Biology : Chemistry of life

Proton : defines the element. the numbers of protons in the nucleus of the atom defines.
# of protons = atomic number = what defines elements
For example, Hydrogen has one proton, helium has two protons..
Electron
Neutron
proton and neutron in the center of the atom=nucleus of the atom
Neutron can change, electron is change, the atom is still the same atom.
protons cannot change.
protons have positive charge.
electrons have negative charge.
they attract each other.
isotope : the same element with a different of neutrons

the Bohr model : model electrons as planets revolving around a star
with more energy, its orbit will become more elliptical
as electrons gets more energy, it will enter the higher energy state
when eletrons get further away from a high energy state the coulomb force is weaker
then they're easier to pluck off
the electron configuration : the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals.
Coulomb force : attraction or repulsion(=repel) of particles or objects because of their electric charge.

valence electrons = electrons that atom will use to when it react
valence electrons : tends to be with highest energy level/furthest out from the center(for s and p block, not for transition metals )
in the same group elements : are going to have same # of Valence eletron
Carbon's electron configuration is [He]2s² 2p²
How many electrons does it have in its outermost shell=not been completed yet
These four [He]2s² 2p²
in carbon's group, they are all going to have 4 Valence electrons
covalent bond :
Fe(iron)'s electron configuration with Ar(argon) as a base = [Ar] 4s² 3d⁶
transition metals
D block : known as transition metals(bridge between s-block and p-block)
F block : known as inner transition metals(bridge between s-block and d-block)

the most part the elements in the column(group) have very similar properties\
and same bonding behavior
because they tend to have the same number of electrons in their outermost shell(=same # of valence electrons)
group 1, alkali metals(except for Hydrogen), very reactive(one valence electron left to react)
group 2, alkaline earth metals, 2 valence electrons in their the outermost shell, reasonably reactable
electron configuration for Sc : [Ar] 4s² 3d¹(backfill)
group 17, Halogen, love to react with alkali metals
group 18, noble gases(=atomic nirvana), have similar properties not being reacted
because they have 8 valence electron, filled their outermost shell
octet rule : Most of the elements important in biology need eight electrons in their outermost shell in order to be stable
Subshells are designated by the letters s, p, d, and f, and each letter indicates a different shape
each orbital can hold up to two electrons. p subshell has 3 dimensions then it can hold up to 6 electrons at most.
d orbital, but this orbital is considerably higher in energy than the 3s and 3p orbitals and does not begin to fill until the fourth row of the periodic table

Ionic, covalent, and metallic bonds
ionic bond : not sharing electrons, just handed over electrons, then attracted force is coming(due to different charges)
ionic bond forms ion. cation(positive charge), anion(negative charge)
covalent bond : is a chemical bond that involves the sharing of 2 electrons between atoms. (when atoms aren't very different in terms of their electronegativity)
polar covalent bond : one side of the molecule is going to be more negative/positive
non polar covalent bond : form between two atoms of the same element, so between atoms of different elements that share electrons equally.
metallic bond : they love to share electrons, make a pool of electrons, which make them malleable(easy to bend)

Electron affinity : how much does the atom attract electrons
Electronegativity : high or low electron density. when that atom is part of a covalent bond, how likely does it want to hog(keep) electrons in that covalent bond?
in case of H2O, oxygen is more electronegativity, so electrons spend more time around oxygen
(on groups)from left to right, it is more electronegative
(on period)from top to bottom, it is less electronegative. because atoms on the bottom have more shells, so the electron in the furthest shell is easier to grab off(give up the electron)

Pauling scale for electronegativity
Oxygen is more electronegative than carbon, it is partially negative.(meanwhile, carbon is partially positive)=polarized situation. polar covalent bond.
<->non-polar covalent bond
if the difference of electronegativity more than 0.5, consider to be polar covalent bond
in case of Na-Cl, the difference of electronegativity(2.1) so big, they're not gonna share electrons. Cl steals electrons.
Cl gets former negative charge, Na gets former positive charge=the ionic bond
if the difference of electronegativity more than 1.7, consider to be ionic bond
those numbers(0.5 and 1.7) are not absolute.

means forces between molecules
dipole-dipole interaction(acetone molecule)
oxygen(partially +), carbon(partially -)=two different poles=polar molecule
there's going to be an electrostatic attraction between O(from molecule A) and C(from molecule B)
its intermolecular force holds molecules as a liquid at room temperature.
it depends on the electronegativity.
hydrogen bonding(water molecule) : stronger version of dipole-dipole, the strongest intermolecular force(O-H-O)
it need more energy to pull these water(boiling temp. 100'c) molecule apart than acetone(boiling temp. 56'c)
FON : fluorine, oxygen, nitrogen = electronegative atoms participate in hydrogen bonding
london dispersion focrces(methane) : the weakest intermolecular force
van der Waals forces : a general term for intermolecular interactions that do not involve covalent bonds or ions

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