Atoms can form bonds with each other by sharing unpaired electrons such that
each bond contains two electrons. In Topic A1, we identified that a carbon atom
has two unpaired electrons and so we would expect carbon to form two bonds.
However, carbon forms four bonds! How does a carbon atom form four bonds
with only two unpaired electrons?
So far, we have described the electronic configuration of an isolated carbon
atom. However, when a carbon atom forms bonds and is part of a molecular structure,
it can emixf the s and p orbitals of its second shell (the valence shell). This is
known as hybridization and it allows carbon to form the four bonds which we
observe in reality.
There are three ways in which this mixing process can take place.
œ the 2s orbital ismixedwith all three 2p orbitals. This isknownas sp3 hybridization;
œ the 2s orbital is mixed with two of the 2p orbitals. This is known as sp2
hybridization;
œ the 2s orbital is mixed with one of the 2p orbitals. This is known as sp
hybridization.
In sp3 hybridization, the s and the p orbitals of the second shell are ‘mixed’
to form four hybridized sp3 orbitals of equal energy.
Each hybridized orbital contains a single unpaired electron and so four
bonds are possible.
Each sp3 orbital is shaped like a deformed dumbbell with one lobe much
larger than the other. The hybridized orbitals arrange themselves as far
apart from each other as possible such that the major lobes point to the corners
of a tetrahedron. sp3 Hybridization explains the tetrahedral carbon in
saturated hydrocarbon structures.
Sigma (σ) bonds are strong bonds formed between two sp3 hybridized carbons
or between an sp3 hybridized carbon and a hydrogen atom. A σ bond
formed between two sp3 hybridized carbon atoms involves the overlap of
half filled sp3 hybridized orbitals from each carbon atom. A σ bond formed
between an sp3 hybridized carbon and a hydrogen atom involves a halffilled
sp3 orbital from carbon and a half-filled 1s orbital from hydrogen.
Nitrogen, oxygen, and chlorine atoms can also be sp3 hybridized in organic
molecules. This means that nitrogen has three half-filled sp3 orbitals and can
form three bonds which are pyramidal in shape. Oxygen has two half-filled
sp3 orbitals and can form two bonds which are angled with respect to each
other. Chlorine has a single half-filled sp3 orbital and can only form a single
bond. All the bonds which are formed are σ bonds.
adapted from G. L. Patrick
Department of Chemistry and Chemical Engineering,
Paisley University, Paisley, Scotland
Tuesday, August 28, 2012
Monday, August 27, 2012
ATOMIC STRUCTURE OF CARBON
Atomic orbitals
The atomic orbitals available for the six electrons of carbon are the s orbital
in the first shell, the s orbital in the second shell and the three p orbitals in
the second shell. The 1s and 2s orbitals are spherical in shape. The 2p
orbitals are dumbbell in shape and can be assigned 2px, 2py or 2pz depending
on the axis along which they are aligned.
Energy levels
The 1s orbital has a lower energy than the 2s orbital which has a lower
energy than the 2p orbitals. The 2p orbitals have equal energy (i.e. they
are degenerate).
Electronic configuration
Carbon is in the second row of the periodic table and has six electrons which
will fill up lower energy atomic orbitals before entering higher energy
orbitals (aufbau principle). Each orbital is allowed a maximum of two electrons
of opposite spin (Pauli exclusion principle). When orbitals of equal
energy are available, electrons will occupy separate orbitals before pairing
up (Hund’s rule). Thus, the electronic configuration of a carbon atom is 1s2
2s2 2px
1 2py
1.
Covalent bonding
A covalent bond binds two atoms together in a molecular structure and is formed
when atomic orbitals overlap to produce a molecular orbital – so called because
the orbital belongs to the molecule as a whole rather than to one specific atom. A
simple example is the formation of a hydrogen molecule (H2) from two hydrogen
atoms. Each hydrogen atom has a half-filled 1s atomic orbital and when the atoms
approach each other, the atomic orbitals interact to produce two MOs (the number
of resulting MOs must equal the number of original atomic orbitals, Fig. 1).
The MOs are of different energies. One is more stable than the original atomic
orbitals and is called the bonding MO. The other is less stable and is called the
antibonding MO. The bonding MO is shaped like a rugby ball and results from
the combination of the 1s atomic orbitals. Since this is the more stable MO, the
valence electrons (one from each hydrogen) enter this orbital and pair up. The
antibonding MO is of higher energy and consists of two deformed spheres. This
remains empty. Since the electrons end up in a bonding MO which is more stable
than the original atomic orbitals, energy is released and bond formation is
favored. In the subsequent discussions, we shall concentrate solely on the bonding
MOs to describe bonding and molecular shape, but it is important to realize
that antibonding molecular orbitals also exist.
adapted from G. L. Patrick
Department of Chemistry and Chemical Engineering,
Paisley University, Paisley, Scotland
The atomic orbitals available for the six electrons of carbon are the s orbital
in the first shell, the s orbital in the second shell and the three p orbitals in
the second shell. The 1s and 2s orbitals are spherical in shape. The 2p
orbitals are dumbbell in shape and can be assigned 2px, 2py or 2pz depending
on the axis along which they are aligned.
Energy levels
The 1s orbital has a lower energy than the 2s orbital which has a lower
energy than the 2p orbitals. The 2p orbitals have equal energy (i.e. they
are degenerate).
Electronic configuration
Carbon is in the second row of the periodic table and has six electrons which
will fill up lower energy atomic orbitals before entering higher energy
orbitals (aufbau principle). Each orbital is allowed a maximum of two electrons
of opposite spin (Pauli exclusion principle). When orbitals of equal
energy are available, electrons will occupy separate orbitals before pairing
up (Hund’s rule). Thus, the electronic configuration of a carbon atom is 1s2
2s2 2px
1 2py
1.
Covalent bonding
when atomic orbitals overlap to produce a molecular orbital – so called because
the orbital belongs to the molecule as a whole rather than to one specific atom. A
simple example is the formation of a hydrogen molecule (H2) from two hydrogen
atoms. Each hydrogen atom has a half-filled 1s atomic orbital and when the atoms
approach each other, the atomic orbitals interact to produce two MOs (the number
of resulting MOs must equal the number of original atomic orbitals, Fig. 1).
The MOs are of different energies. One is more stable than the original atomic
orbitals and is called the bonding MO. The other is less stable and is called the
antibonding MO. The bonding MO is shaped like a rugby ball and results from
the combination of the 1s atomic orbitals. Since this is the more stable MO, the
valence electrons (one from each hydrogen) enter this orbital and pair up. The
antibonding MO is of higher energy and consists of two deformed spheres. This
remains empty. Since the electrons end up in a bonding MO which is more stable
than the original atomic orbitals, energy is released and bond formation is
favored. In the subsequent discussions, we shall concentrate solely on the bonding
MOs to describe bonding and molecular shape, but it is important to realize
that antibonding molecular orbitals also exist.
adapted from G. L. Patrick
Department of Chemistry and Chemical Engineering,
Paisley University, Paisley, Scotland
Interactions of the Platinum(II) Complexes with Nitrogen- and Sulfur-Bonding Bio-Molecules in Chronic Lymphocytic Leukemia
by: Jovana Bogojeski, Biljana Petrović and Živadin D. Bugarčić*
University of Kragujevac, Faculty of Science, Department of Chemistry
Serbia
Introduction
Transition metals and their reactions are in general important in the environment, in
technical processes (catalysis, extraction and purification of metal complexes) and in biology
and medicine (biological electron transfer, toxicology and use of metal complexes as drugs).
Moreover, nonessential metal ions are very often used in biological systems either for
therapeutic application or as diagnostic aids. For instance, metal complexes have been used
for the treatment of many diseases (cancer, arthritis, diabetes, Alzheimer, etc.), but with little
understanding of their mechanism of action in biological systems.(Ronconi & Sadler, 2007;
Bruijnincx & Sadler, 2009) Biochemical studies have not clearly established the molecular
basis for the activity and mechanism of action. The growing field of bioinorganic chemistry
is presently dealing with the clarification of the mechanisms of action of metal complexes in
biological systems.(Ronconi & Sadler,2007; Bruijnincx & Sadler, 2009; Jakupec et al., 2008)
Research in the area of application of metal complex compounds in medicine began with the
discovery of antitumor properties of cisplatin. (Rosenberg, 1965, 1967, 1969, 1970) Today
cisplatin is in routine use as therapeutics worldwide. Following the success of cisplatin a
large number of analogous compounds were synthesized. All these compounds have a
several common characteristics:
1. bifunctional complex compounds with cis-geometry
2. PtX2(amin)2 is general formula of this compounds, where X2 are two labile monodentate
or one labile bidentate ligand, and (amine)2 are inert nitrogen-donor ligands
3. nitrogen-donor ligands have to containe at least one NH bond.
Despite the large number of synthesized compounds only a few of them entered the
medicinal use and most are still in preclinical investigation. (Jakupec et al., 2003; Reedijk,
2009) At the Fig. 1. are presented some of platinum complexes that are in the medicinal use
worldwide.
Chronic lymphocytic leukemia is the most frequent type of leukemia and it accounts for
approximately 25% of all leukemias. (Chiorazzi et al., 2005) Although at the present there is
no curative treatment, combinations of cytotoxic agents and of immunotherapies that
generate high complete remission rates hold promise for altering the natural history of this
340 Chronic Lymphocytic Leukemia
disease. (Wierda et al., 2005) Fludarabine (9-beta-D-arabinofuranosyl-2-fluoroadenine 5’-
phosphate) is the most effective purine nucleoside analogue for the treatment of indolent
lymphoproliferative disorders, including Chronic lymphocytic leukemia, low-grade
lymphoma, and prolymphocytic leukemia. (Eichhorst et al., 2005)
The studies show that among the best drugs in the treatment of Chronic lymphocytic
leukemia are the combination of Pt(II) complexes (cisplatin and oxaliplatin) and alkylating
agents and nucleoside analogues such as fluradabine. (Zecevic et al., 2011) The
nonoverlapping side effect profiles of oxaliplatin and fludarabine and their different but
potentially complementary mechanisms of action provide a basis for investigation of the
activity of the drugs in combination. The rationale for combining oxaliplatin with
fludarabine is based on preclinical data showing synergistic cytotoxicity between cisplatin
in combination with the nucleoside. (Wang et al., 1991; Yamauchi et al., 2001)
Consequently, knowledge of the interaction of the different Pt(II) complexes and nitrogenand
sulfur-bonding bio-molecules, and the results obtained from in vitro studies of this type
of interactions will help in finding of good antitumor drug for the treatment of many tumors
including the Chronic lymphocytic leukemia. The main topic of this chapter will be to show
the results obtained in numerous studies of the interactions of the potential antitumor Pt(II)
complexes and different biomolecules.
Platinum(II) has a high affinity for sulphur, so after administrating Pt(II) complex in the
human body there is a strong possibility for binding with sulphur-donor bio-molecules.
Sulphur-donor bio-molecules are present in large amounts in the form of peptides, proteins
and enzymes. Binding of platinum complexes with sulphur-donor bio-molecules are
responsible for the occurrence of toxic effects. (Lippert, 1999; Reedijk, 1999) However, a
certain amount of platinum complexes being bound to nitrogen-donor bio-molecules (amino
acids or DNA). Today it is generally accepted that the anti-tumor activity of platinum drugs
can be ascribed to interactions between the metal complex and DNA, primarily with the
genetic DNA, which is located in the nucleus. The interactions with mitochondrial DNA are
less responsible for the antitumor activity of the platinum complexes. (Fuertes et al., 2003)
When the Pt(II) complexe reach the DNA, the possibilities for coordination are different.
Binding of Pt(II) complexes to DNA primarily occurs through the N7 atoms of guanine,
while a binding to N7 and N1 of adenine and N3 of cytosine occurs in small amount.
(Lippert, 1999; Reedijk, 1999) Since the DNA molecule containing a different sequence of
purine and pyrimidine bases, it was found that with 60% represented the coordination of
the type 1,2-(GPG), i.e., the coordination realizes via two molecules of guanosine-5’-
monophosphate (5’-GMP), which are located on opposite strands of DNA. About 25% is
represented by coordination of the type 1,2-(APG), i.e. coordination with adenosine-5'-
monophosphate (5’-AMP) and 5’-GMP placed on opposite DNA strands. Other ways of
coordinations (monofunctional binding of the type 1,3-(GPG), coordination via guanosine
located on the same chain of DNA, etc.) are less frequent. On the Fig. 2. is shown the
different ways of coordination of cisplatin to DNA. (Jakupec et al., 2003; Kozelka et al., 1999)
However, as noted above, the cells contain other bio-molecules which can also react with
platinum complexes. High affinities for the platinum complexes show the bio-molecules that
contain sulphur, as the thiols and the thioethars. Namely, Pt(II) as "soft" acid forms very stable
compounds with sulphur donor ("soft" bases). The resulting compounds are responsible for
the occurrence of toxicity (nephrotoxicity, neurotoxicity, resistance, etc.). Since the
concentration of thiols, including glutathione (GSH) and L-cysteine, in intracellular liquid is
about 10 mM, it is assumed that most of the platinum complex bound to sulphur before it
comes to the molecules of DNA. (Jakupec et al., 2003; Reedijk, 2009; Lippert, 1999; Reedijk,
1999) Binding of platinum complexes to sulphur from thioethars are the kinetically favored
process. The resulting Pt-S(thioethar) bond may be terminated in the presence of DNA, i.e. N7
atom of 5’-GMP can substitute the molecule of thioethar. (Reedijk, 1999; Soldatović & Bugarčić,
2005) For these reasons the compounds of the type Pt-S(thioethers) are believe to be the
reservoirs of “platinum complexes’’ in the body, i.e. they are suitable intermediates in the
reaction of Pt(II) complexes and DNA. Pt-S(thioethers) bond can be terminated in the presence
of thiol molecules. The product of this substitution is thermodynamically stable. Also, Pt(II)
complex can direct bind to sulphur from thiol molecules and the resulting Pt-S(thiol) bond is
very stable and can not be easy broken. It is believed that compounds of the type Pt-S(thiol)
are responsible for the occurrence of toxic effects during the use of Pt(II) complexes as
anticancer reagents. The Pt-S(thiol) bond can be terminated in the presents of compounds
known as "rescue agents″, which are compounds with sulphur and they are very strong
nucleophiles (diethyldithiocarbamate, thiourea, thiosulfate, GSH, cysteine, biotin, etc.).
(Jakupec et al., 2003; Fuertes et al., 2003; Soldatović & Bugarčić, 2005)
University of Kragujevac, Faculty of Science, Department of Chemistry
Serbia
Introduction
Transition metals and their reactions are in general important in the environment, in
technical processes (catalysis, extraction and purification of metal complexes) and in biology
and medicine (biological electron transfer, toxicology and use of metal complexes as drugs).
Moreover, nonessential metal ions are very often used in biological systems either for
therapeutic application or as diagnostic aids. For instance, metal complexes have been used
for the treatment of many diseases (cancer, arthritis, diabetes, Alzheimer, etc.), but with little
understanding of their mechanism of action in biological systems.(Ronconi & Sadler, 2007;
Bruijnincx & Sadler, 2009) Biochemical studies have not clearly established the molecular
basis for the activity and mechanism of action. The growing field of bioinorganic chemistry
is presently dealing with the clarification of the mechanisms of action of metal complexes in
biological systems.(Ronconi & Sadler,2007; Bruijnincx & Sadler, 2009; Jakupec et al., 2008)
Research in the area of application of metal complex compounds in medicine began with the
discovery of antitumor properties of cisplatin. (Rosenberg, 1965, 1967, 1969, 1970) Today
cisplatin is in routine use as therapeutics worldwide. Following the success of cisplatin a
large number of analogous compounds were synthesized. All these compounds have a
several common characteristics:
1. bifunctional complex compounds with cis-geometry
2. PtX2(amin)2 is general formula of this compounds, where X2 are two labile monodentate
or one labile bidentate ligand, and (amine)2 are inert nitrogen-donor ligands
3. nitrogen-donor ligands have to containe at least one NH bond.
Despite the large number of synthesized compounds only a few of them entered the
medicinal use and most are still in preclinical investigation. (Jakupec et al., 2003; Reedijk,
2009) At the Fig. 1. are presented some of platinum complexes that are in the medicinal use
worldwide.
Chronic lymphocytic leukemia is the most frequent type of leukemia and it accounts for
approximately 25% of all leukemias. (Chiorazzi et al., 2005) Although at the present there is
no curative treatment, combinations of cytotoxic agents and of immunotherapies that
generate high complete remission rates hold promise for altering the natural history of this
340 Chronic Lymphocytic Leukemia
disease. (Wierda et al., 2005) Fludarabine (9-beta-D-arabinofuranosyl-2-fluoroadenine 5’-
phosphate) is the most effective purine nucleoside analogue for the treatment of indolent
lymphoproliferative disorders, including Chronic lymphocytic leukemia, low-grade
lymphoma, and prolymphocytic leukemia. (Eichhorst et al., 2005)
The studies show that among the best drugs in the treatment of Chronic lymphocytic
leukemia are the combination of Pt(II) complexes (cisplatin and oxaliplatin) and alkylating
agents and nucleoside analogues such as fluradabine. (Zecevic et al., 2011) The
nonoverlapping side effect profiles of oxaliplatin and fludarabine and their different but
potentially complementary mechanisms of action provide a basis for investigation of the
activity of the drugs in combination. The rationale for combining oxaliplatin with
fludarabine is based on preclinical data showing synergistic cytotoxicity between cisplatin
in combination with the nucleoside. (Wang et al., 1991; Yamauchi et al., 2001)
Consequently, knowledge of the interaction of the different Pt(II) complexes and nitrogenand
sulfur-bonding bio-molecules, and the results obtained from in vitro studies of this type
of interactions will help in finding of good antitumor drug for the treatment of many tumors
including the Chronic lymphocytic leukemia. The main topic of this chapter will be to show
the results obtained in numerous studies of the interactions of the potential antitumor Pt(II)
complexes and different biomolecules.
Platinum(II) has a high affinity for sulphur, so after administrating Pt(II) complex in the
human body there is a strong possibility for binding with sulphur-donor bio-molecules.
Sulphur-donor bio-molecules are present in large amounts in the form of peptides, proteins
and enzymes. Binding of platinum complexes with sulphur-donor bio-molecules are
responsible for the occurrence of toxic effects. (Lippert, 1999; Reedijk, 1999) However, a
certain amount of platinum complexes being bound to nitrogen-donor bio-molecules (amino
acids or DNA). Today it is generally accepted that the anti-tumor activity of platinum drugs
can be ascribed to interactions between the metal complex and DNA, primarily with the
genetic DNA, which is located in the nucleus. The interactions with mitochondrial DNA are
less responsible for the antitumor activity of the platinum complexes. (Fuertes et al., 2003)
When the Pt(II) complexe reach the DNA, the possibilities for coordination are different.
Binding of Pt(II) complexes to DNA primarily occurs through the N7 atoms of guanine,
while a binding to N7 and N1 of adenine and N3 of cytosine occurs in small amount.
(Lippert, 1999; Reedijk, 1999) Since the DNA molecule containing a different sequence of
purine and pyrimidine bases, it was found that with 60% represented the coordination of
the type 1,2-(GPG), i.e., the coordination realizes via two molecules of guanosine-5’-
monophosphate (5’-GMP), which are located on opposite strands of DNA. About 25% is
represented by coordination of the type 1,2-(APG), i.e. coordination with adenosine-5'-
monophosphate (5’-AMP) and 5’-GMP placed on opposite DNA strands. Other ways of
coordinations (monofunctional binding of the type 1,3-(GPG), coordination via guanosine
located on the same chain of DNA, etc.) are less frequent. On the Fig. 2. is shown the
different ways of coordination of cisplatin to DNA. (Jakupec et al., 2003; Kozelka et al., 1999)
However, as noted above, the cells contain other bio-molecules which can also react with
platinum complexes. High affinities for the platinum complexes show the bio-molecules that
contain sulphur, as the thiols and the thioethars. Namely, Pt(II) as "soft" acid forms very stable
compounds with sulphur donor ("soft" bases). The resulting compounds are responsible for
the occurrence of toxicity (nephrotoxicity, neurotoxicity, resistance, etc.). Since the
concentration of thiols, including glutathione (GSH) and L-cysteine, in intracellular liquid is
about 10 mM, it is assumed that most of the platinum complex bound to sulphur before it
comes to the molecules of DNA. (Jakupec et al., 2003; Reedijk, 2009; Lippert, 1999; Reedijk,
1999) Binding of platinum complexes to sulphur from thioethars are the kinetically favored
process. The resulting Pt-S(thioethar) bond may be terminated in the presence of DNA, i.e. N7
atom of 5’-GMP can substitute the molecule of thioethar. (Reedijk, 1999; Soldatović & Bugarčić,
2005) For these reasons the compounds of the type Pt-S(thioethers) are believe to be the
reservoirs of “platinum complexes’’ in the body, i.e. they are suitable intermediates in the
reaction of Pt(II) complexes and DNA. Pt-S(thioethers) bond can be terminated in the presence
of thiol molecules. The product of this substitution is thermodynamically stable. Also, Pt(II)
complex can direct bind to sulphur from thiol molecules and the resulting Pt-S(thiol) bond is
very stable and can not be easy broken. It is believed that compounds of the type Pt-S(thiol)
are responsible for the occurrence of toxic effects during the use of Pt(II) complexes as
anticancer reagents. The Pt-S(thiol) bond can be terminated in the presents of compounds
known as "rescue agents″, which are compounds with sulphur and they are very strong
nucleophiles (diethyldithiocarbamate, thiourea, thiosulfate, GSH, cysteine, biotin, etc.).
(Jakupec et al., 2003; Fuertes et al., 2003; Soldatović & Bugarčić, 2005)
Evidence for single electron transfer (SET) pathway in the reaction of primary alkylcadmium reagents with p-benzoquinone
Abstract
The reaction of primary alkylcadmium reagents with p-benzoquinone at various conditions was studied. On the basis of our
results, reaction proceeds through a SET mechanism that forms loose and tight intermediates, which produce quinole (1) and
substituted hydroquinone (2). In both cases, hydroquinone (3) is obtained in different yields. © 2001 Elsevier Science B.V. All
rights reserved.
Introduction
The organocadmium reagents are known as a very
mild and regioselective reagent in organic synthesis [1a].
The most important synthetic application of
organocadmium reagents has been in the preparation of
ketones in reaction with acyl chlorides [1b,c]. Although
this reagent does not react with ketones and esters [2],
it reacts with a,b-unsaturated ketones mainly through
1,4-addition [3]. Results obtained from the reaction of
Grignard reagents with some ketones and benzoquinone
have shown that it proceeds via SET mechanism
[4].
On the basis of recent reported results [5], and our
studies on the reaction of several organocadmium
reagents with benzoquinone [6], we decided to investigate
the mechanism of these reactions. We are glad to
report the operation of a SET mechanism in the reaction
of organocadmium reagents with benzoquinone.
Results and discussion
The reaction of several organocadmium reagents
with p-benzoquinone was carried out at low and high temperatures. Products were identified by the comparison
of their spectroscopic data with authentic samples.
The results are shown in Tables 1 and 2.
On the basis of our results (Table 1), it seems likely
that the quinol formation has arisen via a SET mechanism
through the formation of a-complex between the
substrate and reagent and subsequent single electron
transfer from the reagent to benzoquinone which leads
to the formation of cross-conjugated tight intermediate
(CCTI) in solvent cage (Scheme 1). The appearance of
the deep blue color during the addition of the reagent
to benzoquinone supports the SET mechanism [4b].
Moreover, when we carried out the scavenging studies
by addition of p-dinitrobenzene to the reaction contents,
the starting material benzoquinone was recovered
The reaction of several organocadmium reagents
with p-benzoquinone was carried out at low and high temperatures. Products were identified by the comparison
of their spectroscopic data with authentic samples.
The results are shown in Tables 1 and 2.
On the basis of our results (Table 1), it seems likely
that the quinol formation has arisen via a SET mechanism
through the formation of a-complex between the
substrate and reagent and subsequent single electron
transfer from the reagent to benzoquinone which leads
to the formation of cross-conjugated tight intermediate
(CCTI) in solvent cage (Scheme 1). The appearance of
the deep blue color during the addition of the reagent
to benzoquinone supports the SET mechanism [4b].
Moreover, when we carried out the scavenging studies
by addition of p-dinitrobenzene to the reaction contents,
the starting material benzoquinone was recovered
Conclusions
From this investigation, it can be concluded that the
reaction of the primary alkylcadmium reagent with
p-benzoquinone proceeds through a SET mechanism.
The products and yields are different and depend on
the temperature, solvent and the nature of the alkyl
group. Reaction at low and high temperature leads to
1,2 and 1,4-addition products, respectively. The yield of
the 1,4-addition product is less than the 1,2-addition
product, since radical ion pairs diffusing out of the
solvent cage is enhanced at higher temperatures. The
formation of high percentage yield of hydroquinone at
high temperature and in the case of all alkyl groups
supports this proposal, as well. Diffusing out of the
solvent cage also depends on the viscosity and basicity
of the solvent. Comparing the yields of hydroquinone
in diethyl ether (DEE) and THF at high temperature
shows the increasing yield in DEE, which has, lower
basicity and viscosity. The nature of the primary alkyl
group is also an important factor in reaction mechanism,
since unlike the other primary alkylcadmium
reagents, the benzyl cadmium reagent leads to 1,4-addition
product even at low temperature.
adapted from:
Mansour Shahidzadeh, Mehdi Ghandi *
Department of Chemistry, Uni6ersity of Tehran, PO Box 13145 -143, Tehran, Iran
Received 18 September 2000; accepted 15 November 2000
Homologous
Series A series of compounds of similar structure in which each member differs from the next by
a common repeating unit, CH2 . The members of the series are called homologues.
• All share the same general formula.
• Formula of a homologue differs from its neighbour by CH2. (e.g. CH4, C2H6, . . . etc )
• Contain the same functional group(s).
• Have similar chemical properties.
• Show a gradual change in physical properties as molar mass increases.
• Can usually be prepared by similar methods.
Basic definitions for organic chemistry
Scope
Organic chemistry is a vast subject so it is easier to split it into small sections for study.
This is usually done by studying compounds which behave in a similar way because they
have a particular atom, or group of atoms, (FUNCTIONAL GROUP) in their structure.
Catenation
The ability to form bonds between atoms of the same element. Carbon catenates to
form chains and rings, with single, double and/or triple covalent bonds
Some common functional groups
GROUP ENDING GEN. FORMULA / STRUCTURE EXAMPLE
ALKANE - ane RH C2H6 ethane
ALKENE - ene C2H4 ethene
ALKYNE - yne C2H2 ethyne
HALOALKANE halo - RX C − Cl C2H5Cl chloroethane
ALCOHOL - ol ROH C2H5OH ethanol
ALDEHYDE -al RCHO CH3CHO ethanal
KETONE - one RCOR CH3COCH3 propanone
CARBOXYLIC - oic acid RCOOH CH3COOH ethanoic acid
ACID
ACYL - oyl chloride RCOCl CH3COCl ethanoyl chloride
CHLORIDE
AMIDE - amide RCONH2 CH3CONH2 ethanamide
ESTER - yl - oate RCOOR CH3COOCH3 methyl ethanoate
NITRILE - nitrile RCN CH3CN ethanenitrile
AMINE - amine RNH2 C − NH2 CH3NH2 methylamine
NITRO - nitro RNO2 CH3NO2 nitromethane
SULPHONIC - sulphonic RSO3H C6H5SO3H benzene sulphonic
ACID acid acid
ETHER - oxy - ane ROR R-O-R C2H5OC2H5 ethoxyethane
Elucidation of the structures of organic compounds - a brief summary
Introduction Organic chemistry is so vast that the identification (characterisation) of a compound can be quite
involved. The characterisation takes place in a series of stages (see below). In earlier times relatively
large amounts of substance were required to elucidate the structure but, with the advance in technology
and the increased use of electronic instrumentation, only very small amounts are now required.
Elemental
composition One assumes that organic compounds contain carbon and hydrogen but it can be proved by letting the
compound undergo combustion. Carbon is converted to carbon dioxide and hydrogen to water.
Percentage
composition The percentage composition by mass is found by dividing the mass of an element present by the mass
of the compound present, then multiplying by 100. Elemental mass of C and H can be found by allowing
the substance to undergo complete combustion. From this one can find...
• mass of carbon = 12/44 of the mass of CO2 produced
• mass of hydrogen = 2/18 of the mass of H2O produced
Empirical
formula This gives the simplest ratio of elements present in the substance. It can be calculated by dividing the
mass or percentage mass of each element present by its molar mass and finding the simplest ratio
between the answers. Empirical formula is converted to the molecular formula using molecular mass.
Molecular
mass Molecular mass determination was traditionally carried out using a variety of techniques such as ...
• volumetric analysis or
• molar volume methods such as the Dumas, Victor-Meyer or gas syringe experiments.
Nowadays mass spectrometry is used. The position of the last m/z signal is due to the molecular ion
and gives the molecular mass. The fragmentation pattern also gives information about the compound.
Molecular
formula The molecular formula is an exact multiple of the empirical formula. Comparing the molecular mass with
the empirical mass allows one to find the true formula.
e.g. if the empirical formula is CH (relative mass = 13) and the molecular mass is 78
the molecular formula will be 78/13 or 6 times the empirical formula i.e. C6H6 .
Structural
formula Because of the complexity of organic molecules, there can be more than one structure for a given
molecular formula. To work out the structure, one can carry out different tests...
Chemical Use chemical reactions to identify the functional group(s) present.
Spectroscopy e.g. IR detects bond types due to absorbance of i.r. radiation
NMR gives information about the position and relative
numbers of hydrogen atoms present in a molecule
Confirmation By comparison of spectra and melting point or boiling point.
Monday, August 20, 2012
The Twelve Principles of Green Chemistry*
The Twelve Principles of Green Chemistry*
- Prevention
It is better to prevent waste than to treat or clean up waste after it has been created. - Atom Economy
Synthetic methods should be designed to maximize the incorporation of all materials used in the process into the final product. - Less Hazardous Chemical Syntheses
Wherever practicable, synthetic methods should be designed to use and generate substances that possess little or no toxicity to human health and the environment. - Designing Safer Chemicals
Chemical products should be designed to effect their desired function while minimizing their toxicity. - Safer Solvents and Auxiliaries
The use of auxiliary substances (e.g., solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used. - Design for Energy Efficiency
Energy requirements of chemical processes should be recognized for their environmental and economic impacts and should be minimized. If possible, synthetic methods should be conducted at ambient temperature and pressure. - Use of Renewable Feedstocks
A raw material or feedstock should be renewable rather than depleting whenever technically and economically practicable. - Reduce Derivatives
Unnecessary derivatization (use of blocking groups, protection/ deprotection, temporary modification of physical/chemical processes) should be minimized or avoided if possible, because such steps require additional reagents and can generate waste. - Catalysis
Catalytic reagents (as selective as possible) are superior to stoichiometric reagents. - Design for Degradation
Chemical products should be designed so that at the end of their function they break down into innocuous degradation products and do not persist in the environment. - Real-time analysis for Pollution Prevention
Analytical methodologies need to be further developed to allow for real-time, in-process monitoring and control prior to the formation of hazardous substances. - Inherently Safer Chemistry for Accident Prevention
Substances and the form of a substance used in a chemical process should be chosen to minimize the potential for chemical accidents, including releases, explosions, and fires.
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