faculty of science - department of chemistry - division of quantum chemistry and physical chemistry...

Faculty of Science - Department of Chemistry - Division of Quantum Chemistry and Physical Chemistry

KatholiekeUniversiteit

Leuven

Structure-Activity Relationships -

Mechanism development

Luc Vereecken

Research group on reaction kineticsDepartment of Chemistry

Quantum Chemistry and Physical ChemistryK.U.Leuven, Belgium

Structure activity relationships : WP2

Introduction

Task 2.1 : alkoxy decomposition and isomerisation

Task 2.2 : Site-specific NO3 and OH addition on alkenes

Task 2.3 : O3 cycloaddition on alkenes

Task 2.4 : H-abstraction by OH from hydrocarbons

Mechanism development : WP3 - WP5

Task 3.1 : OH + -pinene

Task 3.2 : O3 + -pinene, -humulene, -caryophyllene

Task 5 : Oxygenates + OH : T,P-dependent mechanism

Chemical mechanisms for modeling

Introduction - SARs

Large, explicit mechanisms (e.g. MCM)100s to 1000s of reactions/compounds

But no direct experimental or theoreticaldata on many of these

Use of SAR’s, predictive correlations

Increasing demand for ever-better accuracy Policy-supporting predictions, what-if analyses: - Smog-episodes, chemical weather, climate - Emission control (compounds and quantities)

Need for accurate Structure Activity Relationships

SAR’s and correlations

Structure-Activity Relationship or Predictive Correlation:

Good predictive accuracyEasy to useContinuous development

Working model:

Independent, additive site-specific rate coefficientsktot = ksite (even for different types of reaction)

Most rate coefficients depend primarily on local effects Inductive, hyperconjugative effects don’t carry very far H-bonds, resonances, … must be treated explicitly

Linear models are easy to work with

Addition of OH-radicals on (poly-)alkenes

Introduction

OH-addition on (poly-)alkenes

AlkenesThe rate of addition depends mainly on the substituents of the radical site Cb after addition : X3 X4

OH

Ca CbOH .

Ca Cbk i

x3

x4

x1

x2 x4x2

x1

x3kprim = 0.4510-11 cm3 s‑1

ksec = 3.010-11 cm3 s‑1

ktert = 5.510-11 cm3 s‑1

Conjugated Alkenes : some contribution from second radical siteksec/prim = 3.010-11 cm3 s‑1

ksec/sec = 3.810-11 cm3 s‑1

ksec/tert = 5.110-11 cm3 s‑1

ktert/prim = 5.710-11 cm3 s‑1

ktert/sec = 8.310-11 cm3 s‑1

ktert/tert = 9.910-11 cm3 s‑1

C CH C CR

R

ROH

kC CH C C

OH R R

R

.

C CH C C

R R

R

OH.

resonance

sec/tert


0 5 10 15 20 250

5

10

15

20

25

k SA

R /

10

-11 c

m3 s

-1

kexp

/ 10-11 cm3 s-1

Non-cyclic compounds: Average deviation 9%

All compounds: Average deviation 13% Max. deviation 54%

Can this be improved ? Yes

Residual errors mostly due to H-abstraction contributions

Publication submitted to J. Phys. Chem. A


0 10 20 300

10

20

30

40

Addition Addition+abstraction

k SA

R /

10-1

1 cm

3 mol

ec-1

s-1

kexp / 10-11 cm3 molec-1 s-1

Linear and mono-cyclic compounds


0 10 20 300

10

20

30

40

Addition Addition+abstraction

k SA

R /

10-1

1 cm

3 mol

ec-1

s-1

kexp / 10-11 cm3 molec-1 s-1

+ bicyclic and (near-)conjugated compounds

H-abstraction by OH-radicals

Introduction

H-abstraction by OH radicals

-15

-14

-13

-12

-11

-10

60 70 80 90 100 110D(C-H) / kcal mol-1 ( B3LYP-DFT/6-31G(d5d,p) )

log

(k a

bs

tr /

cm

3 m

ole

c-1 s

-1 )

p

er H

AlkanesAldehydesAlcoholsEthersketones/aldehydesAcidsAlkenesAlkadienesHyperconjugationVinoxy resonance

super-allyl

allyl

vinoxy

hyperconjugation

H-abstraction by OH radicals

Excellent correlation with bond strengthRate coefficient of abstraction determined by D(CH)Correlation is non-linear (data can be fitted by quadratic eq.)

log (k298K) = -0.00328D2 + 0.3869D - 19.392

Resonance stabilization shifts curve: e.g. vinoxy stabilisationlog (k298K) = -0.00315D2 + 0.3840D – 21.860

Dependence similar for all compoundsAngle and curvature similar for all resonances:

Hyperconjugation, allyl, super-allyl, vinoxy.In 1st order approximation: use same value for all

Different resonance stabilizations have different shift

Correlation will break down for oxygenates/H-bonding at low TAt room temperature: Carboxylic acids are already different

Addition of NO3-radicals on (poly-)alkenes

Introduction

NO3-addition on (poly-)alkenes

Addition of NO3 radicals: double interactionThe rate of addition depends on substitution on both carbons:

Fprim = 1.2810-8 cm3/2 s‑1/2 fprim = 1.2810-8 cm3/2 s‑1/2

Fsec = 7.2710-7 cm3/2 s‑1/2 fsec = 3.3010-7 cm3/2 s‑1/2

Ftert = 3.8510-5 cm3/2 s‑1/2 ftert = 7.0210-7 cm3/2 s‑1/2

N

O

OO N O

O

OF

fRadical site: factor FAddition site: factor f

kadd = F f

kadd,site = F f kadd,tot = ksite

Open questions: - Corrections for allyl-resonance stabilization of radical - H-abstraction (e.g. with allyl-resonance stabilization)


1E-16 1E-15 1E-14 1E-13 1E-12 1E-11 1E-101E-16

1E-15

1E-14

1E-13

1E-12

1E-11

1E-10

k NO

3(SA

R)

/ cm

3 s-1

kNO3

(exp) / cm3 s-1

Regular compounds Bicyclic compounds Conjugated alkenes (lin & cyc) Other

Average deviation 1.2


1E-16 1E-15 1E-14 1E-13 1E-12 1E-11 1E-101E-16

1E-15

1E-14

1E-13

1E-12

1E-11

1E-10

k NO

3(SA

R)

/ cm

3 s-1

kNO3

(exp) / cm3 s-1


Average deviation 2.2


1E-16 1E-15 1E-14 1E-13 1E-12 1E-11 1E-101E-16

1E-15

1E-14

1E-13

1E-12

1E-11

1E-10

k NO

3(SA

R)

/ cm

3 s-1

kNO3

(exp) / cm3 s-1


Systematic underestimation


1E-16 1E-15 1E-14 1E-13 1E-12 1E-11 1E-101E-16

1E-15

1E-14

1E-13

1E-12

1E-11

1E-10

k NO

3(SA

R)

/ cm

3 s-1

kNO3

(exp) / cm3 s-1



k(alkene+NO3)

0

5E-15

1E-14

1.5E-14

2E-14

2.5E-14

0 2 4 6 8

# carbons in 1-alkene

rate

coe

ffici

ent c

m3

s-1

ktot(NO3+alkene)

ktot - kabstr(est) ~ kadd(SAR)

Possible influence of H-abstraction: e.g. series of 1-alkenes- Could be sizable for large hydrocarbons- Affected by addition followed by HNO3 elimination ?


Addition to conjugated alkadienes: Substitution effect different than for OH-addition

(partial stabilisation of radical electron by allyl-resonance)

Underestimation seems different for linear and cyclicLinear: underestimation by 0.3Cyclic: underestimation by 0.1

Different addition scheme across -bonds ?

NO

O

ON

OO

O

NO

O

O

Allyl-resonance Interaction across -bonds

Decomposition of alkoxy radicals

Introduction

Alkoxy radical decomposition

Decomposition barrier depends mostly on , -substituents

A first version of this SAR was published as: J. Peeters, G. Fantechi, L. Vereecken, J. Atmos. Chem. 48, 59 (2004)

k(T) = × 1.8×1013 exp(-Eb/RT) s-1

Eb / kcal mol-1 = 17.5 + 2.1 n-alkyl + 3.1 n-alkyl + 8.0 n,-hydroxy + 8.0 n-oxo + 12.0 n-oxo

curvature for small Eb < 7 kcal mol-1 : Eb

' / kcal mol‑1 = Eb + 0.027 (9.0-Eb)2


0

2

4

6

8

10

12

14

16

18

20

0 2 4 6 8 10 12 14 16 18 20

Eb(SAR) (E'b for < 7 kcal/mol)

Eb(e

xptl

; a

b in

itio

)

B3LYP-DFT/6-31G(d(6), p)

B3LYP-DFT/6-31G(d(5), p)

B3LYP-DFT/SVP

G2(MP2/SVP)

Experimental


Current developments (in progress) :

- More quantum chemical methods6-31G(d,p), 6-311++G(2df,2pd), aug-cc-pVTZMPW1K, BB1K, MPWKCIS1K, (CC, Gx, QCI)

- Multi-rotamer TST with (modified) Arrhenius fit SAR for Ea, A, (n)

- More substituents (preliminary) / kcal mol-1:-OR : -9.1 -OR : -9.0-OOR : -7.5 -OOR : =C : +21.1 =C : +4.6-C=C : -5.0 -C=C : -9.6-ONO2 : -3.1 -ONO2 : -2.7 -ONO : -4.2 -ONO : -6.2


Future work:

- Use multi-rotamer TST for alkoxy isomerisation (H-shift)L. Vereecken, J. Peeters, J. Chem. Phys. 119, 5159 (2003)

- Perform URESAM calculations on these systems: Pressure dependence

SAR for Troe Parameters: Fc, k0, …

O3 cycloaddition

No results yet, but see literature

Conclusions - I

OH-addition SAR: Very good accuracyCan only be improved by explicitly incorporating H-abstraction

H-Abstraction correlationVery good correlation with bond strengthCurvature and slope similar, delocalisation shifts curve

NO3 addition SARVery good accuracy for most compounds (1.2, 2.2)Conjugated alkenes are underpredicted delocalisation effects

Alkoxy decomposition SAR:Being extended (substituents and methodology)Data serves as basis for alkoxy isomerisation SAR

Four site-specific predictive SARs:

Part II: Mechanism developmentTerpenes and sesquiterpenes

Introduction - Mechanism development

OH-initiated oxidation of -pinene using traditional chemistry:

Chemistry of -pinene + OH

OHCH2OH

OO-pinene

promptring opening

70%

+OH

+O2

90%

NO

NO2

CH2OH

O

CH2OH

+ acetone

Prediction of 60 % acetone formation

Experiment: acetone yields 8% (Aschmann et al, 1998)2% (Orlando et al., 2000)13% (Wisthaler et al., 2001)

?

Peroxy ringclosure in isoprene / terpenes :

-pinene

-pinene

peroxy ring closure+ O2

OO

OO

OH

OH+ OHring opening+ O2

OO

OHOO

OO

OO+ OHring opening+ O2

OHperoxy ring closure+ O2

Chemistry of unsaturated (per)oxy radicals

Ring closure in -pinene + OHO

+NO

-NO2

+O2

+ CH2OHOH

CH2OH

OO

-pinene

promptring opening

30%

70%

+OH

CH2OH

OO

ringclosure

OO

CH2OH

+NO

-NO2

+O2

OO

CH2OHO syn: 7.09 kcal/mold

anti: 7.90 kcal/mold

10.2 kcal/mols

OO

O

OO

OHO

+ CH2OH

+NO

-NO2

CH2OH

O

CH2OH

O

CH2OH

O

O+NO

-NO2

+O2

2.8 kcal/mols

12.3 kcal/mols

O

CH2OH

O

+NO

-NO2

+O2O

O

O

+ CH2OH

CH2OH

O

+NO -NO2

+O2

CH2OH

O

O

anti; 5.70 kcal/mold

syn: 8.28 kcal/moldanti: 3.78 kcal/mold

syn: 3.98 kcal/mold

10.2 kcal/mols

O

O

+ CH2OH

O

O OH

OO

+NO

-NO2

+O2

O

HO

OHO

O

6 ring closure

5 ring closure

anti: 8.7 kcal/mold

syn: 5.05 kcal/mold

O

OHO

O

CH2OH + O2 CH2O + HO2

spont.

OHO

O+ acetone

HO

OHO

O

7.1 kcal/mols

0 kcal/mole

11 kcal/mold HO

OHO

O

*

HO

OHO

O

HO

OHO

- CO

collision

activated

56 kcal/mold + Etherm

+NO

-NO2

+O2

HO

OHO

HO

- CH2O

11.3 kcal/mols

HO

OO

HO

HO

OHO

O

+O2-HO2

2.76 kcal/mold

+NO

-NO2

+O2

- CO2

5.5 kcal/mols

8.15 kcal/mold

HO

OHO

HO

HO

OHO

HO

11.26 kcal/mold

H-shift

+ O2

- HO2

O O

OHO

O O

OHO

O

+O2

O O

OO

HO

O

+NO

-NO2

+O2

O O

OHO

HO

O O

OHO

HO

O O

OHO

HO

-HO2

3 kcal/mole

9.5 kcal/mole

7 kcal/mole

O O

OHO

- CH2O

11.3 kcal/mols

syn: 5.15 kcal/mold

anti: 1.9 kcal/mols

syn: 4.04 kcal/mold

syn: 4.10 kcal/mold

anti: 2.96 kcal/mold

Mininum C

Mininum B

16.19 kcal/mold

O

CH2OH

O

HO

H-shift

ringclosesyn: 13.3 kcal/mold

activated

46 kcal/mold + Etherm

ether ringopenanti: 18.3 kcal/mold

- acetone

CH2OH

+O2

-pinene + OH

O

+NO

-NO2

+O2

+ CH2OHOH

CH2OH

OO

-pinene

promptring opening

30%

70%

+OH

+O2

Nopinone: 25 %

CH2OH

OO

ringclosure

+NO

-NO2

OO

CH2OH

+NO

-NO2

+O2

OO

CH2OHO

OO

OHO

O

OHO

Ospont.

HO

OHO

O

HO

OHO

+NO

-NO2

+O2

HO

OHO

O

HO

OO

HO

- COCH2OH

O

H-shift

+O2 -HO2

-pinene + OH

Peroxy ring closure path forms dicarbonyl dihydroxy compound

-pinene + OH

CH2OH

O

CH2OH

+ acetone

CH2OH

O

CH2OH

O

O

O

O

O O

OO

HO

About 4 %

Chemistry with oxy ring closure finds low acetone yield comparable to experimental findings

Compounds formed are highly oxygenated cyclic esters, formates

0%

10%

20%

30%

40%

50%

60%

70%

80%

10 31.6 100 316 1000 3162 10000 31620 100000 316226 1000000

-pinene + OH

10ppt

100ppt

1ppb

10ppb

100ppb

1ppm[NO]

Peroxy chemistry ROO + R’OO/HOO(pre- and post ring closure)

Peroxy ring closuredi-OH-di-carbonyl

Oxy ring closure

Degradation mechanism depends on [NO], [HO2/RO2]

-pinene + OH

.

bpineneRC3

1

5

4

3

2

8

7

610

9

1. +O2

2. +NO -NO2

3. 1,6-H-shift+ 27% nitrate

1. +O2

2. +NO -NO2

3. breaking(3-4)+ 27% nitrate

1

5

4

3

2

8

7

610

9

OH

bpineneOH3RC10

.

1. +O2

2. +NO -NO2

3. 1,5-H-shift+13% nitrate .

1

5

4

3

2

8

7

610

9

OHHO

bpineneOH3OH10RC4

1. +O2

2. +NO -NO2

3. breaking(3-4)+ 28% nitrate

1. +O2

2. +NO -NO2


.

1

5

4

3

2

8

7

610

9

OHHO

R7RC10

1. +O2

2. -HO2.

1

5

4

3

2

8

7

610

9

OHO

R7O10

.

1

5

4

32

8

7

610

9

OH

HO

O

R6RC3

1. +O2

2. +NO -NO2

3. breaking(2-3) -HCOOH

.

1

5

4

2

8

7

610

9

HO

O

S1RC2

1. +O2

2. +NO -NO2

.

1

5

4

2

8

7

610

9

HO

O

O

S1RO2

. 1

5

4

2

8

7

610

9

HO

O

O

S1RC1

High NO concentration, at laboratory conditions

. 1

5

4

32

8

7

610

9

OH

HO

O

R6RC1

.

1

54

32

8

7

610

9

OH

HO

O

OH1. +O2

2. +NO -NO2


1

5

4

32

8

7

610

9

O

HO

OR6O3

1. +O2

2. -HO2.

1

5

4

3

2

8

7

610

9

O

.

P1RC4

1. +O2

2. +NO -NO2


1

54

32

8

7

610

9

.

O

OH

P1OH4RC3

1. +O2

2. +NO -NO2

3. breaking(2-3) -CO2

1

54

2

8

7

610

9

.

OH

R1RC2

1. +O2

2. +NO -NO2

1

54

2

8

7

610

9

.

OH

R1RO2

O

1

54

32

8

7

610

9

. O

OH

P1OH4RC1

1

54

2

8

7

610

9

.

OH

R1RC1

O

1. +O2

2. +NO -NO2

3. breaking(1-2) -CH2O + 13% nitrate

54

2

8

7

610

9

.

OH

S5RC2

O

1. +O2

2. +NO -NO2

3. breaking(2-7) -CO2

54

8

7

610

9

.

OH

T1RC7

1. +O2

2. +NO -NO2

3. breaking(7-8)5

4

8

7

10

9

.OH

O6

U1RC8

1. +O2

2. +NO -NO2

3. 1,5-H-shift+ 9% nitrate 5

4

8

7

10

9

.

OH

O6

V1RC7

HO

1. +O2

2. +NO -NO2

3. breaking (6-7) -CO2 5

4

8

10

9

.

OH

6

W1RC6

HO

. 1

5

4

3

2

8

7

610

9

bpineneRC1

1. +O2

2. +NO

-NO2

3. +O2

4. -HO2.

+ 13% nitrate

1

5

4

3

2

8

7

610

9

bpineneO1

O

52%

48%

8%

92%

S2RC4

64%

36%

Minor H-abstraction channels (Klara Petrov)

Mainly formation of larger (multisubstituted) oxygenates. Larger products should nearly all be reactive to OH, O3, NO3

-pinene + O3

Other mechanisms

Some additional theoretical verification on impact of- ring closure- low-NOx chemistry

Mechanism sufficiently mature for modeling (see BIRA)

Sesquiterpenes + O3

No results yet

Oxygenates + OH

Introduction

General mechanism:

Oxygenates + OH

T,P-dependences:

Oxygenates + OH

Barriers above reactants: Formation of pre-reactive complexes not too important

Positive T-dependence (except at low T: tunneling)No P-dependence

Barriers below reactants: Chemical activation effects

Negative T-dependence at all TPressure dependent

See: Peeters and Vereecken, Int. Symp. Gas Kin. 2006

Specific issues for theoretical work on oxygenate+OH reactions

Oxygenates + OH

- Calculation of tunneling contributionsSmall-curvature corrections most often usede.g. Masgrau et al., J. Phys. Chem. A 106, 11760 (2002)

tunneling contribution 22 at 202 Kfor acetone+OH

- Variational effectsH-abstraction over H-bonds: low and broad TSVariational effects can be important

(kinetic bottleneck not at energy maximum)e.g. Masgrau et al. 2002 (acetone+OH)

variational effects up to order of magnitude

- Specific reaction pathways(See acids)

Acetone + OH

The reaction of acetone + OH shows a curved Arrhenius plot:

Wollenhaupt, Carl, Horowitz, Crowley, J. Phys. Chem. A 104, 2695 (2000)

Gierczak, Gilles, Bauerle, Ravishankara, J. Phys. Chem. A

107, 5014 (2003); Talukdar et al., J. Phys. Chem. A 107, 5021 (2003)

Acetone + OH

Theoretical work shows the general features of the PES:

Vandenberk, Vereecken and Peeters, PCCP 4, 461 (2002)

Similar PESes by Masgrau et al., J. Phys. Chem. A 106, 11760 (2002)Vasvári et al., PCCP 3, 551 (2001)

Hydroxyacetone + OH

The reaction of hydroxyacetone + OH : Negative T-dependence

Dillon, Horowitz, Hölscher, Crowley, Vereecken, Peeters, PCCP, 8, 236, 2006

Hydroxyacetone + OH

Accuracy of barrier heights did not allow for finaltheoretical kinetic predictions.

Glycolaldehyde + OH

The reaction of CH2OHCHO+ OH : No T-dependence

Karunanandan, Hölscher, Dillon, Horowitz, Crowley, Vereecken, Peeters, submitted for publication

-Slowdown relative to CH3CHO: due to charge distribution - Lack of T-dependence: due to specific barrier height:

200 300 400 500 600 700 8002.0

2.1

2.2

2.3

2.4

2.5

2.6

2.7

2.8

2.9

3.0

k eff (

a.u

.)

Temperature / K

RRKM-MEsimulation

Stringent requirements for theoretical methodologies

Oxygenates + OH

Quantum chemical methods: very high level needed Calculation of energiesBut also for calculation of geometries and frequencies

Mechanism developmentUnexpected mechanisms can exist

Kinetic methodologies: Important effects ofTunneling (SCT or better needed)Variational effectsAnharmonicity effectsMulti-conformer (multi-well) effectsMultiple pathwaysInternal rotors

Conclusions - II

-pinene + OH Very complex reaction mechanismDepends strongly on [NOx] versus [ROO/HOO]Many fast unimolecular reaction steps

reduction of mechanism possibleIn progress

Terpenoids + O3

In progress

Oxygenates + OH :

Very complex kineticsStringent demands on theoretical methodologyT,P-dependence of k(T) or product distribution still difficult

Mechanism development

faculty of science - department of chemistry - division of quantum chemistry and physical chemistry...

Documents

oh addition

cm3 s1ohaddition

oh radicalshabstraction

cm3 s1ktert

cm3 s1ksec

cm3 s1 kterttert

cm3 s1 ksecsec

cm3 s1 ksectert