Molecular Modeling Computational Chemistry Bonds Lewis Structures Resonance

Molecular Modeling Computational Chemistry Bonds, Lewis Structures, Resonance, Molecular Shapes, Polarity Dr. Ron Rusay

Molecular Modeling Computational Chemistry Bonds, Lewis Structures, Resonance, Dr. Ron Rusay

Electronegativity Differences

Covalent Bonding Hydrogen? and Fluorine?

Bonding. H? and F?

Molecular Modeling (Individual or Collaborative) Report Form (Replacement pages for Molecular Model Lab pp. 97 -103) http: //chemconnections. org/general/chem 108/Chemistry%20108%20 Molecular%20 Modeling%20 Fo rm%20 Fall%202017. pdf Computers & Internet available in PS 110, if needed http: //molview. org Turn-in individually or one per group Consult Calendar for Due Date

Lewis Electron-Dot Drawings H Covalent Bonding-Valence Electrons Periods 2 & 3 . H

Computational Chemistry Covalent Bonding Polarity: Molview (http: //molview. org) Covalent Bond . . . Close opening screen; caffeine appears. Click trash; now build hydrogen fluoride

Computational Chemistry Covalent Bonding Polarity: Molview (http: //molview. org) Covalent Bond . . . From Jmol dropdown menu click MEP surface lucent

Covalent Bonded Compounds Polarity: Molview (http: //molview. org) Jmol Covalent Bond . . . Color coded electron density distribution scale: redhighest δ-, blue highest δ+, green balanced NOTE: These colors may vary from model to model.

Bond Polarity A molecule, such as HF, that has a center of positive charge and a center of negative charge is polar; It has a “dipole moment”. The partial charge is represented by and the polarity with a vector arrow.

Hydrogen Halides What happens to the electronegativities, bond lengths and bond energies going down the column of halogens?

Question ¥ Which of the following bonds is the most polar? ¥ ¥ A) B) C) D) ¥ ¥

Answer ¥ Which of the following bonds is the most polar? ¥ ¥ A) B) C) D) ¥ ¥

Polarity /Visual Portrayal 0. 143 nm 0. 094 nm 0. 158 nm Color coded electron density distribution: blue-lowest, red highest, green balanced NOTE: These colors do vary.

Question In which of the compounds below is the + for Hydrogen (H) the greatest? A) B) C) D) CH 4 NH 3 Si. H 4 H 2 O

Answer In which of the compounds below is the + for H the greatest? A) B) C) D) CH 4 NH 3 Si. H 4 H 2 O

Question ¥ ¥ Which of the following bonds is the most polar? A) B) 0. 143 nm ¥ C) 0. 129 nm 0. 122 nm D) 0. 116 nm Bond length: single > double > triple

Answer ¥ ¥ Which of the following bonds is the most polar? A) B) 0. 143 nm ¥ C) 0. 129 nm 0. 122 nm D) 0. 116 nm Bond length: single > double > triple

Polar Covalent Bonds ¥ Electrons tend to shift away from lower electronegativity atoms to higher electronegativity atoms. ¥ The greater the difference in electronegativity, the more polar the bond.

Professor Gilbert Newton Lewis (circa 1940) G. N. Lewis Photo Bancroft Library, University of California/LBNL Image Library Footnote: G. N. Lewis, despite his insight and contributions to chemistry, was never awarded the Nobel prize. Notes from Lewis’s notebook and his “Lewis” structure.

Lewis Structures ¥ For simple Lewis structures: 1. Draw the individual atoms using dots to represent the valence electrons. 2. Put the atoms together so they share PAIRS of electrons to make complete octets. Cannot use more than the total number of valence electrons. ¥ NH 3, for example: http: //chemconnections. org/general/movies/Lewis. Dot. Structures. swf

Lewis Structures equals 1 pair of e-s H H C H H H Methane H H . . Ethyl Alcohol (Ethanol) . . F . . CH 3 CH 2 OH C 2 H 5 OH C 2 H 6 O C H CF 4 C Carbon dioxide . . F. . C CH 4 F. . . H . . O. . H Carbon Tetrafluoride Note the carbon “double bond”; equals 2 pairs of e- s

Lewis Structures H Ammonia H N N H + C H O . . H N . . H H. . H . N. H H H Ammonium Ion Urea Note the carbon “double bond”; equals 2 pairs of e-s

Important Bond Numbers (Neutral Atoms!) one bond two bonds three bonds four bonds H F Cl O Br I 2 single or 1 double N 3 single or 1 single + 1 double or 1 triple 4 single or 2 single + 1 double or 1 single + 1 triple or 2 double C

http: //chemconnections. org/general/movies/Lewis%20 structures. html

Resonance Considered when more than one valid Lewis structure can be written for a molecule without changing the atoms’ positions. It is used to explain variations in bond lengths and chemical behavior. These are shorthand structures. Each point of an angle in the hexagon equals a carbon atom, the hydrogen atoms are not shown & must be deduced from the fact that carbon forms 4 bonds.

Shorthand “Bond Line”Structures Each point of an angle in the hexagon equals a carbon atom, the hydrogen atoms are not shown & must be deduced from the fact that carbon forms 4 bonds. C 6 H 6

Resonance Moving electrons: The overall structure is considered to be a weighted average of all of the possible valid Lewis structures where some are more favored than others. Resonance structures are mental images used to explain the observed arrangement of the atoms and their bond lengths and bond angles.

Carbonate Ion Resonance The 3 -d structure is an average of the resonance structures. The normal bond length of a C=O bond is ~0. 120 nm and C-O is ~0. 142 nm.

Molecular Modeling Computational Chemistry Molecular Shapes, Polarity Dr. Ron Rusay

Shapes of Molecules View: What is the shape of a molecule? George Zaidan and Charles Morton https: //www. youtube. com/watch? v=Jq_Ca-HKh 1 g

Shapes of Molecules View: What is the shape of a molecule? George Zaidan and Charles Morton https: //www. youtube. com/watch? v=Jq_Ca. HKh 1 g http: //chemconnections. org/general/chem 1 08/Molecular%252520 Shapes-Guide. html

Molecular Shapes Molecular Models for C, H, N, O ¥ Fundamental repeating shapes found in every biological molecule C =black H = gray N = blue O = red pink = generic atom

http: //molview. org Molecular Shapes → Lewis Structures Ammonia Molecular Modeling: Bonding & Lewis Structures Computational Chemistry: Molecular Modeling Report Form Replaces Lab Manual pp. 53 -58

http: //molview. org Molecular Shapes → Lewis Structures Mol. View: Visual On-line Molecular Modeling Ammonia Molecular Modeling: Bonding & Lewis Structures Computational Chemistry: Molecular Modeling Report Form Replaces Lab Manual pp. 53 -58

Lewis Structures → Molecular Shapes ¥ For simple Lewis structures: 1. Draw the individual atoms using dots to represent the valence electrons. 2. Put the atoms together so they share PAIRS of electrons to make complete octets. ¥ NH 3 Ammonia:

http: //molview. org Molecular Shapes → Lewis Structures Ammonium Molecular Modeling: Bonding & Lewis Structures Computational Chemistry: Molecular Modeling Report Form Replaces Lab Manual pp. 53 -58

http: //molview. org Molecular Shapes → Lewis Structures Mol. View: Visual On-line Molecular Modeling Ammonium Molecular Modeling: Bonding & Lewis Structures Computational Chemistry: Molecular Modeling Report Form Replaces Lab Manual pp. 53 -58

Lewis Structures → Molecular Shapes ¥ For simple Lewis structures: 1. Draw the individual atoms using dots to represent the valence electrons. 2. Put the atoms together so they share PAIRS of electrons to make complete octets. ¥ NH 4+ + H + + Ammonium

Molecular Geometry – Overview Numbers of atoms or (“lone” / “free”) pairs of electrons about the central atom from Lewis Structure Four Three Two Molecular Geometry Assignment

Molecular Polarity Trigonal Pyramid Tetrahedral Trigonal Planar http: //chemconnections. org/COT/VSEPR 1/ DVC Student Project Group Tetrahedral

Molecular Polarity The vector sum of the magnitude and the direction of the individual bond dipoles determine the overall polarity (dipole moment) of a molecule

Isomers Molecular Shapes & Stereochemistry Dr. Ron Rusay

Isomerism http: //chemconnections. org/general/movies/Isomerism. MOV

Isomerism • Isomers: two compounds with the same formulas but different arrangements of atoms. ___________ • Structural isomers have different connectivity of atoms. • Geometrical isomers and optical isomers are stereoisomers (i. e. have the same bonds, but different spatial arrangements of atoms). • Stereoisomers have the same connectivity but different spatial arrangements of atoms.

Isomerism cis - trans Enantiomers (Chiral: Non-superimposable Mirror Images)

Stereoisomers: cis-trans · To maintain orbital overlap in the pi bond, C=C double bonds cannot freely rotate. · Although the two molecules below have the same connectivity, they are NOT identical. cis trans

Chemical Communication cis/ Pheromones Smell http: //chemconnections. org/organic/chem 226/Labs/Smell/Chem. Comm. html http: //www. learner. org/resources/series 61. html Pheromone Synthesis [20: 40 -23: 51]

Chemical Communication Smell / Pheromones http: //chemconnections. org/organic/chem 226/Labs/Smell/Chem. Comm. html cis https: //embed. molview. org/v 1/? mode=balls&cid=5363527&bg=white http: //www. learner. org/resources/series 61. html Pheromone Synthesis [20: 40 -23: 51]

Molecular Modeling Bonus Choose any biologically active molecule, pharmaceutical, natural product, etc. Using molview’s search, find & open the file, use the Tool Menu to find the Embed URL Computers & Internet available in PS 110, if needed http: //molview. org Paste the Embed URL into an e-mail, Provide the molecule’s name as the e-mail subject, send to Dr. R

Stereoisomers: Enantiomers Chirality & Carbon Atoms Each carbon atom with four different substituents are chiral. http: //chemconnections. org/general/movies/Chirality. mov

Chirality

Stereoisomerism ¥ ¥ ¥ • Enantiomers are chiral: i. e. They are non-superimposable mirror images. Most physical and chemical properties of enantiomers are identical. Therefore, enantiomers are very difficult to separate eg. Tartaric acid… Louis Pasteur: Enantiomers can have very different physiological effects: eg. (+) and (-) carvone, Advil (ibuprofen) …… (thalidomide)

Shapes & Interactions: Mirror Images & Smell What is the molecular formula of carvone? S-(+)-d- S-(+)- caraway R-(-)-l- mirror R-(-)- spearmint http: //chemconnections. org/organic/chem 226/Labs/Smell/Chem. Comm. html

Shapes & Interactions: Mirror Images & Smell What is the molecular formula of carvone? S-(+)-d- R-(-)-l- C 10 H 14 O Identify the chiral carbon atom in the stucture above. S-(+)- caraway R-(-)- spearmint http: //chemconnections. org/organic/chem 226/Labs/Smell/Chem. Comm. html

From the late 1950 s – early 1960 s more than 10, 000 children in 46 countries were born with deformities caused by one of the two enantiomers. 50% survived.

https: //embed. molview. org/v 1/? mod e=balls&cid=92142&bg=white https: //embed. molview. org/v 1/? mode=balls 75792&bg=white The S-(-) enantiomer, which is on the left, caused the deformities. The severity and location of the deformities depended on when thalidomide was taken: On the 20 th day of pregnancy it caused central brain damage in the fetus, on Day 21 it would damage the eyes, on Day 22 the ears and face, on Days 24 -28 arm and leg damage would occur. Thalidomide did not damage the fetus if taken after 42 days gestation.

What is the shape of water? a. b. c. d. Tetrahedral Bent Trigonal planar Linear

What is the electronic geometry of NH 3? a. Linear b. Trigonal Planar c. Tetrahedral d. Trigonal Pyramidal H N H H

What is the electronic geometry of NH 3? a. Linear b. Trigonal Planar c. Tetrahedral d. Trigonal Pyramidal N has 4 groups around it; thus, it is a tetrahedral electron geometry H N H H Answer: C

Which of these molecules has a linear molecule geometry? a. b. c. d. CO 2 O 3 Both Neither

Which molecule could be represented by this model? a. b. c. BH 3 CH 4 NH 3

What is the molecular geometry of H 2 S? a. Linear b. Tetrahedral c. Trigonal planar d. Trigonal pyramidal e. Bent

What is the molecular geometry of H 2 S? Answer: D a. Linear b. Tetrahedral c. Trigonal planar d. Trigonal pyramidal e. Bent S H H

What is the molecular geometry of formaldehyde CH 2 O? a. Linear b. Tetrahedral c. Trigonal planar d. Trigonal pyramidal e. Bent Singha lists formaldehyde as a preservative in its beer!

Formaldehyde on the left is a polar molecule. Is the following statement True or False for the molecule to the right? “The similar nitrogen molecule shown next to formaldehyde is non-polar. ”

Formaldehyde on the left is a polar molecule. Is the following statement True or False for the molecule to the right? “The similar nitrogen molecule shown next to formaldehyde is non-polar. ” False

I II IV III, I, IV

The molecular formula (shown above) of thalidomide is: a. b. c. d. e. C 12 H 9 NO 4 C 12 H 10 N 2 O 4 C 13 H 9 N 2 O 4 C 13 H 10 N 2 O 4 C 15 H 10 NO 4

Thalidomide has one chiral carbon atom. The carbon atom circled above is the chiral carbon atom. a. b. TRUE FALSE

FALSE chiral carbon atom

Biological Activity Molecular Structures Continued Stereospecific interactions of Amino acids / Proteins / Enzymes Dr. Ron Rusay

Amino Acids Legos of Chemical Biology Amino acids contain carbon, hydrogen, oxygen, and nitrogen, which resemble the following shapes & structural components • 20 different amino acids are encoded by the genetic code, which is archived in DNA. • Hundreds of amino acids link together to form proteins, which provide the physical structure and chemical machinery for life. • There are less than 20, 000 total proteins produced from humans’ entire DNA genome, each coded by a specific gene in DNA’s ~3 billion genetic bases.

Lewis Structures → Molecular Shapes Molecular Models for C, H, N, O ¥ Fundamental repeating shapes found in every biological molecule C =black H = gray N = blue O = oxygen pink = generic atom

Proteins: Indispensible Biopolymers Acetylcholinesterase (ACE) ACE, an enzyme, which catalyzes a key reaction in a repetitive neurochemical cycle that is crucial to the physiological functions in humans…. and insects among others. 4, 496 atoms; 4, 404 bonds 574 amino acid residues

Proteins & Small Molecules Acetylcholinesterase (ACE) ACE catalyzes the conversion of the neurotransmitter acetylcholine to choline.

Proteins & Small Molecules Acetylcholinesterase (ACE) The ACE enzyme has a receptor, a site in the molecule defined by the 3 amino acids in the image on the right. It binds acetylcholine, which then hydrolyzes to choline.

Proteins & Small Molecules Acetylcholinesterase (ACE) Animation of acetylcholinesterase with acetylcholine http: //chemconnections. org/general/movies/richard. mpg

Detecting molecules we cannot see: the Sense of Smell Models, Receptors & Interactions http: //ep. llnl. gov/msds/orgchem/Chem 226/smell-links. html Structure-Odor Relationships Karen J. Rossiter, Chem. Rev. , 1996, 3201 -3240

Historical view of a few smell receptors. 4 October 2004 Vanillin (Smell) Sensitivity ~ 1 x 10 -5 mol / L air The Nobel Assembly at Karolinska Institutet has today decided to award The Nobel Prize in Physiology or Medicine for 2004 jointly to Richard Axel and Linda B. Buck for their discoveries of "odorant receptors and the organization of the olfactory system"

S-(+)-d-carvone caraway R-(-)-l-carvone spearmint Axel & Buck discovered a large gene family, comprised of some 1, 000 different genes (three per cent of our genes) that give rise to an equivalent number of olfactory receptor types. These receptors are located on the olfactory receptor cells, which occupy a small area in the upper part of the nasal epithelium and detect the inhaled odorant molecules.

Shapes & Interactions: Mirror Images & Smell S-(+)-d- S-(+)- caraway R-(-)-l- R-(-)- spearmint http: //chemconnections. org/organic/chem 226/Labs/Smell/Chem. Comm. html

Importance of Stereochemistry · Enzymes are capable of distinguishing between stereoisomers:

Opioid Addiction Neurologically active drugs like opioids mimic neurotransmitters that are naturally produced in the body, such as endorphins, which slow breathing, block pain and produce a calming, pleasant, anti-depressing sensation. However, opiates bind to receptors and flood the nervous system with dopamine, which regulates pleasure among other emotions & functions, producing a level of euphoria that stimulates a craving for more and more, which can never be satisfied!!!! https: //www. sciencedaily. com/releases/2007/ 10/071014163647. htm Dopamine Heroin

4 N 6 H: Structure of human delta opioid receptor DOI: 10. 2210/pdb 4 N 6 H/pdb Classification: SIGNALING PROTEIN Organism(s): Escherichia coli, Homo sapiens Molar Mass: 52, 088. 38 g/mol; Atoms: 3, 481; Amino Acid Residues: 414 Trans-membrane

Opioid receptor agonist Agonist: A substance that initiates a physiological response when combined with a receptor.

Opioid agonists: More powerful than fentanyl itself http: //sciencemag. org/content/355/6332/ 1364. full

Opioid receptor inhibitor (antagonist)

http: //chemconnections. org/general/ movies/106 -nicotine-smoking. mov

Proteins & Small Molecules Weapons aimed at Acetylcholinesterase Two images of Sarin, a potent nerve agent, which inhibits acetylcholinesterase and causes convulsions leading to death if not antidoted with atropine. Sarin

Proteins & Small Molecules Acetylcholinesterase Sarin out competes acetylcholine, binds with the ACE enzyme, and ACE cannot work.

Proteins & Small Molecules Acetylcholinesterase Sarin & VR bind in place of acetylcholine and inhibit acetylcholinesterase, interrupting vital physiological processes, which leads to death. Nerve Agent Attacks: Japan (1995) Syria (2013 -2018) Great Britain (2018) https: //www. youtube. com/watch? v=748 w. LBWdch. U

Proteins & Small Molecules Acetylcholinesterase Sarin binds in place of acetylcholine and inhibits acetylcholinesterase, Interrupting vital physiological processes which leads to death. Sarin: Weapon of Mass Destruction Syria (2013 -2018) http: //chemconnections. org/general/movies/richard. mpg

VSEPR Polarity / Biomimicry Dr. Ron Rusay

Lewis Structures → Molecular Shapes Classic Worldwide Model: VSEPR “Valence Shell Electron Pair Repulsion” http: //chemconnections. org/general/movies/VSEPR. MOV Basis of the model: Molecular structure’s shape is determined by minimizing electron pair repulsions through maximizing separations.

Molecular Polarity & Dipole Moment When identical polar bonds point in opposite directions, the effects of their polarities cancel, giving no net dipole moment. When they do not point in opposite directions, there is a net effect and a net molecular dipole moment, designated .

Molecular Dipole Moment The vector sum of the magnitude and the direction of the individual bond dipole determines the overall dipole moment of a molecule

Polarity & Physical Properties Chloroform (polar) vs. Carbon tetrachloride (non-) An electrically charged rod attracts a stream of chloroform but has no effect on a stream of carbon tetrachloride.

Ammonia and in the Ammonium Ion

Water

Polarity & Physical Properties Ozone and Water 0. 1278 nm • • Resultant Molecular Dipoles > 0 Solubility: Polar molecules that dissolve or are dissolved in like • molecules • The Lotus flower Water & dirt repellancy: solubility?

Polarity & Physical Properties Solubility Generally likes dissolves like: ¥ Polar compounds dissolve other polar compounds & ionic compounds. Eg. ethanol and water, sodium chloride and water, sugar and water ¥ Nonpolar compounds are soluble in other nonpolar compounds. Eg. carbon tetrachloride and oil, diesel and gasoline

Acetic acid • Is acetic acid polar or non-polar? • Will acetic acid be miscible (dissolve) in water? Based on the Molview model?

The “Lotus Effect” Biomimicry Wax ¥ ¥ Water not only dissolves some dirt, but attracts and removes it like a snowball rolling downhill. Lotus petals have micrometer-scale roughness, resulting in water contact angles up to 170°

The “Lotus Effect” Biomimicry ¥ ¥ ¥ Isotactic polypropylene (i-PP) melted between two glass slides and subsequent crystallization provided a smooth surface. Atomic force microscopy tests indicated that the surface had root mean square (rms) roughness of 10 nm. A) The water drop on the resulting surface had a contact angle of 104° ± 2 B) the water drop on a superhydrophobic i. PP coating surface has a contact angle of 160°. Science, 299, (2003), pp. 1377 -1380, H. Yldrm Erbil, A. Levent Demirel, Yonca Avc, Olcay Mert http: //www. sciencemag. org/cgi/content/full/299/5611/1377/DC 1

The red spheres are oxygen and the white/gray are hydrogen. 2 H 2(g) + O 2(g) → 2 H 2 O(l) Balanced Chemical Equation How many oxygens are there? How many hydrogens are there?

https: //www. youtube. com/watch? v=UV 8 Kb. Qy. F 228 The red spheres are oxygen and the white/gray are hydrogen. 2 H 2(g) + O 2(g) → 2 H 2 O(l) Balanced Chemical Equation # of molecules 6 H 2(g) + 3 O 2(g) → 6 H 2 O(l) How many oxygens are there? 6 How many hydrogens are there? 12

https: //www. youtube. com/watch? v=UV 8 Kb. Qy. F 228 http: //www. youtube. com/watch? v=a 6 q. GIMq. DKw. A&index=4&list=PLA 3383 CE 72437 FC 43 The red spheres are oxygen and the white/gray are hydrogen. 2 H 2(g) + O 2(g) → 2 H 2 O(l) Balanced Chemical Equation Chemical Reactions: Three Balloons # of molecules 7 H 2(g) + 3 O 2(g) → 6 H 2 O(l) + 1 H 2(g) Unbalanced How many oxygens are there? 6 How many hydrogens are there? 14 The oxygen limited how much water could form.

QUESTION The electrolysis of water is the reverse of burning (combustion). Which equation best represents the change that takes place when water is electrolyzed? A) H 2 O(l) → H 2 O(g) B) H 2 O(g) → H 2 O(l) C) 2 H 2 O(l) → 2 H 2(g) + O 2(g) D) 2 H 2(g) + O 2(g) → 2 H 2 O(l)

Answer The electrolysis of water is the reverse of burning (combustion). Which equation best represents the change that takes place when water is electrolyzed? A) H 2 O(l) → H 2 O(g) B) H 2 O(g) → H 2 O(l) C) 2 H 2 O(l) → 2 H 2(g) + O 2(g) D) 2 H 2(g) + O 2(g) → 2 H 2 O(l)

Amino Acids Legos of Chemical Biology Amino acids contain carbon, hydrogen, oxygen, and nitrogen, which resemble the following shapes & structural components • 20 different amino acids are encoded by the genetic code, which is archived in DNA. • Hundreds of amino acids link together with amide (peptide) bonds to form proteins, which are the machinery for the chemistry of life. • There are less than 20, 000 total proteins produced from humans’ entire genome, each coded by a specific gene in DNA’s ~3 billion genetic bases.

Lewis Structures → Molecular Shapes Molecular Models for C, H, N, O ¥ Fundamental repeating shapes found in every biological molecule http: //chemconnections. org/general/movies/htmlswf/vsepr_four_electron. htm C =black H = gray N = blue O = oxygen pink = generic atom

Question ¥ ¥ ¥ In which of the following pairs is oxygen the more positive end of the bond? A) O and F B) O and N C) O and S D) O and H

Answer ¥ ¥ ¥ Which of the following is oxygen the positive end of the bond dipole? A) O-F B) N-O C) S-O D) H-O

QUESTION Receptor Sensitivity If 1. 0 gram of vanillin was placed in an open container at center court in the Oakland Coliseum and dispersed, it might be possible to detect it sitting in a seat in the top row. How many grams of vanillin would there be per Literair assuming that vanillin’s concentration was at its detection limit? Vanillin (C 8 H 8 O 3) Smell detection limit ~ 1. 0 x 10 -5 mol / Literair A) 0. 015 g B) 1. 5 mg C) 3. 0 mg D) 0. 030 mg