Molecular Shape and Bonding

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Questions and Answers

Which functional group is characterized by the presence of a carbonyl group (C=O) likely found in ketones?

Carboxylic acids (correct)

Alcohols

Aromatics

Amines

In the context of drug design, what determines the absorption characteristics from the gastrointestinal tract?

Solubility in water

Nature of functional groups (correct)

Molecular weight

Concentration of the drug

Which of the following is NOT a characteristic of sulfonic acids?

Are commonly used as antimicrobial agents

Have a carbon connected to a sulfuric acid group

Contain a sulfur atom

Are classified as primary amines (correct)

Which type of reaction is likely to be affected by the steric arrangement of functional groups?

Electrophilic substitution reactions Signup and view all the answers

What term describes the study of how molecules interact and how their shape affects their bonding and reactivity?

Molecular shape and bonding Signup and view all the answers

What represents the formula for calculating the number of moles in a substance?

Number of moles = mass of substance (g) / Molecular mass (Mr) Signup and view all the answers

Which statement accurately describes electronegativity trends in the periodic table?

Electronegativity decreases as you move down a group. Signup and view all the answers

When comparing elements with valence shells that are less than half full, what is typically easier?

To lose electrons to form cations. Signup and view all the answers

What is the correct calculation for the molecular mass of ethanol, C2H6O?

Mr = (2 x 12.011) + (6 x 1.008) + (1 x 15.9994) = 46.0694 amu Signup and view all the answers

What is the significance of the Avogadro number in the context of the mole?

It determines the number of atoms in a mole. Signup and view all the answers

What is the primary characteristic of the nucleus of an atom?

It contains protons and neutrons. Signup and view all the answers

Which statement accurately describes isotopes?

Isotopes are atoms of the same element with different numbers of neutrons. Signup and view all the answers

What occurs when an atom gains an electron?

The atom becomes negatively charged. Signup and view all the answers

How can the number of neutrons in an atom be determined?

By subtracting the atomic number from the mass number. Signup and view all the answers

What fraction of naturally occurring carbon is composed of the isotope 12C?

Approximately 98.89% Signup and view all the answers

Which of the following statements about atomic mass is true?

Atomic mass is a weighted average of all isotopes of an element. Signup and view all the answers

What defines the atomic number of an element?

The total number of protons in the nucleus. Signup and view all the answers

Which of the following is NOT a characteristic of the electron cloud?

Electrons are found in a defined orbit around the nucleus. Signup and view all the answers

What is the term used to describe the number of bonds an atom can form?

Valency Signup and view all the answers

Which of the following statements about lone pair electrons is correct?

They contribute to the dipole moment. Signup and view all the answers

How is formal charge calculated?

Valence electrons - (lone pair electrons + bonding electrons) Signup and view all the answers

Which of the following elements is described as having four bonds?

Carbon (C) Signup and view all the answers

Which statement about a neutral atom gaining two electrons is true?

It becomes negatively charged. Signup and view all the answers

Why might the equation method for determining formal charge be considered impractical in organic chemistry?

It is a lengthy process. Signup and view all the answers

In which scenario does a 'free radical' occur?

When one atom has a single unpaired electron. Signup and view all the answers

What effect do lone pair electrons have on molecular shape?

They contribute to bond angles and molecular geometry. Signup and view all the answers

What distinguishes the shape of p orbitals from s orbitals?

P orbitals are dumbbell-shaped while s orbitals are spherical. Signup and view all the answers

Which rule dictates that electrons fill the lowest energy orbitals first?

Aufbau Principle Signup and view all the answers

What is the maximum number of electrons that can occupy the third shell?

18 Signup and view all the answers

Which of the following statements regarding orbital nodes is correct?

P orbital nodes are characterized by planes with zero electron density. Signup and view all the answers

Why is fluorine considered the most electronegative element?

It possesses a small atomic radius and high effective nuclear charge. Signup and view all the answers

What does the Pauli Exclusion Principle state regarding electrons in an orbital?

A maximum of two electrons can occupy an orbital with opposite spins. Signup and view all the answers

Which of the following orbitals has a cloverleaf shape?

d orbital Signup and view all the answers

What type of electron configuration is classified as 'ground-state'?

The configuration with the lowest energy and most stability. Signup and view all the answers

How do the sizes of orbital shells in an atom change?

Each subsequent shell is larger than the previous one. Signup and view all the answers

What is a key characteristic of electron clouds in orbitals?

They have varying densities, indicating electron probabilities. Signup and view all the answers

Which types of orbitals are most relevant in pharmaceutical chemistry?

s and p orbitals. Signup and view all the answers

What phenomenon explains the wave-like properties of electrons?

Quantum Mechanical Model. Signup and view all the answers

In which configuration does nitrogen have the highest degree of electron sharing?

1s2 2s2 2px1 2py1 2pz1 Signup and view all the answers

Which term describes the three p orbitals of equal energy that are mutually perpendicular?

Degenerate p orbitals Signup and view all the answers

What occurs when s and p orbitals hybridise?

They create four orbitals with the same energy levels. Signup and view all the answers

What is the outcome when a covalent bond forms?

Atoms become more stable and the energy of the system decreases. Signup and view all the answers

What distinguishes ionic compounds from covalent compounds?

Ionic compounds result from the transfer of electrons. Signup and view all the answers

Which statement about dipole moments is true?

Dipole moments can indicate molecular polarity. Signup and view all the answers

What is the role of valence electrons in bonding?

They occupy the outermost electron shell and engage in bond formation. Signup and view all the answers

What does the inductive effect of an atom refer to?

Its ability to polarize a bond through electron-withdrawing. Signup and view all the answers

Which of the following bonds is formed between atoms with similar electronegativity?

Non-polar covalent bond Signup and view all the answers

What is represented by Lewis structures?

Covalent bonds through dot representations of electrons. Signup and view all the answers

In which scenario would an atom gain an electron?

To stabilize its outer electron shell configuration. Signup and view all the answers

What defines the strength of covalent bonds?

The overlap of atomic orbitals during bond formation. Signup and view all the answers

What does the term 'octet' refer to in covalent bonding?

Eight electrons achieving stability in the valence shell. Signup and view all the answers

Why do elements with low ionization energies typically form cations?

They lose electrons readily due to their electron configuration. Signup and view all the answers

What is a key characteristic of covalent compounds?

They do not conduct electricity in any state. Signup and view all the answers

What role does electronegativity play in bond formation?

It affects the type of bond formed between atoms, either ionic or covalent. Signup and view all the answers

Study Notes

Week 9

MPharm Programme, PHA111: Molecular Shape and Bonding
Lecturer: Dr. Stephanie Myers
Date: 1.21
Contact: [email protected], 0191 5152760

Pharmaceutical Chemistry

Molecules, bonding, and shape: - Functional groups: alkenes, alcohols, alkyl halides, ketones, carboxylic acid derivatives, amines, aromatics. - Canvas - Functional Groups Handout
Acids and bases: - carboxylic acids, sulfonic acids, sulfonamides, imides, β-diketones, thiols, phenols. - Amines (primary, secondary, tertiary, aromatic, heterocyclic), imines, amidines, guanidines.
Stereochemistry
Kinetics
Thermodynamics
The identity of functional groups in a drug determines factors like the route of administration, absorption from the gastrointestinal tract (if oral), first-pass metabolism, bioavailability, binding to receptors (pharmacokinetics), and the time course of effect (pharmacokinetics).

Learning Outcomes

Consider chemical structure: - Describe the differences between ionic and covalent bonds. - Appreciate the shapes of chemical structures and the hybridization of atoms. - Identify functional groups (polar/non-polar, ionisable/neutral). - Deduce relevant properties (solubility, absorption, distribution, metabolism, excretion). - Understand how binding to a receptor produces a therapeutic effect. - Rationalise clinical care based on medicinal properties and side effects. - Design new medicines for specific purposes. - Provide advice on various levels.

A Pharmaceutical Chemistry Example: Atorvastatin

Atorvastatin, a synthetic statin used to control cholesterol, launched in January 1997.
Its patent expired in 2011.
In 2008, it was the most expensive prescribed drug (by gross ingredient cost).
It was the top-selling small-molecule drug globally, reaching ~$10 billion in 2010, peaking at ~$15 billion in 2007/2008.

Atorvastatin (detailed)

It's a competitive inhibitor of HMG-CoA reductase.
This enzyme is crucial for cholesterol production.
By inhibiting this enzyme, atorvastatin lowers cholesterol production and, consequently, the total amount of LDL (low-density lipoprotein) cholesterol.
It also lowers triglycerides and slightly increases HDL (high-density lipoprotein) cholesterol levels.

Organic Chemistry

All organic compounds contain carbon (a 4A element).
Carbon shares four electrons to form four strong covalent bonds.
It bonds to other carbons to create chains and rings.
Not all carbon compounds are derived from living organisms.
Over 99% of 37 million known compounds contain carbon. - Examples include ethynylestradiol, cetirizine, oxytetracycline.

The Periodic Table

A table of elements organized by atomic number and properties.
The table helps to understand relationships between elements, including electronegativity, oxidation states, etc.

Common Elements in Carbon-Containing Compounds

Elements and colours to represent them in organic compounds.

Atomic Structure

Nucleus: - Positively charged, containing protons and neutrons - Small and dense (10−14 to 10−15 m in diameter)
Electron Cloud: - Negatively charged electrons in a cloud around the nucleus - Atomic diameter is approximately 2Å (10−10 m or 100 pm).
Charge on a proton equals the charge on an electron.
Neutral atoms have equal numbers of protons and electrons.

Atomic and Mass Numbers

Atomic number (Z): - Number of protons in an atom's nucleus. - All atoms of a given element have the same atomic number.
Mass number (A): - Number of protons plus neutrons in an atom's nucleus. - Number of neutrons = Mass number (A) - Atomic number (Z).
Isotopes: - Atoms of the same element with different numbers of neutrons but the same atomic number. - Therefore, they have different mass numbers (A).

Atomic and Molecular Mass

Atomic mass (atomic weight): - Represents the weighted average mass in atomic mass units (amu) of naturally occurring isotopes of an element.
Molecular Mass (molecular weight): - The total of atomic masses of all atoms in a molecule.

Calculating Moles

The mole (symbol: mol) is the SI unit of amount of substance.
One mole contains exactly 6.02214076 × 10²³ elementary entities—Avogadro's number.
Calculate the number of moles = (mass of substance in grams) / (Molecular mass).

Periodic Table Trends

Atomic radius: Decreases across a period, increases down a group.
Ionization energy: Increases across a period, decreases down a group.
Electron affinity: Increases across a period, decreases down a group.
Nonmetallic character: Increases across a period, decreases down a group.
Metallic character: Decreases across a period, increases down a group.

Electronegativity

Measures an atom's ability to attract electrons.
Electronegativity increases across a period.
Electronegativity decreases down a group.
Fluorine (4.0) is the most electronegative element.

Atomic Structure: Orbitals

Electrons are not discrete particles but can be described as both particles and waves.
Possible to determine regions or volumes where electrons are most likely found (orbitals).
Orbitals are denoted by Greek letter psi (Ψ).

Atomic Structure: Electron Configuration

Ground-state electron configuration: - Most stable, lowest-energy electron configuration of an atom. - Aufbau principle: Lower energy orbitals fill first. - Pauli exclusion principle: Each orbital holds a maximum of two electrons with opposite spins. - Hund's rule: If multiple orbitals of equal energy are available, electrons occupy each one singly before pairing up.

Time for a Break

A break

Orbital Hybridisation

Carbon forms four bonds with other atoms—hybridisation helps explain this
Energy is required to promote an electron to a higher energy level
S and p orbitals combine to form hybrid orbitals with the same energy levels
This allows for equal bond strengths

sp³ Hybridisation Video

Reference to a YouTube video related to sp³ hybridisation.

Chemical Bonding Theory

Atoms bond to become more stable and lower in energy than the separated atoms.
Energy released when forming bonds and consumed when breaking bonds.
Valence shell: - Outermost electron shell of an atom. - Eight electrons (octet) give noble gases stability.

Chemical Bonding Theory: Ionic Compounds

Some elements achieve octet configuration by gaining or losing electrons to form ions.
Charged ions (cations and anions) are held together by electrostatic attraction, forming an ionic bond.

Chemical Bonding Theory: Covalent Compounds

Covalent bonds form through electron sharing between atoms.
Covalent bonds result in neutral molecules, and atoms in covalent molecules achieve an octet configuration through electron sharing.

Sodium (Na): Ionic Bond

Sodium as an electropositive element readily loses its outermost electron (3s electron) to achieve a stable noble gas configuration.
This loss of an electron forms a positive ion (Na+).

Chlorine (Cl): Ionic Bond

Chlorine as an electronegative element readily gains an electron to complete its outer electron shell, forming a negatively charged ion (Cl-).

Covalent Bonds

Covalent bonds result from the overlap of atomic orbitals.
Electrons are paired in overlapping orbitals, attracting them to the nuclei of both atoms and forming the bond.
Nonpolar Covalent Bonds.
Polar Covalent Bonds

Types of Bonds

A continuum exists between ionic and non-polar bonds and are determined by electronegativity differences.

As a General Rule... (Bond Type)

Ionic bond formation when electronegativity difference is > 1.7
Covalent bond formation when electronegativity difference is < 1.7

Electrostatic Potential Maps

Visual representation of charge distribution in molecules using colors to show the attraction between species.

Inductive Effect/Dipole Moment

Inductive effect: polarization of a bond caused by the electronegativity of nearby atoms.
Dipole moment: measure of the net polarity of a molecule; dependent on bond polarities and lone pairs.

Bond Representations

Lewis structures (electron-dot structures): Dot diagrams representing valence electrons in covalent molecules.
Kekulé structures (line-bond structures): Simplified diagrams with lines representing covalent bonds between atoms.

Representing Structures

Formula-like structures, zig-zag chains, and abbreviations for alkyl portion.

Skeletal Structure/Line-Bond Structure

A shorthand method of representing structures.
Carbon atoms implicitly located at intersections and ends of lines bonded.

Valency

Valency represents the combining capacity of an atom, determined by the number of additional electrons needed to reach a noble gas configuration.

Lone Pair Electrons

Non-bonding electrons in filled orbitals; they play a role in molecular geometry and charge distribution.

Assignment of Formal Charge

Calculations to determine the apparent charge on an atom in a molecule; help in understanding bonding and structure.

Summary of Formal Charges

Summary of formal charges on atoms in molecules across different groups in the periodic table.

To be continued...

The class continues with additional material, like sp2, sp, hybridisations and bonding.

Week 10

Valence Bond Theory: A covalent bond arises from the overlap of atomic orbitals.
sp³ Orbitals: Four equivalent orbitals formed by hybridization of one s and three p orbitals, exhibiting tetrahedral geometry.
sp³ Bonding - Structure of Methane & Ethane: Describes bonding in methane (CH4) and ethane (C2H6) utilizing sp³ hybrid orbitals.
sp² Orbitals: Three equivalent orbitals generated by hybridizing one s and two p orbitals, demonstrating trigonal planar geometry. sp² Bonding - Structure of Ethene.
sp Orbitals: Two equivalent orbitals resulting from the hybridization of one s and one p orbital, appearing as a linear shape (180°). sp Bonding -Structure of Ethyne.
Bond Strengths, Bond Lengths, and Bond Angles: Table summarizing bonding properties for various molecules (e.g., methane, ethane, ethene, ethyne).
Bonding in the Methyl Cation: An analysis of bonding related to a positively charged carbon with three hydrogen atoms.
Bonding in the Methyl Radical: Examination of bonding present in the methyl radical.
Hybridisation of Nitrogen & Hybridisation of Oxygen: Discussion of hybridization properties in molecules containing nitrogen and oxygen.
Hybridisation of Sulfur: Review of sp³ hybridization in molecules containing sulfur.
Hybridisation of Phosphorus: Analysis of sp³ hybridization properties in organophosphates molecules (e.g., ATP, ADP, methyl phosphates).
Hybridisation Summary: A general summary of hybridisation patterns (sp, sp2, sp3) and relationships to bond types and strengths.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

Test your knowledge on organic chemistry functional groups, their characteristics, and their implications in drug design. This quiz covers carbonyl groups found in ketones, absorption characteristics, sulfonic acids, and the influence of molecular shape on reactivity.