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Biological Chemistry > Chemical Bonds > Flashcards

Chemical Bonds Flashcards

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1
Q

Quantum Mechanics

A
  • particles = waves, ie. they can be described as a wave function
  • wave functions of electrons in atoms can be described by PSI x,y,z
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2
Q

Electron Density

A

electron distribution in space for an orbital

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3
Q

Coulomb’s Law

A
  • electrostatic potential energy

- closer an electron is to the nuclear the greater energy it has (greater attraction)

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4
Q

Aufbau Principle

A

electrons placed in orbitals starting with lowest energy and working up

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5
Q

Pauli Exclusion Principle

A

2 electrons per orbital with spins paired

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6
Q

Hunds Rule

A

when multiple orbitals of the same energy are available electrons are distributed amongst them

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7
Q

Molecular Orbitals

A

combining atomic orbitals to form molecular orbitals (sigma and pi)
bonding orbitals: wave functions together. high probability electron is between nucleus to give a favorable electrostatic attraction
- favorable coloumb interaction with both nuclei
anti bonding orbitals: wave functions opposite no electron density between nuclei, ie. energetically unfavorable

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8
Q

Bonding and Antibonding Orbitals

A
  • bonding orbitals filled first
  • when anti bonding orbitals are filled, the energy comes from putting electron in bonding orbital
  • this cancels out gain in energy and determines whether two atoms will bond spontaneously
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9
Q

Hybridization

A

the idea that atomic orbitals fuse to form newly hybridised orbitals, which in turn, influences molecular geometry and bonding properties
- sigma: hybridized
- pi: unhybridized
repositioning of orbitals so the electrons are in optimal locations for being shared in covalent bond formation

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10
Q

Configuration

A

conversion between isomers needs a single bond to break

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11
Q

Enantiomers

A

Non superimposable mirror images of each other

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12
Q

Diastereoisomers

A

Not mirror images but are non superimposable

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13
Q

Glucose Polymers

A

Amylose vs Cellulose

  • amylose has alpha linkages with bends and twists
  • celulose has beta linkages and is flat with straight chains
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14
Q

Features Defining Molecular Shape and Structure

A
  1. bond length
  2. bond angles (VSEPR theory)
  3. bond rotation
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15
Q

Conformation

A

how atoms are joined, is fixed
molecules will adopt a configuration minimizing repulsion forces
- Eclipsed: same orientation of groups
- Staggered: opposite orientations of groups (preferred because of steric hindrance)

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16
Q

Isomers

A

Same molecular formula but different structural formulas

  • structural: different bonding
  • constitutional: geometrical isomerism
17
Q

Constitutional isomers

A

You can’t interconvert them without breaking a covalent bond. Configurational change needed. Cis Trans nomenclature needed

18
Q

Types of staggered conformation

A

Gauche: R groups next to each other

Anti (favored): R groups opposite

19
Q

Conjugated Double bonds

A

Different types of double bonds
The single and double bonds alternate. These enables the electrons to be delocalised over the whole system and so be shared by many atoms. This means that the delocalised electrons may move around the whole system.

20
Q

Aromatic Compounds

A

Hydrocarbons which contain benzene, or some other related ring structure. These pi-bonds are delocalized around the ring, leading to an unusual stability for the benzene ring compared to other alkenes.

21
Q

Heterocyclic Aromatic Systems

A

Pyridine
Pyrimidine
Pyrrole
- carbon in ring replaced by one or more nitrogens

22
Q

Wavelength and Frequency

A

increase in frequency = energy increase

smaller wavelength = energy increase

23
Q

Electron Orbital Movement

A

Energy goes into moving electrons between orbitals
Electrons use energy to move to antibonding orbitals
sigma to antisigma = highest energy
pi to anti pi = lowest energy

24
Q

Molecular Vibrations

A

Electrons vibrate within an orbital/energy level
Stretching, rocking, scissoring, wobbling, etc
Absorbance vs wavelength graph gives a broad peak causes by this vibration

25
Q

Beer Lambert Law

A

A = E x c x l

Absorbance proportional to concentration

26
Q

Fluoresence

A

When going back to the ground state, electrons move down to lower energy molecular vibrator levels releasing heat
When going back to bonding orbitals they drop from lowest level of anti sigma to highest sigma level
We see this lowest energy difference

27
Q

Electronic Properties of Phosphate

A
  • hydridize orbitals to make 4 sp3 orbitals and one 3d electron
  • tetrahedral geometry with all oxygens being equivalent and having partial negative charge
  • phosphate ion is very stable and exists in different resonance forms
  • this stability means it can pull reaction forwards of ATP hydrolysis
28
Q

Delocalisation

A
  • resonance is a type of delocalisation where electrons move around
  • conjugation is another type of delocalisation where multiple double bonds are allowing electrons to move around in molecular orbitals beyond the 2 atoms
29
Q

Electronic Properties of Oxygen

A
  • 2p orbitals form bond
  • 1s/2s orbitals non bonding
  • filled sigma, pi, and anti pi orbitals
  • anti pi bond cancels out one of the bonding pairs
30
Q

Bond Order

A

electrons in bonding orbitals - electrons in anti bonding orbitals / 2
Gives net number of shared electron pairs

31
Q

Oxygen Paramegnetism

A
  • electrons in antibonding orbitals line up their spins with each other so have paramagnetism
  • explains oxygen’s reactivity
32
Q

Electronegativity

A
  • attraction between electron and nucleus and the ability of the nucleus to pull electrons
  • increases across periods (increased nuclear charge)
  • decreases down groups (electron shielding)
  • leads to partial charges on atoms
33
Q

Steric Clash

A

Two atoms closer than the sum of their VDW radii

34
Q

VDW Attraction

A

Little more than sum of VDW radii

  • transient dipoles created by random change
  • weak interactions
35
Q

Hydrogen Bonds

A
  • linear bonds
  • dipoles in H bonds align (directionality)
  • essentially a form of dipole dipole interaction only between H and C,N,O,F
36
Q

Hydrophobic Effect

A
  • water molecules form organised clathrates when in contact with non polar structures
  • this organised structure is energetically unfavorable
  • bringing non polar faces together relaxes the organised water
37
Q

Bond Energies

A 
Covalent bonds: 350 kj
H bond: 5-20 kj
VDW: 0.2-2 kj
hydrophobic: entropy
rotational conformations: 10 kj

Biological Chemistry (7 decks)

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