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A Review on Computational Organic Chemistry: Basic Concepts and Applications ,[object Object]
Contents ,[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],Calculations are now performed by not only  computational chemists but also experimental chemists.
[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Differences Between   Molecular Mechanics and Quantum Methods ,[object Object],[object Object]
Differences Between   Molecular Mechanics and Quantum Methods (Cont.)‏ ,[object Object],[object Object]
Differences Between   Molecular Mechanics and Quantum Methods (Cont.)‏ ,[object Object]
Range of Molecular Mechanics and Quantum Methods Method  Range (heavy atoms)‏ Molecular Mechanics   > 1000 Semi-Empirical   < 200 Ab initio  Hartree-Fock(HF)   < 50 Ab initio  Correlated   < 20 Density Functional (DFT)   < 100
Relative Computation Times Methylcyclohexane (C 7 H 14 )‏ 14 2 pBP/DN* ( DFT )‏ .06 8 54 - f 1 7 100 AM1 ( Semi-Empirical )‏ HF/3-21G ( Ab initio )‏ HF/6-31G* ( Ab initio )‏ MP2/6-31G*  ( Ab   initio  Correlated )‏ f f MMFF94 ( MM )‏ Geometry Optimization Single-Point Energy Level of Calculation
Comparison of the Performance of Molecular Mechanics( MM ) and Quantum Methods( QM )   S= satisfactory; U= unsatisfactory   Task      MM   Semi-  Ab   initio   DFT     Empirical  HF  Correlated Geometry  S  S  S  S  S Transition-state  -    S  S  S  S Geometry Conformation  S  U  S  S  S Thermochemistry  -      U  S  S  S
[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
Widely Used Software Packages for  MM ,  QM ,[object Object],[object Object],[object Object],[object Object],[object Object],Each software has  different user interface, operating feature, price, manual and so on .
[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],Dihedral angle  0  90  180 
Relation between Dihedral Angle and Relative Conformer Energy in 1,3-Butadiene s- trans s- cis twisted Order of stability: s- trans  > s- cis  > twisted
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Advantage and Disadvantage of X-ray and CD Method ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Advantages and Disadvantages of  Total Synthesis ,[object Object],[object Object],[object Object],[object Object],[object Object]
Advantages and Disadvantages of  NMR   (2D-NMR, 1D-NMR with Chiral Derivatizing Agents   )‏ ,[object Object],[object Object],[object Object],[object Object],[object Object]
Advantages and Disadvantages of Computational Chemistry ,[object Object],[object Object],[object Object],[object Object],[object Object]
Determination of Absolute Configuration in  A Macrocyclic System  by a Combination of Computational Chemistry and Another Method
The distance between H-2 and H-13 is  4.0 Å  in 13( R )configuration . This is  not consistent with  information based on NOESY.
The distance between H-2 and H-13 is 2.4 Å  in   13( S )configuration. This is  consistent with  information based on NOESY.
CD Spectrum Negative  Cotton Effect - CD also supports 13( S )configuration.
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Investigation of  Basicity (Proton Affinity) ,  Acidity , and More…
4-Aminopyridine: Where is the Basic Site ? ,[object Object], H(A) = 193.6,   H(B) = 169.1 kcal/mol  B  is more stable than  A , and thus the ring  N  is more basic.
[object Object],The ring  N  is more negatively charged , and thus is likely to be more basic. Colors near red represent more negative charge , while colors near blue represent more positive charge.
Imidazole: Where is the Basic Site ? The  N-3  is negatively charged , and thus is the basic site . Electrostatic Potential Map
Acidities of Alcohols stronger stronger weaker weaker 15.5 Methanol 15.9 Ethanol 7.2 4-Nitrophenol 10.0 Phenol 12.4 2,2,2-Trifluoroethanol pKa’s (acidities)‏
Electrostatic Potential (ESP) Map for the Alcohols ,[object Object],[object Object]
[object Object],[object Object],[object Object],Examination of  frontier molecular orbital ( HOMO  and  LUMO )  is an important method because most chemical reactions involve  electron movement between them .
References of  Frontier Molecular Orbital   (FMO)  Theory and Reaction ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],Examination of  FMO  Energies
Acrolein/BF 3 : What is the role of Lewis Acids ? ,[object Object]
[object Object],[object Object]
[object Object],[object Object],[object Object],Examination of  FMO  Shape (Value)‏
Ester Enolate: Where is the reactive site ? ,[object Object],The ester enolate has two possible sites,  which may react with  electrophiles ;  the anion  and  the terminal carbon .
HOMO of the Enolate HOMO Map of the Enolate The color near red indicates minimum value, and  the color near blue indicates maximum value of HOMO. The terminal carbon,where  HOMO shape (value) is   larger , generally reacts with  electrophile .
Electrophilic Substitution of Indole; What should be favorite position for electrophilic attack ? ,[object Object]
Stereochemistry of Nucleophilic Additions to Carbonyl Compounds Cyclohexanones has two possible faces, which may undergo  nucleophilic  attack;  the axial   and  the equatorial  face. ,[object Object]
Nucleophilic Additions to Dioxanone Ring LUMO   map for the axial face LUMO   map for the equatorial face Nucleophililes  preferentially attack from the  axial  face.
Nucleophilic Additions to Dithianone Ring LUMO   map for the axial face LUMO   map for the equatorial face Nucleophililes  preferentially attack from the  equatorial   face.
[object Object],[object Object],[object Object],The development of several methods  is  in progress   for the  calculation in solution.
[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],They have recently begun to be widely applied  in not only organic chemistry but also biochemistry and closely related fields such as drug design . Explosive developments in computer hardware and software
[object Object],[object Object],[object Object],[object Object],Quantum chemical calculations ( QM ) are expected to become an important method for drug design in the future.

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Computational Organic Chemistry

  • 1.
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11. Range of Molecular Mechanics and Quantum Methods Method Range (heavy atoms)‏ Molecular Mechanics > 1000 Semi-Empirical < 200 Ab initio Hartree-Fock(HF) < 50 Ab initio Correlated < 20 Density Functional (DFT) < 100
  • 12. Relative Computation Times Methylcyclohexane (C 7 H 14 )‏ 14 2 pBP/DN* ( DFT )‏ .06 8 54 - f 1 7 100 AM1 ( Semi-Empirical )‏ HF/3-21G ( Ab initio )‏ HF/6-31G* ( Ab initio )‏ MP2/6-31G* ( Ab initio Correlated )‏ f f MMFF94 ( MM )‏ Geometry Optimization Single-Point Energy Level of Calculation
  • 13. Comparison of the Performance of Molecular Mechanics( MM ) and Quantum Methods( QM ) S= satisfactory; U= unsatisfactory Task     MM Semi- Ab initio DFT     Empirical HF Correlated Geometry S S S S S Transition-state -   S S S S Geometry Conformation S U S S S Thermochemistry -    U S S S
  • 14.
  • 15.
  • 16.
  • 17.
  • 18.
  • 19. Relation between Dihedral Angle and Relative Conformer Energy in 1,3-Butadiene s- trans s- cis twisted Order of stability: s- trans > s- cis > twisted
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25. Determination of Absolute Configuration in A Macrocyclic System by a Combination of Computational Chemistry and Another Method
  • 26. The distance between H-2 and H-13 is 4.0 Å in 13( R )configuration . This is not consistent with information based on NOESY.
  • 27. The distance between H-2 and H-13 is 2.4 Å in 13( S )configuration. This is consistent with information based on NOESY.
  • 28. CD Spectrum Negative Cotton Effect - CD also supports 13( S )configuration.
  • 29.
  • 30.
  • 31.
  • 32. Imidazole: Where is the Basic Site ? The N-3 is negatively charged , and thus is the basic site . Electrostatic Potential Map
  • 33. Acidities of Alcohols stronger stronger weaker weaker 15.5 Methanol 15.9 Ethanol 7.2 4-Nitrophenol 10.0 Phenol 12.4 2,2,2-Trifluoroethanol pKa’s (acidities)‏
  • 34.
  • 35.
  • 36.
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
  • 42. HOMO of the Enolate HOMO Map of the Enolate The color near red indicates minimum value, and the color near blue indicates maximum value of HOMO. The terminal carbon,where HOMO shape (value) is larger , generally reacts with electrophile .
  • 43.
  • 44.
  • 45. Nucleophilic Additions to Dioxanone Ring LUMO map for the axial face LUMO map for the equatorial face Nucleophililes preferentially attack from the axial face.
  • 46. Nucleophilic Additions to Dithianone Ring LUMO map for the axial face LUMO map for the equatorial face Nucleophililes preferentially attack from the equatorial face.
  • 47.
  • 48.
  • 49.
  • 50.

Editor's Notes

  1. Thank you Dr. XYZ for your kind introduction. It is my pleasure to speak to you my seminar “A Review on Computational Organic Chemistry: Basic Concepts and Applications”. I am not computational chemist, but today I would like to introduce usefulness of computational chemistry.
  2. QM can calculate ……… These futures are applied for investigation of…..
  3. dark blue