Can Quantum Chemistry Simulations Help Trace the Origin of Life?

Oh, how I cherished my PhD days in the UK. The pub gatherings, the student community, the non-hierarchical chats with professors… Jamie, my PhD supervisor, was all about work-life balance before it became a mainstream thing. And then there was Peter Knowles, my PhD reviewer, whose grasp on quantum mechanics was simply awe-inspiring. How many hours I spent trying to understand Dirac’s physics! Amid all this, my Beatles fandom grew even stronger. After all, Cardiff isn’t too far from Liverpool. Yep, I absolutely adored the UK. But after wrapping up my PhD, the pull to return home, to Italy, was too strong to resist. So, back I went, landing a post-doc at SISSA, one of Europe’s leading research centers. Those Monday afternoons, filled with lectures from visiting professors, were a delight. It wasn’t just the Nobel laureates that left an impression—it was the sheer intellect of the students and colleagues around me. So, what’s the connection between all of this and the quantum chemistry simulations of the prebiotic origin of life? Today, we’re delving into this very topic, guided by the comprehensive review by Fabio Petrucci, a dear colleague from my SISSA days. Can quantum chemistry simulations really help us understand how lifeless molecules sparked life? Let’s get ready to be amazed.

Genesis Psychedelica | DALL·E

Quantum Chemistry Simulations and the Prebiotic Origin of Life

Remember our story about Darwin—yes, that very Darwin—who back in 1871 casually speculated about life beginning in a warm little pond? And how we dived into Miller and Urey’s 1953 experiment of this pond, the so-called primordial soup, showing us how amino acids might have come to be on a young and hot Earth?

That experiment marked a turning point for prebiotic chemistry and the study of life’s origins, capturing the human imagination and transforming it from a mere academic pursuit into a gripping narrative.

But what exactly is prebiotic chemistry? It’s the scientific discipline that investigates how simple, lifeless molecules on our ancient Earth—and elsewhereevolved into the complex biochemical systems that harbor life.

Naturally, being here on From Atoms To Words, you’re expecting a deep dive into simulations, right? I know, I know, you are thirsty for the technical juice. And we’ve certainly explored a wide array of computational tools in a variety of applications, from enzymatic reactions to DNA and surface adsorptions:

Quantum Chemistry of Enzymatic Reactions
QM/MM Calculations of Molecule-Surface Adsorption
Chemical Simulations of the Early Universe
All-atom Molecular Dynamics of the SARS-CoV-2 Virus
Multiscale Simulations of DNA
Quantum Nanoreactor Simulations of the Primordial Soup

Yet, only recently have we begun to harness all this computational power for exploring the prebiotic origin of life itself. Why? Because to understand how life sprang up on Earth is to embark on a grand scientific adventure that spans across biology, chemistry, and physics.

That, dear reader, is a hefty task, and so is our mission today. So, without further ado, let’s dive straight in—I bet you’re hungry for some delicious details.

Can Quantum Chemistry Simulations Help Tracing the Origin of Life? | From Atoms To Words | Arturo Robertazzi
Snapshots of a Miller-Urey-like experiment. CO2 molecules react with NH3. Quantum chemistry simulations performed with QuantistryLab

Quantum Chemistry Simulations of 4 Prebiotic Scenarios

Alright, let’s dive into the heart of the matter. Of all computational tools, we’re centering our conversation on quantum chemistry simulations, from DFT to high-level methods and ab initio molecular dynamics. Inspired by the excellent review article by Fabio Petrucci, we’re launching into a voyage through cosmic crucibles and Earth’s primordial soups, exploring the effect of shockwaves, interactions with mineral substrates, and the interplay of light and lifeless molecules—all in pursuit of understanding how life’s building blocks were formed. Let’s begin with our first topic: chemistry in the interstellar medium.

▸ Prebiotic Scenario 1: Chemistry in the Interstellar Medium

For enthusiasts of prebiotic chemistry, the interstellar medium is like an extraterrestrial treasure trove, presenting a smorgasbord of conditions—chilly temperatures (typically dipping way below 100 Kelvin), varying densities, and a cocktail of chemical processes.

Thanks to the marvels of experimental spectroscopy, we’ve discovered a diverse array of molecules adrift in this space. But here’s the catch: the multitude of reactions occurring in the interstellar medium—from gas-phase to surface-mediated processes, not to mention the occasional jolt from proton irradiation—makes it a complex, albeit fascinating, puzzle.

So, could quantum chemistry simulations be our guiding light?

Of course. Quantum chemistry steps into the fray, shedding light on high-energy, low-temperature reactions that could have given rise to organic molecules with prebiotic potential. Through this lens, we gain unparalleled insights into the atomistic subtleties of these early processes.

Take the work by Barone and team. Using advanced DFT approaches (B2PLYPD3 | CBS-QB3), they explored the formation of formamide, a multifunctional prebiotic precursor to the biochemical compounds of life, from a simple mix of NH2 and H2CO. Their findings? This reaction faces no energetic barrier, making it highly probable even within the chilly confines of the interstellar medium.

Glycine, the simplest amino acid | QuantistryLab

But the story doesn’t end with gas-phase chemistry. The dust grain surfaces and icy mantles within the interstellar medium serve as havens where organic molecules can seek refuge and engage in reactions.

The DFT calculations by Rimola and team showed how icy comets may act as cosmic crucibles, where ammonia, formaldehyde, and hydrogen cyanide undergo Strecker-like reactions to synthesize glycine—as we have seen in previous stories, a fundamental amino acid crucial for life.

Within this prebiotic scenario, the DFT calculations unveil a thrilling chapter: the formation of aminoacetonitrile, a key precursor to glycine, safely cradled in the icy embrace of dust particles.

I imagine these interstellar icebergs, rocketing through the emptiness of space, only to deliver their precious cargo to ancient Earth. Upon their dramatic rendezvous with the primordial oceans, a transformative alchemy turns aminoacetonitrile into glycine. Well, isn’t that a mighty display of nature’s genius?

More on From Atoms To Words:
7 Noncovalent Interactions in Proteins: The Hidden Architects of Structures and Functions
Quantum Biology: The Fuzzy Connection Between Quantum Mechanics and Living Things
Computational Chemistry 2043: A Quantum Peep into the Future

▸ Prebiotic Scenario 2: Organic molecules exposed to radiation

When the Sun was just a fledgling star, shining with a gentler glow than the powerhouse we orbit today, primitive Earth was enveloped in a reductive atmosphere—a world without the welcoming embrace of oxygen and ozone. This inhospitable environment set the perfect stage for energetic short-wavelength light to shape early Earth’s chemical makeup.

It’s this very light that may have tilted life’s preference for the well-known and yet mysterious molecular orientation, known as homochirality. The exclusivity of amino acids and sugars in adopting one spatial arrangement out of two possible mirror images is crucial as it ensures that biomacromolecules, like proteins, can fold and function correctly.

Yet another showcase of nature’s molecular mastery. But let me not get too carried away.

So, let’s rewind to the late ’60s. As The Beatles were cooking up Sgt. Pepper in the studio, Ferris and Orgel were busy synthesizing purine nucleobases from cis-diaminomaleonitrile. Under the glow of UV light, this molecule is transformed into 4-aminoimidazole-5-carbonitrile (or AICN for short), a precursor to purine nucleobases like adenine, a key piece of DNA and RNA structures. What’s truly impressive is AICN’s remarkable stability when exposed to radiation—a testament to the resilience of these molecular structures under early Earth’s extreme conditions. Makes you pause and wonder, doesn’t it?

But the question we’re really interested in is: Can we really reproduce and rationalize the interplay of light and matter with quantum chemistry simulations?

Well, investigating such complex photochemical reactions requires the precision of sophisticated ab initio methods, way beyond the approximations of DFT. We are talking about advanced techniques like second-order perturbation theory and multireference methods. But keep in mind that, as indispensable as these methods are for their accuracy, their thirst for computational resources is a tall order.

Enter Szabla and team, who have applied these rigorous quantum chemistry calculations to the photochemistry of AICN–water clusters, factoring in six water molecules (and believe me, that is not a small model to be handled with high-level ab initio methods). Now, these studies revealed that the charge transfer to the solvent is coupled with the formation of an H3O+ cation, hinting a broader chemical story of potential photostability for organic molecules swimming in the vast ocean of bulk water.

And what about the essential bricks in the nucleic acids structures? Quantum chemistry has also played a key role in that camp, identifying pathways toward the synthesis of pyrimidine ribonucleotides against the backdrop of Earth’s nascent UV exposure. Szabla and team, for example, explored the photostability of critical precursors, uncovering mechanisms by which molecules like 2-aminooxazole can avoid decay or undergo transformation when exposed to light.

Pretty stellar, isn’t it, what quantum chemistry simulations can show us?

Can Quantum Chemistry Simulations Help Tracing the Origin of Life? | From Atoms To Words | Arturo Robertazzi
DNA repair in a model system – a thymine dimer surrounded by liquid water | Ab Initio Molecular Dynamics | Credit

More on From Atoms To Words:
Is Machine Learning Going to Replace Computational Chemists?
60 Years in the Making: AlphaFold’s Historical Breakthrough in Protein Structure Prediction
When Will RNA Structure Prediction Get Its AlphaFold Breakthrough?

▸ Prebiotic Scenario 3: Mineral surfaces as catalysts to life

Back in the late ’40s, John D. Bernal recognized that mineral particles, like clays, can act as catalysts in the synthesis of small polypeptides. Now, how does this fact tie into our scenario? Well, a crucial question in the chemistry of life’s origin concerns the active role of mineral inorganic surfaces in coming into contact with prebiotic molecules.

These mineral surfaces excel at adsorbing and concentrating organic material, such as amino acids, from their water environment, which in turn helps their assembly into more complex structures. We’re talking about the polymerization of simple amino acids into polypeptides, or what could essentially be considered the early precursors to proteins.

So, where do quantum chemistry simulations come into play?

The DFT calculations of Ugliengo and team offer exemplary insights into these organic molecule-mineral interactions. They analyzed the adsorption of amino acids on silica surfaces, shedding light on the delicate balance between peptide bond formation and hydrolysis. Their calculations demonstrated that peptide bonds are more likely to form on these substrates, confirming the potential of mineral surfaces to catalyze biomolecular polymerization.

But what about DNA nucleobases? How do they interact with these surfaces? The quantum chemistry simulations of Mignon and team give an atomistic picture of how the strength of these interactions varies with the proximity of the nucleobase to the clay surfaces. They also explored how nucleobases like cytosine interact within mineral layers, showing the dynamics of the stabilization, mostly occurring via noncovalent interactions, such as van der Waals.

And then, there’s the curious case of ribose, the backbone of RNA, known for its structural flexibility—a trait that poses both challenges and opportunities in prebiotic chemistry. When Sponer and team took a closer look with DFT, they discovered that the electrostatic field from the mineral surface can influence the orientation of nearby ribose’s hydroxyl groups, with the ribose-surface complex being stabilized by strong hydrogen bonding.

My takeaway? Quantum chemistry simulations shine at mapping how life’s essentials polymerize under prebiotic conditions into life’s molecules. Not bad, eh?

▸ Prebiotic Scenario 4: Extreme conditions on Earth

So far, we’ve explored the interstellar medium, delved into the effects of radiation, and examined how organic molecules interact with mineral surfaces. Now, let’s have a taste of Earth’s primordial soup, where the recipe for life wasn’t just a pinch of this or a dash of that, but a whole bubbling mix of hot surface pools and extreme hydrothermal vents.

One key player that might have nudged lifeless molecules towards life in such settings is the shock waves from meteorite impacts. These dramatic events could unleash extreme pressures and temperatures, sparking chemical reactions that otherwise would be slow or just not happening at all. It’s a scenario straight out of a sci-fi movie, where the universe’s very chaos plants the seeds of life.

So, can quantum chemistry simulations also shed light on the reactions driven by these shock waves?

Absolutely. Computational models grounded in ab initio molecular dynamics are tailor-made for this line of inquiry, since the blink-and-you-miss-it lifespan of shock waves—mere picoseconds—is something ab initio molecular dynamics can handle.

Looking into Goldman and team‘s research gives us a window into this. They showed how even moderate impacts with icy mixtures rich in CO2 can whip up complex nitrogen-based cycles, which then morph into aromatic hydrocarbons as they cool off. Yet, when the conditions get tougher, we see a different scenario, with simpler organic compounds like methane and formaldehyde being formed. This variety just goes to show the wide spectrum of chemical events that extreme conditions can trigger.

What’s truly interesting is that certain events, like oblique impacts, can potentially lower the shock wave temperatures and pressures, playing a role in keeping these prebiotic ingredients intact.

Kind of amazing, isn’t it? It hints that Earth’s tumultuous early days might have serendipitously created the ideal nursery for life to emerge.

Can Quantum Chemistry Simulations Help Tracing the Origin of Life? | From Atoms To Words | Arturo Robertazzi
Bihydroxide anion deprotonating a silanol group at the silica surface | Ab Initio Molecular Dynamics | Credit

More on From Atoms To Words:
The Evolution of Quantum Chemistry: From Pencil and Paper to Quantum Computing
Large Language Models for Chemistry: Is the Beginning of a New Era?
Chemical Space to Material Discovery: Simulations and Machine Learning Leading the Way

A Final Personal Touch

Wow, you stuck with me all the way to the end. Well done! So, now we can answer today’s question: Yes, quantum chemistry simulations can help trace the prebiotic origin of life.

And yet, we’ve really just nibbled at the edges of a huge topic. Prebiotic chemistry, quantum chemistry simulations, the origins of life… it’s an enormous and complex field. Honestly, the more I dive into it, the more it feels like I’m just scratching the surface.

Today, we zeroed in on the quantum side of things, but the arsenal of computational tools and experimental methods at our disposal is vast and varied. There’s so much more to explore.

What really gets me excited is the long list of unanswered questions that tickle the curiosity of my inner scientist. Where did life kick off? Was it in some forgotten corner of Earth, out there in the cold stretches between stars, or on a comet zipping through space? It’s an ancient mystery that ties us back to where we all came from, reminding us that we’re just a small part of a much bigger universe. Hopefully filled with life.

Right, the age-old question – are we alone?

I doubt it. But I won’t believe until we have an ultimate proof.

The thing is, tracing life back to its roots, from the simplest molecules to the marvels of living machinery, is a goal in itself. It’s a journey that is as much about gazing into the infinity of the cosmos as it is about looking within us.

If you enjoyed this dive into quantum chemistry simulations of prebiotic scenarios, I’d love to hear your thoughts. Agree, disagree, or have a totally wild theory of your own? Let’s connect! Subscribe to my LinkedIn newsletter and let’s keep the conversation rolling.


From Atoms To Words

Today’s Story Filed Under: