RMGStudyGroup 06 Group Additivity

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RMG group meeting, 11/01/2013

Thermo in RMG




Group additivity



The experimentalist’s problem…

3


S

SH SH2

What are the dominant reaction paths? What are the intermediates?

?

REACTANT

PRODUCTS

REACTOR



Modeling reaction mechanisms

4

•

Required information – How fast does each reaction proceed? (rate

coefficients k )

– Energy balance: during reactions energy is

exchanged between the enironment and the

compounds (H ! S and c p)

• "hat is aailable? – #f we are luc$y:

•

experimental data (%#&')• (empirical) correlations between $inetic and thermodynamic

parameters! eg Eans*olanyi

– &tructural information: atoms and their connectiity

(bonds)




The benefits of sizing down

*roperty (molecule) + , property (subsystem)

'R-%&.ER-/#0#'1


Chinese characters:

33334! each word one

character

Alphabet:

25 letters to ma$e all

possible words

anestri asterin eranist nastier

ratines resiant restain retainsretinas retsina sainter stainer

starnie stearin



Towards smaller entities

!

REACTONS

REACTOR SDE

CO!POUNDS

"ROUPS

SH 4 S 4

r

r

G

RT K e

∆ °−

=

r f ( )ii

G v G i∆ ° = ∆ °∑

f gr ( ) ( ) g

G i G g ∆ ° = ∆ °∑

CH

CH# CH#

C

CH#

CH CH#

C

$ONDS gr bond( ) ( )

b

G g G b∆ ° = ∆ °∑C % C•C• % H




Group contribution methods for thermo

"

6- methods differ:a) 7efinition of the groups

b) 'he way properties are calculated from the 6-8s

CHCH#CH#

CH# 9obac$ : ;H 4 < ;H<

/enson : ;(;)<(H) 4 < ;(;)(H)<

9obac$ :

∆f H ° (298 K) = 68.3 + ∑i GAV H

S ° (298 K) = (14.4 + ∑i GAV H ─ G )/298

/enson:

∆f H ° (298 K) = ∑i GAV H

S ° (298 K) = ∑i GAVS + R ln (nop/!)




6roup + central atom with all of

its neighboring ligands

eg S&'C('H(

C&'S('C('H()

C&'C()'H()

C&'C('H(#

4 nonnearest neighbor

interactions (NNs)

• /enson diided molecules into (functional) groups

•

%%#s are often hard to recogni=e (eg >han et al 9 *hys;hem - 233 < @5A)

• 8arious Baa applets are aailable:

#enson group additivity

$

http:CCwebboo$nistgoCchemistryCgrpaddC

http:CCrmgmiteduCmoleculeDsearch


http://var/www/apps/conversion/tmp/My%20Documents/Artikels%20GAVs%20thermo%20S/Khan_JPhysChemA_2009_thermo%20of%20O%20N%20radicals%20and%20molecules.pdf

http://webbook.nist.gov/chemistry/grp-add/

http://rmg.mit.edu/molecule_search

http://rmg.mit.edu/molecule_search

http://webbook.nist.gov/chemistry/grp-add/

http://var/www/apps/conversion/tmp/My%20Documents/Artikels%20GAVs%20thermo%20S/Khan_JPhysChemA_2009_thermo%20of%20O%20N%20radicals%20and%20molecules.pdf




%MG thermo



– 6roups: /enson groups

– Radicals: hydrogen bond increments

– 6auche

–

! – ther: cis C trans

– Ring

– *olycyclic

&verview of the thermo libraries

'(


H;H

<

H;H

<

H

H

H

H

H

HH

HH

;H< H

;H<

H

HH

H

-nti 6auche

WE** DE+NED,

*ESS WE**

DE+NED-



)mplementation

''


• 6raph based recognition of (corrector) groups

2 6auche F F

G ;s 3 2!&I <!&I A!&I !&I

2 ;s 3 !&I 5!&I @!&I J!&I

< ;s 3 !&I !&I 3!&I !&I

A ;d!;dd!;t!;b!;bf!s!;!HI 3 !&I ;d!;dd!;t!;b!;bf!s!;!HI 3 !&I

5 ;s 3 2!&I

@ ;s 3 2!&I

J ;s 3 2!&I

;s 3 <!&I

3 ;s 3 <!&I

;s 3 <!&I

Cs.

Cs

H H

Cs

Cs

Cs

Cs

Cs

Cs

Cs



Group library

'*


• 0ibrary K 7ictionary K 'ree files containing the

group alues! group definitions and

dependencies respectiely

• #n contrast to $inetic libraries there is no

automated filling of the tree – Eery node needs a 6- alue or reference

– Example:

33 & Ss&CsCs

<2 &sHH <@ 32 J JAJ JJ 25 33J L

<< &s;sH 3 <<5J 5@ 522 5A3 55 @J L

<A Ss&CsCs 52@ < 522 5J@ @25 @ @A L

6roup 4 6-8(H) 4 6-8(&) 4 6-8(cp <33 A33 33 533 J33 333 33)

dH d& dcp ;omments



Group library

'3


• ;hanging this library should Kin my opinionK be

aoided to all cost – 0inear dependencies

– ;orrections (gauche! cisCtransL) depend on the

alues assigned to the groups

!odi/0in1 the 1ro2p 3al2es can ha3e /ar reachin1

conse42ences,

• -dding new groups (&! %! ;l! /rL) can be done

relatiely easy

i / /



%adical library

'4


• Hydrogen bond increments – -dantage oer radical centered groups (eg ;M(;)

( H)<) in flexibility and interpretability

– 7escribe the influence of the loss of a hydrogen atom

on the enthalpy (related to /7E)! entropy and c pN

– ne drawbac$ is their use for biradicals as they

normally account for the spin multiplicity of 2

RMG i / /



Gauche library

'


Read the manuscript and what the corrections

account forO

R!" $enson Sabbe

2 x ;s(;s(;s;s;s);s;s;s)

5 6 "AUCHE CORR7 5 6 "AUCHE CORR7 5 8 "AUCHE CORR7

H;H

< H;H

<

H ;H<H ;H

<

H;H

<H;H

<

RMG i / /



'+ library

'!


• ;rowded methyls

RMG ti / /



%ing,-olyring library

'"


• Ring corrections are added to account for the

strain caused by a ring

• ther %%#Ps are accounted for as they wouldappear in the open ring analogue

•

*olyring tree deiates slightly from the othertrees as priority can be assigned:

"hen two hits are receied RQ6 only uses the first hitO

)"r#ng($%&))'()&(&(GAV")n*lopn( 22f +−=∆ H

RMG ti 11/01/2013




Thermo from .)

RMG group meeting 11/01/2013



• *artition functions describe the statistical properties of a

system and can be used to derie thermodynamic

properties (enthalpy! entropy! heat capacity)

• /ut there is a snatchL

/ow do theoreticians calculate thermo0

'1

2

lnln( )

ln

V

V

p

p

qS R q e RT

T

q

H RT RT T

H C

T

∂ = + ÷∂ ∂

= + ÷∂ ∂ = ÷∂

,

-

1 1

i jnk T

i j

q e

ε ∞ −

= =

= ∑∑n + number of modes

#*-;:“Chemical species = an ensemble of chemically identical molecular

entities that can explore the same set of molecular energy levels on

the time scale of the experiment.”





2pecies fT 5

*(

99 );#

τ 5 <7; ns τ 5 = da0s

One species,

ts S > 5 )87) @mol&< &<7

detect to di//erent speciesB

their S > 5 ))79 @ mol&< &<7





• #mportant to $now how the 6-8s hae been

obtained: fitting to experimental data! calculated

data (H S n7HR S multiconformer)

• Experimental data + measuring mixture of

arious conformers

6 <) <8 )9 # #6

)

9

6

8

<

6hat’s in a name0

*'θ (N)

( $ 9

m o l : )





6roup + central atom with all of

its neighboring ligands

eg S&'C('H(

C&'S('C('H()

C&'C()'H()

C&'C('H(#

4 nonnearest neighbor

interactions (NNs)

• /enson diided molecules into (functional) groups

#enson group additivity

**


f f

op

(298 ) ( )

(298 ) ( ) ln( / )

( ) ( ) p

H ii

S i

i

p C i

i

H K GAV X

S K GAV X R n

C T GAV X

σ

∆ °

°

°

∆ ° =

° = −

° =

∑∑

∑




2ymmetry numbers

*3

• &ymmetry numbers are used to aoid

oercounting of equialent energy leels

•

! Cnopt can depend on the interpretation of theresearcher

o #n σ σ σ =

#n 3σ =

36 (0 )σ =

#n 1 or 2σ =

1σ =





• ;onstruction of a matrix lin$ing the 6-8Ts with

the molecules in the training set

•0inear regression 4 statistics – -oiding linear dependencies

– Qinimi=ing sum of squares: ∑(y i" i)2

7erivation of the G.8’s from ab initio data

*4

H&;H2;H<

H&;H2;H2;H<

&(;)(H) ;(&)(;)(H)2 ;(;)(H)<∆f H °

4.3

68.2

1

1

1 1

1 1

H&;H2;H2;H2;H< 88.1 1 1 1

;(;)2(H)2

1

2

yGAV 1

5)55( −=

+ set of linear equations

&ignificance of regression

( )

( )∑

∑

=

=

−−

−><−

=n

i

ii

n

i

i

y y pn

y y p

F

1

2

2

1

1

1

1

; &HH

H

H

&(;)(H);(&)(H)<





• 8arious groups contributions will be set to fixed

alues (of a similar group)

• "hen combining arious sets of 6-8Us care

need to be ta$en that those fixed groups were

assigned the same alue

9inear dependent set of e:uations

*


; &H

H

H

H

&(;)(H);(&)(H)<

a C&centered 1ro2p ha3in1 a S li1and ill

ala0s be accompa1nied b0 a S&'C( 1ro2p

and can not be sol3ed independentl0,

;()(H)< 4 (;)2

>han et al K 333 K 333 K 2<J + KA<2 $cal mol

;ohen et al K 333 K 333 K 2<J + KA<J $cal mol




• Hydrocarbons and organosulfur compounds

– Q-7(Vf H N) + 2 $9 mol

– Q-7(SN) + 9 mol >

– Q-7(c pN) + < 9 mol >

• -mount of groups increases fast with the

inclusion of heteroelements

•"hat to do if groups are not aailable?

#enson group contribution method

*!


;H C Cd Ct Cb 5 ;

O CO 5 )<

S CS 5 9=

9obac$WX and 6aniW2X Y 3 $9 mol W<X

Y methods of 9obac$ and 6ani W<X

;(&)(;)(H2) + 235J $9 mol ;(&)(;2)(H) + J2 $9 mol

;(&)(;t)(H2) + 2@ $9 mol ;(&)(;)(;t)(H) + ? $9 mol

&87)= '&<<7); F '&)768(( 5 <7<) G@ mol&<

WX 9obac$ and Reid Chem. #ng. Comm. @: 2<<2A< (J@)! W2X ;onstantinou and 6ani $iche %. A3: 5@@3 (A)! W<X discussed in Z'he properties of gases and liquids[ by *oling! *rausnit= and Tconnell (2333)





6hat if ) want to

calculate ' ringcorrection0




.tomic,bond corr vs %eaction

*$


• ;/&F/< calculation:

9*3 H (2J >) + <JJ@2A h

• ;alculated energy contains errors in relatiistic

effects! diagonal / corrections! extrapolation

errorsL but errors tend to be structure specific

• Error canceling transformations: reaction

enthalpies

4 H) CH9<<<

so10ric reaction : n2mber o/ electron pairs is conser3ed

5 AAC 'atom additi3e corrections(




Method selection

*1

G g oup meeting, /0 / 0 3

#sogyric #sodesmic Hypohomo

desmotic

Homodes

motic

Hyperhomo

desmotic

sodesmic reaction : t0pe o/ bonds is conser3ed

H0pohomodesmotic : same h0bridiation 'e4 spB sp) and sp# C atoms(Homodesmotic : bonds in3ol3in1 same h0bridiation




%outine

3(

g p g, / / 3

?

• ;hec$ if corrections are

applied and correctlydefined +

'hermodataEstimator

• Ring correction +

difference between RQ6

predicted alue and the

calculated alues

•

-dd node to tree! libraryand dictionary

• ;hec$ if RQ6 estimate

corresponds with

calculated alue




%outine

3'

g p g, / / 3

4 ) CH9+4

sodesmic

E\*: 33 3J ] 3 ? @A5 ] 3<

Vr H (2J >) + 223J $9 mol

Vf H (2J >) + 3 $9 mol

R&; (H& + 2<< $9 mol

"hat if RQ6 predictsa wrong symmetry

number?




.dvantages of inclusion in groups

g p g, / / 3

OOH OOH O

4 OH

OO