Thermodynamics of Potential CHO Metabolites in a Reducing Environment

How did metabolism arise and evolve? What chemical compounds might be suitable to support and sustain a proto-metabolism before the advent of more complex co-factors? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHO compounds in aqueous solution, allowing us to probe the thermodynamics of core extant cycles and their closely related chemical cousins. By framing our analysis in terms of the simplest feasible cycle and its permutations, we analyze potentially favorable thermodynamic cycles for CO2 fixation with H2 as a reductant. We find that paying attention to redox states illuminates which reactions are endergonic or exergonic. Our results highlight the role of acetate in proto-metabolic cycles, and its connection to other prebiotic molecules such as glyoxalate, glycolaldehyde, and glycolic acid.

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Predicting metastable phase boundaries in Al–Cu alloys from first-principles calculations of free energies: The role of atomic vibrations

EPL (Europhysics Letters) ◽

10.1209/epl/i2005-10462-x ◽

2006 ◽

Vol 73 (5) ◽

pp. 719-725 ◽

Cited By ~ 53

Author(s):

C Ravi ◽

C Wolverton ◽

V Ozoliņš

Keyword(s):

First Principles ◽

Metastable Phase ◽

First Principles Calculations ◽

Free Energies ◽

Phase Boundaries ◽

Cu Alloys ◽

Atomic Vibrations

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Chemical equilibrium and chemical kinetics

10.1093/oso/9780198782957.003.0014 ◽

2018 ◽

Author(s):

Dennis Sherwood ◽

Paul Dalby

Keyword(s):

Free Energy ◽

Equilibrium Constant ◽

Gibbs Free Energy ◽

Chemical Kinetics ◽

Chemical Equilibrium ◽

First Principles ◽

Effect Of Temperature ◽

Total System ◽

Free Energies

Building on the previous chapter, this chapter examines gas phase chemical equilibrium, and the equilibrium constant. This chapter takes a rigorous, yet very clear, ‘first principles’ approach, expressing the total Gibbs free energy of a reaction mixture at any time as the sum of the instantaneous Gibbs free energies of each component, as expressed in terms of the extent-of-reaction. The equilibrium reaction mixture is then defined as the point at which the total system Gibbs free energy is a minimum, from which concepts such as the equilibrium constant emerge. The chapter also explores the temperature dependence of equilibrium, this being one example of Le Chatelier’s principle. Finally, the chapter links thermodynamics to chemical kinetics by showing how the equilibrium constant is the ratio of the forward and backward rate constants. We also introduce the Arrhenius equation, closing with a discussion of the overall effect of temperature on chemical equilibrium.

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Role of dislocations in the bcc-hcp transition under high pressure: A first-principles approach in beryllium

Physical Review Materials ◽

10.1103/physrevmaterials.4.063609 ◽

2020 ◽

Vol 4 (6) ◽

Author(s):

Vanessa Riffet ◽

Bernard Amadon ◽

Nicolas Bruzy ◽

Christophe Denoual

Keyword(s):

High Pressure ◽

First Principles

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IKBKB siRNA-Encapsulated Poly (Lactic-co-Glycolic Acid) Nanoparticles Diminish Neuropathic Pain by Inhibiting Microglial Activation

International Journal of Molecular Sciences ◽

10.3390/ijms22115657 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5657

Author(s):

Seounghun Lee ◽

Hyo-Jung Shin ◽

Chan Noh ◽

Song-I Kim ◽

Young-Kwon Ko ◽

...

Keyword(s):

Neuropathic Pain ◽

Microglial Activation ◽

Glycolic Acid ◽

Nuclear Factor Kappa B ◽

Decisive Role ◽

Plga Nanoparticles ◽

Spinal Nerve ◽

Nuclear Factor ◽

Interfering Rna

Activation of nuclear factor-kappa B (NF-κB) in microglia plays a decisive role in the progress of neuropathic pain, and the inhibitor of kappa B (IκB) is a protein that blocks the activation of NF-κB and is degraded by the inhibitor of NF-κB kinase subunit beta (IKBKB). The role of IKBKB is to break down IκB, which blocks the activity of NF-kB. Therefore, it prevents the activity of NK-kB. This study investigated whether neuropathic pain can be reduced in spinal nerve ligation (SNL) rats by reducing the activity of microglia by delivering IKBKB small interfering RNA (siRNA)-encapsulated poly (lactic-co-glycolic acid) (PLGA) nanoparticles. PLGA nanoparticles, as a carrier for the delivery of IKBKB genes silencer, were used because they have shown potential to enhance microglial targeting. SNL rats were injected with IKBKB siRNA-encapsulated PLGA nanoparticles intrathecally for behavioral tests on pain response. IKBKB siRNA was delivered for suppressing the expression of IKBKB. In rats injected with IKBKB siRNA-encapsulated PLGA nanoparticles, allodynia caused by mechanical stimulation was reduced, and the secretion of pro-inflammatory mediators due to NF-κB was reduced. Delivering IKBKB siRNA through PLGA nanoparticles can effectively control the inflammatory response and is worth studying as a treatment for neuropathic pain.

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The Affinity of Carboplatin to B-Vitamins and Nucleobases

International Journal of Molecular Sciences ◽

10.3390/ijms22073634 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3634

Author(s):

Beata Szefler ◽

Przemysław Czeleń ◽

Przemysław Krawczyk

Keyword(s):

Vitamin B6 ◽

Pyridoxal Phosphate ◽

Antitumor Agents ◽

Lone Pair ◽

Chemical Compounds ◽

Free Energies ◽

Aromatic Rings ◽

Anti Cancer ◽

Potential Impact ◽

Reactive Molecule

Platinum compounds have found wide application in the treatment of various types of cancer and carboplatin is one of the main platinum-based drugs used as antitumor agents. The anticancer activity of carboplatin arises from interacting with DNA and inducing programmed cell death. However, such interactions may occur with other chemical compounds, such as vitamins containing aromatic rings with lone-pair orbitals, which reduces the anti-cancer effect of carboplatin. The most important aspect of the conducted research was related to the evaluation of carboplatin affinity to vitamins from the B group and the potential impact of such interactions on the reduction of therapeutic capabilities of carboplatin in anticancer therapy. Realized computations, including estimation of Gibbs Free Energies, allowed for the identification of the most reactive molecule, namely vitamin B6 (pyridoxal phosphate). In this case, the computational estimations indicating carboplatin reactivity were confirmed by spectrophotometric measurements.

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A first-principles study of the atomic layer deposition of ZnO on carboxyl functionalized carbon nanotubes: the role of water molecules

Physical Chemistry Chemical Physics ◽

10.1039/d0cp05283c ◽

2021 ◽

Vol 23 (5) ◽

pp. 3467-3478

Author(s):

J. I. Paez-Ornelas ◽

H. N. Fernández-Escamilla ◽

H. A. Borbón-Nuñez ◽

H. Tiznado ◽

Noboru Takeuchi ◽

...

Keyword(s):

First Principles ◽

Ligand Exchange ◽

Functional Group ◽

Atomic Layer ◽

High Reactivity ◽

Water Molecules ◽

Exchange Reactions ◽

Layer Deposition ◽

The Right

Atomic description of ALD in systems that combine large surface area and high reactivity is key for selecting the right functional group to enhance the ligand-exchange reactions.

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