1. Modeling of the molecular and electron structure 2. Different methods

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Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**

Consortium leader

PÁZMÁNY PÉTER CATHOLIC UNIVERSITY

Consortium members

SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER

The Project has been realised with the support of the European Union and has been co-financed by the European Social Fund ***

**Molekuláris bionika és Infobionika Szakok tananyagának komplex fejlesztése konzorciumi keretben

***A projekt az Európai Unió támogatásával, az Európai Szociális Alap társfinanszírozásával valósul meg.

PÁZMÁNY PÉTER CATHOLIC UNIVERSITY SEMMELWEIS

UNIVERSITY

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WORLD OF MOLECULES

CHEMICAL COMPOUNDS, STOICHIOMETRY

(Molekulák világa)

(Vegyületek, sztöchiometria)

KRISTÓF IVÁN

semmelweis-egyetem.hu

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1. Modeling of the molecular and electron structure 2. Different methods

3. MM

4. Hartree-Fock 5. Semi-empirical 6. DFT

7. Møller Plesset 8. Approximations

9. Display options and methods

World of Molecules: Chemical compounds, stoichiometry

Previously – Modeling of electron and molecular structure

(4)

Previously - Different approximation methods

Schrödinger equation nuclei are fixed

guess electron correlation

electrons are independent, LCAO-MO

parametrization

Density Functional

Models

Møller Plesset Models

Ab initio Hartree-

Fock models Hartree-Fock MO methods AOs don’t interact, parametrization

Semi-empirical Models correct for electron

interaction

(5)

in proteins or polypeptides

• α-helical structures

• β-sheet structure in DNA, RNA or

polynucleotides

• α-helical structures

• β-helical structures

Previously - Displaying structural information

CRYSTAL STRUCTURE OF HUMAN

INSULIN-DEGRADING ENZYME IN COMPLEX WITH INSULIN

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Previously - Displaying electrostatic potential surfaces

acetic acid EP surface IsoVal: -6.6

E = -27.62 kJ/mol

benzene EP surface IsoVal: -6.6

pyridine EP surface IsoVal: -6.6

E = -27.62 kJ/mol

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1. Compounds

2. Chemical composition

3. Ambiguity of the chemical formula 4. Stoichiometry

5. Main groups of chemical compounds 6. Grouping of inorganic compounds 7. Salts

8. Properties of water

Chemical compounds

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• described by chemical formulas (e.g. NaHCO₃)

• list the constituent elements by their symbol and in

subscript the number indicates the amount of that type of element - in a single molecule

• structural formulas contain information about the spatial structure, bonds and connectivity in a

molecule

• condensed~, skeletal~, stereochemistry~,

• perspective drawings: projections

• widespread use in organic chemistry

Chemical compounds

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• in general and inorganic chemistry the chemical formula is used

• a priori information is necessary to derive the connectivity from the chemical formula

• basic properties of elements, number of possible bonds, oxidation number, electronegativity,

• furthermore the structural information can also be derived from the followings

• Lewis theory

• hybridization of atomic orbitals, VSEPR theory

Chemical compounds

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A given chemical formula can mean

• different chemical compounds

• same chemical compound with different molecular geometry (isomers)

therefore only the structural formula defines

unambiguously a given chemical substance and its properties

the chemical formula is used for convenient purposes, and also for the description of chemical reactions

Ambiguity of a chemical formula

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of a compound describes the ratio of the constituents (Law of definite proportions)

of a reaction describes the ratio of the compounds

taking part in the reaction, the ratio of the reactants and products is typically an integer numbers.

• the law of conservation of mass always applies to reactions

• e.g.:

• the total number of nitrogens and hydrogens are the same on both sides

Stoichiometry

3 2

2

3 H 2 NH

N + ⇔

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• organic, which has – C – C – bonds

• inorganic, which lacks – C – C – bonds

• acids

• the reaction result of water and oxydes of non-metallic compounds

• bases

• the reaction result of water and oxydes of metallic compounds

• salts

• produced from the reaction of acids and bases

• metal complexes

• a central, metallic atom or ion is bonded to the surrounding

molecules/ligands, which usually donate dative bond to the metal

Grouping of chemical compounds

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• acids - chemical characteristics

• usually consist of one or more Hydrogen ions, and an anion (e.g. H₂SO₄ ⇌2H⁺ + SO₄^2-)

• strength is defined by the acid dissociation constant (K_a)

• number of hydrogen ions that a molecule can donate (monoprotic, diprotic, ..., polyprotic acids)

• grouping based on the constituents

• e.g. halids, oxoacids, ...

• grouping based on the amount of water a molecule contains

• e.g. phosphoric acid: P₂O₅ + n H₂O, meta- (n=1), pyro- (n=2), ortho- (n=3),

Grouping of inorganic compounds

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Phosphoric acid

http://en.wikipedia.org/wiki/File:Phosphoric-acid-3D-vdW.png | http://en.wikipedia.org/wiki/File:Pyrophosphoric-acid-3D-vdW.png

orthophosphoric acid H₃PO₄

pyrophosphoric acid H₄P₂O₇

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• bases - chemical characteristics

• usually consist of one or more hydroxide ion and a cation (e.g. Ca(OH)₂ ⇌2OH^- + Ca²⁺)

• strength is defined by the base dissociation constant (K_b)

• the dissociation constant of the conjugate acid (BH⁺) is also a good definition (BH⁺ + OH^- ⇌ B + H₂O, which is the reverse reaction of the dissociation equilibrium)

• number of hydroxyl ions that a molecule can dissociate

• grouping based on constituents

• hydroxyl group, thiol group,...

• grouping based on the amount of water a molecule

Grouping of inorganic compounds

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• salts - chemical characteristics , composition

• product of the neutralization reaction of an acid and a base

• based on the original strength of the acid and base

• normal salt (e.g. K₂SO₄ )

where the acid and base have similar strength

• acid salts (e.g. NaHSO₄ )

where the acid is stronger than the base

• basic/alkali salts (e.g. Na₂CO₃ )

where the base is stronger than the acid

Grouping of inorganic compounds

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Salt (crystalline)

copper(II) sulphate CuSO₄

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• salts - chemical characteristics, composition

• mixed salts (two different acids or bases are used in the neutralization reaction)

(e.g. Ca(OH)Cl +HF = CaFCl + H₂O )

• cocrystals

two or more salts are crystallized simultaneously

• double salts (e.g. KAl(SO₄)₂ from K₂SO₄ and Al₂(SO₄)₃)

• coordination salts

• prepared with coordination ligands (e.g. K₄[Fe(CN)₆])

Grouping of inorganic compounds

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Salt (cocrystal)

Alum crystal KAl(SO₄)₂

with a small amount of chrome alum

KCr(SO₄)₂

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Coordination salt ion

ferrocyanide ion [Fe(CN)₆]^4-

with LUMO+ orbitals plotted

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• Life on Earth depends on this molecule

• composition: H₂O

• structure is not linear, but tetrahedral, since the Oxygen atom (electron structure: 1s² 2s² 2p⁴)

is in a sp³ hybrid state with 6 valence electrons and the electrons from the two Hydrogen, altogether 8

electrons = 4 electron pairs, i.e. tetrahedral molecular geometry

• the oxygen atom has two non-bondin electron pairs in two spatial directions

Properties of water

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Water

http://commons.wikimedia.org/wiki/File:GeysirEruptionNear.jpg

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• the tetrahedral geometry is the source of the unique properties of water

• polar molecule (has a dipole moment of 1.85 Debyes)

• a multitude of water molecules can develop secondary bonds between each other

• develops Hydrogen bonds, max. 4 per molecule

• due to the high number of Hydrogen bonds it is liquid at room temperature

• compared to NH₃ which is a gas, since it can develop fewer Hydrogen bonds per molecule

Properties of water

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Hydrogen bonds in hexagonal ice crystals

http://en.wikipedia.org/wiki/File:Hex_ice.GIF

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• due to its polarity it is a good solvent for polar or ionic compounds

• develops hydrogen bonds with capable molecules

• develops a solvation shell around ionic compounds (mode of solving these compounds)

• crystallizes into several different types of phases (molecular lattice)

• ice has a lower density (due to its organized crystal structure than liquid water)

Properties of water

(27)

Solvation shell of Na

⁺

ion

http://en.wikipedia.org/wiki/File:Na%2BH2O.svg

(28)

Different phases of crystalline water

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• density of water is lowest at 4 º C

• between 0 and 4ºC liquid water still contains ordered crystalline structured Hydrogen bonds

which is a less dense spatial molecular distribution

• above 4ºC the random motion from heat

compensates this and the density is monotonously increasing until 100ºC

• water is one of the few liquids which have a very low compressibility (often termed incompressible)

Properties of water

(30)

• water is a neutral molecule but has amphoteric nature

• but due to the high amount of Hydrogen bonds in liquid state the following reaction occurs

• H₂O + H₂O ⇌ H₃O⁺ + OH^–

• it is called autodissociation or autoprotolysis

• amphoteric: it can act as an acid and also as a base

• the corresponding dissociation constant is K_w=10^-14M²

• i.e. the concentration of each ion in equilibrium is c=10^-7M

• so, even in distilled water there are some ions present

Properties of water

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Network of Hydrogen bonds with 500 molecules

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1. Chemical equilibria

• equilibria in gases

• acid-base equilibria

2. Acid-base theories

• Arrhenius theory

• Brønsted-Lowry theory

• Lewis theory

• Pearson theory (HSAB)

3. Superacids and superbases

Next – Chemical equilibria, acid-base theories

1. Modeling of the molecular and electron structure 2. Different methods

1. Modeling of the molecular and electron structure 2. Different methods

3. MM

4. Hartree-Fock 5. Semi-empirical 6. DFT

7. Møller Plesset 8. Approximations

9. Display options and methods

Previously - Different approximation methods

in proteins or polypeptides

• α-helical structures

• β-sheet structure in DNA, RNA or

polynucleotides

• α-helical structures

• β-helical structures

Previously - Displaying structural information

Table of Contents

Chemical compounds

Chemical compounds

Chemical compounds

A given chemical formula can mean

Ambiguity of a chemical formula

Stoichiometry

3 H 2 NH

N + ⇔

Grouping of chemical compounds

Grouping of inorganic compounds

Phosphoric acid

Grouping of inorganic compounds

• salts - chemical characteristics , composition

Grouping of inorganic compounds

Salt (crystalline)

• salts - chemical characteristics, composition

Grouping of inorganic compounds

Salt (cocrystal)

Coordination salt ion

Properties of water

Water

Properties of water

Hydrogen bonds in hexagonal ice crystals

• crystallizes into several different types of phases (molecular lattice)

Properties of water

Solvation shell of Na

ion

Different phases of crystalline water

• density of water is lowest at 4 º C

Properties of water

Properties of water

Network of Hydrogen bonds with 500 molecules