#molecular structure

[reality-detective]

I’m pretty sure you will appreciate "Laminin"🤔

[science-lover33]

Exploring the Marvels of Biological Macromolecules: The Molecular Machinery of Life (Part 3)

Proteins and Enzymes: Catalysts of Molecular Reactions

Proteins are the central players in macromolecular interactions. Enzymes, a specialized class of proteins, catalyze biochemical reactions with remarkable specificity. They bind to substrates, facilitate reactions, and release products, ensuring that cellular processes occur with precision.

Protein-Protein Interactions: Orchestrating Cellular Functions

Proteins often interact with other proteins to form dynamic complexes. These interactions are pivotal in processes such as signal transduction, where cascades of protein-protein interactions transmit signals within cells, regulating diverse functions such as growth, metabolism, and immune responses.

Protein-Ligand Interactions: Molecular Recognition

Proteins can also interact with small molecules called ligands. Receptor proteins, for instance, bind to ligands such as hormones, neurotransmitters, or drugs, initiating cellular responses. These interactions rely on specific binding sites and molecular recognition.

Protein-DNA Interactions: Controlling Genetic Information

Transcription factors, a class of proteins, interact with DNA to regulate gene expression. They bind to specific DNA sequences, promoting or inhibiting transcription, thereby controlling RNA and protein synthesis.

Membrane Proteins: Regulating Cellular Transport

Integral membrane proteins participate in macromolecular interactions by regulating the transport of ions and molecules across cell membranes. Transport proteins, ion channels, and pumps interact precisely to maintain cellular homeostasis.

Cooperativity and Allosteric Regulation: Fine-Tuning Cellular Processes

Cooperativity and allosteric regulation are mechanisms that modulate protein function. In cooperativity, binding one ligand to a protein influences the binding of subsequent ligands, often amplifying the response. Allosteric regulation occurs when a molecule binds to a site other than the active site, altering the protein's conformation and activity.

Interactions in Signaling Pathways: Cellular Communication

Signal transduction pathways rely on cascades of macromolecular interactions to transmit extracellular signals into cellular responses. Kinases and phosphatases, enzymes that add or remove phosphate groups, play pivotal roles in these pathways.

Protein Folding and Misfolding: Disease Implications

Proteins must fold into specific three-dimensional shapes to function correctly. Misfolded proteins can lead to Alzheimer's, Parkinson's, and prion diseases. Chaperone proteins assist in proper protein folding and prevent aggregation.

References

Voet, D., Voet, J. G., & Pratt, C. W. (2016). Fundamentals of Biochemistry: Life at the Molecular Level. Wiley.

Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry. W. H. Freeman.

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry. W. H. Freeman

[polarmolecule]

molecular geometry my sweetheart my baby. electron orbitals kill yourself.

[omniscientopal]

I’m dumb but convinced this says something, does anyone know how to read molecular structures?? Got this at the thrift shop yesterday.

[moaan]

Hey! by Katsuaki Shoda Via Flickr: Canon EOS R6m2 + RF24-105mm F4L IS USM

[angelnumber27]

Small Molecule Developed That Makes Immunotherapy Available to All Cancer Patients

[aanews69]

All our links in one place:https://sleekbio.com/aanews69Visit our Patreonhttps://www.patreon.com/DNPLServicesWe deliver stories. We also give you guides, tip...

[prose2passion]

very clearly a model of the hydrocarbon C20H20 dodecahedrane.

[tenth-sentence]

In the next several sections, we describe how these measurements are made for nuclear spin states of these two isotopes and then how this information can be correlated with molecular structure.

"Chemistry" 2e - Blackman, A., Bottle, S., Schmid, S., Mocerino, M., Wille, U.

[gudmould]

3 minutes to understand a plastic | polycarbonate PC

Polycarbonate PC Polycarbonate is a thermoplastic resin containing -[ORO-CO]-links in main chain of molecule. According to different ester groups in molecular structure, it can be divided into aliphatic, cycloaliphatic, and aliphatic-aromatic types. Among them, aromatic polycarbonates are of practical value, and bisphenol A polycarbonate is important, molecular weight is usually…

[studentbyday]

Lewis dot structures Pt. 1

Normal valence and hypervalent states and why we need formal charge

Intro to bonding

Chemical bonds are strong forces of attraction, specifically electrostatic forces, between atoms - follows Coulomb's law. Like charges repelling and opposite charges attracting explains what makes a stable bond and what doesn't.

2 main kinds of bonds:

Ionic bonds: electrons are transferred from 1 atom to another to form ions → the oppositely charged ions (cation lost electron to what is now an anion) are electrostatically attracted to each other by Coulomb's law. No bonds are 100% ionic. Point of ions forming is to obtain a noble gas electron configuration, which is more stable.

Ionic bonds form because metals have low ionization energies and low electron affinities, so they tend to form cations to achieve a full octet.

Non-metals have high electron affinities and high ionization energies, so they tend to form anions to achieve a full octet. Down the group, atomic radius increases, so even if it's a non-metal, the big atomic radius means lower electron affinity, so it's less likely to want to gain electrons to form an anion. Compounds formed from such non-metals are probably not gonna be stable.

Covalent bonds: electrons = shared so each atom achieves a full octet. Usually covalent bonds follow the octet rule. Mostly happens between non-metal atoms.

Intro to Lewis structures & the normal valence state

Lewis dot structures are a simple model of how bonding works, explaining simple bond behaviors and simple molecular shapes and geometries. Lewis structures only contain valence electrons because we assume the inner core electrons aren't involved in chemical bonding since they're held tightly to the nucleus and not involved in electron sharing or transfer.

Valence is the number of bonds an atom can have in a molecule. Since Lewis structures deal with valence electrons, we need to know the valence of every atom in a molecule if we want to create a Lewis structure of it.

If we were to draw the ground-state Lewis dot structures of the n = 2 elements in groups 1A-8A, we'd get:

The ground-state Lewis structures correlate to the ground-state electron configurations for these elements (if we're just looking at the valence shells of those elements).

But in this table of normal valences, we see that elements in groups 1-4 have valences that match the group number, but elements in groups 5-8 have valences that go from 3 to 0. This is because when atoms form bonds, the electrons don't always stay in the ground-state configuration. Atoms move and bang around, get energized, and when the atom forms a bond with another, the electrons in some atoms like Be, B, and C (group 2, 3, and 4) are in a more stable configuration when they're unpaired. Which orbitals these unpaired electrons are found in is the topic of this post. So with this reality, we can say that the valence of an atom = the number of unpaired electrons in that atom. An atom can only form as many bonds as it has unpaired electrons. So the Lewis structures for these elements when they're in their normal valence state are:

We can split up the lone pairs in Be, B, and C because n = 2 has 4 orbitals (2s and 3 degenerate 2p orbitals) into which we can put electrons without spending too much energy. We can't split lone pairs in N, O, or F because we're already at the 4 orbital limit so the only option would be to move some electrons into orbitals in n = 3 which would cost too much energy. What counts as too much energy? The energy put into making bonds, into moving electrons around to form their normal valence state, must be returned by the bond forming. If too much energy is put into forming the valence state, not all of it may be returned by bond formation.

These n = 2 elements tend to follow the octet rule, which is the simplest view of bonding: all atoms tend to lose or gain electrons to achieve a valence (outermost) shell of 8 electrons. It was called a "rule" because most atoms in the n = 2 and n = 3 periods of the periodic table want to form a valence shell that had 8 electrons. But there are many ways of breaking the octet rule, so in reality it's more like a guideline than a rule.

Some ways to break the octet rule include:

Duet rule: atoms that only have 1s orbital occupied while higher energy orbitals aren't involved in the atom's chemistry, i.e. n = 1 elements H and He

Some boron compounds - boron has a normal valence of 3 with no lone pairs (e.g. BF3 is a very stable molecule in which boron has 6 electrons). Boron can't complete its octet and remain electrically neutral: in BF4, fluoride is attracted to the empty orbital in B → the fluoride shares one of its lone pairs with the boron → B and every F has a full octet and there's a net negative charge on the molecule. In other words, when B fills its octet in a compound, it becomes a polyatomic ion that can form ionic compounds like NaBF4

Expanded valence aka hypervalence → hypervalent states: while N, O, F, and Ne with valence shell n = 2 can't split their lone pairs further because it's too much energy to move the would-be unpaired electrons into the n = 3 energy level, elements in rows 3 and onwards have d orbitals. Having more orbitals in an energy level means more lone pairs can be split → more unpaired valence electrons and it won't necessarily be too much of an energy cost to do it.

Here's a more concise and complete version of the table of normal and hypervalent states. Hypervalent states only occur when atoms have extra electrons in lone pairs that can be split up to make extra bonding sites. This is why you don't see hypervalent states for groups 1A-4A in the table. Regardless of how far down you get in these groups, even though they have the extra unfilled orbitals in their valence shells, they don't have enough valence electrons to fill all of them. This table gives us a cheatsheet for drawing pretty much any Lewis structure.

That being said, these are the goals for drawing Lewis diagrams for covalent molecules and ionic compounds:

Goals for every Lewis diagram:

Have the correct number of total valence electrons (v.e.)

Each atom has the correct number of valence electrons for that atom

Ensure the way electrons are shared fulfills the octet rule for every atom unless it's an exception (see above for the exceptions)

To make sure we fulfill these goals, we need to keep track of the electrons and the easiest way to do that is to make assumptions about the nature of the bonds (even if they aren't true in reality). There's 2 ways to do this and both use the notion of core charge:

Formal charge (this is the one we use for Lewis structures) - assumes 100% covalent bonds → each element gets 1 electron of each bonding pair. Formal charge is the difference between the number of electrons in the isolated, neutral atom and the atom when it's bonded to the other atom(s).

There's 2 ways to figure out the formal charge on each element in a molecule: mathematically and intuitively (i.e. using the table of valences and hypervalences). Intuition is, ofc, much faster.

Intuitive method says that if the atom's valence and lone pair numbers match with a cell in their proper column of the table of valences and hypervalences, the atom has no charge. If the element isn't in its normal valence or hypervalence states, then you can assign a formal charge to the atom by comparing it with the valence states of neighboring atoms.

Number of bonds an atom forms is related to its formal charge. N with formal charge of +1 acts like a group 4 element in its normal valence state: instead of N's normal valence state of 3 bonds, it can actually form 4 bonds with F.C. of +1

You can think of it as:

If the sum of the formal charges = the overall charge on the species (i.e. the molecule), the Lewis structure is correct.

Oxidation number (this is used in redox chemistry) - assumes 100% ionic bonds → both electrons in the bond "go to" the more electronegative element in the bond.

to find the oxidation numbers for atoms in a compound:

figure out which atoms are more electronegative, so you can figure out which one gets the bonding electrons. (e.g. Cl is more electronegative than H, so the bonding electrons go to Cl and Cl becomes an "ion" [not really, but for the sake of oxidation numbers, that's what we assume])

calculate oxidation numbers

oxidation # for more electronegative atom = core charge aka # of v.e. in neutral, isolated atom - # of electrons in lone pairs - # of bonded electrons oxidation # of Cl = 7 - 6 - 2 = -1

oxidation # for less electronegative atom = core charge aka # of v.e. in neutral, isolated atom - # of lone pairs oxidation # of H = 1 - 0 = +1

Charges determined by oxidation number and formal charge don't reflect reality except in perfect diatomic molecular elements where the charge on each atom in the molecule is truly 0.

>> Next: How to draw Lewis structures

[kyannnite]

murderous tendencies be damned my boy can work a violin

[themellowyellowmomma]

[tsuchinokoroyale]

You are what you eat and baby I’m always making that jello jigglers resippy 😏

[myheartisbro-ken]

My brain, every other second for the past 6 weeks straight gay: what if we rewatched Agatha All Along?

[enderwoah]

what's stronger than a diamond?

take this antarctic empire inspired fusion design of phil and techno! he was real fun to design (my favourite bit is his cape, it turns into mist at the very bottom like a waterfall (or into snow, your choice)) :D

also fun fact, this was lined with a feather pen that i had to dip into an inkwell :D my lining pen was broken by my siblings but this had the perfect nib !

red king design by @cherrifire + the gemcyt au by @chrisrin!

stupid doodle under the cut: