Molecules are groups of of COVALENTLY-BONDED ATOMS and ATOMS are like basic “units” of ELEMENTS. If you were to look at a periodic table of elements and “menu” and “order” 1 of an element, they’d bring you an atom. In biochemistry, some of the most popular “orders” are carbon (C ), hydrogen (H), oxygen (O), nitrogen, (N), and phosphorus (P) and they have different properties .
But instead of “ordering” them a la carte, you order “shish-kebobs” of them – atoms can bond to one another through strong covalent bonds so they stick together to form MOLECULES, which can be small things like water (just 3 atoms – 2 hydrogen & 1 oxygen) or “big” things like the “macromolecules” proteins & DNA which have lots of atoms.
Regardless of how many atoms are in a molecule, each of those ATOMS is made up of even smaller things – 3 basic SUBATOMIC PARTICLES 👉 most “boring” are NEUTRONS 👉 Like name suggests, they’re NEUTRal (not charged)😴 BUT the other 2 types *are* charged ⚡️👇
- PROTONS (p⁺) are POSITIVELY charged ➕ & live w/neutrons in a central hub called the NUCLEUS
- ELECTRONS (e⁻) are negatively charged ➖ & orbit the nucleus in an ELECTRON CLOUD ☁️ We can predict where within that cloud e⁻ are most likely to be using molecular orbital theory 👉 takes into account # of e⁻ & how they can optimize their housing arrangement 🏘
If # of p⁺==# of e⁻ 👉 NEUTRAL BUT the separation of the charges means even neutral molecules have ➖ parts (cloud) & ➕ part (nucleus). Most of an atom’s e⁻ are tightly held bc they’re attracted to ➕nucleus BUT e⁻ on clouds’ outer edge (VALENCE ELECTRONS) are further from ➕ nucleus, so they’re less tightly held ⏩ can interact w/other atoms
# of p⁺ = Z is an element’s ATOMIC NUMBER 👉 determines seating arrangement at periodic table (#p increases like you read a book 📖left to right, top to bottom) & DEFINES an element 👉 if you were to change this #, you’d have a different element
Opposite charges attract 😍 & like charges repel 👻 So if 2 separate atoms get too close, their ➖ e⁻ clouds will clash & they’ll repel each other 👻 The closest they can get w/o repelling each other is VAN DER WAALS RADIUS (vdW radius)(aka non-bonded radius)(aka hard sphere radius)👇
- 1/2 the distance between nuclei of 2 NON-BONDED atoms of same element (imagine the atoms are 🎱🎱 that can only “just touch” each other)
- If you 👀 “space filling” models of proteins (they look blobby instead of ball-stick-y or ribbony) you’re likely “seeing” vdW radii
Different elements have different vdW radii bc they have different # of subatomic particles👇
- As you go left to right ➡️ across periodic table, radii tend to ⬇️ bc they have more p⁺ pulling e⁻ in tighter (its a trend)
- & as you go top to bottom ⬇️ radii tend to ⬆️ bc all they have so many electrons that the ones on the inside of the cloud shield the outer ones
the vdW radius is how close 2 atoms can get w/o clouds overlapping 👍 BUT atoms can get CLOSER if they agree to SHARE some of their clouds 👇
🔹 e⁻ clouds can only hold a certain # of e⁻ 👉 If there’s still room, atoms can overlap parts of their clouds to share e⁻(s) to fill vacancies 👉 we call these COVALENT BONDS
Since they’re overlapping their clouds, they can get closer than their vdW radii 👉 & when they get closer bond gets stronger 💪🏻(think of trying to grip something w/just your fingertips 👉👈 vs your whole fingers) 🤝
If they share even more of their clouds they can get even closer and stronger 👉 sharing 2 pairs gets you a DOUBLE BOND & sharing 3 pairs gets you a TRIPLE BOND
But even TRIPLY-BONDed atoms need to avoid getting TOO CLOSE 👉 if they do, parts that aren’t “supposed” to overlap start clashing ⏩ electrostatic REPULSION 👻
The “sweet spot” 🍭 is COVALENT BOND DISTANCE (aka bond length) 👉 distance between nuclei (internuclear distance) of 2 BONDED atoms (similarly COVALENT BOND RADIUS is 1/2 this distance)
This is my 2nd official post as Student Ambassador for The International Union of Biochemistry and Molecular Biology @theIUBMB. I’ll be bringing you weekly posts for them so I hope you’ll follow along – and follow them too!