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Chymotrypsin
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Chymotrypsin
Crystallographic structure of Bos taurus chymotrypsinogen.[1]
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3.4.21.1
CAS number
9004-07-3
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Chymotrypsin C
Identifiers
EC number
3.4.21.2
CAS number
9036-09-3
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Chymotrypsin (EC 3.4.21.1, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum where it performs proteolysis, the breakdown of proteins and polypeptides.[2] Chymotrypsin preferentially cleaves peptide amide bonds where the side-chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their sidechain that fits into a 'hydrophobic pocket' (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 sidechain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme.[3][4] Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine and methionine at the P1 position.
Structurally, it is the archetypal structure for its superfamily, the PA clan of proteases.
Contents
[hide]
1 Activation
2 Mechanism of action and kinetics
3 Isozymes
4 See also
5 References
6 Further reading
7 External links
Activation[edit]
Chymotrypsin is synthesized in the pancreas by protein biosynthesis as a precursor called chymotrypsinogen that is enzymatically inactive. Trypsin activates chymotrypsinogen by cleaving peptidic bonds in positions Arg15 - Ile16 and produces π-Chymotrypsin. In turn, aminic group (-NH3+) of the Ile16 residue interacts with the side chain of Glu194, producing the "oxyanion hole" and the hydrophobic "S1 pocket". Moreover, Chymotrypsin induces its own activation by cleaving in positions 14-15, 146-147 and 148-149, producing α-Chymotrypsin (which is more active and stable than π-Chymotrypsin).[citation needed] The resulting molecule is a three-polypeptide molecule interconnected via disulfide bonds.
Mechanism of action and kinetics[edit]
See also: Catalytic triad
In vivo, chymotrypsin is a proteolytic enzyme (Serine protease) acting in the digestive systems of many organisms. It facilitates the cleavage of peptide bonds by a hydrolysis reaction, which despite being thermodynamically favorable occurs extremely slowly in the absence of a catalyst. The main substrates of chymotrypsin are peptide bonds in which the amino acid N-terminal to the bond is a tryptophan, tyrosine, phenylalanine, or leucine. Like many proteases, chymotrypsin will also hydrolyse amide bonds in vitro, a virtue that enabled the use of substrate analogs such as N-acetyl-L-phenylalanine p-nitrophenyl amide for enzyme assays.
Mechanism of peptide bond cleavage in α-chymotrypsin
Chymotrypsin cleaves peptide bonds by attacking the unreactive carbonyl group with a powerful nucleophile, the serine 195 residue located in the active site of the enzyme, which briefly becomes covalently bonded to the substrate, forming an enzyme-substrate intermediate. Along with histidine 57 and aspartic acid 102, this serine residue constitutes the catalytic triad of the active site.
These findings rely on inhibition assays and the study of the kinetics of cleavage of the aforementioned substrate, exploiting the fact that the enzyme-substrate intermediate p-nitrophenolate has a yellow colour, enabling us to measure its concentration by measuring light absorbance at 410 nm.
It was found that the reaction of chymotrypsin with its substrate takes place in two stages, an initial “burst” phase at the beginning of the reaction and a steady-state phase following Michaelis-Menten kinetics. The mode of action of chymotrypsin explains this as hydrolysis takes place in two steps. First acylation of the substrate to form an acyl-enzyme intermediate and then deacylation in order to return the enzyme to its original state. This occurs via the concerted action of the three amino acid residues in the catalytic triad.[5] Aspartate hydrogen bonds to the N-δ hydrogen of histidine, increasing the pKa of its ε nitrogen and thus making it able to deprotonate serine. It is this deprotonation that allows the serine side chain to act as a nucleophile and bind to the electron-deficient carbonyl carbon of the protein main chain. Ionization of the carbonyl oxygen is stabilized by formation of two hydrogen bonds to adjacent main chain N-hydrogens. This occurs in the oxyanion hole. This forms a tetrahedral adduct and breakage of the peptide bond. An acyl-enzyme intermediate, bound to the serine, is formed, and the newly formed amino terminus of the cleaved protein can dissociate. In the second reaction step, a water molecule is activated by the basic histidine, and acts as a nucleophile. The oxygen of water attacks the carbonyl carbon of the serine-bound acyl group, resulting in formation of a second tetrahedral adduct, regeneration of the serine -OH group, and release of a proton, as well as the protein fragment with the newly formed carboxyl terminus [5]
Isozymes[edit]
Chymotrypsinogen B1
Identifiers
Symbol
CTRB1
Entrez
1504
HUGO
2521
OMIM
118890
RefSeq
NM_001906
UniProt
P17538
Other data
EC number
3.4.21.1
Locus
Chr. 16 q23.1
Chymotrypsinogen B2
Identifiers
Symbol
CTRB2
Entrez
440387
HUGO
2522
RefSeq
NM_001025200
UniProt
Q6GPI1
Other data
EC number
3.4.21.1
Locus
Chr. 16 q22.3
Chymotrypsin C (caldecrin)
Identifiers
Symbol
CTRC
Entrez
11330
HUGO
2523
OMIM
601405
RefSeq
NM_007272
UniProt
Q99895
Other data
EC number
3.4.21.2
Locus
Chr. 1 p36.21
See also[edit]
Trypsin
PA clan of proteases
References[edit]
Jump up ^ PDB: 1CHG; Freer ST, Kraut J, Robertus JD, Wright HT, Xuong NH (April 1970). "Chymotrypsinogen: 2.5-angstrom crystal structure, comparison with alpha-chymotrypsin, and implications for zymogen activation". Biochemistry. 9 (9): 1997–2009. doi:10.1021/bi00811a022. PMID 5442169.
Jump up ^ Wilcox PE (1970). "Chymotrypsinogens — chymotrypsins". Methods in Enzymology. Methods in Enzymology. 19: 64–108. doi:10.1016/0076-6879(70)19007-0. ISBN 978-0-12-181881-4.
Jump up ^ Appel W (December 1986). "Chymotrypsin: molecular and catalytic properties". Clin. Biochem. 19 (6): 317–22. doi:10.1016/S0009-9120(86)80002-9. PMID 3555886.
Jump up ^ Berger A, Schechter I (February 1970). "Mapping the active site of papain with the aid of peptide substrates and inhibitors". Philos. Trans. R. Soc. Lond. B Biol. Sci. 257 (813): 249–64. doi:10.1098/rstb.1970.0024. PMID 4399049.
^ Jump up to: a b Petsko, Gregory; Ringe, Dagmar (2009). Protein Structure and Function. Oxford: Oxford University Press. pp. 78–79. ISBN 978-0-19-955684-7.
Further reading[edit]
Stryer L, Berg JM, Tymoczko JL (2002). Biochemistry. San Francisco: W.H. Freeman. ISBN 0-7167-4684-0.
Grisham CM, Reginald H (2005). Biochemistry. Australia: Thomson Brooks/Cole. ISBN 0-534-49033-6.
External links[edit]
The MEROPS online database for peptidases and their inhibitors: S01.001
Chymotrypsin at the US National Library of Medicine Medical Subject Headings (MeSH)
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Hypervalent molecule
From Wikipedia, the free encyclopedia
Jump to: navigation, search
A hypervalent molecule (the phenomenon is sometimes colloquially known as expanded octet) is a molecule that contains one or more main group elements apparently bearing more than eight electrons in their valence shells. Phosphorus pentachloride (PCl5), sulfur hexafluoride (SF6), chlorine trifluoride (ClF3), the chlorite (ClO2−) ion, and the triiodide (I3−) ion are examples of hypervalent molecules.
Contents
[hide]
1 Definitions and nomenclature
1.1 N-X-L notation
2 History and controversy
3 Criticism
4 Alternative definition
5 Bonding in hypervalent molecules
5.1 Molecular orbital theory
5.2 Valence bond theory
6 Structure, reactivity, and kinetics
6.1 Structure
6.1.1 Hexacoordinated phosphorus
6.1.2 Pentacoordinated silicon
6.2 Reactivity
6.2.1 Silicon
6.2.2 Phosphorus
6.3 Ab initio calculations
7 See also
8 References
Definitions and nomenclature[edit]
Hypervalent molecules were first formally defined by Jeremy I. Musher in 1969 as molecules having central atoms of group 15–18 in any valence other than the lowest (i.e. 3, 2, 1, 0 for Groups 15, 16, 17, 18 respectively, based on the octet rule).[1]
Several specific classes of hypervalent molecules exist:
Hypervalent iodine compounds are useful reagents in organic chemistry (e.g. Dess–Martin periodinane)
Tetra-, penta- and hexacoordinated phosphorus, silicon, and sulfur compounds (ex. PCl5, PF5, SF6, sulfuranes and persulfuranes)
Noble gas compounds (ex. xenon tetrafluoride, XeF4)
Halogen polyfluorides (ex. ClF5)
N-X-L notation[edit]
N-X-L nomenclature, introduced in 1980,[2] is often used to classify hypervalent compounds of main group elements, where:
N represents the number of valence electrons
X is the chemical symbol of the central atom
L the number of ligands to the central atom
Examples of N-X-L nomenclature include:
XeF2, 10-Xe-2
PCl5, 10-P-5
SF6, 12-S-6
IF7, 14-I-7
History and controversy[edit]
The debate over the nature and classification of hypervalent molecules goes back to Gilbert N. Lewis and Irving Langmuir and the debate over the nature of the chemical bond in the 1920s.[3] Lewis maintained the importance of the two-center two-electron (2c-2e) bond in describing hypervalence, thus using expanded octets to account for such molecules. Langmuir, on the other hand, upheld the dominance of the octet rule and preferred the use of ionic bonds to account for hypervalence without violating the rule (e.g. SF42+, 2F−).
In the late 1920s and 1930s, Sugden argued for the existence of a two-center one-electron (2c-1e) bond and thus rationalized bonding in hypervalent molecules without the need for expanded octets or ionic bond character; this was poorly accepted at the time.[3] In the 1940s and 1950s, Rundle and Pimentel popularized the idea of the three-center four-electron bond, which is essentially the same concept which Sugden attempted to advance decades earlier; the three-center four-electron bond can be alternatively viewed as consisting of two collinear two-center one-electron bonds, with the remaining two nonbonding electrons localized to the ligands.[3]
The attempt to actually prepare hypervalent organic molecules began with Hermann Staudinger and Georg Wittig in the first half of the twentieth century, who sought to challenge the extant valence theory and successfully prepare nitrogen and phosphorus-centered hypervalent molecules.[4] The theoretical basis for hypervalency was not delineated until J.I. Musher's work in 1969.[1]
In 1990, Magnusson published a seminal work definitively excluding the role of d-orbital hybridization in bonding in hypervalent compounds of second-row elements. This had long been a point of contention and confusion in describing these molecules using molecular orbital theory. Part of the confusion here originates from the fact that one must include d-functions in the basis sets used to describe these compounds (or else unreasonably high energies and distorted geometries result), and the contribution of the d-function to the molecular wavefunction is large. These facts were historically interpreted to mean that d-orbitals must be involved in bonding. However, Magnusson concludes in his work that d-orbital involvement is not implicated in hypervalency.[5]
Criticism[edit]
Both the term and concept of hypervalency still fall under criticism. In 1984, in response to this general controversy, Paul von Ragué Schleyer proposed the replacement of 'hypervalency' with use of the term hypercoordination because this term does not imply any mode of chemical bonding and the question could thus be avoided altogether.[3]
The concept itself has been criticized by Ronald Gillespie who, based on an analysis of electron localization functions, wrote in 2002 that "as there is no fundamental difference between the bonds in hypervalent and non-hypervalent (Lewis octet) molecules there is no reason to continue to use the term hypervalent."[6]
For hypercoordinated molecules with electronegative ligands such as PF5 it has been demonstrated that the ligands can pull away enough electron density from the central atom so that its net content is again 8 electrons or fewer. Consistent with this alternative view is the finding that hypercoordinated molecules based on fluorine ligands, for example PF5 do not have hydride counterparts e.g. phosphorane PH5 which is unknown.
The ionic model holds up well in thermochemical calculations. It predicts favorable exothermic formation of PF4+F− from phosphorus trifluoride PF3 and fluorine F2 whereas a similar reaction forming PH4+H− is not favorable.[7]
Alternative definition[edit]
Durrant has proposed an alternative definition of hypervalency, based on the analysis of atomic charge maps obtained from Atoms in molecules theory.[8] This approach defines a parameter called the valence electron equivalent, γ, as “the formal shared electron count at a given atom, obtained by any combination of valid ionic and covalent resonance forms that reproduces the observed charge distribution”. For any particular atom X, if the value of γ(X) is greater than 8, that atom is hypervalent. Using this alternative definition, many species such as PCl5, SO42−, and XeF4, that are hypervalent by Musher's definition, are reclassified as hypercoordinate but not hypervalent, due to strongly ionic bonding that draws electrons away from the central atom. On the other hand, some compounds that are normally written with ionic bonds in order to conform to the octet rule, such as ozone O3, nitrous oxide NNO, and trimethylamine N-oxide (CH3)3NO, are found to be genuinely hypervalent. Examples of γ calculations for phosphate PO43− (γ(P) = 2.6, non-hypervalent) and orthonitrate NO43− (γ(N) = 8.5, hypervalent) are shown below.
Calculation of the valence electron equivalent for phosphate and orthonitrate
Bonding in hypervalent molecules[edit]
Early considerations of the geometry of hypervalent molecules returned familiar arrangements that were well explained by the VSEPR model for atomic bonding. Accordingly, AB5 and AB6 type molecules would possess a trigonal bi-pyramidal and octahedral geometry, respectively. However, in order to account for the observed bond angles, bond lengths and apparent violation of the Lewis octet rule, several alternative models have been proposed.
In the 1950s an expanded valence shell treatment of hypervalent bonding was adduced to explain the molecular architecture, where the central atom of penta- and hexacoordinated molecules would utilize d AOs in addition to s and p AOs. However, advances in the study of ab initio calculations have revealed that the contribution of d-orbitals to hypervalent bonding is too small to describe the bonding properties, and this description is now regarded as much less important.[5] It was shown that in the case of hexacoordinated SF6, d-orbitals are not involved in S-F bond formation, but charge transfer between the sulfur and fluorine atoms and the apposite resonance structures were able to account for the hypervalency (See below).
Additional modifications to the octet rule have been attempted to involve ionic characteristics in hypervalent bonding. As one of these modifications, in 1951, the concept of the 3-center 4-electron (3c-4e) bond, which described hypervalent bonding with a qualitative molecular orbital, was proposed. The 3c-4e bond is described as three molecular orbitals given by the combination of a p atomic orbital on the central atom and an atomic orbital from each of the two ligands on opposite sides of the central atom. Only one of the two pairs of electrons is occupying a molecular orbital that involves bonding to the central atom, the second pair being non-bonding and occupying a molecular orbital composed of only atomic orbitals from the two ligands. This model in which the octet rule is preserved was also advocated by Musher.[3]
Qualitative model for a three-center four-electron bond
Molecular orbital theory[edit]
A complete description of hypervalent molecules arises from consideration of molecular orbital theory through quantum mechanical methods. A LCAO in, for example, sulfur hexafluoride, taking a basis set of the one sulfur 3s-orbital, the three sulfur 3p-orbitals, and six octahedral geometry symmetry-adapted linear combinations (SALCs) of fluorine orbitals, a total of ten molecular orbitals are obtained (four fully occupied bonding MOs of the lowest energy, two fully occupied intermediate energy non-bonding MOs and four vacant antibonding MOs with the highest energy) providing room for all 12 valence electrons. This is a stable configuration only for SX6 molecules containing electronegative ligand atoms like fluorine, which explains why SH6 is not a stable molecule. In the bonding model, the two non-bonding MOs (1eg) are localized equally on all six fluorine atoms.
Valence bond theory[edit]
For hypervalent compounds in which the ligands are more electronegative than the central, hypervalent atom, resonance structures can be drawn with no more than four covalent electron pair bonds and completed with ionic bonds to obey the octet rule. For example, in phosphorus pentafluoride (PF5), 5 resonance structures can be generated each with four covalent bonds and one ionic bond with greater weight in the structures placing ionic character in the axial bonds, thus satisfying the octet rule and explaining both the observed trigonal bipyramidal molecular geometry and the fact that the axial bond length (158 pm) is longer than the equatorial (154 pm).[9]
Phosphorus pentafluoride. There are 2 structures with an axial ionic bond, plus 3 structures with an equatorial ionic bond.
For a hexacoordinate molecule such as sulfur hexafluoride, each of the six bonds is the same length. The rationalization described above can be applied to generate 15 resonance structures each with four covalent bonds and two ionic bonds, such that the ionic character is distributed equally across each of the sulfur-fluorine bonds.
Sulfur hexafluoride. There are 12 structures with the two ionic bonds in adjacent (cis) positions, plus 3 structures with the two ionic bonds in opposite (trans) positions.
Spin-coupled valence bond theory has been applied to diazomethane and the resulting orbital analysis was interpreted in terms of a chemical structure in which the central nitrogen has five covalent bonds;
Chemical formula of diazomethane, showing hypervalent nitrogen
This led the authors to the interesting conclusion that "Contrary to what we were all taught as undergraduates, the nitrogen atom does indeed form five covalent linkages and the availability or otherwise of d-orbitals has nothing to do with this state of affairs."[10]
Structure, reactivity, and kinetics[edit]
Structure[edit]
Hexacoordinated phosphorus[edit]
Hexacoordinate phosphorus molecules involving nitrogen, oxygen, or sulfur ligands provide examples of Lewis acid-Lewis base hexacoordination.[11] For the two similar complexes shown below, the length of the C-P bond increases with decreasing length of the N-P bond; the strength of the C-P bond decreases with increasing strength of the N-P Lewis acid-Lewis base interaction.
Relative bond strengths in hexacoordinated phosphorus compounds. In A, the N-P bond is 1.980Å long and the C-P is 1.833Å long, and in B, the N-P bond increases to 2.013Å as the C-P bond decreases to 1.814Å.[11]
Pentacoordinated silicon[edit]
This trend is also generally true of pentacoordinated main-group elements with one or more lone-pair-containing ligand, including the oxygen-pentacoordinated silicon examples shown below.
Relative bond strengths in pentacoordinated silicon compounds. In A, the Si-O bond length is 1.749Å and the Si-I bond length is 3.734Å; in B, the Si-O bond lengthens to 1.800Å and the Si-Br bond shortens to 3.122Å, and in C, the Si-O bond is the longest at 1.954Å and the Si-Cl bond the shortest at 2.307A.[11]
The Si-halogen bonds range from close to the expected van der Waals value in A (a weak bond) almost to the expected covalent single bond value in C (a strong bond).[11]
Reactivity[edit]
Silicon[edit]
Observed third-order reaction rate constants
for hydrolysis (displacement of chloride from silicon)[12]
Chlorosilane
Nucleophile
kobs (M−2s−1)
at 20 °C in anisole
Ph3SiCl HMPT 1200
Ph3SiCl DMSO 50
Ph3SiCl DMF 6
MePh2SiCl HMPT 2000
MePh2SiCl DMSO 360
MePh2SiCl DMF 80
Me(1-Np)PhSiCl HMPT 3500
Me(1-Np)PhSiCl DMSO 180
Me(1-Np)PhSiCl DMF 40
(1-Np)Ph(vinyl)SiCl HMPT 2200
(1-Np)Ph(vinyl)SiCl DMSO 90
(1-Np)(m-CF3Ph)HSiCl DMSO 1800
(1-Np)(m-CF3Ph)HSiCl DMF 300
Corriu and coworkers performed early work characterizing reactions thought to proceed through a hypervalent transition state.[12] Measurements of the reaction rates of hydrolysis of tetravalent chlorosilanes incubated with catalytic amounts of water returned a rate that is first order in chlorosilane and second order in water. This indicated that two water molecules interacted with the silane during hydrolysis and from this a binucleophilic reaction mechanism was proposed. Corriu and coworkers then measured the rates of hydrolysis in the presence of nucleophilic catalyst HMPT, DMSO or DMF. It was shown that the rate of hydrolysis was again first order in chlorosilane, first order in catalyst and now first order in water. Appropriately, the rates of hydrolysis also exhibited a dependence on the magnitude of charge on the oxygen of the nucleophile.
Taken together this led the group to propose a reaction mechanism in which there is a pre-rate determining nucleophilic attack of the tetracoordinated silane by the nucleophile (or water) in which a hypervalent pentacoordinated silane is formed. This is followed by a nucleophilic attack of the intermediate by water in a rate determining step leading to hexacoordinated species that quickly decomposes giving the hydroxysilane.
Silane hydrolysis was further investigated by Holmes and coworkers [13] in which tetracoordinated Mes2SiF2 (Mes = mesityl) and pentacoordinated Mes2SiF3− were reacted with two equivalents of water. Following twenty-four hours, almost no hydrolysis of the tetracoordinated silane was observed, while the pentacoordinated silane was completely hydrolyzed after fifteen minutes. Additionally, X-ray diffraction data collected for the tetraethylammonium salts of the fluorosilanes showed the formation of hydrogen bisilonate lattice supporting a hexacoordinated intermediate from which HF2− is quickly displaced leading to the hydroxylated product. This reaction and crystallographic data support the mechanism proposed by Corriu et al..
Mechanism of silane hydrolysis and structure of the hydrogen bisilonate lattice
The apparent increased reactivity of hypervalent molecules, contrasted with tetravalent analogues, has also been observed for Grignard reactions. The Corriu group measured[14] Grignard reaction half-times by NMR for related 18-crown-6 potassium salts of a variety of tetra- and pentacoordinated fluorosilanes in the presence of catalytic amounts of nucleophile.
Though the half reaction method is imprecise, the magnitudinal differences in reactions rates allowed for a proposed reaction scheme wherein, a pre-rate determining attack of the tetravalent silane by the nucleophile results in an equilibrium between the neutral tetracoordinated species and the anionic pentavalent compound. This is followed by nucleophilic coordination by two Grignard reagents as normally seen, forming a hexacoordinated transition state and yielding the expected product.
Grignard reaction mechanism for tetracoordinate silanes and the analogous hypervalent pentacoordinated silanes
The mechanistic implications of this are extended to a hexacoordinated silicon species that is thought to be active as a transition state in some reactions. The reaction of allyl- or crotyl-trifluorosilanes with aldehydes and ketones only precedes with fluoride activation to give a pentacoordinated silicon. This intermediate then acts as a Lewis acid to coordinate with the carbonyl oxygen atom. The further weakening of the silicon–carbon bond as the silicon becomes hexacoordinate helps drive this reaction.[15]
Phosphorus[edit]
Similar reactivity has also been observed for other hypervalent structures such as the miscellany of phosphorus compounds, for which hexacoordinated transition states have been proposed. Hydrolysis of phosphoranes and oxyphosphoranes have been studied [16] and shown to be second order in water. Bel'skii et al.. have proposed a prerate determining nucleophilic attack by water resulting in an equilibrium between the penta- and hexacoordinated phosphorus species, which is followed by a proton transfer involving the second water molecule in a rate determining ring-opening step, leading to the hydroxlyated product.
Mechanism of the hydrolysis of pentacoordinated phosphorus
Alcoholysis of pentacoordinated phosphorus compounds, such as trimethoxyphospholene with benzyl alcohol, have also been postulated to occur through a similar octahedral transition state, as in hydrolysis, however without ring opening.[17]
Mechanism of the base catalyzed alcoholysis of pentacoordinated phosphorus
It can be understood from these experiments that the increased reactivity observed for hypervalent molecules, contrasted with analogous nonhypervalent compounds, can be attributed to the congruence of these species to the hypercoordinated activated states normally formed during the course of the reaction.
Ab initio calculations[edit]
The enhanced reactivity at pentacoordinated silicon is not fully understood. Corriu and coworkers suggested that greater electropositive character at the pentavalent silicon atom may be responsible for its increased reactivity.[18] Preliminary ab initio calculations supported this hypothesis to some degree, but used a small basis set.[19]
A software program for ab initio calculations, Gaussian 86, was used by Dieters and coworkers to compare tetracoordinated silicon and phosphorus to their pentacoordinate analogues. This ab initio approach is used as a supplement to determine why reactivity improves in nucleophilic reactions with pentacoordinated compounds. For silicon, the 6-31+G* basis set was used because of its pentacoordinated anionic character and for phosphorus, the 6-31G* basis set was used.[19]
Pentacoordinated compounds should theoretically be less electrophilic than tetracoordinated analogues due to steric hindrance and greater electron density from the ligands, yet experimentally show greater reactivity with nucleophiles than their tetracoordinated analogues. Advanced ab initio calculations were performed on series of tetracoordinated and pentacoordinated species to further understand this reactivity phenomenon. Each series varied by degree of fluorination. Bond lengths and charge densities are shown as functions of how many hydride ligands are on the central atoms. For every new hydride, there is one less fluoride.[19]
For silicon and phosphorus bond lengths, charge densities, and Mulliken bond overlap, populations were calculated for tetra and pentacoordinated species by this ab initio approach.[19] Addition of a fluoride ion to tetracoordinated silicon shows an overall average increase of 0.1 electron charge, which is considered insignificant. In general, bond lengths in trigonal bipyramidal pentacoordinate species are longer than those in tetracoordinate analogues. Si-F bonds and Si-H bonds both increase in length upon pentacoordination and related effects are seen in phosphorus species, but to a lesser degree. The reason for the greater magnitude in bond length change for silicon species over phosphorus species is the increased effective nuclear charge at phosphorus. Therefore, silicon is concluded to be more loosely bound to its ligands.
Effects of fluorine substitution on positive charge density
Comparison of Charge Densities with Degree of Fluorination for Tetra and Pentacoordinated Silicon
In addition Dieters and coworkers [19] show an inverse correlation between bond length and bond overlap for all series. Pentacoordinated species are concluded to be more reactive because of their looser bonds as trigonal-bipyramidal structures.
Calculated bond length and bond overlap with degree of fluorination
Comparison of Bond Lengths with Degree of Fluorination for Tetra and Pentacoordinated Silicon
Comparison of Bond Lengths with Degree of Fluorination for Tetra and Pentacoordinated Phosphorus
By calculating the energies for the addition and removal of a fluoride ion in various silicon and phosphorus species, several trends were found. In particular, the tetracoordinated species have much higher energy requirements for ligand removal than do pentacoordinated species. Further, silicon species have lower energy requirements for ligand removal than do phosphorus species, which is an indication of weaker bonds in silicon.
See also[edit]
Charge-shift bond
References[edit]
^ Jump up to: a b Musher, J.I. (1969). "The Chemistry of Hypervalent Molecules". Angew. Chem. Int. Ed. 8: 54–68. doi:10.1002/anie.196900541.
Jump up ^ Perkins, C. W.; Martin, J. C.; Arduengo, A. J.; Lau, W.; Alegria, A,; Kochi, J. K.; An Electrically Neutral a-Sulfuranyl Radical from the Homolysis of a Perester with Neighboring Sulfenyl Sulfur: 9-S-3 species J.Am. Chem. Soc. 1980, 102, 7753–7759 doi:10.1021/ja00546a019
^ Jump up to: a b c d e Jensen, W. (2006). "The Origin of the Term "Hypervalent"". J. Chem. Educ. 83 (12): 1751. Bibcode:2006JChEd..83.1751J. doi:10.1021/ed083p1751. | Link
Jump up ^ Kin-ya Akiba. Chemistry of Hypervalent Compounds. New York: Wiley VCH. ISBN 0-471-24019-2.
^ Jump up to: a b E. Magnusson. Hypercoordinate molecules of second-row elements: d functions or d orbitals? J. Am. Chem. Soc. 1990, 112, 7940–7951. doi:10.1021/ja00178a014
Jump up ^ Gillespie, R (2002). "The octet rule and hypervalence: Two misunderstood concepts". Coordination Chemistry Reviews. 233–234: 53–62. doi:10.1016/S0010-8545(02)00102-9.
Jump up ^ Predicting the Stability of Hypervalent Molecules Mitchell, Tracy A.; Finocchio, Debbie; Kua, Jeremy. J. Chem. Educ. 2007, 84, 629. Link
Jump up ^ Durrant, M. C. (2015). "A quantitative definition of hypervalency". Chemical Science. 6: 6614–6623. doi:10.1039/C5SC02076J.
Jump up ^ Curnow, Owen J. (1998). "A Simple Qualitative Molecular-Orbital/Valence-Bond Description of the Bonding in Main Group "Hypervalent" Molecules". Journal of Chemical Education. 75 (7): 910–915. Bibcode:1998JChEd..75..910C. doi:10.1021/ed075p910.
Jump up ^ Gerratt, Joe (1997). "Modern valence bond theory". Chemical Society Reviews. 26 (2): 87–100. doi:10.1039/CS9972600087.
^ Jump up to: a b c d Holmes, R.R. (1996). "Comparison of Phosphorus and Silicon: Hypervalency, Stereochemistry, and Reactivity". Chem. Rev. 96 (3): 927–950. doi:10.1021/cr950243n. PMID 11848776.
^ Jump up to: a b Corriu, RJP; Dabosi, G.; Martineau, M. (1978). "Mécanisme de l'hydrolyse des chlorosilanes, catalysée par un nucléophile: étude cinétique et mise en evidence d'un intermediaire hexacoordonné". J. Organomet. Chem. 150: 27–38. doi:10.1016/S0022-328X(00)85545-X.
Jump up ^ Johnson, SE; Deiters, JA; Day, RO; Holmes, RR (1989). "Pentacoordinated molecules. 76. Novel hydrolysis pathways of dimesityldifluorosilane via an anionic five-coordinated silicate and a hydrogen-bonded bisilonate. Model intermediates in the sol-gel process". J. Am. Chem. Soc. 111 (9): 3250. doi:10.1021/ja00191a023.
Jump up ^ Corriu, RJP; Guerin, Christian.; Henner, Bernard J. L.; Wong Chi Man, W. W. C. (1988). "Pentacoordinated silicon anions: reactivity toward strong nucleophiles". Organometallics. 7: 237–8. doi:10.1021/om00091a038.
Jump up ^ Kira, M; Kobayashi, M.; Sakurai, H. (1987). "Regiospecific and highly stereoselective allylation of aldehydes with allyltrifluorosilane activated by fluoride ions". Tetrahedron Letters. 28 (35): 4081–4084. doi:10.1016/S0040-4039(01)83867-3.
Jump up ^ Bel'Skii, VE (1979). J. Gen. Chem. USSR. 49: 298. Missing or empty |title= (help)
Jump up ^ Ramirez, F; Tasaka, K.; Desai, N. B.; Smith, Curtis Page. (1968). "Nucleophilic substitutions at pentavalent phosphorus. Reaction of 2,2,2-trialkoxy-2,2-dihydro-1,3,2-dioxaphospholenes with alcohols". J. Am. Chem. Soc. 90 (3): 751. doi:10.1021/ja01005a035.
Jump up ^ Brefort, Jean Louis; Corriu, Robert J. P.; Guerin, Christian; Henner, Bernard J. L.; Wong Chi Man, Wong Wee Choy (1990). "Pentacoordinated silicon anions: Synthesis and reactivity". Organometallics. 9 (7): 2080. doi:10.1021/om00157a016.
^ Jump up to: a b c d e Dieters, J. A.; Holmes, R. R. (1990). "Enhanced Reactivity of Pentacoordinated Silicon Species. An ab Initio Approach". J. Am. Chem. Soc. 112 (20): 7197–7202. doi:10.1021/ja00176a018.
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