This paper will discuss that the 10 member and nine members ring in enediynechromophores c
1027
The primary mechanism util...
Strain (chemistry)
From Wikipedia, the free encyclopedia
In chemistry, a molecule experiences strain when its chemical str...
3 See also
Summary
Thermodynamics
The equilibrium of two molecular conformations is determined by the difference in Gibbs ...
Determining molecular strain
Images of cyclohexane and methylcyclopentane.
Images of cyclohexane and methylcyclopentane.
T...
Reaction of trialkylamines and trimethylboron.
Reaction of trialkylamines and trimethylboron.
Syn-pentane strain
Main arti...
originally measured along with other methods using the Gibbs free energy equation and, for
example, the Meerwein–Ponndorf–...
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 a...
References
Anslyn and Dougherty, Modern Physical Organic Chemistry, University Science Books, 2006, ISBN
978-1-891389-31-3...
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 dissociatio...
$DATA
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 -4.273...
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 4.5...
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This paper will discuss that the 10 member and nine members ring in enediyne chromophores c 1027 jjjjj

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This paper will discuss that the 10 member and nine members ring in enediyne chromophores c 1027 jjjjj

  1. 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 2. NBO 3. ONLY USE 2 REFS AT FIRST deardrjusufi- i am looking for a computational chem position. in am familiar which a variet of computational platforms-VMD, Gaussian 09 9r thateaaly well), and learning amber, CHARRM, iaslso know firefly/PC GAMMESS- i want to work partime or full- would you know anyone who neeedssome one familiar whith these platform?? idonot know does that much python, but a lot of c++, and fortram is ok, i am ok whith LINUX softear like AMBER, and NBO 6.0 AmberTools 1.4 and Amber 11 on Microsoft Windows
  2. 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. 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. 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. 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. 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. 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. 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. 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 ! File created by the GAMESS Input Deck Generator Plugin for Avogadro $BASIS GBASIS=STO NGAUSS=3 $END $CONTRL SCFTYP=ROHF RUNTYP=ENERGY MULT=2 $END
  10. 10. $DATA 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 MARK 45 GAUSSAIAN Z MATRIX AFTER BAJUE %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. 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

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