Wednesday, 15 June 2011

Electronic Configuration of the Elements

Here's a useful table for your chemistry homework or general use! This is a compilation of the electron configurations of the elements up through number 104, broken into three pages (the table was too large for anything less). To arrive at the electron configurations of atoms, you must know the order in which the different sublevels are filled. Electrons enter available sublevels in order of their increasing energy. A sublevel is filled or half-filled before the next sublevel is entered. For example, the s sublevel can only hold two electrons, so the 1s is filled at helium (1s2). The p sublevel can hold six electrons, the d sublevel can hold 10 electrons, and the f sublevel can hold 14 electrons. Common shorthand notation is to refer to the noble gas core, rather than write out the entire configuration. For example, the configuration of magnesium could be written [Ne]3s2, rather than writing out 1s22s22p63s2.

No. Element K L M N O P Q
1 2 3 4 5 6 7
s s p s p d s p d f s p d f s p d f s
1 H 1
2 He 2
3 Li 2 1
4 Be 2 2
5 B 2 2 1
6 C 2 2 2
7 N 2 2 3
8 O 2 2 4
9 F 2 2 5
10 Ne 2 2 6
11 Na 2 2 6 1
12 Mg 2 2 6 2
13 Al 2 2 6 2 1
14 Si 2 2 6 2 2
15 P 2 2 6 2 3
16 S 2 2 6 2 4
17 Cl 2 2 6 2 5
18 Ar 2 2 6 2 6
19 K 2 2 6 2 6 - 1
20 Ca 2 2 6 2 6 - 2
21 Sc 2 2 6 2 6 1 2
22 Ti 2 2 6 2 6 2 2
23 V 2 2 6 2 6 3 2
24 Cr 2 2 6 2 6 5* 1
25 Mn 2 2 6 2 6 5 2
26 Fe 2 2 6 2 6 6 2
27 Co 2 2 6 2 6 7 2
28 Ni 2 2 6 2 6 8 2
29 Cu 2 2 6 2 6 10 1*
30 Zn 2 2 6 2 6 10 2
31 Ga 2 2 6 2 6 10 2 1
32 Ge 2 2 6 2 6 10 2 2
33 As 2 2 6 2 6 10 2 3
34 Se 2 2 6 2 6 10 2 4
35 Br 2 2 6 2 6 10 2 5
36 Kr 2 2 6 2 6 10 2 6

Valence Bond Theory and Hybrid Atomic Orbitals

This picture is an image of a Centaur from Sphinx Stargate. The Centaur is a race of monsters in Greek mythology, hybrid animal having the head, arms and torso of a man united to the body and legs of a horse. Mixing a number of atomic orbitals to form the same number of hybrid orbitals to explain chemical bonding and shapes and molecular structures is a rather recent myth. The most significant development in the first half of the 20th century is the human's ability to understand the structure of atoms and molecules. Computation has made mathematical concepts visible to the extent that we now can see the atomic and molecular orbitals. On the other hand, Using everyday encountered materials or toys can also generate beautiful illustrations of hybrid atomic orbitals.
The valence bond (VB) approach is different from the molecular orbital (MO) theory. Despite their differences, most of their results are the same, and they are interesting.

The valence bond (VB) theory

The valence-bond approach considers the overlap of the atomic orbitals (AO) of the participation atoms to form a chemical bond. Due to the overlapping, electrons are localized in the bond region. The overlapping AOs can be of different types, for example, a sigma bond may be formed by the overlapping the following AOs.

Chemical bonds formed due to overlap of atomic orbitals
s-s s-p s-d p-p p-d d-d
H-H
Li-H
H-C
H-N
H-F
H-Pd in
palladium
hydride
C-C
P-P
S-S
F-S
in SF6
Fe-Fe

However, the atomic orbitals for bonding may not be "pure" atomic orbitals directly from the solution of the Schrodinger Equation. Often, the bonding atomic orbitals have a character of several possible types of orbitals. The methods to get an AO with the proper character for the bonding is called hybridization. The resulting atomic orbitals are called hybridized atomic orbitals or simply hybrid orbitals.
We shall look at the shapes of some hybrid orbitals first, because these shapes determine the shapes of the molecules.

Hybridization of atomic orbitals

The solution to the Schrodinger Equation provides the wavefunctions for the following atomic orbitals:
1s, 2s, 2p, 3s, 3p, 3d, 4s, 4p, 4d, 4f, etc. For atoms containing two or more electrons, the energy levels are shifted with respect to those of the H atom. An atomic orbital is really the energy state of an electron bound to an atomic nucleus. The energy state changes when one atom is bonded to another atom. Quantum mechanical approaches by combining the wave functions to give new wavefunctions are called hybridization of atomic orbitals. Hybridization has a sound mathematical fundation, but it is a little too complicated to show the details here. Leaving out the jargons, we can say that an imaginary mixing process converts a set of atomic orbitals to a new set of hybrid atomic orbitals or hybrid orbitals.
At this level, we consider the following hybrid orbitals:
sp
sp
2
sp3
sp3d
sp3d2

The sp hybrid atomic orbitals

The sp hybrid atomic orbitals are possible states of electron in an atom, especially when it is bonded to others. These electron states have half 2s and half 2p characters. From a mathematical view point, there are two ways to combine the 2s and 2p atomic orbitals: sp1 = 2s + 2p
sp2 = 2s - 2p
These energy states (sp1 and sp2) have a region of high electron probability each, and the two atomic orbitals are located opposite to each other, centered on the atom. The sp hybrid orbitals are represented by this photograph.
H-Be-H 1s             1s
H sp1 Be sp2 H
1s             1s
For example, the molecule H-Be-H is formed due to the overlapping of two 1s orbitals of 2 H atoms and the two sp hybridized orbitals of Be. Thus, the H-Be-H molecule is linear. The diagram here shows the overlapping of AOs in the molecule H-Be-H.
The ground state electronic configuration of Be is 1s22s2, and one may think of the electronic configuration "before" bonding as 1s2sp2. The two electrons in the sp hybrid orbitals have the same energy.

Linear molecules
ClBeCl HCCH
HCN
O=C=O
You may say that the concept of hybridizing AOs for the bonding is just a story made up to explain the molecular shape of Cl-Be-Cl. You are right! The story is lovely and interesting, though.
In general, when two and only two atoms bond to a third atom and the third atom makes use of the sp hybridized orbitals, the three atoms are on a straight line. For example, sp hybrid orbitals are used in the central atoms in the molecules shown on the right.

The sp2 hybrid orbitals

The energy states of the valence electrons in atoms of the second period are in the 2s and 2p orbitals. If we mix two of the 2p orbitals with a 2s orbital, we end up with three sp2 hybridized orbitals. These three orbitals lie on a plane, and they point to the vertices of a equilateral triangle as shown here. When the central atom makes use of sp2 hybridized orbitals, the compound so formed has a trigonal shape. BF3 is such a molecule:

Molecules with sp2 Hybrid orbitals
F
|
B
/     \
F         F
        . .     -2
:O:
|
C
/     \\
:O::         O

.
N
//     \\
O         O

. .
O
//     \\
O         O

. .
S
//     \\
O         O

Not all three sp2 hybridized orbitals have to be used in bonding. One of the orbitals may be occupied by a pair or a single electron. If we do not count the unshared electrons, these molecules are bent, rather than linear. The three molecules shown together with the BF3 molecule are such molecules.
Carbon atoms also makes use of the sp2 hybrid orbitals in the compound H2C=CH2. In this molecule, the remaining p orbital from each of the carbon overlap to form the additional pi, p, bond.

Planar molecules with sp2 Hybrid orbitals
H               H
\             /
C = C
/             \
H               H
O               2-
\            
C = O
/            
O                
O               1-
\            
N = O
/            
O                

Other ions such as CO32-, and NO3-, can also be explained in the same way.

The sp3 hybrid orbitals

Mixing one s and all three p atomic orbitals produces a set of four equivalent sp3 hybrid atomic orbitals. The four sp3 hybrid orbitals points towards the vertices of a tetrahedron, as shown here in this photograph. When sp3 hybrid orbitals are used for the central atom in the formation of molecule, the molecule is said to have the shape of a tetrahedron.
The typical molecule is CH4, in which the 1s orbital of a H atom overlap with one of the sp3 hybrid orbitals to form a C-H bond. Four H atoms form four such bonds, and they are all equivalent. The CH4 molecule is the most cited molecule to have a tetrahedral shape. Other molecules and ions having tetrahedral shapes are SiO44-, SO42-,
As are the cases with sp2, hybrid orbitals, one or two of the sp3 hybrid orbitals may be occupied by non-bonding electrons. Water and ammonia are such molecules.

Tetrahedral arrangements of
CH4, NH3E and OH2E2
H         H
\       /
C
/  \
H   H
H         H
\       /
N
/  \
:   H
H         H
\       /
O
/  \
:   :
The C, N and O atoms in CH4, NH3, OH2 (or H2O) molecules use the sp3 hybrid orbitals, however, a lone pair occupy one of the orbitals in NH3, and two lone pairs occupy two of the sp3 hybrid orbitals in OH2. The lone pairs must be considered in the VSEPR model, and we can represent a lone pair by E, and two lone pairs by E2. Thus, we have NH3E and OH2E2 respectively.
The VSEPR number is equal to the number of bonds plus the number of lone pair electrons. Does not matter what is the order of the bond, any bonded pair is considered on bond. Thus, the VSEPR number is 4 for all of CH4, :NH3, ::OH2.
According the the VSEPR theory, the lone electron pairs require more space, and the H-O-H angle is 105 deegrees, less than the ideal tetrahedral angle of 109.5 degrees.

The dsp3 hybrid orbitals

The five dsp3 hybrid orbitals resulted when one 3d, one 3s, and three 3p atomic orbitals are mixed. When an atom makes use of fice dsp3 hybrid orbitals to bond to five other atoms, the geometry of the molecule is often a trigonalbipyramidal. For example, The molecule PClF4 displayed here forms such a structure. In this diagram, the Cl atom takes up an axial position of the trigonalbipyramid. There are structures in which the Cl atom may take up the equatorial position. The change in arrangement is accomplished by simply change the bond angles. This link discusses this type of configuration changes of this molecule. Some of the dsp3 hybrid orbitals may be occupied by electron pairs. The shapes of these molecules are interesting. In TeCl4, only one of the hybrid dsp3 orbitals is occupied by a lone pair. This structure may be represented by TeCl4E, where E represents a lone pair of electrons. Two lone pairs occupy two such orbitals in the molecule BrF3, or BrF3E2. These structures are given in a VSEPR table of 5 and 6 coordinations.
The compound SF4 is another AX4E type, and many interhalogen compounds ClF3 and IF3 are AX3E2 type. The ion I3- is of the type AX2E3.

The d2sp3 hybrid orbitals

The six d2sp3 hybrid orbitals resulted when two 3d, one 3s, and three 3p atomic orbitals are mixed. When an atom makes use of six d2sp3 hybrid orbitals to bond to six other atoms, the molecule takes the shape of an octahedron, in terms of molecular geometry. The gas compound SF6 is a typical such structure. This link provides other shapes as well. There are also cases that some of the d2sp3 hybrid orbitals are occupied by lone pair electrons leading to the structures of the following types:

AX6,   AX5E,   AX4E2   AX3E3   and   AX2E4
IOF5,   IF5E,   XeF4E2
No known compounds of AX3E3 and AX2E4 are known or recognized, because they are predicted to have a T shape and linear shape respectively when the lone pairs of electrons are ignored.

Molecular shapes of compounds

While the hybridized orbitals were introduced, in the foregoing discussion, Valence-shell Electron-pair Repulsion (VSEPR) Model were included to suggest the shapes of various molecules. Specifically, the VSEPR model counts unshared electron pairs and the bonded atoms as the VSEPR number. A single-, double- and tripple-bond is considered as 1. After having considered the hybridized orbitals and the VSEPR model, we can not take a systematic approach to rationalize the shapes of many molecules based on the number of valence electrons. A summary in the form of a table is given here to account for the concepts of hybrid orbitals, valence bond theory, VSEPR, resonance structures, and octet rule. In this table, the geometric shapes of the molecules are described by linear, trigonal planar, tetrahedral, trigonal bypyramidal, and octahedral. The hybrid orbitals use are sp, sp2, sp3, dsp3, and d2sp3.
The VSEPR number is the same for all molecules of each group. Instead of using NH3E, and OH2E2, we use :NH3, ::OH2 to emphasize the unshared (or lone) electron pairs.
A summary of hybrid orbitals, valence bond theory, VSEPR,
resonance structures, and octet rule.
Linear Trigonal
planar
Tetrahedral Trigonal
bipyramidal
Octahedral
sp sp2sp3 dsp3 d2sp3
BeH2
BeF2
CO2
HCN
HCยบCH
BH3
BF3
CH2O
(>C=O)
>C=C<
CO32-
benzene
graphite
fullerenes
•NO2
N3-
:OO2 (O3)
:SO2
SO3
CH4
CF4
CCl4
CH3Cl
NH4+
:NH3
:PF3
:SOF2
::OH2
::SF2

SiO44-
PO43-
SO42-
ClO4-
PF5
PCl5
PFCl4
:SF4
:TeF4
::ClF3
::BrF3
:::XeF2
:::I3-
(:::I I2-)
:::ICl2-
SF6
IOF5
PF6-
SiF62-
:BrF5
:IF5
::XeF4
• a lone odd electron         : a lone electron pair
This table correlates a lot of interesting chemical concepts in order to understand the molecular structures of these compounds or ions. There are some intriqueing chemical relationships among the molecules in each column for you to ponder. Only Be and C atoms are involved in linear molecules. In gas phase, BeH2 and BeF2 are stable, and these molecules do not satisfy the octet rule. The element C makes use of sp hybridized orbitals and it has the ability to form double and triple bonds in these linear molecules.
Carbon compounds are present in trigonal planar and tetrahedral molecules, using different hybrid orbitals. The extra electron in nitrogen for its compounds in these groups appear as lone unpaired electron or lone electron pairs. More electrons in O and S lead to compounds with lone electron pairs. The five-atom anions are tetrahedral, and many resonance structures can be written for them.
Trigonal bipyramidal and octahedral molecules have 5 and 6 VSEPR pairs. When the central atoms contain more than 5 or 6 electrons, the extra electrons form lone pairs. The number of lone pairs can easily be derived using Lewis dot structures for the valence electrons.
In describing the shapes of these molecules, we often ignore the lone pairs. Thus, •NO2, N3-, :OO2 (O3), and :SO2 are bent molecules whereas :NH3, :PF3, and :SOF2 are pyramidal. You already know that ::OH2 (water) and ::SF2 are bent molecules.
The lone electron pair takes up the equatorial location in :SF4, which has the same structure as :TeF4 described earlier. If you lay a model of this molecule on the side, it looks like a butterfly. By the same reason, ::ClF3 and ::BrF3 have a T shape, and :::XeF2, :::I3-, and :::ICl2- are linear.
Similarly, :BrF5 and :IF5 are square pyramidal whereas ::XeF4 is square planar.

The Center Atom

A nice student asked a brilliant question. Which atom in the formula is usually the center atom?
Usually, the atom in the center is more electropositive than the terminal atoms. However, the H and halogen atoms are usually at the terminal positions because they form only one bond.
Take a look at the chemical formulas in the table, and see if the above statement is true.
However, the application of VSEPR theory can be expanded to complicated molecules such as
H H         H   O
    | |         |  //
  H-C-C=C=C-C=C-C-C
    |           |  \
    H           N   O-H
               / \
              H   H
By applying the VSEPR theory, one deduces the following results:
  • H-C-C bond angle = 109o
  • H-C=C bond angle = 120o, geometry around C trigonal planar
  • C=C=C bond angle = 180o, in other words linear
  • H-N-C bond angle = 109o, tetrahedral around N
  • C-O-H bond angle = 105 or 109o, 2 lone electron pairs around O

ATOMIC ORBITAL

An atomic orbital is a mathematical function that describes the wave-like behavior of either one electron or a pair of electrons in an atom. This function can be used to calculate the probability of finding any electron of an atom in any specific region around the atom's nucleus. The term may also refer to the physical region defined by the function where the electron is likely to be.
Within a physical context atomic orbitals are the basic building blocks of the electron cloud model (alternatively referred to as the wave mechanics model or atomic orbital model), a modern framework for describing the placement of electrons in an atom. In this model, the atom consists of a nucleus surrounded by orbiting electrons. These electrons exist in atomic orbitals, which are a set of quantum states of the negatively charged electrons trapped in the electrical field generated by the positively charged nucleus. The electron cloud model can only be described by quantum mechanics, in which the electrons are most accurately described as standing waves surrounding the nucleus.

Atomic orbitals are typically described as “hydrogen-like” (meaning one-electron) wave functions over space, categorized by n, l, and m quantum numbers, which correspond to the electrons' energy, angular momentum, and an angular momentum direction, respectively. Each orbital is defined by a different set of quantum numbers and contains a maximum of two electrons. The simple names s orbital, p orbital, d orbital and f orbital refer to orbitals with angular momentum quantum number l = 0, 1, 2 and 3 respectively. These names indicate the orbital shape and are used to describe the electron configurations. They are derived from the characteristics of their spectroscopic lines: sharp, principal, diffuse, and fundamental, the rest being named in alphabetical order (omitting j).





The wavefunction for the electron cloud of a complex atom may be seen as being built up (in approximation) in an electron configuration that is a sum of simpler hydrogen-like atomic orbitals. In such a configuration, pairs of electrons are arranged in simple repeating patterns of increasing odd numbers (1,3,5,7..), each of which represents a set of electron pairs with a given energy and angular momentum. The repeating periodicity of the blocks of 2, 6, 10, and 14 elements in the periodic table arises naturally from the total number of electrons which occupy a complete set of s, p, d and f atomic orbitals, respectively.

Tuesday, 14 June 2011

Cholesterol Synthesis

Statins HMG-CoA reductase inhibitors

Statins

  • Facts:



    Lower cholesterol by inhibiting the enzyme HMG-CoA reductase (rate-limiting enzyme of the mevalonate pathway of cholesterol synthesis)

    Inhibition of this enzyme in the liver results in decreased cholesterol synthesis and increased synthesis of LDL receptors, resulting in an increased clearance of LDL

  • Side Effects:



    Myalgias, muscle cramps
    Rhabdomyolysis

  • Notes:



    Mevalonate is also used for the production of dolichol and CoQ10
    Reduced CoQ10 is implicated in the pathogenesis of statin-induced myopathy

Aufbau Rule for filling electrons in orbitals

The Aufbau principle or building-up principle is used to determine the electron configuration of an atom, molecule or ion. The principle postulates a hypothetical process in which an atom is "built up" by progressively adding electrons. As they are added, they assume their most stable conditions with respect to the nucleus and those electrons already there.
According to the principle, electrons fill orbitals starting at the lowest available (possible) energy states before filling higher states (e.g. 1s before 2s). The number of electrons that can occupy each orbital is limited by the Pauli exclusion principle.

Unoccupied orbitals will be filled before occupied orbitals are reused.

The Madelung energy ordering rule

Order in which orbitals are arranged by increasing energy according to the Madelung rule. Each diagonal red arrow corresponds to a different value of n+l.
  The rule is based on the total number of nodes in the atomic orbital, n+l, which is related to the energy. In the case of equal n+l values, the orbital with a lower n value is filled first. The fact that most of the ground state configurations of neutral atoms fill orbitals following this n+l,n pattern was obtained experimentally, by reference to the spectroscopic characteristics of the elements.
The Madelung energy ordering rule applies only to neutral atoms in their ground state, and even in that case, there are several elements for which it predicts configurations that differ from those determined experimentally. Copper and chromium are common examples of this property. According to the Madelung rule, the 4s orbital (n+l = 4+0 = 4) is occupied before the 3d orbital (n+l = 3+2 = 5). The rule then predicts the configuration of 29Cu to be 1s22s22p63s2 3p64s23d9, abbreviated [Ar]4s23d9 where [Ar] denotes the configuration of Ar (the preceding noble gas). However the experimental electronic configuration of the copper atom is [Ar]4s13d10. By filling the 3d orbital, copper can be in a lower energy state. Similarly, chromium takes the electronic configuration of [Ar]4s13d5 instead of [Ar]4s23d4. In this case, chromium has a half-full 3d shell.