Cundari Th.R. -- Computational Organometallic Chemistry-0824704789

TABLE 1

Summary of the Application of Molecular Mechanics to Organometallic Catalysis, with Examples

Reaction

Catalyst

Program

Force field

Added parameters

Purpose

Ref.

Allylation

3

-Allyl palladium com-

MacMimic

MM2

3

-Allyl-Pd interaction

Model the stereoselectivity

93

η

η

plexes with chiral

(91,92)

in complexes with confor-

phenanthroline li-

mationally flexible li-

gands

gands in asymmetric ally-

lation

Allylation

3

-allyl palladi-

MacroModel

MM2

Derived from crystal struc-

Determine the factors that

94

Chiral η

um(II) catalysts

ture data; available as

govern stereodifferenti-

supplementary material

ation in [(chiral diphosphi-

3

com-

ne)Pd(η -allyl)]

plexes

Allylation

3

-Allyl palladium(II) cat-

MacMimic

MM2

Obtained from the litera-

Quantify the steric interac-

95

η

alysts

ture (91)

tion between an incom-

3

ing nucleophile and η -al-

lyl palladium complex

during allylation

Dihydroxylation

Osmium tetraoxide with

MacroModel,

Modified

NH

-type nitrogen parame-

Explain enantiofacial selec-

97

3

various other ligands

MacMimic

MM2, MM3

ters taken from MM2(91);

tivities and selectivity

osmium parameters

trends observed for the

taken from the literature

various olefin classes

(96)

Epoxidation

Mn(salen) complexes

MacroModel

MM3

Parameters for Mn ob-

Probe mechanism of epoxi-

99

MM3

tained from crystal struc-

dation by Mn(salen) com-

ture data (98)

plexes via metallaoxe-

tane intermediates

Force field devel-

Metallocenes (M Fe,

CHEM-X

CHARMM

Vibrational data

Develop a self-consistent

25

opment

Ru, Os, V, Cr, Co, Fe,

molecular mechanics

Ni)

force field, based on spec-

troscopic data, for linear

metallocenes

Force field devel-

Bent Ti, Zr, and Hf met-

CHARMM

Modified

Derived from vibrational

Generate a self-consistent,

27

opment

allocenes

CHARMM

data of [Cp

MCI

] com-

accurate force field for

2

2

(27)

plexes

bent metallocenes

Inorganic

Fe

2

and Ni

2

complexes with N-do-

nor ligands

Vanadium-oxo com-

plexes

Low-spin Ni(II) com-

plexes with tetraaza

macrocycles

Allylic nickel phosphine

complexes

Vanadium peroxides

(L

V(O )

; m

0–4)

n

2

m

Transition metal car-

bonyl clusters

WCl CHR (R H, CH

,

4

3

CH

CH )

2

3

Cobalt(II), nickel(II), and

copper(II) complexes

with amine and imine

ligands

CHARMM

CHARMM

Augmented with values for

pyridine and metal

MM2

MM2

X-ray data and quantum cal-

culations to determine

metal-dependent parame-

ters

MOLMEC

MM2

Extensions for aliphatic

amines and aromatic sys-

tems from crystal struc-

ture data

PCMODEL

MM2

Crystallographic data and

ab initio calculations

MM2

MM2

Metal-dependent parame-

ters derived from quan-

tum mechanical calcula-

tions and crystallography

Custom

MM2

Presented in paper

PCMODEL

METMOD1

Crystal structure data

DOMMINO

CLFSE MM

Crystal structure data

(106)

Generate parameters appro-

2

priate for modeling the

selectivity of the macrocy-

clic reagents to the size

of the metal atom

Develop force field for vana-

100

dium-oxos; compare MM

and SEQC methods

Use trial-and-error process

101

to derive force field pa-

rameters for the Ni(II)

part of the molecule that

gave the best fit with X-

ray data

Develop force field to pre-

102

dict diastereo-induction

in intramolecular Ni-cata-

lyzed [4 4] cycloaddi-

tions

Demonstrate utility of esti-

103

mating missing metal-de-

pendent molecular me-

chanics parameters from

quantum calculations

Develop a new force field

104

for the molecular mechan-

ics simulation of ligand

structures in transition

metal carbonyl clusters

Develop and evaluate tung-

105

sten carbene parameters

Extend molecular mechan-

107

ics scheme with cellular li-

gand field ligand stabiliza-

tion energy (CLFSE)

terms that explicitly treat

the electronic effects aris-

ing from changes in the

d-orbital energies

Rhodium diphosphine

complexes

[Rh(modified xan-

thene)H(CO)L] and

[Rh(diphos-

phine)(H)(CO)

]

2

complexes

Rh diphosphine com-

plexes

[Rh(chiral bisphosphi-

ne)(MAC)] com-

plexes

Cinchona-modified Pt/

alumina catalysts

Rh(I) aminophosphine-

phosphinite com-

plexes

Ir complexes with chiral

dithioether ligands

that form seven-

membered rings

[Rh(S,S-CHIRAPHOS)]

enamide complexes

Osmium tetraoxide

MacroModel

Amber

Augmented with values for

Probe the different alde-

tertiary phosphines (19)

hyde regioselectivity of

phosphine ligands

SYBYL

TRIPOS

Crystal structure data and

Develop new bidentate di-

Ref. 121

phosphines by modeling

the effect of bite angle on

regioselectivity

CHEM-X

COSMIC

Crystal structure fragments

Define the source of stereo-

COSMIC

assembled in COSMIC

selectivity in binding of

prochiral enamide to the

chiral Rh diphosphine

fragment

QUANTA

SHAPES (24) Presented in paper

Probe structural features

CHARMM

that give rise to the en-

antioselectivity observed

in the hydrogenation of

the substrates

AMBER

MacroModel

Unknown origin of parame-

Rationalize interaction be-

ters

tween chiral modifier and

substrate

CAChe

MM2

Presented in paper

Support thermodynamically

controlled asymmetric hy-

drogenation of ketopanto-

lactone

2

UFF

UFF parameters only

Study the relative stability

Cerius

of possible isomers

CHEM-X

MMX

Crystallography and within

Analyze the addition of H

2

PCMODEL

MMX

to the major and minor di-

asteremeric [Rh(S,S)-

CHIRAPHOS)] fragments

MacroModel

MM2

Used values for RuO

4

Explained selectivity trends

for various olefins

Supported tungsten

phenoxides

Tungsta-carbenes

TADDOL-TiCl

2

Co

(CO)

8

2

Redox active cavitand li-

gands with ferrocenyl

redox centers

Bleomycin (BLM) bound

to Fe(III)

Bridged zirconocene di-

chlorides

Cu(I) carboxylates

Ansa zirconocenes with

chiral ethylene

bridges

Insight II

ESFF

Crystal structure data

Model the surface structure

135

to determine the pre-

ferred arrangement of

the tungsten diphenoxide

species on the hydroxyl-

ated support

PCMODEL

METMOD1

MMX parameters and crys-

Create an adequate model

136

MMX

tal structure data

to study the catalysts, the

intermediates, and prod-

ucts of this reaction type

Chem3D

MM2

None specified

Measure the influence that

137

substituents on the dioxo-

lane ring exert on stereo-

selectivity

PCMODEL

MMX

None specified

Model proposed cobalta-

138

cycle intermediates of bi-

cyclization of substrate

CHEMMOD

CHEMMIN

Taken from CHEMMIN

Find the minimum-energy

139

position of the ligand

within the cavitand

MM2MX

1.5MM2/MX

General metal complex val-

Make a qualitative study of

140

ues used

Fe(III)BLM bound to

HOOH

Discover

Modified

Unpublished data

Use molecular mechanics

141

cff91

to study equilibration be-

tween conformers of the

catalysts

MOPAC

PM3 and

None specified

Propose possible mecha-

142

PCMODEL

MMX

nism of the dimerization

of 1-alkynes

Not specified

Not specified

None specified

Rationalize stereoregularity

143

of polypropene samples

in the presence of diaste-

reomeric complexes with

different bridges

TABLE 1

Continued

Reaction

Catalyst

Program

Force field

Added parameters

Purpose

Ref.

Polymerization

[WCl

]/[SnMe

]

METMOD

MM2

Collected from literature or

Create a model for study-

144

6

4

spectroscopic data

ing the steric effects gov-

erning the stereoselectiv-

ity of olefin metathesis in

the elementary steps of

olefin polymerization

Polymerization

Silylene-bridged zir-

MM2

MM2

None reported (Zr treated

Investigate the effects of al-

55

conocene

as a pseudoatom)

kyl substituents on the

Cp rings and the olefin

substrate

Polymerization

Zirconocenes

Custom code

Modified

From the literature (69)

Determine relationship be-

59

CHARMM

tween regiospecificity

(27,33)

and type of stereoselectiv-

AMBER

ity in propene polymeri-

zation

Polymerization

Cyclopentadienyl com-

Custom code

CHARMM

None specified

Present a geometrical and

60

plexes of Ti and Zr

MM2

nonbonded energy analy-

sis on possible catalytic

intermediates

Polymerization

Bis-(2-phenylindenyl) zir-

Custom code

CHARMM

From the literature (69)

Analyze the stereospecific-

61

conium chloride pre-

(27,33)

ity and enantioselectivity

cursor

caused by the isomeriza-

tion of the catalyst

Shape selectivity

Fe(II)/Fe(III) complexes

SYBYL

TAFF (145)

Added parameters to de-

Model the formation of the

146

of DIPIC, 2PP C, and

scribe Fe(II) and Fe(III)

complexes of Fe(II) and

6

CHOX

with these ligands

Fe(III) of linear NO

-donor

2

set ligands

Shape selectivity

Bis(pentamethylcyclop

CHARMM

CHARMM

Parameters obtained from

Understand why these met-

26

entadienyl) com-

the literature (27)

allocenes are bent

plexes of Ca, Sr, Ba,

Sm, Eu, and Yb

Vanadium oxo com-

plexes

Rh/SiO

2

and Rh[Sn(n-

C

H )

]

y

/SiO

4

9

x

2

Pt/SiO

2

and Sn(n-C

H )

4

9

MoS

2

slab

Zeolite L

Silicalite and zeolite

NaY

Zeolite NaY

H

x

ZSM-5/benzene

complexes (x 4)

Mordenite, zeolite L

FER, ZSM-48, EUO, MFI

zeolites (small-, me-

dium-, and large-pore

zeolites)

Custom code

MM2

Metal-dependent parame-

ters were derived as out-

lined in paper

SYBYL

TRIPOS

Listed in paper, obtained

from Refs. 147–149

SYBYL

TRIPOS

Listed in paper and Ref.

149

PC-CHEMMOD

Dreiding in

Used values from literature

CHEMMIN

(152)

Chemgraph

Only van der

Parameters taken from the

Waals

literature (154)

terms

ZEOLITHEN-

Only van der

Reported in papers

ERGIE

Waals

terms

ZEOLITHEN-

Reported in

Crystal structure data

ERGIE

paper

Custom

Only van der

Listed in paper and modi-

method

Waals

fied from literature for

(160,161)

terms

sorbate (162,163)

Insight II Dis-

CVFF

Obtained from the litera-

cover

ture (78)

CATALYSIS

CVFF and

Within CATALYSIS and

cff91

computed structures com-

pared with crystal struc-

ture data

Compare quantum and mo-

100

lecular mechanics meth-

ods in analysis of the ste-

ric and electronic energy

differences between iso-

mers

Calculate steric hindrance

150

for Sn complexes grafted

on the metallic surface

Calculate steric hindrance

151

for Sn complexes grafted

on the metallic surface

Model the active site of

153

MoS

2

and binding of thio-

phene

Calculate minimum-energy

155

position of pyridine in ze-

olite L

Use molecular mechanics

156–159

to develop a molecular

dynamics approach to

studying small molecules

in zeolites

Determine adsorption sites

74

and locations of aromatic

molecules in zeolite NaY

under catalytic conditions

Predict preferred proton lo-

76

cations in zeolite

Obtain the minimum-en-

77

ergy profiles for the selec-

tive isopropylation of

naphthalene

Determine the minimum-en-

80

ergy pathway for the dif-

fusion of the substrates

through the zeolites

TABLE 1

Continued

Reaction

Catalyst

Program

Force field

Added parameters

Purpose

Ref.

Zeolites

Y, mordenite, ZSM-5

2

Burchart (zeo-

Cerius

2

Estimate adsorption

81

Cerius

and beta zeolites

lite), Dreid-

strength of all the carbe-

ing (sor-

nium ion isomers derived

bate)

from the olefins on the ze-

olites

Zeolites

Zeolite-Y with lanthan-

QUANTA/

Reported in

From crystal structure data

Study C–S bond cleavage

82

ide and actinide ions

CHARMM

paper

in N-substituted car-

bonimido dithiolates

Zeolites

HZSM-5

ZEOLITHEN-

Parameters taken from the

Determine the location of

83

ERGIE

literature (164)

naphthalene and 2-meth-

ylnaphthalene in the

HZSM-5

Zeolites

Faujasite-type zeolites

Dizzy (79)

Reported in

Vibrational spectra

Develop a force field to ex-

79

paper

plicitly distinguish be-

tween Al and Si in FAU-

type zeolites

Ziegler–Natta

Ansa zirconocenes and

None speci-

Modified

None specified

Rationalize dependence of

64

hafnocenes

fied

CHARMM

the stereoselectivity of

the catalyst on the π-li-

gand alkyl substitutions

Ziegler–Natta

Meso- and rac-bis(2-pen-

MCM

UFF

No parameters needed

Model the source of barrier

165

ylindenyl)zirconium

between meso and rac

dichloride

forms of the catalyst; de-

termine the role of π-

stacking on polymer for-

mation

5

-

rac-(1,2-Ethylenebis(η

indenyl))Zr(IV) cata-

lysts

Ansa metallocenes

Ansa zirconocenes

Zirconocene-based and

titanocene-based cata-

lysts

CpZrC

H

and

5

2

Cp

ZrC H

9

with the

2

4

various bridging li-

gands

BIOGRAF

Dreiding

Ab initio calculations for ac-

tivated complex; molecu-

lar mechanics parameters

reported in paper

2

UFF and VAL-

No additional parameters

Cerius

BOND

necesary

BIOGRAF, PO-

Dreiding

Dreiding extended to in-

LYGRAF

clude tetrahedral Zr and

pseudoatoms for Cp, al-

lyl, and olefin centroids;

parameters reported in

paper

None given

Modified

None specified

CHARMM

CHARMM

Unspecified

DFT calculations; additional

parameters from the liter-

ature (33,65–67)

Determine effect of catalyst

166

substituents on the tac-

ticity of polypropylene

Develop a force field capa-

167

ble of calculating transi-

tion states and kinetic iso-

tope effects for the

systems of interest

Evaluate ability of the force

54

field to predict tacticity of

known and unknown zir-

conocene catalysts

Rationalize the probability

57

distributions of stereo-

chemical configurations

of the regioirregular units

in isotactic polymer units

Evaluate steric effects due

62

to bulky substituents