a pplications of ets-nocv method in description of various t ypes of chemical bonds
DESCRIPTION
A pplications of ETS-NOCV method in description of various t ypes of chemical bonds. Mariusz P. Mitoraj. Jagiellonian University Cracow, Poland Department of Theoretical Chemistry. ADF webinar, Kraków-rest-of-the-world, 28th Feb., 2014. - PowerPoint PPT PresentationTRANSCRIPT
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Applications of ETS-NOCV method in description of varioustypes of chemical bonds
Mariusz Mariusz P. P. MitorajMitoraj
Jagiellonian UniversityCracow, Poland
Department of Theoretical Chemistry
ADF webinar, Kraków-rest-of-the-world, 28th Feb., 2014
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Examples of theoretical quantities for visualization of chemical bond
ADF webinar, Kraków-restoftheworld, 28th Feb., 2014
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Formation of chemical bond in H2 – based picture
H H
H2
HH 22 Deformation density (Differential density)
(1) qualitative databy inspection of the signof : negative (outflow),positive (inflow) of densitydue to bond formation
H H
1. Start from promolecular state (atom/fragments)
H=1s2 H=1s2
ADF webinar, Kraków-restoftheworld, 28th Feb., 2014
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The Natural Orbitals for Chemical Valence (NOCV)The Natural Orbitals for Chemical Valence (NOCV)
NOCV’s also decompose the deformation density :
useful qualitative databy inspection of the signof : negative (outflow),positive (inflow) of density
M
1k
2kk )r(ψv)r(ρ
Mitoraj, M.; Michalak, A. Organometallics 2007, 26(26); 6576., Michalak, A.; Mitoraj, M.; Ziegler, T. J. Phys. Chem. A. 2008, 112 (9), 1933, Mitoraj, M.; Michalak, A. J. Mol. Model., 2008, 14, 681, Mitoraj,
M.; Zhu, H.; Michalak, A.; Ziegler, T. 2008, International Journal of Quantum Chemistry, DOI: 10.1002/qua.21910., Mitoraj, M.; Michalak, A. J. Mol. Model. 2008, 14, 681.
NOCV’s ( ) diagonalize the deformation density matrix:
PCi v iCi ; i =1,M
where P=P-P0 , density matrix of the combined molecule,P0- density matrix of the considered molecular fragments.
i
iiji λ*Cψ
(r) vk[ k2 (r) k
2
k1
M / 2
(r)] k (r)k1
M / 2
NOCV’s are in pairs:
Radoń, M. Theor Chem Account 2008, 120,337.
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backdonation
donation
backdonation
The contours of the deformation density (The contours of the deformation density () and the contributions) and the contributionsfrom the pairs of complementary orbitals for the heme/CO systemfrom the pairs of complementary orbitals for the heme/CO system
rr i
n
ii
2
1
)(
q = 0.74q = 1.04
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-De=Etotal= Edist + Eelstat + EPauli + Eorb ETS:
λ μ
TSλμ
orbλμorb FPE
2/M
k
korb
TSk
2/M
1k
TSkkorb E]FF[vE Energetic estimation
of k
A combination of ETS and NOCV - (ETS-NOCV)A combination of ETS and NOCV - (ETS-NOCV)
NOCV:
2/N
1kk
2/N
1k
2k
2kk
orb )r(ρ)]r(ψ)r(ψ[v)r(ρ
2/N
1k
orbk
2/N
1k
TSk,k
TSk,kk
TSorbTSorborb E]FF[v)CFCCPC(Tr)FPTr( E
ETS-NOCV:
Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler „A combined charge and energy decom-
Position scheme for bond analysis” J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.
electronic factor
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Dative bonds – systems with symmetry Dative bonds – systems with symmetry
(CO)5Cr=CH2
donation
backdonation
:CN- > PH3 > NH3 > C2H4 > CS > CO > N2 > NO+
:NO+ > CS > CO > N2 > C2H4 > PH3 > CN- > NH3
for Ni(NH3)3 X complexes:Donor/acceptor properties of ligands
Mitoraj Mariusz, Michalak A (2007) „ Donor-Acceptor Properties of Ligands from the Natural Orbitals for Chemical Valence” Organometallics, 26, 6576-6580
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Dative Bond NHDative Bond NH33BHBH3 3 - Calculations- Calculations
• Define closed shell fragments, NH3 and BH3
• Run SP calculations to get the fragment MO’s• Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s
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Dative Bond NHDative Bond NH33BHBH3 3 - Calculations- Calculations
M.Mitoraj J. Phys. Chem. A, 2011, 115 (51), pp 14708–14716
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Crystal of Ammonia Borane, NHCrystal of Ammonia Borane, NH33BHBH33
M.Mitoraj J. Phys. Chem. A, 2011, 115 (51), pp 14708–14716
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Inter-Molecular-Hydrogen BondsInter-Molecular-Hydrogen Bonds
Adenine-Thyminekcal/mol,
(BP86/TZ2P)A-T
Eint -13.0
Eorb -22.0
EPauli 38.7
Eprep 2.1
Eelstat -31.9
Etotal-experiment99 -12.1
Etotal – other
theoreticalresults
-13.2
Eorb=-22.0
Rafał Kurczab, Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler J. Phys. Chem. A,2010, 114, 8581.
N*(H-N)
H-N covalency!
O-H
O*(H-N)
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Hydrogen Bond A-T CalculationsHydrogen Bond A-T Calculations
• Define closed shell fragments, Adenine and Thymine• Run SP calculations to get the fragment MO’s• Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s
ADF webinar, Kraków-restoftheworld, 28th Feb., 2014
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Covalent bondsCovalent bonds
CHCH33-CH-CH33 CHCH22=CH=CH22GeHGeH22=GeH=GeH22 HH33CCCCCCHCCH33
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Quadruple bond; ReQuadruple bond; Re22ClCl882-2-
[-1.3 kcal/mol]
1[-65.5 kcal/mol]
2[-65.5 kcal/mol]
[-84.3 kcal/mol]
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Etotal=-31.3kcal/molEorb=-242.7Esteric=211.4
Cr2, formally sixtuple bond, bCr2-Nal = 6.01
Eorb=-242.7 kcal/mol
Typical-Multiple bonds-TMTypical-Multiple bonds-TM
J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.
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Ethane Built from two methyl radicalsEthane Built from two methyl radicals
1. Define CH3 regions (uneven number of electrons);2. Run SP RESTRICTED ! Calculations for CH3 fragments to get the fragment MO’s; (1/2 + 1/2 electrons for SOMO of CH3)3. Use fragoccupations keyword in order to keep the right occupations for each CH3
fragoccupations f1 A 5 // 4 subend f2 A 4 // 5 subend End
4. Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s -alpha-and beta-NOCV’s
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Etotal=-31.3kcal/molEorb=-242.7Esteric=211.4
Cr2, sextuple bond, bCr2-Nal = 6.01
Eorb=-242.7 kcal/mol
Typical-Multiple bonds-TMTypical-Multiple bonds-TM
J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.
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CrCr22 Built from two Cr Built from two Cr++CrCr
1. Define Cr regions (uneven number of electrons);2. Run SP RESTRICTED ! Calculations for Cr fragments using OCCUPATION keyword (A 18 1 1 1 1 1 1);Should be like CrShould be like Cr but it is Cr 6* but it is Cr 6* (1/2 + 1/2) so we must:3. Use fragoccupations keyword in order to keep the right occupations for each Cr.
fragoccupations
Region_1
A 15//9
subend
Region_2
A 9//15
subend
End
4. Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s
CrCr
CrCr
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Better Fragment MO’s from unrestriced run:Better Fragment MO’s from unrestriced run: advanced ’manual’ usageadvanced ’manual’ usage
1. Run open shell calculations for a given fragment;
2. Save tape21 ascii (dmpkf) copy the final MO’s(from the section Eig-CoreSFO_A, MO’s expressed in SFO);
3. Run fragment calculations by setting SCF=0 wrong MO’ssave tape21asciifind Eig-CoreSFO_A section, then:
4. Take MO’s and occupations, energies, from step 2 and paste them toTape21 from step 3…..it gives you right fragment MO’sTransform asciibinary(udmpkf);
ADF uses in principle only ‚rectricted’ fragments, however, one might cheat him
5. Rerun final ETSNOCV calculations (do not recalculate the fragments!)
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Agostic intramolecular RH---Metal interactionAgostic intramolecular RH---Metal interaction
Ni-diimine cationic Brookhart model catalyst
Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler „On the Nature of the Agostic Bond between Metal Centers and -Hydrogen Atoms in Alkyl Complexes. An Analysis Based on the Extended Transition State Method and the Natural Orbitals for Chemical Valence Scheme (ETS-NOCV)”
Organometallics, 2009, 28 (13), pp 3727
Ni-C
C-Hpolarization
C-C
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ETSNOCV(red-outflow,blue-inflow) -8.3 kcal/mol
Halogen Bonding CFHalogen Bonding CF33I---NHI---NH33 from ETS-NOCV perspective from ETS-NOCV perspective
N
H
H
H
I CF
FF
N-I covalency
N*(C-F)
charge accumulation, increase s-character (pointed out by prof. Grabowski)
Charge outflow, increase positive charge
Grabowski S. Chem. Rev., 2011, 111 (4), pp 2597–2625
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Domination of the electrostatic factor is due to the presense of σ-holeon iodine atom:
FF
F I
Halogen Bonding CFHalogen Bonding CF33I---NHI---NH33 from ETS-NOCV perspective from ETS-NOCV perspective
(Politzer P, Lane P, Concha MC, Ma Y, Murray J (2007) JMolModel, 13, 305, „An Overview of Halogen Bonding”
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Halogen Bonding CFHalogen Bonding CF33I---NHI---NH33 from ETS-NOCV perspective from ETS-NOCV perspective
Prof. Politzer, „Program & Book of Abstracts”, MIB 2011,„….The weakness of this interpretation (electrostatic) is that it is simple and straightforward, and therefore is viewed by some with suspicion.
C
F
F
F
I
FF
F I
Electrostatic potential picture
ETS-NOCV picture
(C-F) bond
-hole
Charge Anisotropy
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Can ETS-NOCV discriminate between halogen and hydrogenCan ETS-NOCV discriminate between halogen and hydrogen bonding within the same molecule?bonding within the same molecule?
Anion receptor based on urea, which involve hydrogen and halogenBonding at the same time|:
Chudzinski, et all, JACS, 2011, 133, 10559
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Can ETS-NOCV discriminate between halogen and hydrogenCan ETS-NOCV discriminate between halogen and hydrogen bonding within the same molecule?bonding within the same molecule?
-22.3 kcal/mol -6.3 kcal/mol
Yes: ETS-NOCV can separate halogen and hydrogen connections
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Cl- / restCl- / rest
• Define closed shell fragments, Cl minus + rest of the complex• Run SP calculations to get the fragment MO’s• Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s
ADF webinar, Kraków-restoftheworld, 28th Feb., 2014
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Thank You very much for Thank You very much for Your Attention! Your Attention!
ADF webinar, Kraków-restoftheworld, 28th Feb., 2014