Chem 150 Unit 1 - Molecules Organic and Biological Chemistry substances are made of molecules. Being able to predict the structures and interactions of

Chem 150Chem 150Unit 1 - MoleculesUnit 1 - Molecules

Organic and Biological Chemistry Organic and Biological Chemistry substances are made of molecules. Being substances are made of molecules. Being

able to predict the structures and able to predict the structures and interactions of molecules is important to interactions of molecules is important to

our understanding of Organic and our understanding of Organic and Biological ChemistryBiological Chemistry

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Atomic StructureAtomic Structure

Atoms are made up of three types of subatomic particles:Atoms are made up of three types of subatomic particles:• protonsprotons• neutronsneutrons• electronselectrons

Two important properties of these particles are Two important properties of these particles are massmass and and chargecharge..

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• The protons and neutrons packed The protons and neutrons packed in the center of the atom in a in the center of the atom in a region called the region called the nucleusnucleus..

• The electrons occupy a diffuse The electrons occupy a diffuse region surrounding the nucleus.region surrounding the nucleus.

• The diameter of the volume The diameter of the volume occupied by the electrons isoccupied by the electrons is≈ 10,000 times that of the nucleus.≈ 10,000 times that of the nucleus.

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The electrons have a specific arrangement in the the diffuse The electrons have a specific arrangement in the the diffuse cloud that surround the nucleus.cloud that surround the nucleus.• The Bohr model of the atomThe Bohr model of the atom• Electrons circle the nucleus in specific orbits, with each orbit corresponding to a Electrons circle the nucleus in specific orbits, with each orbit corresponding to a

different energy level.different energy level.

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The electrons have a specific arrangement in the the diffuse The electrons have a specific arrangement in the the diffuse cloud that surround the nucleus.cloud that surround the nucleus.• The Bohr model of the atom only works if the atom has a The Bohr model of the atom only works if the atom has a

single electron.single electron.• Quantum mechanics was able to produce a better model.Quantum mechanics was able to produce a better model.

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According to quantum mechanics the electrons occupy According to quantum mechanics the electrons occupy orbitalsorbitals in pairs. in pairs.• The volumes of these orbitals have specific shapes.The volumes of these orbitals have specific shapes.

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The electrons in each energy level are divided into the The electrons in each energy level are divided into the orbitals.orbitals.• Each orbital can hold a maximum of 2 electrons.Each orbital can hold a maximum of 2 electrons.• The number of orbitals in each energy level, or shell, The number of orbitals in each energy level, or shell,

increases with the number of the energy level.increases with the number of the energy level.

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For the For the ground statesground states of the of the elements, the electrons fill elements, the electrons fill the orbitals in a predictable the orbitals in a predictable way.way.• In the ground state the In the ground state the

electrons occupy the electrons occupy the available orbitals that are available orbitals that are nearest to the center of the nearest to the center of the atom atom

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The ground state distribution of the electrons is reflected in The ground state distribution of the electrons is reflected in the organization of the periodic table the organization of the periodic table

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Valence ElectronsValence Electrons

The electrons that are most important for determining the The electrons that are most important for determining the chemical and physical properties of an atom are those chemical and physical properties of an atom are those located on the surface in the highest occupied energy level.located on the surface in the highest occupied energy level.

• This energy level is called the This energy level is called the valence shellvalence shell..

• The electrons in the valence shell are called the The electrons in the valence shell are called the valence valence electronselectrons..

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Valence ElectronsValence Electrons

• For the For the representative elementsrepresentative elements, the number of valence , the number of valence electrons can be determined from the group number for electrons can be determined from the group number for that element.that element.

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Electron Dot StructuresElectron Dot Structures

The The Lewis electron dot structuresLewis electron dot structures are a convenient way of are a convenient way of showing the number of valence electrons that an atom has.showing the number of valence electrons that an atom has.

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The Octet RuleThe Octet Rule

Except for helium (He), the inert gases, (He, Ne, Ar, Kr, Xe & Except for helium (He), the inert gases, (He, Ne, Ar, Kr, Xe & Rn) each have 8 electrons in their valence shellRn) each have 8 electrons in their valence shell

InertInertGasGas

EnergyEnergyLevelLevel

Total No.Total No.ElectronsElectrons

Valence Valence ElectronsElectrons

Max No.Max No.allowedallowed

in Energyin EnergyLevelLevel22nn22

HeliumHelium(He)(He) 11 22 22 22

NeonNeon(Ne)(Ne) 22 1010 88 88

ArgonArgon(Ar)(Ar) 33 1818 88 1818

KryptonKrypton(Kr)(Kr) 44 3636 88 3232

XenonXenon(Xe)(Xe) 55 5454 88 5050

RadonRadon(Rn)(Rn) 66 8686 88 7272

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The Octet Rule:The Octet Rule:

Atoms gain, lose, or share valence electrons in Atoms gain, lose, or share valence electrons in order to end up with eight valence electrons.order to end up with eight valence electrons.

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Chemistry is all about the different strategies that the Chemistry is all about the different strategies that the elements use to attain 8 electrons in their valence shellelements use to attain 8 electrons in their valence shell

• When an element has the same number of electrons as When an element has the same number of electrons as one of the inert gases, it is said to be one of the inert gases, it is said to be isoelectronisoelectron with that with that inert gas.inert gas.

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For more discussion on the octet rule, see the Chem 150For more discussion on the octet rule, see the Chem 150Elaboration - The Octet RuleElaboration - The Octet Rule

http://www.chem.uwec.edu/Chem150_S07/elaborations/unit1/unit-1b-octet-rule.html

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Monoatomic IonsMonoatomic Ions

A strategy that the representative elements use is to simply A strategy that the representative elements use is to simply gain or lose electrons to become gain or lose electrons to become isoelectronicisoelectronic with one of the with one of the inert gases.inert gases.

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Predicting the charge on the transition metals is less straight Predicting the charge on the transition metals is less straight forward than for the representative element.forward than for the representative element.

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Predicting the charge on the transition metals is less straight Predicting the charge on the transition metals is less straight forward than for the representative element.forward than for the representative element.

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CompoundsCompounds

Metals and non-metals combine Metals and non-metals combine to form to form binary ionic binary ionic compoundscompounds..• Each monoatomic ion in a Each monoatomic ion in a

binary ionic compound has 8 binary ionic compound has 8 valence electrons.valence electrons.

2 Na2 Na2 Na2 Na ClCl22ClCl22

2 Na2 Na++ + 2 Cl + 2 Cl--2 Na2 Na++ + 2 Cl + 2 Cl--

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Covalent BondsCovalent Bonds

Review the characteristics of Metals and Nonmetals, with Review the characteristics of Metals and Nonmetals, with respect to their approaches to adhering to the octet rule.respect to their approaches to adhering to the octet rule.

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Review the characteristics of Metals and Nonmetals, with Review the characteristics of Metals and Nonmetals, with respect to their approaches to adhering to the octet rule.respect to their approaches to adhering to the octet rule.• When metals combine with nonmetals, the metal give up When metals combine with nonmetals, the metal give up

their valence electrons to the nonmetal and each forms their valence electrons to the nonmetal and each forms and ion:and ion:

• An An ionic compoundionic compound is formed, which is held together by an is formed, which is held together by an ionic bondionic bond..

Sodium Chloride (NaCl): Na Cl

Magnesium Chloride (MgCl2): Mg2+

ClCl

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When nonmetals combine with nonmetals, a different strategy When nonmetals combine with nonmetals, a different strategy is need.is need.• When nonmetals combine with nonmetals, they share When nonmetals combine with nonmetals, they share

valance electrons.valance electrons.

• The electrons are shared in pairs to form a The electrons are shared in pairs to form a covalent bondcovalent bond..

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Compounds con’dCompounds con’d

Compounds that are formed from nonmetals are held Compounds that are formed from nonmetals are held together by covalent bonds.together by covalent bonds.

• A group of atoms held together by covalent bonds is called A group of atoms held together by covalent bonds is called a a moleculemolecule..

• Compounds that are composed of molecules are called Compounds that are composed of molecules are called molecular compounds.molecular compounds.

• Unlike ionic compounds, the group of atoms in a molecular Unlike ionic compounds, the group of atoms in a molecular compound stay together as a group when the compound compound stay together as a group when the compound changes it state (solid, liquid, gas or solution)changes it state (solid, liquid, gas or solution)

• The formula that describes the composition of a molecule The formula that describes the composition of a molecule is called a is called a molecular formulamolecular formula..

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The structures of The structures of molecules can be molecules can be represented by either represented by either electron dot electron dot structural formulasstructural formulasororline-bond structural line-bond structural formulas.formulas.

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Compounds that are formed from nonmetals are held Compounds that are formed from nonmetals are held together by covalent bonds.together by covalent bonds.• In some molecules, more than one pair of electrons is In some molecules, more than one pair of electrons is

shared to form double bonds (2 pairs of electrons) or triple shared to form double bonds (2 pairs of electrons) or triple bonds (3 pairs of electrons).bonds (3 pairs of electrons).

Oxygen (O2): O O O O

Nitrogen (N2): N N N N

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Compounds, con’dCompounds, con’d

For more discussion on the formation of compounds,For more discussion on the formation of compounds, see the Chem 150 see the Chem 150Elaboration - CompoundsElaboration - Compounds

http://www.chem.uwec.edu/Chem150_S07/elaborations/unit1/unit1-c-compounds.html

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Naming binary compounds depends on type of compound you Naming binary compounds depends on type of compound you have.have.

• Binary ionic compounds with a representative metalBinary ionic compounds with a representative metal• Name of metalName of metal

+ name of nonmetal with the “-ide” ending+ name of nonmetal with the “-ide” ending‣ NaClNaCl Sodium chlorideSodium chloride‣ MgFMgF22 Magnesium fluorideMagnesium fluoride

• Binary ionic compound with a transition metalBinary ionic compound with a transition metal• Name the metal with a Roman numeral to indicate the chargeName the metal with a Roman numeral to indicate the charge

+ name of nonmetal with the “-ide” ending+ name of nonmetal with the “-ide” ending‣ CuClCuCl Copper(I) chlorideCopper(I) chloride‣ CuClCuCl22 Copper(II) chlorideCopper(II) chloride

• Binary molecular compoundBinary molecular compound• Name the least electronegative element first with a prefix to indicate its number + Name the least electronegative element first with a prefix to indicate its number +

name of the more electronegative element with a prefix to indicate its number and name of the more electronegative element with a prefix to indicate its number and the “-ide” endingthe “-ide” ending‣ SOSO33 Sulfur trioxideSulfur trioxide‣ NN22OO55 Dinitrogen pentoxideDinitrogen pentoxide

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Polyatomic IonsPolyatomic Ions

There are some species that are held together by covalent There are some species that are held together by covalent bond, but which are also ionic.bond, but which are also ionic.

C O

O

O

2-

Carbonate ion

S OO

O

O

2-

Sulfate ion

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Polyatomic IonsPolyatomic Ions

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Structural FormulasStructural Formulas

Structural formulas are used to explicitly show what atom is Structural formulas are used to explicitly show what atom is connected to what atom in a molecule.connected to what atom in a molecule.• Some molecules share the same molecular formulaSome molecules share the same molecular formula• These are called isomersThese are called isomers

These all have the same molecular formula: CThese all have the same molecular formula: C33HH88OOThese all have the same molecular formula: CThese all have the same molecular formula: C33HH88OO

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Structural FormulasStructural Formulas

The different types of structural formulas include:The different types of structural formulas include:

• Electron dot structural formulaElectron dot structural formula

• Line-bond structural formulaLine-bond structural formula

• Condensed structural formulaCondensed structural formula

• Skeletal structural formulaSkeletal structural formula

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For more discussion on structural formulas,For more discussion on structural formulas, see the Chem 150 see the Chem 150Elaboration - Structural FormulasElaboration - Structural Formulas

http://www.chem.uwec.edu/Chem150_S07/elaborations/unit1/unit1-d-structural-formulas.html

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Noncovalent InteractionsNoncovalent Interactions

Molecules are held together by covalent bonds.Molecules are held together by covalent bonds.Molecules interact with other molecules through Molecules interact with other molecules through noncovalent noncovalent interactionsinteractions..• Characteristics of noncovalent interactionsCharacteristics of noncovalent interactions• Are much weaker than covalent bonds.Are much weaker than covalent bonds.• They are the interactions that hold molecules together in the solid, liquid and They are the interactions that hold molecules together in the solid, liquid and

solution states.solution states.• They are easily disrupted by increasing the temperature.They are easily disrupted by increasing the temperature.• The are primarily electrical in natureThe are primarily electrical in nature

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Charge/Charge InteractionCharge/Charge Interaction• Also called a Also called a salt bridgesalt bridge..• Arises from permanent charges that attract or repel one Arises from permanent charges that attract or repel one

another.another.• Permanent charges are also called Permanent charges are also called formal chargesformal charges..

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Calculating the formal charge on an atom in a molecule or Calculating the formal charge on an atom in a molecule or polyatomic ion.polyatomic ion.

• When calculating the number of electrons around an atom When calculating the number of electrons around an atom in a compound, divide the bonding electrons equally in a compound, divide the bonding electrons equally between the two atoms participating in a bond.between the two atoms participating in a bond.

Formal Charge = number of valence electronsfor a neutral atom

– number of electrons around the atomin the compound

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N

H

H

H

H

Formal Charge on hydrogens = 1 - 1 = 0Formal Charge on hydrogens = 1 - 1 = 0Formal Charge on hydrogens = 1 - 1 = 0Formal Charge on hydrogens = 1 - 1 = 0

Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1

N

H

H

H

H

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Formal Charge on singly bonded oxygens = 6 - 7 = -1Formal Charge on singly bonded oxygens = 6 - 7 = -1Formal Charge on singly bonded oxygens = 6 - 7 = -1Formal Charge on singly bonded oxygens = 6 - 7 = -1

Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1Formal Charge on nitrogen = 5 - 4 = +1

N

O

O O

N

O

O O

Formal Charge on doubly bonded oxygen = 6 - 6 = 0Formal Charge on doubly bonded oxygen = 6 - 6 = 0Formal Charge on doubly bonded oxygen = 6 - 6 = 0Formal Charge on doubly bonded oxygen = 6 - 6 = 0

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Dipole/Dipole and Ion Dipole InteractionsDipole/Dipole and Ion Dipole Interactions• Some molecules, which are uncharged, have their valence Some molecules, which are uncharged, have their valence

electrons distributed unevenly, leading to a molecule electrons distributed unevenly, leading to a molecule having a positive and a negative end.having a positive and a negative end.

• This situation leads to a permanent dipole.This situation leads to a permanent dipole.• These dipoles can interact with ions and other dipoles.These dipoles can interact with ions and other dipoles.


δδ++δδ++δδ--δδ-- δδ++δδ++δδ--δδ-- δδ++δδ++δδ--δδ--

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Determining if a molecule is polar or not:Determining if a molecule is polar or not:• Determining the electron distribution in a molecule is a very Determining the electron distribution in a molecule is a very

complicated calculation, there are, however, some simple complicated calculation, there are, however, some simple rules that can be applied to determine if a molecule is polar rules that can be applied to determine if a molecule is polar or not.or not.


Two questions are asked:Two questions are asked:

1.1.Does the molecule contain any polar covalent Does the molecule contain any polar covalent bond?bond?

2.2.If so, are these bonds arranged in a way that they If so, are these bonds arranged in a way that they will cancel each other out?will cancel each other out?

Two questions are asked:Two questions are asked:

1.1.Does the molecule contain any polar covalent Does the molecule contain any polar covalent bond?bond?

2.2.If so, are these bonds arranged in a way that they If so, are these bonds arranged in a way that they will cancel each other out?will cancel each other out?

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To answer the first question, identify any polar covalent To answer the first question, identify any polar covalent bonds that the molecule has:bonds that the molecule has:• This is done by comparing the electronegativity of the two This is done by comparing the electronegativity of the two

atoms participating in each of the bonds.atoms participating in each of the bonds.• If the one atom has a substantially higher electronegativity If the one atom has a substantially higher electronegativity

that the other, the valence electrons are not shared equally that the other, the valence electrons are not shared equally and the bond is polar.and the bond is polar.


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The electronegativity values for the elements (Table 4.1 in The electronegativity values for the elements (Table 4.1 in Raymond)Raymond)


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The electronegativities can be used to predict whether a The electronegativities can be used to predict whether a bond is ionic, polar covalent, or pure covalent:bond is ionic, polar covalent, or pure covalent:


ΔΔE.N. E.N. > 2> 2ΔΔE.N. E.N. > 2> 2 0.5 > 0.5 > E.N.E.N.0.5 > 0.5 > E.N.E.N.

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The electronegativities can be used to predict The electronegativities can be used to predict whether a bond is ionic, polar covalent, or whether a bond is ionic, polar covalent, or pure covalent:pure covalent:

In general:In general:• The bond is The bond is polarpolar if N, O, F or Cl are if N, O, F or Cl are

bonded any of the other non-metals, bonded any of the other non-metals, including H.including H.

• The bond is The bond is nonpolarnonpolar if C or H are bond to if C or H are bond to any of the other non-metals, except N, O, F any of the other non-metals, except N, O, F or Cl; or if N, O, F or Cl are bonded to N, or Cl; or if N, O, F or Cl are bonded to N, O, F or ClO, F or Cl


C N

C O

C O

H N

H O

C F

δ−δ+ δ−δ+

C C

C H

O O

O O

F FC S

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Some examples of polar covalent bonds:Some examples of polar covalent bonds:


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If a molecule contains more than one polar covalent bond, If a molecule contains more than one polar covalent bond, you then need to determine the geometry and shape of the you then need to determine the geometry and shape of the molecule around the atoms participating in the polar covalent molecule around the atoms participating in the polar covalent bonds.bonds.

• This is done by counting up the groups of electrons around This is done by counting up the groups of electrons around each atomeach atom

• Groups of electrons include:Groups of electrons include:• A non-bonding pair of electronsA non-bonding pair of electrons• A single covalent bondA single covalent bond• A double covalent bond (counts as a single group of electrons)A double covalent bond (counts as a single group of electrons)• A triple covalent bond (counts as a single group of electrons)A triple covalent bond (counts as a single group of electrons)


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Use arrows to represent the polar bonds and look to see if Use arrows to represent the polar bonds and look to see if the arrows cancel one another outthe arrows cancel one another out


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Putting is all together:Putting is all together:


Does the molecule contain any polar covalent bonds?

Does the molecule contain any polar covalent bonds?

Determine the shape of the molecule.

Determine the shape of the molecule.

Are the polar covalent bonds arranged in space in a way that causes them to cancel one another out?

Are the polar covalent bonds arranged in space in a way that causes them to cancel one another out?

Nonpolar

Nonpolar

Polar

No

No

Yes

Yes

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Putting is all together:Putting is all together:


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For more discussion on determining polar molecules,For more discussion on determining polar molecules, see the Chem 150 see the Chem 150Elaboration - PolarityElaboration - Polarity

http://www.chem.uwec.edu/Chem150_S07/elaborations/unit1/unit1-e-polarity.html

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The non-covalent interactions include:The non-covalent interactions include:• ion/ion (salt bridge)ion/ion (salt bridge)• dipole/dipoledipole/dipole• ion/dipoleion/dipole• hydrogen bondhydrogen bond• coordinate covalentcoordinate covalent• induced dipole (London dispersion forces)induced dipole (London dispersion forces)


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Hydrogen BondHydrogen Bond• A very important noncovalent interaction in biochemistry is A very important noncovalent interaction in biochemistry is

the hydrogen bond.the hydrogen bond.• The hydrogen bond is an extension of the the dipole/dipole The hydrogen bond is an extension of the the dipole/dipole

interaction.interaction.


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Requirements for hydrogen bonding:Requirements for hydrogen bonding:• DonorDonor: Hydrogen atom that is covalently bonded to a : Hydrogen atom that is covalently bonded to a

electronegative atom. In biological molecules this is usually electronegative atom. In biological molecules this is usually either an oxygen (O) or a nitrogen (N).either an oxygen (O) or a nitrogen (N).

• AcceptorAcceptor: An electronegative atom on another molecule : An electronegative atom on another molecule that contains a non-bonded pair of electrons. In biological that contains a non-bonded pair of electrons. In biological molecules this is usually also an oxygen (O) or a nitrogen molecules this is usually also an oxygen (O) or a nitrogen (N).(N).

Examples:Examples:


N H O

donor acceptor

O H O H

donor acceptor

δ+ δ+δ− δ−δ−δ−

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Water molecules are particularly good at hydrogen bonding to Water molecules are particularly good at hydrogen bonding to themselves.themselves.

Molecular Structure of WaterMolecular Structure of Water

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Noncovalent interactionsNoncovalent interactions

Water is particularly effective at forming Hydrogen bondsWater is particularly effective at forming Hydrogen bonds

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hydrogen bondshydrogen bondshydrogen bondshydrogen bonds

dipole/dipoledipole/dipoledipole/dipoledipole/dipole

Ion/dipoleIon/dipoleIon/dipoleIon/dipole

Ion/ionIon/ion(salt bridge)(salt bridge)

Ion/ionIon/ion(salt bridge)(salt bridge)

coordinatecoordinatecovalentcovalent

coordinatecoordinatecovalentcovalent

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Induced dipole interactionsInduced dipole interactions

• Ion/induced dipole and dipole/induced dipole interactionsIon/induced dipole and dipole/induced dipole interactions• In this interaction the presence of an ion or permanent dipole in one molecule In this interaction the presence of an ion or permanent dipole in one molecule

will induce a dipole in another molecule by distorting the electron cloud in that will induce a dipole in another molecule by distorting the electron cloud in that moleculemolecule

• This interaction is always attractive.This interaction is always attractive.

• Induced dipole/induced dipole interaction.Induced dipole/induced dipole interaction.• To understand this interaction you have to view even nonpolar molecules as To understand this interaction you have to view even nonpolar molecules as

having a fluctuating dipole.having a fluctuating dipole.

• When brought near another molecule, the fluctuating dipoles synchronize to When brought near another molecule, the fluctuating dipoles synchronize to produce an attractive interaction.produce an attractive interaction.

• All molecules experience this interaction.All molecules experience this interaction.

• It is also called the London dispersion forceIt is also called the London dispersion force

• This interaction increases in strength as the molecules get larger.This interaction increases in strength as the molecules get larger.


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Induced dipoleInduced dipoleInteract ionsInteract ions

Induced dipoleInduced dipoleInteract ionsInteract ions

The EndThe End

Documents

Chem 150 Unit 1 - Molecules Organic and Biological Chemistry substances are made of molecules. Being able to predict the structures and interactions of