command. In ID WIN-NMR process the FID using zero filling of Sl(r+i) 32k and an exponential window function with a LB value of 1.0 Hz. 

One significant characteristic of the program is the Command Line. Hereby, the visualization of the molecules is directed in the viewer with commands from a script language. The scripts, such as loop or batch files, can be saved, lutp //openrasmoi.org... 

The four Build Menus ia REACCS are Stmcture, Query, Top, and HighlightRxn. Stmcture menu contains the basic drawiag commands used to constmct the backbone of the stmcture. Query menu contains the commands used to add flexible stmctural parameters to the query. Top menu contains commands used to build reactions and to store and retrieve reactions, molecules, and graphic queries. HighlightRxn menu contains commands that apply atom/atom mapping and reaction centers to the current reaction. Atom/atom mapping is used to identify the reaction centers and iacrease accuracy and efficiency by letting the searcher specify that a particular atom ia a reactant must correspond to a particular atom ia the product. 

Each chapter in this book provides many problems of different sorts. The inchapter problems are placed for immediate reinforcement of ideas just learned, while end-of-ebapter problems provide additional practice and are of several types. They begin with a short section called "Visualizing Chemistry," which helps you "see" the microscopic world of molecules and provides practice for working in three dimensions. After the visualizations are many "Additional Problems." Early problems are primarily of the drill type, providing an opportunity for you to practice your command of the fundamentals. Later problems rend to be more thought-provoking, and some are real challenges. 

First we need to locate the part of the molecule where resonance is an issue. Remember that we can push electrons only from lone pairs or bonds. We don t need to worry about all bonds, because we can t push an arrow from a single bond (that would violate the first commandment). So we only care about double or triple bonds. Double and triple bonds are called pi bonds. So we need to look for lone pairs and pi bonds. Usually, only a small region of the molecule will possess either of these features. 

Notice that we have two resonance structures, each of which has charge separation. Even though the molecule has no net charge, nevertheless, we cannot draw a single resonance structure that is free of charge. If we try to do so, we will end up with a structure that violates the second commandment ... 

Once they reach acetylcholine receptors, BZ molecules hang on for dear life. So tenacious is their grip that they take hit after hit from the weaker acetylcholine molecules. For tens of hours acetylcholine is unable to exert command and control of mental activities. Like sugar in a gas tank, BZ gums up the transmission. The result is incapacitation. 

Now we are in a position to expand our command of molecules by introducing organic molecules that contain atoms of oxygen, nitrogen, sulfur, and phosphorus. That forms the substance of the next three chapters. 

The information retrieval in MAECIS is accomplished using one of three available commands SHOW, FIND, or SEARCH. The SHOW command is the simplest one to use and requires only a code number or registry number. It allows the user to retrieve all chemical structures and associated information stored under a particular code number. In most cases this fulfills the user s needs. The FIND command is used for complex searches involving various combinations of multiple data fields, handles substructure searching. Queries such structures with a molecular weight between 200 and 250 containing an ester substructure" are handled by the FIND command. Finally, the SEARCH command is used for chemical structure searches. This search takes only seconds and allows the chemist to determine if a particular molecule is already in the database. 

The result of any retrieval command in MAECIS is a set of chemical structures which is referred to as the "current set". If a second retrieval is made, the current set is moved into another internal storage area and is referred to as the "prior set". In this way, MAECIS automatically keeps track of at least two retrievals for the user. However, it is often necessary to establish several sets of molecules during a single computer session. In MAECIS, any number of sets can be retained using a SAVE command which allows the user to name and save any set of molecules created by a retrieval command. Any stored set in MAECIS can also be referenced in a subsequent FIND command. Thus, new sets can be generated from old sets through the find command s boolean operations. Sets retained with the SAVE command are in temporary memory. To make them permanent, the STORE and RESTORE commands are available to move sets to and from permanent disk files. 

Given a set of molecules, the REVIEW command is used to display the chemical structure and associated information of any member of the set. The review mode allows the user to both page through the current set of molecules, one after another, as well as to jump to a specific entry within the set. The chemical structure currently displayed is referenced by MAECIS as the "current" structure. The user can also designate a second member of the set as the "alternate" structure. This allows for comparison of structures which will be described in the section on chemical structure manipulation. 

One of the more powerful manipulation commands in MAECIS is COMPARE which allows the current molecule to be superimposed upon the alternate molecule. This is accomplished in the following steps. First, the user specifies the atom pairs in the two structures which are to be overlapped. At least three pairs of atoms must be specified. The program then performs a nonlinear least-squares calculation to minimize the distance between these atom pairs. Finally, the user specifies that the molecules are to be drawn superimposed upon each other. The superimposed molecules can be drawn with any of the options available with the DRAW command. An illustration of this is contained in Figure 2 where two musk odorants are compared. Thus, a chemist can obtain an idea of the structural similarity of any two molecules. 

In addition to the manipulation commands, several molecular properties can be calculated for a molecule. The molecular weight is calculated using the exact mass (5) of the most abun-... 

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