BOND command

Example 14.6 Graphite. Graphite has a layerlike stmcture. Each carbon is bonded to three other carbons forming a framework of planar benzenoid rings, with bond lengths of 1.42 A [279]. Two of these bonds command the use of Sj, while Sg must be used for the third one. Now we calculate acc A c- The graphite carbons are electroneutral hence Aqc = —13.2 me. Using agj(1.42) = —0.352 kcal/moU me (for m = —0.814), one finds... 

This is also done on the Bond menu with the Network Bonds command. This shows a similar list as for the short interactions, but now all bonds in the red network are shown. It is also convenient to sort this list by atom labels. 

The BOND command determines whether bonds occur in chains, rings or both. 

One can start building up a list of MM3 parameters by use of the TINKER analyze command. Don t expect to build up the entire set, which occupies about 100 pages in the MM3 user s manual, but do obtain a few representative examples to get an idea of how a parameter set is constr ucted. From previous exercises and projects, you should have input and output geometries for an alkene, an alkane, and water. From these, the object is to determine the stretching and bending parameters for the C—C, C=C, C—H, and O—H bonds. The C—H bond parameters are not the same... 

Mazza, J.J. and Kuhbander, R.J., Grit blast/silane (GBS) aluminum surface preparation for structural adhesive bonding, WL-TR-94-4111. Materials Laboratory, Air Force Materiel Command, September 1999. 

Potter, D.L. et al.. Primary Adhesive Bonded Structure Technology (PABST) Design Handbook for Adhesive Bonding. Report AFFDL-TR-79-3129, Douglas Aircraft Co., Air Force Flight Development Laboratory (FBA), Air Force Systems Command, WPAFB (November, 1979). 

French et al, Descriptions And Requirements For Explosive, Nylon Plastic-Bonded Molding Powder PBXN-1 , NAVORD Syst Command, OS11632A (1968) 51) EE. Kilmer, Heat... 

Never exceed an octet for second-row elements. Elements in the second row (C, N, O, F) have only four orbitals in their valence shell. Each of these four orbitals can be used either to form a bond or to hold a lone pair. Each bond requires the use of one orbital, and each lone pair requires the use of one orbital. So the second-row elements can never have five or six bonds the most is four. Similarly, they can never have four bonds and a lone pair, because this would also require five orbitals. For the same reason, they can never have three bonds and two lone pairs. The sum of (bonds) + (lone pairs) for a second-row element can never exceed the number four. Let s see some examples of arrow pushing that violate this second commandment ... 

At first it is difficnlt to see that the arrow on the left structnre violates the second commandment. Bnt when we connt the hydrogen atoms, we can see that the arrow above wonld give a carbon atom with five bonds. 

Onr two commandments (never break a single bond, and never violate the octet rule ) reflect the two parts of a curved arrow (the head and the tail). A bad tail violates the first commandment, and a bad head violates the second commandment. 

Answer First we need to ask if the first commandment has been violated did we break a single bond To determine this, we look at the tail of the arrow. If the tail of the arrow is coming from a single bond, then that means we are breaking that single bond. If the tail is coming from a double bond, then we have not violated the first... 

Now we need to ask if the second commandment has been violated did we violate the octet rule To determine this, we look at the head of the arrow. Are we forming a fifth bond Remember that C+ only has three bonds, not four. When we push the arrow shown above, the carbon atom will now get four bonds, and the second commandment has not been violated. 

Notice that if we stopped here, we would be violating the second commandment. The central carbon atom is getting five bonds. To avoid this problem, we must immediately draw the second arrow. The C=C disappears (which solves our octet problem) and becomes a lone pair on carbon. 

In this example, we can see that one of the lone pairs on oxygen is coming down to form a bond, and the C=C double bond is being pushed to form a lone pair on a carbon atom. When both arrows are pushed at the same time, we are not violating either of the two commandments. So, let s focus on how to draw the resonance structure. Since we know what arrows mean, it is easy to follow the arrows. We just get rid of one lone pair on oxygen, place a double bond between carbon and oxygen, get rid of the carbon-carbon double bond, and place a lone pair on carbon ... 

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. 

Can we convert any lone pairs into pi bonds without violating the two commandments ... 

The only way to avoid forming a fifth bond for carbon would be to push an arrow that takes electrons away from that carbon. If we try to do this, we will break a single bond and we will be violating the first commandment ... 

This might seem better at first, because we get rid of the charges, but our two commandments show us why it cannot be drawn like this the nitrogen atom would have five bonds, which would violate the octet rule. 

When we learned how to draw resonance structures, we saw two conunand-ments that we must not violate (1) never break a single bond, and (2) never exceed an octet for second-row elements. When drawing mechanisms, we are trying to understand where the electrons actually moved to break and form bonds. Therefore, it is OK to break single bonds. In fact, it happens in almost every reaction. So when drawing mechanisms there is only one commandment to follow never exceed an octet for second-row elements. 

Violates second commandment— nitrogen cannot have five bonds... 

Violates second commandment— oxygen cannot have three bonds and two lone pairs... 

Violates first commandment— cannot break a single bond... 

Fig. 4-5. Use of the Auto Build command to create a query structure. A any atoms Ch chain bond Rn ring bond [S,0] oxygen or sulfur atom.

The monomeric metaphosphate ion itself commands a fair amount of attention in discussions of metaphosphates. It is postulated as an intermediate of numerous hydrolysis reactions of phosphoric esters 52 S4,S5) and also of phosphorylation reactions S6> kinetic and mechanistic studies demonstrate the plausibility of such an assumption. In addition, the transient formation of ester derivatives of meta-phosphoric acid — in which the double-bonded oxygen can also be replaced by thio and imino — has also been observed they were detected mainly on the basis of the electrophilic nature of the phosphorus. 

But, we expect that the majority of readers will be those with only a rudimentary command of quantum chemistry and chemical bonding theory (e.g., at the level of junior-year physical chemistry course) who wish to learn more about the emerging ab initio and density-functional view of molecular and supramolecular interactions. While this is not a textbook in quantum chemistry per se, we believe that the book can serve as a supplement both in upper-level undergraduate courses and in graduate courses on modern computational chemistry and bonding theory. 

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