This document discusses ring strain in 9-membered enediyne chromophores. It focuses on three species - Mark 42, Mark 45, and Mark 48. The document proposes removing the anthraquinone bridge from these molecules using Maestro and performing calculations using MP2, RHF/6-311G, and B3LYP to examine them as transition states in a solvent-free system. It also mentions that the 9 natural products in this family contain a common bicyclo[7.3.0]dodeca-1,3,5,7,9,11-hexaene chromophore.

1. This paper will discuss that the 10 member and nine members ring in enediynechromophores c
1027
The primary mechanism utilized by nine member enediyne producing organisms of interest the
most biologically relevant species is the enediynediradical.
The mode of action of nine membered enediynes, which is generally accepted is the ability to
produce single stranded or double stranded DNAlesions, this short paper will look at c1027,
and the common me thechism which includes only three species mark 42, mark 45 amd mark
48.
biological importance of plants
begin from "the nine -membered chromoprotein family of enediynee has steadily grown of if 12th
of thing that up and chief
theantroquinone bridge repeats it self in the three molecules
lets remove it using Maestro and make calculations on Mark 45, mark 45 ANION , an mark 48,
lets assume a solvent free system. lets use MP2, RHF/6-311G, and B3YL
look at the 3 species as transition states-they are actually-a family all nine national
products is having a common remember system
bicyclo[7.3.0] dodecjadiynene
the nine natural pruthatcts are that's: necarzinostatin, kedarcidin, c-1027 fifth with, an
maduropeptin and N that1199A2
Although old all the known nine membered enediynes that contain a common bicyclo[7.3.0]
dodecjadiynenechromphore, only five have complete structures
Recently humorous crytpic gene clusters encoding enediyne biosynthesis in a variety
ofactinycetes have neenunvieled, subjectsthingthat these organismshave the potential to
produce uncharacterized enediynes.
The latter finng may significantly increase the pool of nine membered enediynes in the years to
come.
That if if
1. FINISH NEXT PARA
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3. ONLY USE 2 REFS AT FIRST
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AmberTools 1.4 and Amber 11 on Microsoft Windows

2. Strain (chemistry)
From Wikipedia, the free encyclopedia
In chemistry, a molecule experiences strain when its chemical structure undergoes some stress
which raises its internal energy in comparison to a strain-free reference compound. The internal
energy of a molecule consists of all the energy stored within it. A strained molecule has an
additional amount of internal energy which an unstrained molecule does not. This extra internal
energy, or strain energy, can be likened to a compressed spring.[1] Much like a compressed spring
must be held in place to prevent release of its potential energy, a molecule can be held in an
energetically unfavorable conformation by the bonds within that molecule. Without the bonds
holding the conformation in place, the strain energy would be released.
Contents
1 Summary
1.1 Thermodynamics
1.2 Determining molecular strain
2 Kinds of strain
2.1 Van der Waals strain
2.1.1 Syn-pentane strain
2.1.2 Allylic strain
2.1.3 1,3-diaxial strain
2.2 Torsional strain
2.3 Ring strain
2.3.1 Small Rings
2.3.2 Transannular strain
2.3.3 Bicyclic systems
2.4 References

3. 3 See also
Summary
Thermodynamics
The equilibrium of two molecular conformations is determined by the difference in Gibbs free
energy of the two conformations. From this energy difference, the equilibrium constant for the two
conformations can be determined.
lnK_{eq}=frac{-Delta {G^o}}{RT},
If there is a decrease in Gibbs free energy from one state to another, this transformation is
spontaneous and the lower energy state is more stable. A highly strained, higher energy molecular
conformation will spontaneously convert to the lower energy molecular conformation.
Examples of the anti and gauche conformations of butane.
Examples of the anti and gauche conformations of butane.
Enthalpy and entropy are related to Gibbs free energy through the equation(at a constant
temperature):
Delta{G^o}=Delta{H^o}-TDelta{S^o},.
Enthalpy is typically the more important thermodynamic function for determining a more stable
molecular conformation.[1] While there are different types of strain, the strain energy associated
with all of them is due to the weakening of bonds within the molecule. Since enthalpy is usually
more important, entropy can often be ignored.[1] This isn't always the case; if the difference in
enthalpy is small, entropy can have a larger say in the equilibrium. For example, n-butane has two
possible conformations, anti and gauche. The anti conformation is more stable by 0.9 kcal/mol.[1]
We would expect that butane is roughly 82% anti and 18% gauche at room temperature. However,
there are two possible gauche conformations and only one anti conformation. Therefore, entropy
makes a contribution of 0.4 kcal in favor of the gauche conformation.[2] We find that the actual
conformational distribution of butane is 70% anti and 30% gauche at room temperature.

4. Determining molecular strain
Images of cyclohexane and methylcyclopentane.
Images of cyclohexane and methylcyclopentane.
The heat of formation (ΔHfo) of a compound is described as the enthalpy change when the
compound is formed from its separated elements.[3] When the heat of formation for a compound is
different from either a prediction or a reference compound, this difference can often be attributed
to strain. For example, ΔHfo for cyclohexane is -29.9 kcal/mol while ΔHfo for methylcyclopentane is
-25.5 kcal/mol.[1] Despite having the same atoms and number of bonds, methylcyclopentane is
higher in energy than cyclohexane. This difference in energy can be attributed to the ring strain of
a five-membered ring which is absent in cyclohexane. Experimentally, strain energy is often
determined using heats of combustion which is typically an easy experiment to perform.
Determining the strain energy within a molecule requires knowledge of the expected internal
energy without the strain. There are two ways do this. First, one could compare to a similar
compound that lacks strain, such as in the previous methylcyclohexane example. Unfortunately, it
can often be difficult to obtain a suitable compound. An alternative is to use Benson group
increment theory. As long as suitable group increments are available for the atoms within a
compound, a prediction of ΔHfo can be made. If the experimental ΔHfo differs from the predicted
ΔHfo, this difference in energy can be attributed to strain energy.
Kinds of strain
Van der Waals strain
Main article: Van der Waals strain
Van der Waals strain, or steric strain, occurs when nonbonded atoms are forced closer to each
other than their Van der Waals radii allow. Specifically, Van der Waals strain is considered a form
of strain where the interacting atoms are at least four bonds away from each other.[4] The amount
on steric strain in similar molecules is dependent on the size of the interacting groups; bulky tert-
butyl groups take up much more space than methyl groups and often experience greater steric
interactions.
The effects of steric strain in the reaction of trialkylamines and trimethylboron were studied by
Brown et al.[5] They found that as the size of the alkyl groups on the amine were increased, the
equilibrium constant decreased as well. The shift in equilibrium was attributed to steric strain
between the alkyl groups of the amine and the methyl groups on boron.

5. Reaction of trialkylamines and trimethylboron.
Reaction of trialkylamines and trimethylboron.
Syn-pentane strain
Main article: Pentane interference
There are situations where seemingly identical conformations are not equal in strain energy. Syn-
pentane strain is an example of this situation. There are two different ways to put both of the bonds
the central in n-pentane into a gauche conformation, one of which is 3 kcal/mol higher in energy
than the other.[1] When the two methyl-substituted bonds are rotated from anti to gauche in
opposite directions, the molecule assumes a cyclopentane-like conformation where the two terminal
methyl groups are brought into proximity. If the bonds are rotated in the same direction, this
doesn't occur. The steric strain between the two terminal methyl groups accounts for the difference
in energy between the two similar, yet very different conformations.
Allylic strain
Main article: Allylic strain
Allylic methyl and ethyl groups are close together.
Allylic methyl and ethyl groups are close together.
Allylic strain, or A1,3 strain is closely associated to syn-pentane strain. An example of allylic strain
can be seen in the compound 2-pentene. It's possible for the ethyl substituent of the olefin to rotate
such that the terminal methyl group is brought near to the vicinal methyl group of the olefin. These
types of compounds usually take a more linear conformation to avoid the steric strain between the
substituents.[1]
1,3-diaxial strain
Main article: Cyclohexane conformation
1,3-diaxial strain is another form of strain similar to syn-pentane. In this case, the strain occurs due
to steric interactions between a substituent of a cyclohexane ring ('α') and gauche interactions
between the alpha substituent and both methylene carbons two bonds away from the substituent in
question (hence, 1,3-diaxial interactions). When the substituent is axial, it is brought near to an
axial gamma hydrogen. The amount of strain is largely dependent on the size of the substituent and
can be relieved by forming into the major chair conformation placing the substituent in an
equatorial position. The difference in energy between conformations is called the A value and is
well known for many different substituents. The A value is a thermodynamic parameter and was

6. originally measured along with other methods using the Gibbs free energy equation and, for
example, the Meerwein–Ponndorf–Verley reduction/Oppenauer oxidation equilibrium for the
measurement of axial versus equatorial values of cyclohexanone/cyclohexanol (0.7kcal/mol).[6]
Torsional strain
Further information: Alkane stereochemistry
Torsional strain is the resistance to bond twisting. In cyclic molecules, it is also called Pitzer strain.
Torsional strain occurs when atoms separated by three bonds are placed in an eclipsed
conformation instead of the more stable staggered conformation. The barrier of rotation between
staggered conformations of ethane is approximately 2.9 kcal/mol.[1] It was initially believed that
the barrier to rotation was due to steric interactions between vicinal hydrogens, but the Van der
Waals radius of hydrogen is too small for this to be the case. Recent research has shown that the
staggered conformation may be more stable due to a hyperconjugative effect.[7] Rotation away
from the staggered conformation interrupts this stabilizing force.
More complex molecules, such as butane, have more than one possible staggered conformation. The
anti conformation of butane is approximately 3.8 kcal/mol more stable than the gauche
conformation.[1] Both of these staggered conformations are much more stable than the eclipsed
conformations. Instead of a hyperconjugative effect, such as that in ethane, the strain energy in
butane is due to both steric interactions between methyl groups and angle strain caused by these
interactions.
Ring strain
Main article: Ring strain
According to the VSEPR theory of molecular bonding, the preferred geometry of a molecule is that
in which both bonding and non-bonding electrons are as far apart as possible. In molecules, it is
quite common for these angles to be somewhat compressed or expanded compared to their optimal
value. This strain is referred to as angle strain, or Baeyer strain.[8] The simplest examples of angle
strain are small cycloalkanes such as cyclopropane and cyclobutane, which are discussed below.
Furthermore, there is often eclipsing in cyclic systems which cannot be relieved.
Strain of some common cycloalkane ring-sizes[1] Ring size Strain energy (kcal/mol)
Ring size Strain energy (kcal/mol)
3 27.5 10 12.4

7. 4 26.3 11 11.3
5 6.2 12 4.1
6 0.1 13 5.2
7 6.2 14 1.9
8 9.7 15 1.9
9 12.6 16 2.0
In principle, angle strain can occur in acyclic compounds, but the phenomenon is rare.
Small Rings
Cyclohexane is considered a benchmark in determining ring strain in cycloalkanes and it is
commonly accepted that there is little to no strain energy.[1] In comparison, smaller cycloalkanes
are much higher in energy due to increased strain. Cyclopropane is analogous to a triangle and thus
has bond angles of 60°, much lower than the preferred 109.5° of an sp3 hybridized carbon.
Furthermore, the hydrogens in cyclopropane are eclipsed. Cyclobutane experiences similar strain,
with bond angles of approximately 88° (it isn't completely planar) and eclipsed hydrogens. The
strain energy of cyclopropane and cyclobutane are 27.5 and 26.3 kcal/mol, respectively.[1]
Cyclopentane experiences much less strain, mainly due to torsional strain from eclipsed hydrogens,
and has a strain energy of 6.2 kcal/mol.
Transannular strain
Main article: Transannular strain
Perhaps surprisingly, medium sized rings (7–13 carbons) experience more strain energy than
cyclohexane. This transannular strain occurs when the cycloalkanes attempt to avoid angle and
torsional strain. In doing so, CH2 units across from each other are brought into proximity and
experience Van der Waals strain.
Bicyclic systems
Main article: Bicyclic molecule
The amount of strain energy in bicyclic systems is commonly the sum of the strain energy in each
individual ring.[1] This isn't always the case, as sometimes the fusion of rings induces some extra
strain.

8. References
Anslyn and Dougherty, Modern Physical Organic Chemistry, University Science Books, 2006, ISBN
978-1-891389-31-3
Coxon and Norman, Principles of Organic Synthesis, 3rd ed., Blackie Academic &Pro., 1993, ISBN
978-0-7514-0126-4
Levine, Physical Chemistry, 5th ed., McGraw-Hill, 2002, ISBN 978-0-07-253495-5
Brown, Foote, and Iverson, Organic Chemistry, 4th ed., Brooks/Cole, 2005, ISBN 978-0-534-
46773-9
Brown, H.C.; Johannesen, R.B. (1952)."Dissociation of the Addition Compounds of Trimethlboron
with n-Butyl- and Neopentyldimethylamines; Interaction of Trimethylboron and Boron Trifluoride
with Highly Hindered Bases". J. Am. Chem. Soc. 75: 16–20. doi:10.1021/ja01097a005.
Eliel, E.L., Wilen, S.H., The Stereochemistry of Organic Compounds,Wiley-Interscience, 1994.
Weinhold, F. (2001). "Chemistry: A New Twist on Molecular Shape". Nature 411 (6837): 539–541.
doi:10.1038/35079225. PMID 11385553.
Wiberg, K. (1986). "The Concept of Strain in Organic Chemistry".Angew. Chem. Int. Ed. Engl. 25
(4): 312–322. doi:10.1002/anie.198603121.
Calculating Bond Dissociation Energy
Back to Top
Let us see the example of the C-H bond dissociation energy in an organic compound like Ethane
having the molecular formula as C2H6. The corresponding bond dissociation energy equation and
bond dissociation energy calculation is as follows.
CH3CH2-H → CH3CH2 + H
Here, the Hydrogen bond gets dissociated from Ethane and the energy used to dissociate this
Hydrogen atom from the molecule of Ethane is termed as Bond dissociation energy.
The value of bond dissociation energy for this reaction is

9. ΔH = 102 Kcal/mol or 424.0 KJ/mol
and in short it is denoted as Do.
It has been seen that Bond energy and Bond dissociation energy have similar values, but they differ
in case of some diatomic molecules. This is because, in diatomic molecules, the average of the total
energy becomes the bond energy while BDE remains the same. This is how we can calculate bond
dissociation energy and form bond dissociation energy table or chart.
Bond dissociation energy should not be confused with Bond energy, as both are different terms. The
former one is the measure of the bonds strength while the later one is the total energy contained in
a chemical bond.
Bond Dissociation Energy Table
Back to Top
The principal measure of the ease of homolytic cleavage is the bond-dissociation energy. The bond
dissociation energies indicate the energy required to break a specific bond in a particular molecule,
whereas the average bond energies are calculated from a set of experimental data assuming that all
C-H bonds have the same energy.
Both types of values are useful bond dissociation energies provide an accurate assessment of the
energy required to break a particular bond homolytically; average bond energies can be used to
estimate changes in energy for the transformations from one stable species to another, especially in
cases where π bonds are broken and made.
Bond Dissociation Energy
M
MARK 45 GAMESS Z MATRIX AFTER BAJUE
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Title
C1
C 6.0 -6.33290 0.18750 1.50950
C 6.0 -5.38240 -0.77170 1.50780
C 6.0 -4.10710 -0.12540 1.50660
C 6.0 -4.27340 1.20300 1.50740
C 6.0 -5.70190 1.57030 1.50940
H 1.0 -7.39840 0.01230 1.51070
H 1.0 -5.54230 -1.83810 1.50750
H 1.0 -5.98310 2.12800 2.40710
H 1.0 -5.98530 2.12890 0.61290
C 6.0 -0.29250 2.45860 1.50370
C 6.0 -1.26130 3.47620 1.50510
C 6.0 -2.62500 3.16890 1.50640
C 6.0 -2.98440 1.83570 1.50620
C 6.0 -2.01050 0.81100 1.50480
C 6.0 -0.66010 1.11230 1.50350
H 1.0 -0.93750 4.51340 1.50520
H 1.0 -3.37200 3.95470 1.50750
H 1.0 0.09720 0.33710 1.50240
C 6.0 -2.67760 -0.54930 1.50480
H 1.0 -2.42060 -1.11210 2.40650
H 1.0 -2.42250 -1.11120 0.60190
$END
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%NProcShared=2
#n B3LYP/6-31G(d) Opt Freqgfoldprint pop=full
Title
0 1
C -6.33290 0.18750 1.50950
C -5.38240 -0.77170 1.50780
C -4.10710 -0.12540 1.50660
C -4.27340 1.20300 1.50740
C -5.70190 1.57030 1.50940
H -7.39840 0.01230 1.51070
H -5.54230 -1.83810 1.50750
H -5.98310 2.12800 2.40710
H -5.98530 2.12890 0.61290
C -0.29250 2.45860 1.50370
C -1.26130 3.47620 1.50510

11. C -2.62500 3.16890 1.50640
C -2.98440 1.83570 1.50620
C -2.01050 0.81100 1.50480
C -0.66010 1.11230 1.50350
H -0.93750 4.51340 1.50520
H -3.37200 3.95470 1.50750
H 0.09720 0.33710 1.50240
C -2.67760 -0.54930 1.50480
H -2.42060 -1.11210 2.40650
H -2.42250 -1.11120 0.60190