Jarrid Rector-Brooks, Théophile Lambert, Marta Skreta
et al.
Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes without pre-specifying catalytic residues. We introduce DISCO (DIffusion for Sequence-structure CO-design), a multimodal model that co-designs protein sequence and 3D structure around arbitrary biomolecules, as well as inference-time scaling methods that optimize objectives across both modalities. Conditioned solely on reactive intermediates, DISCO designs diverse heme enzymes with novel active-site geometries. These enzymes catalyze new-to-nature carbene-transfer reactions, including alkene cyclopropanation, spirocyclopropanation, B-H, and C(sp$^3$)-H insertions, with high activities exceeding those of engineered enzymes. Random mutagenesis of a selected design further confirmed that enzyme activity can be improved through directed evolution. By providing a scalable route to evolvable enzymes, DISCO broadens the potential scope of genetically encodable transformations. Code is available at https://github.com/DISCO-design/DISCO.
Nicole Arulanantham, Colette Salyk, Klaus Pontoppidan
et al.
Mid-infrared spectroscopy of protoplanetary disks provides a chemical inventory of gas within a few au, where planets are readily detected around older stars. With the JWST Disk Infrared Spectral Chemistry Survey (JDISCS), we explore demographic trends among 31 disks observed with MIRI (MRS) and with previous ALMA millimeter continuum imaging at high angular resolution (5-10 au). With these S/N $\sim$200-450 spectra, we report emission from H$_2$O, OH, CO, C$_2$H$_2$, HCN, CO$_2$, [Ne II], [Ne III], and [Ar II]. Emission from H$_2$O, OH and CO is nearly ubiquitous for low-mass stars, and detection rates of all molecules are higher than for similar disks observed with Spitzer-IRS. Slab model fits to the molecular emission lines demonstrate that emission from C$_2$H$_2$, HCN, and possibly CO$_2$ is optically thin; thus since column densities and emitting radii are degenerate, observations are actually sensitive to the total molecular mass. C$_2$H$_2$ and HCN emission also typically originate in a hotter region ($920^{+70}_{-130}$, $820^{+70}_{-130}$ K, respectively) than CO$_2$ ($600^{+200}_{-160}$ K). The HCN to cold H$_2$O luminosity ratios are generally smaller in smooth disks, consistent with more efficient water delivery via icy pebbles in the absence of large dust substructures. The molecular emission line luminosities are also correlated with mass accretion rates and infrared spectral indices, similar to trends reported from Spitzer-IRS surveys. This work demonstrates the power of combining multi-wavelength observations to explore inner disk chemistry as a function of outer disk and stellar properties, which will continue to grow as the sample of observed Class II systems expands in the coming JWST observation cycles.
Tian-Yu Tu, Prathap Rayalacheruvu, Liton Majumdar
et al.
Cosmic rays (CRs) have strong influences on the chemistry of dense molecular clouds (MCs). To study the detailed chemistry induced by CRs, we conducted a Yebes W band line survey towards an unshocked MC (which we named as 3C391:NML) associated with supernova remnant (SNR) 3C391. We detected emission lines of 18 molecular species in total and estimated their column densities with local thermodynamic equilibrium (LTE) and non-LTE analysis. Using the abundance ratio N(HCO+)/N(CO) and an upper limit of N(DCO+)/N(HCO+), we estimated the CR ionization rate of 3C391:NML is $ζ\gtrsim 2.7\times 10^{-14}\rm \ s^{-1}$ with an analytic method. However, we caution on adopting this value because chemical equilibrium, which is a prerequisite of using the equations, is not necessarily reached in 3C391:NML. We observed lower N(HCO+)/N(HOC+), higher N(HCS+)/N(CS), and higher X($l$-C3H+) by an order of magnitude in 3C391:NML than the typical values in quiescent dense MCs. We found that an enhanced CR ionization rate (of order $\sim 10^{-15}$ or $\sim 10^{-14}\rm \ s^{-1}$) is needed to reproduce the observation with chemical model. This is higher than the values found in typical MCs by 2--3 orders of magnitude.
Oliver A. Thompson, Alexander J. Richings, Brad K. Gibson
et al.
Our ability to trace the star-forming molecular gas is important to our understanding of the Universe. We can trace this gas using CO emission, converting the observed CO intensity into the H$_2$ gas mass of the region using the CO-to-H$_2$ conversion factor (Xco). In this paper, we use simulations to study the conversion factor and the molecular gas within galaxies. We analysed a suite of simulations of isolated disc galaxies, ranging from dwarfs to Milky Way-mass galaxies, that were run using the FIRE-2 subgrid models coupled to the CHIMES non-equilibrium chemistry solver. We use the non-equilibrium abundances from the simulations, and we also compare to results using abundances assuming equilibrium, which we calculate from the simulation in post-processing. Our non-equilibrium simulations are able to reproduce the relation between CO and H$_2$ column densities, and the relation between Xco and metallicity, seen within observations of the Milky Way. We also compare to the xCOLD GASS survey, and find agreement with their data to our predicted CO luminosities at fixed star formation rate. We also find the multivariate function used by xCOLD GASS overpredicts the H$_2$ mass for our simulations, motivating us to suggest an alternative multivariate function of our fitting, though we caution that this fitting is uncertain due to the limited range of galaxy conditions covered by our simulations. We also find that the non-equilibrium chemistry has little effect on the conversion factor (<5\%) for our high-mass galaxies, though still affects the H$_2$ mass and Lco by $\approx$25\%.
Théophile De Donder, a Belgian mathematician born in Brussels, elaborated two important ideas that created a bridge between thermodynamics and chemical kinetics. He invented the concept of the degree of advancement of a reaction, and, in 1922, he provided a precise mathematical form to the already known chemical affinity by translating Clausius's uncompensated heat into formal language. These concepts merge in an important inequality that was the starting point for the formalization of out-of-equilibrium thermodynamics. The present article aims to reconstruct how De Donder elaborated his ideas and how he developed them by exploring his teaching activity and its connection with his scientific production. Furthermore, it emphasizes the role played by the discussions with his disciples who became his collaborators. The paper analyzes De Donder's efforts in participating in the second Solvay Chemistry Council in 1925 to call the attention of the international community of chemists. Even if his mathematical approach did not receive much attention at the time, his work on chemical affinity was the basis for the birth of the so-called Brussels school of thermodynamics.
Kevin Maik Jablonka, Qianxiang Ai, Alexander Al-Feghali
et al.
Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines.
Complex organic molecules (COMs) have been observed to be abundant in the gas phase toward protostars. Deep line surveys have been carried out only for a limited number of well-known high-mass star forming regions using the Atacama Large Millimeter/submillimeter Array (ALMA), which has unprecedented resolution and sensitivity. Statistical studies on oxygen-bearing COMs (O-COMs) in high-mass protostars using ALMA are still lacking. With the recent CoCCoA survey, we are able to determine the column density ratios of six O-COMs with respect to methanol (CH$_3$OH) in a sample of 14 high-mass protostellar sources to investigate their origin through ice and/or gas-phase chemistry. The selected species are: acetaldehyde (CH$_3$CHO), ethanol (C$_2$H$_5$OH), dimethyl ether (DME, CH$_3$OCH$_3$), methyl formate (MF, CH$_3$OCHO), glycolaldehyde (GA, CH$_2$OHCHO), and ethylene glycol (EG, (CH$_2$OH)$_2$). DME and MF have the highest and most constant ratios within one order of magnitude, while the other four species have lower ratios and exhibit larger scatter by 1-2 orders of magnitude. We compare the O-COM ratios of high-mass CoCCoA sources with those of 5 low-mass protostars available from the literature, along with the results from experiments and simulations. We find that the O-COM ratios with respect to methanol are on the same level in both the high- and low-mass samples, which suggests that these species are mainly formed in similar environments during star formation, probably in ice mantles on dust grains during early pre-stellar stages. Current simulations and experiments can reproduce most observational trends with a few exceptions, and hypotheses exist to explain the differences between observations and simulations/experiments, such as the involvement of gas-phase chemistry and different emitting areas of molecules.
Non-equilibrium chemistry is a key process in the study of the InterStellar Medium (ISM), in particular the formation of molecular clouds and thus stars. However, computationally it is among the most difficult tasks to include in astrophysical simulations, because of the typically high (>40) number of reactions, the short evolutionary timescales (about $10^4$ times less than the ISM dynamical time) and the characteristic non-linearity and stiffness of the associated Ordinary Differential Equations system (ODEs). In this proof of concept work, we show that Physics Informed Neural Networks (PINN) are a viable alternative to traditional ODE time integrators for stiff thermo-chemical systems, i.e. up to molecular hydrogen formation (9 species and 46 reactions). Testing different chemical networks in a wide range of densities ($-2< \log n/{\rm cm}^{-3}< 3$) and temperatures ($1 < \log T/{\rm K}< 5$), we find that a basic architecture can give a comfortable convergence only for simplified chemical systems: to properly capture the sudden chemical and thermal variations a Deep Galerkin Method is needed. Once trained ($\sim 10^3$ GPUhr), the PINN well reproduces the strong non-linear nature of the solutions (errors $\lesssim 10\%$) and can give speed-ups up to a factor of $\sim 200$ with respect to traditional ODE solvers. Further, the latter have completion times that vary by about $\sim 30\%$ for different initial $n$ and $T$, while the PINN method gives negligible variations. Both the speed-up and the potential improvement in load balancing imply that PINN-powered simulations are a very palatable way to solve complex chemical calculation in astrophysical and cosmological problems.
F. Espinoza, Department of Physics, Astronomy
et al.
The current public sense of anxiety in dealing with disinformation as manifested by so-called fake news is acutely displayed by the reaction to recent events prompted by a belief in conspiracies among certain groups. A model to deal with disinformation is proposed; it is based on a demonstration of the analogous behavior of disinformation to that of wave phenomena. Two criteria form the basis to combat the deleterious effects of disinformation: the use of a refractive medium based on skepticism as the default mode, and polarization as a filter mechanism to analyze its merits based on evidence. Critical thinking is enhanced since the first one tackles the pernicious effect of the confirmation bias, and the second the tendency towards attribution, both of which undermine our efforts to think and act rationally. The benefits of such a strategy include an epistemic reformulation of disinformation as an independently existing phenomenon, that removes its negative connotations when perceived as being possessed by groups or individuals.
Variational quantum eigensolver~(VQE) typically optimizes variational parameters in a quantum circuit to prepare eigenstates for a quantum system. Its applications to many problems may involve a group of Hamiltonians, e.g., Hamiltonian of a molecule is a function of nuclear configurations. In this paper, we incorporate derivatives of Hamiltonian into VQE and develop some hybrid quantum-classical algorithms, which explores both Hamiltonian and wavefunction spaces for optimization. Aiming for solving quantum chemistry problems more efficiently, we first propose mutual gradient descent algorithm for geometry optimization by updating parameters of Hamiltonian and wavefunction alternatively, which shows a rapid convergence towards equilibrium structures of molecules. We then establish differential equations that governs how optimized variational parameters of wavefunction change with intrinsic parameters of the Hamiltonian, which can speed up calculation of energy potential surface. Our studies suggest a direction of hybrid quantum-classical algorithm for solving quantum systems more efficiently by considering spaces of both Hamiltonian and wavefunction.
In the subject of black hole chemistry, a broad variety of critical phenomena for charged topological black holes (TBHs) with massive gravitons (within the framework of dRGT massive gravity) is discussed in detail. Since critical behavior and nature of possible phase transition(s) crucially depend on the specific choice of ensemble, and, in order to gain more insight into criticality in the massive gravity framework, we perform our analysis in both the canonical (fixed charge, $Q$) and the grand canonical (fixed potential, $Φ$) ensembles. It is shown that, for charged TBHs in the grand canonical ensemble, the van der Waals (vdW) phase transition could take place in $d \ge 5$, the reentrant phase transition (RPT) in $d \ge 6$ and the analogue of triple point in $d \ge 7$ which are different from the results of canonical ensemble. In the canonical ensemble, the vdW phase transition is observed in $d \ge 4$, the vdW type phase transition in $d \ge 6$ and the critical behavior associated with the triple point in $d \ge 6$. In this regard, the appearance of grand canonical $P-V$ criticality and the associated phase transition(s) in black holes with various topologies depend on the effective topological factor $k_{\rm{eff}}^{\rm{(GC)}} \equiv {[k + {m_g^2}c_0^2{c_2} - 2({d_3}/{d_2}){Φ^2}]}$ instead of $k$ in Einstein gravity, where $k$ is the normalized topological factor ($k_{\rm{eff}}^{\rm{(C)}} \equiv [k + {m_g^2}c_0^2{c_2}]$ plays this role in the canonical ensemble of TBHs in massive gravity). Such evidence gives the (grand) canonical study of extended phase space thermodynamics with massive gravitons a special significance.
Jonathan Holdship, Jonathan Rawlings, Serena Viti
et al.
Many species of complex organic molecules (COMs) have been observed in several astrophysical environments but it is not clear how they are produced, particularly in cold, quiescent regions. One process that has been proposed as a means to enhance the chemical complexity of the gas phase in such regions is the explosion of the ice mantles of dust grains. In this process, a build up of chemical energy in the ice is released, sublimating the ices and producing a short lived phase of high density, high temperature gas. The gas-grain chemical code UCLCHEM has been modified to treat these explosions in order to model the observed abundances of COMs towards the TMC-1 region. It is found that, based on our current understanding of the explosion mechanism and chemical pathways, the inclusion of explosions in chemical models is not warranted at this time. Explosions are not shown to improve the model's match to the observed abundances of simple species in TMC-1. Further, neither the inclusion of surface diffusion chemistry, nor explosions, results in the production of COMs with observationally inferred abundances.
L. Ilsedore Cleeves, Edwin A. Bergin, Karin I. Öberg
et al.
We report the first detection of a substantial brightening event in an isotopologue of a key molecular ion, HCO$^+$, within a protoplanetary disk of a T Tauri star. The H$^{13}$CO$^+$ $J=3-2$ rotational transition was observed three times toward IM Lup between July 2014 and May 2015 with the Atacama Large Millimeter Array. The first two observations show similar spectrally integrated line and continuum fluxes, while the third observation shows a doubling in the disk integrated $J=3-2$ line flux compared to the continuum, which does not change between the three epochs. We explore models of an X-ray active star irradiating the disk via stellar flares, and find that the optically thin H$^{13}$CO$^+$ emission variation can potentially be explained via X-ray driven chemistry temporarily enhancing the HCO$^+$ abundance in the upper layers of the disk atmosphere during large or prolonged flaring events. If the HCO$^+$ enhancement is indeed caused by a X-ray flare, future observations should be able to spatially resolve these events and potentially enable us to watch the chemical aftermath of the high-energy stellar radiation propagating across the face of protoplanetary disks, providing a new pathway to explore ionization physics and chemistry, including electron density, in disks.
Philippe Schwaller, Theophile Gaudin, David Lanyi
et al.
There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a novel way of tokenization, which is arbitrarily extensible with reaction information. With this approach, we demonstrate results superior to the state-of-the-art solution by a significant margin on the top-1 accuracy. Specifically, our approach achieves an accuracy of 80.1% without relying on auxiliary knowledge such as reaction templates. Also, 66.4% accuracy is reached on a larger and noisier dataset.
Surface chemistry is important across diverse fields such as corrosion and nanostructure synthesis. Unfortunately, many as-synthesized nanomaterials, including partially dealloyed nanoparticle catalysts for fuel cells, with highly active surfaces are not stable in their reactive environments, preventing widespread application. Thus, understanding instability by focusing on the structure-stability and defect-stability relationship at the nanoscale is crucial and will likely play an important role in meeting grand challenges. To this end, recent advances in imaging nanostructure stability have come via both electron, x-ray, and other techniques such as atomic force microscopy, but tend to be limited to specific sample environments and/or two-dimensional images. Here, we report investigations into the defect-stability relationship of silver nanoparticles to voltage-induced electrochemical dissolution imaged in-situ in three-dimensional (3D) detail by Bragg Coherent Diffractive Imaging (BCDI). We first determine the average dissolution kinetics by Stationary Probe Rotating Disk Electrode (SPRDE) in combination with inductively coupled plasma mass spectrometry (ICP-MS), which allows real-time in-situ measurement of Ag+ ions formation and the corresponding electrochemical current. We then observe the dissolution and redeposition processes in 3D with BCDI in single nanocrystals, providing unique insight about the role of surface strain, defects, and their coupling to the dissolution chemistry. The methods developed and the knowledge gained go well beyond a "simple" silver electrochemistry and are applicable to all electrocatalytic reactions where functional links between activity and stability are controlled by structure and defect dynamics.
Samir F. Matar, Mario Maglione, Michel Nakhl
et al.
From DFT based calculations establishing energy-volume equations of state and electron localization mapping, the electronic structure and crystal chemistry changes from Sn2TiO4 to Sn2TiO6 by oxidation are rationalized; the key effect being the destabilization of divalent tin SnII towards tetravalent state SnIV leading to rutile Sn2TiO6 as experimentally observed. The subsequent electronic structure change is highlighted in the relative change of the electronic band gap which increases from ~1eV up to 2.2 eV and the 1.5 times increase of the bulk modulus assigned to the change from covalently SnII based compound to the more ionic SnIV one. Such trends are also confronted with the relevant properties of black SnIIO characterized by very small band gap.
We study the spatial distribution and chemistry of small hydrocarbons in the Orion Bar PDR. We used the IRAM-30m telescope to carry out a millimetre line survey towards the Orion Bar edge, complemented with ~2'x2' maps of the C2H and c-C3H2 emission. We analyse the excitation of the detected hydrocarbons and constrain the physical conditions of the emitting regions with non-LTE radiative transfer models. We compare the inferred column densities with updated gas-phase photochemical models including 13CCH and C13CH isotopomer fractionation. ~40% of the lines in the survey arise from hydrocarbons (C2H, C4H, c-C3H2, c-C3H, C13CH, 13CCH, l-C3H and l-H2C3). We detect new lines from l-C3H+ and improve its rotational spectroscopic constants. Anions or deuterated hydrocarbons are not detected: [C2D]/[C2H]<0.2%, [C2H-]/[C2H]<0.007% and [C4H-]/[C4H]<0.05%. Our gas-phase models can reasonably match the observed column densities of most hydrocarbons (within factors <3). Since the observed spatial distribution of the C2H and c-C3H2 emission is similar but does not follow the PAH emission, we conclude that, in high UV-flux PDRs, photodestruction of PAHs is not a necessary requirement to explain the observed abundances of the smallest hydrocarbons. Instead, gas-phase endothermic reactions (or with barriers) between C+, radicals and H2 enhance the formation of simple hydrocarbons. Observations and models suggest that the [C2H]/[c-C3H2] ratio (~32 at the PDR edge) decreases with the UV field attenuation. The observed low cyclic-to-linear C3H column density ratio (<3) is consistent with a high electron abundance (Xe) PDR environment. In fact, the poorly constrained Xe gradient influences much of the hydrocarbon chemistry in the more UV-shielded gas. We propose that reactions of C2H isotopologues with 13C+ and H atoms can explain the observed [C13CH]/[13CCH]=1.4(0.1) fractionation level.