Hasil untuk "Organic chemistry"

Marija S. Genčić, Tatjana Ilic-Tomic, Marko Z. Mladenović et al.

Volatile organic compounds produced by microbes are increasingly recognized as modulators of microbial interactions and mediators of both intra- and inter-kingdom communication. This study explored the possible ecophysiological roles of nine amides from <i>Streptomyces</i> sp. NP10 in quorum sensing (QS) and biofilm formation in <i>Pseudomonas aeruginosa</i> PAO1. GC-MS profiling, synthesis, spectral validation, and co-injection experiments confirmed compound identities. Notably, <i>N</i>-(3-methyl-2-butenyl)acetamide is reported as a new natural product and <i>N</i>-(2-methylbutyl)acetamide as a new <i>Streptomyces</i>-produced metabolite. At subinhibitory concentrations (250 μg/mL), most of the amides enhanced <i>P. aeruginosa</i> biofilm formation, with <i>N</i>-(2-methylbutyl)acetamide, <i>N</i>-(3-methyl-2-butenyl)acetamide, and 2-phenylacetamide showing the strongest effects. Simultaneously, these compounds suppressed QS by reducing the production of <i>N</i>-acyl homoserine lactones (AHLs) and 2-alkyl-4-quinolones (AHQs). Aliphatic acetamides preferentially inhibited short-chain AHLs, while <i>N</i>-acetyltyramine and 2-phenylacetamide mainly affected quinolone signaling. These opposing effects on QS and biofilm are consistent with the involvement of alternative regulatory circuits. Motility assays showed biofilm stimulation was not correlated with altered swarming or twitching. Cross-species assays revealed limited QS inhibition, with only <i>N</i>-acetyltryptamine reducing violacein production in <i>Chromobacterium violaceum</i> CV026. Most of the amides were non-cytotoxic at 100 μM (10.5–20.2 μg/mL), except for 2-phenylacetamide. Overall, these amides likely serve as microbial signals influencing QS and biofilm formation, offering leads for anti-virulence strategies.

Adriana GROZAV, Gabriel MARC, Cristina AZAROV et al.

  ABSTRACT. The microwave-assisted improved synthesis of ethyl 2-(2-((6-methyl-4-oxo-4H-chromen-3-yl)methylene)hydrazinyl)thiazole-4-carboxylate is described. The antioxidant potential of the target compound was evaluated using spectrophotometric methods, including the DPPH• and ABTS•⁺ radical scavenging assays, as well as three additional electron-transfer assays employing metal-based oxidizing agents. The title compound exhibited good antioxidant activity compared to reference antioxidants. For the title compound theoretical quantum chemical (DFT) calculations were performed.

Beatriz Martín-García, Davide Spirito, Giulia Biffi et al.

Halide double perovskites are an interesting alternative to Pb-containing counterparts as active materials in optoelectronic devices. Low-dimensional double perovskites are fabricated by introducing large organic cations, resulting in organic/inorganic architectures with one or more inorganic octahedral layers separated by organic cations. Here, we synthesize layered double perovskites based on 3D Cs2AgBiBr6 that consist of double (2L) or single (1L) inorganic octahedral layers, using ammonium cations of different size and chemical structure. Temperature-dependent Raman spectroscopy reveals phase transition signatures in both inorganic lattice and organic moieties by detecting variations in their vibrational modes. Changes in the conformational arrangement of the organic cations to an ordered state coincide with a phase transition in the 1L systems with the shortest ammonium moieties. Significant changes of photoluminescence intensity observed around the transition temperature suggest that optical properties may be deeply affected by the octahedral tilts emerging at the phase transition.

Mahmoud El-Maghrabey, Ali Abdel-Hakim, Shiho Tagaya et al.

Nitrofurantoin is utilized in various industries, including dairy, livestock, poultry, and aquaculture, as a growth promoter and antibacterial agent. Because prolonged use can cause mutagenesis and other side effects, many countries have prohibited its use in food-producing animals. In this work, we introduce a simple, rapid, and highly sensitive chemiluminescence (CL) approach for the quantitation of nitrofurantoin using its redox cycle activity. Nitrofurantoin is reduced to nitrofurantoin radicals by the reducing agent dithiothreitol, and reactive oxygen species (ROS) formed during the reoxidation process (superoxide anion radical) are detected by luminol CL. The CL conditions were optimized, including types of solvents, CL and reducing reagents, and their concentrations. The method was validated as per International Council for Harmonization (ICHQ2(R2)) guidelines, regarding linearity, detection and quantitation limits, accuracy, and precision. A good linearity with <i>r</i> = 0.9992 was obtained between the CL intensity and the nitrofurantoin concentration in the range of 4.0–400.0 ng/mL with a high sensitivity down to 1.15 ng/mL. The method was utilized to determine nitrofurantoin in milk samples, and a good recovery range was obtained (97.5–103.1%; RSD ≤ 4.4%); the results were comparable to the reported method, demonstrating the method’s reliability. Finally, the method demonstrated good practicality using a recently developed assessment tool.

Priyankush Ghosh, Sambit Mishra, Shubham Dey et al.

The launch of the James Webb Space Telescope (JWST) has delivered high-quality atmospheric observations and expanded the known chemical inventory of exoplanetary atmospheres, opening new avenues for atmospheric chemistry modeling to interpret these data. Here, we present XODIAC, a fast, GPU-accelerated, one-dimensional photochemical model with a built-in equilibrium chemistry solver, an updated thermochemical database, and three chemical reaction networks. This framework enables comparative atmospheric chemistry studies, including the newly developed XODIAC-2025 network, a state-of-the-art C-H-O-N-P-S-Metals network, linking 594 species through 7,720 reactions. The other two are existing, publicly available C-H-O-N-S and C-H-O-N-S-Metals networks, from the established photochemical models VULCAN and ARGO, respectively, which are commonly used in the community. The XODIAC model has been rigorously benchmarked on the well-studied hot Jupiter HD 189733 b, with results compared against these two models. Benchmarking shows excellent agreement and demonstrates that, when the same chemical network and initial conditions are used, the numerical scheme for solving atmospheric chemistry does not significantly affect the results. We also revisited the atmospheric chemistry of HD 189733 b and performed a comparative analysis across the three networks. Sulfur chemistry shows the least variation across networks, carbon chemistry shows slightly more, and phosphorus chemistry varies the most, primarily due to the introduction of unique PHO and PN pathways comprising 390 reactions in the XODIAC-2025 network. These findings highlight XODIAC's capability to advance exoplanetary atmospheric chemistry and provide a robust framework for comparative exoplanetology.

Smik Patel, Praveen Jayakumar, Tzu-Ching Yen et al.

Quantum chemistry is among the most promising applications of quantum computing, offering the potential to solve complex electronic structure problems more efficiently than classical approaches. A critical component of any quantum algorithm is the measurement step, where the desired properties are extracted from a quantum computer. This review focuses on recent advancements in quantum measurement techniques tailored for quantum chemistry, particularly within the second quantized framework suitable for current and near-term quantum hardware. We provide a comprehensive overview of measurement strategies developed primarily for the Variational Quantum Eigensolver (VQE) and its derivatives. These strategies address the inherent challenges posed by complexity of the electronic Hamiltonian operator. Additionally, we examine methods for estimating excited states and one- and two-electron properties, extending the applicability of quantum algorithms to broader chemical phenomena. Key aspects of the review include approaches for constructing measurement operators with reduced classical preprocessing and quantum implementation costs, techniques to minimize the number of measurements required for a given accuracy, and error mitigation strategies that leverage symmetries and other properties of the measurement operators. Furthermore, we explore measurement schemes rooted in Quantum Phase Estimation (QPE), which are expected to become viable with the advent of fault-tolerant quantum computing. This review emphasizes foundational concepts and methodologies rather than numerical benchmarks, serving as a resource for researchers aiming to enhance the efficiency and accuracy of quantum measurements in quantum chemistry.

Sonia Kaushik, Manisha Priyadarsini, Avinash G. Khanderao et al.

Organic spintronics has drawn the interest of the science community due to various applications in spin-valve devices. But to date, an efficient room-temperature Organic Spin Valve device has not been experimentally realized due to the complicated spin transport at the metal-organic interfaces. These studies are always challenging due to the complicated spin-polarized charge transfer at the metal-organic interfaces. The present study focuses on a comprehensive understanding of the interfacial properties that are essential for advancing device performance and functionality. The Ferromagnetic metals and half-metallic electrodes such as Co, Co2FeAl, etc., and fullerene (C60) bilayer samples are prepared and studied via different structural and magnetic characterizations. Due to the mechanical softness of C60, deep penetration of ferromagnetic metal atoms is observed inside the C60 film. In-situ MOKE measurements reveal the origin of the 23 Å thick magnetic dead layer at the interface, which is attributed to the diffused ferromagnetic clusters exhibiting superparamagnetic behavior. In contrast to the inorganic substrates, magnetic anisotropy tends to develop at 40 Å thick Co film deposited on C60 which enhances with increasing thickness. The XRD measurements confirm the presence of in-plane compressive strain and texturing along the hcp (002) phase in the Co film. The anomaly observed in the hard axis of magnetization is due to high dispersion in the local magnetic anisotropy. The variation of the magnetic anisotropy axis is observed in the Co2FeAlwedge deposited in the proximity of C60. These findings provide valuable insights into the complex interplay between ferromagnetic materials and organic semiconductors offering potential avenues for tailoring magnetoresistance effects and fundamental understanding of organic spintronic devices.

Jong Min Oh, Yaren Nur Zenni, Zeynep Özdemir et al.

Monoamine oxidase inhibitors (MAOIs) have been crucial in the search for anti-neurodegenerative medications and continued to be a vital source of molecular and mechanistic diversity. Therefore, the search for selective MAOIs is one of the main areas of current drug development. To increase the effectiveness and safety of treating Parkinson’s disease, new scaffolds for reversible MAO-B inhibitors are being developed. A total of 24 pyridazinobenzylpiperidine derivatives were synthesized and evaluated for MAO. Most of the compounds showed a higher inhibition of MAO-B than of MAO-A. Compound <b>S5</b> most potently inhibited MAO-B with an IC₅₀ value of 0.203 μM, followed by <b>S16</b> (IC₅₀ = 0.979 μM). In contrast, all compounds showed weak MAO-A inhibition. Among them, <b>S15</b> most potently inhibited MAO-A with an IC₅₀ value of 3.691 μM, followed by <b>S5</b> (IC₅₀ = 3.857 μM). Compound <b>S5</b> had the highest selectivity index (SI) value of 19.04 for MAO-B compared with MAO-A. Compound <b>S5</b> (3-Cl) showed greater MAO-B inhibition than the other derivatives with substituents of -Cl > -OCH₃ > -F > -CN > -CH₃ > -Br at the 3-position. However, the 2- and 4-position showed low MAO-B inhibition, except <b>S16</b> (2-CN). In addition, compounds containing two or more substituents exhibited low MAO-B inhibition. In the kinetic study, the K_i values of <b>S5</b> and <b>S16</b> for MAO-B were 0.155 ± 0.050 and 0.721 ± 0.074 μM, respectively, with competitive reversible-type inhibition. Additionally, in the PAMPA, both lead compounds demonstrated blood–brain barrier penetration. Furthermore, stability was demonstrated by the 2V5Z-<b>S5</b> complex by pi–pi stacking with Tyr398 and Tyr326. These results suggest that <b>S5</b> and <b>S16</b> are potent, reversible, selective MAO-B inhibitors that can be used as potential agents for the treatment of neurological disorders.

Matthew Otten, Byeol Kang, Dmitry Fedorov et al.

As quantum hardware continues to improve, more and more application scientists have entered the field of quantum computing. However, even with the rapid improvements in the last few years, quantum devices, especially for quantum chemistry applications, still struggle to perform calculations that classical computers could not calculate. In lieu of being able to perform specific calculations, it is important have a systematic way of estimating the resources necessary to tackle specific problems. Standard arguments about computational complexity provide hope that quantum computers will be useful for problems in quantum chemistry but obscure the true impact of many algorithmic overheads. These overheads will ultimately determine the precise point when quantum computers will perform better than classical computers. We have developed QREChem to provide logical resource estimates for ground state energy estimation in quantum chemistry through a Trotter-based quantum phase estimation approach. QREChem provides resource estimates which include the specific overheads inherent to problems in quantum chemistry by including heuristic estimates of the number of Trotter steps and number of necessary ancilla, allowing for more accurate estimates of the total number of gates. We utilize QREChem to provide logical resource estimates for a variety of small molecules in various basis sets, obtaining estimates in the range of $10^7-10^{15}$ for total number of T gates. We also determine estimates for the FeMoco molecule and compare all estimates to other resource estimation tools.

Xiaoyu Fu, Da Cheng, Zhenwu Luo et al.

Abstract Background . Up to 20% of people with HIV (PWH) who undergo virologically suppressed antiretroviral therapy (ART) fail to experience complete immune restoration. We recently reported that plasma anti-CD4 IgG (antiCD4IgG) autoantibodies from immune non-responders specifically deplete CD4 + T cells via antibody-dependent cytotoxicity. However, the mechanism of antiCD4IgG production remains unclear. Methods . Blood samples were collected from 16 healthy individuals and 25 PWH on suppressive ART. IgG subclass, plasma lipopolysaccharide (LPS), and antiCD4IgG levels were measured by ELISA. Gene profiles in B cells were analyzed by microarray and quantitative PCR. Furthermore, a patient-derived antiCD4IgG–producing B cell line was generated and stimulated with LPS in vitro. B cell IgG class switch recombination (CSR) was evaluated in response to LPS in splenic B cells from C57/B6 mice in vitro. Results . Increased plasma anti-CD4 IgGs in PWH were predominantly IgG1 and associated with increased plasma LPS levels as well as B cell expression of TLR2, TLR4, and MyD88 mRNA in vivo. Furthermore, LPS stimulation induced antiCD4IgG production in the antiCD4IgG B cell line in vitro. Finally, LPS promoted CSR in vitro. Conclusion . Our findings suggest that persistent LPS translocation may promote anti-CD4 autoreactive B cell activation and antiCD4IgG production in PWH on ART, which may contribute to gradual CD4 + T cell depletion. This study suggests that reversing a compromised mucosal barrier could improve ART outcomes in PWH who fail to experience complete immune restoration.

Wenjun Zeng, Lulu Chen, Zhihui Xiao et al.

The molecular weight, the triple-helix conformation, the monosaccharide content, the manner of glycosidic linkages, and the polysaccharide conjugates of polysaccharides all affect bioactivity. The purpose of this study was to determine how different molecular weights affected the bioactivity of the <i>Lycium barbarum</i> polysaccharides (LBPs). By ethanol-graded precipitation and ultrafiltration membrane separation, one oligosaccharide (LBPs-1, 1.912 kDa) and two polysaccharides (LBPs-2, 7.481 kDa; LBPs-3, 46.239 kDa) were obtained from <i>Lycium barbarum</i>. While the major component of LBPs-1 and LBPs-2 was glucose, the main constituents of LBPs-3 were arabinose, galactose, and glucose. LBPs-2 and LBPs-3 exhibited triple-helix conformations, as evidenced by the Congo red experiment and AFM data. Sugar residues of LBPs-2 and LBPs-3 were elucidated by NMR spectra. The polysaccharides (LBPs-2 and LBPs-3) exhibited much higher antioxidant capacities than oligosaccharide (LBPs-1). LBPs-3 showed higher oxygen radical absorbance capacity (ORAC) and superoxide dismutase (SOD) activity than LBPs-2, but a lower capability for scavenging ABTS⁺ radicals. In zebrafish, LBPs-2 and LBPs-3 boosted the growth of T-lymphocytes and macrophages, enhanced the immunological response, and mitigated the immune damage generated by VTI. In addition to the molecular weight, the results indicated that the biological activities would be the consequence of various aspects, such as the monosaccharide composition ratio, the chemical composition, and the chemical reaction mechanism.

Nadia Martinez Naya, Jazmin Kelly, Giuliana Corna et al.

Cannabidiol (CBD) is the primary non-psychoactive chemical from Cannabis Sativa, a plant used for centuries for both recreational and medicinal purposes. CBD lacks the psychotropic effects of Δ9-tetrahydrocannabinol (Δ9-THC) and has shown great therapeutic potential. CBD exerts a wide spectrum of effects at a molecular, cellular, and organ level, affecting inflammation, oxidative damage, cell survival, pain, vasodilation, and excitability, among others, modifying many physiological and pathophysiological processes. There is evidence that CBD may be effective in treating several human disorders, like anxiety, chronic pain, psychiatric pathologies, cardiovascular diseases, and even cancer. Multiple cellular and pre-clinical studies using animal models of disease and several human trials have shown that CBD has an overall safe profile. In this review article, we summarize the pharmacokinetics data, the putative mechanisms of action of CBD, and the physiological effects reported in pre-clinical studies to give a comprehensive list of the findings and major effects attributed to this compound.

Aminat Mohammed Ahmed, Menbere Leul Mekonnen, Kebede Nigussie Mekonnen

Nutrient enrichment of the aquatic system promotes eutrophication, which degrades the aesthetic and economic value of water systems. On the other hand, the global supply of nutrients such as phosphate is dwindling. Hence, from the viewpoint of both eutrophication and sustainable use of nutrients, their removal and recovery from wastewater is critical. Among the various technologies practiced today, adsorption represents an economically feasible, and operationally simple technique. However, to utilize the potential of adsorption, finding effective adsorbents has been an ongoing research process preoccupying scientists. Among the various adsorbents, biopolymer nanocomposites (alginate, cellulose, chitosan, and lignin) showed promising potential. This is due to their abundance, non-toxicity, ease of modification, etc. Hence, in this review article, the utility of this class of adsorbents, particularly for nutrient removal and recovery, is addressed. Further, the various approaches to the modification of biopolymers, and their typical features for the simultaneous removal of nutrients are also discussed.

G. Esplugues, M. Rodríguez-Baras, D. San Andrés et al.

Within the project Evolution of Chemistry in the envelope of HOt corinoS (ECHOS), we present a study of sulphur chemistry in the envelope of the Class 0 source B335 through observations in the spectral range 7, 3, and 2 mm. We have modelled observations assuming LTE and LVG approximation. We have also used the code Nautilus to study the time evolution of sulphur species. We have detected 20 sulphur species with a total gas-phase S abundance similar to that found in the envelopes of other Class 0 objects, but with significant differences in the abundances between sulphur carbon chains and sulphur molecules containing oxygen and nitrogen. Our results highlight the nature of B335 as a source especially rich in sulphur carbon chains unlike other Class 0 sources. The low presence or absence of some molecules, such as SO and SO+, suggests a chemistry not particularly influenced by shocks. We, however, detect a large presence of HCS+ that, together with the low rotational temperatures obtained for all the S species (<15 K), reveals the moderate or low density of the envelope of B335. We also find that observations are better reproduced by models with a sulphur depletion factor of 10 with respect to the sulphur cosmic elemental abundance. The comparison between our model and observational results for B335 reveals an age of 10$^4$$<$t$<$10$^5$ yr, which highlights the particularly early evolutionary stage of this source. B335 presents a different chemistry compared to other young protostars that have formed in dense molecular clouds, which could be the result of accretion of surrounding material from the diffuse cloud onto the protostellar envelope of B335. In addition, the analysis of the SO2/C2S, SO/CS, and HCS+/CS ratios within a sample of prestellar cores and Class 0 objects show that they could be used as good chemical evolutionary indicators of the prestellar to protostellar transition.

Antoine Marie, Abdallah Ammar, Pierre-François Loos

We provide an in-depth examination of the $GW$ approximation of Green's function many-body perturbation theory by detailing both its theoretical and practical aspects in the realm of quantum chemistry. First, the quasiparticle context is introduced before delving into the derivation of Hedin's equations. From these, we explain how to derive the well-known $GW$ approximation of the self-energy. In a second time, we meticulously explain each step involved in a $GW$ calculation and what type of physical quantities can be computed. To illustrate its versatility, we consider two contrasting systems: the water molecule, a weakly correlated system, and the carbon dimer, a strongly correlated system. Each stage of the process is thoroughly detailed and explained alongside numerical results and illustrative plots. We hope that the contribution will facilitate the dissemination and democratization of Green's function-based formalisms within the computational and theoretical quantum chemistry community.

Alexey Potapov, Maria Elisabetta Palumbo, Zelia Dionnet et al.

The origin of organic compounds detected in meteorites and comets, some of which could serve as precursors of life on Earth, still remains an open question. The aim of the present study is to make one more step in revealing the nature and composition of organic materials of extraterrestrial particles by comparing infrared spectra of laboratory-made refractory organic residues to the spectra of cometary particles returned by the Stardust mission, interplanetary dust particles, and meteorites. Our results reinforce the idea of a pathway for the formation of refractory organics through energetic and thermal processing of molecular ices in the solar nebula. There is also the possibility that some of the organic material formed already in the parental molecular cloud before it entered the solar nebula. The majority of the IR "organic" bands of the studied extraterrestrial particles can be reproduced in the spectra of the laboratory organic residues. We confirm the detection of water, nitriles, hydrocarbons, and carbonates in extraterrestrial particles and link it to the formation location of the particles in the outer regions of the solar nebula. To clarify the genesis of the species, high-sensitivity observations in combination with laboratory measurements like those presented in this paper are needed. Thus, this study presents one more piece of the puzzle of the origin of water and organic compounds on Earth and motivation for future collaborative laboratory and observational projects.

Michele Pizzochero, Efthimios Kaxiras

Although the unconventional $π$-magnetism at the zigzag edges of graphene holds promise for a wide array of applications, whether and to what degree it plays a role in their chemistry remains poorly understood. Here, we investigate the addition of a hydrogen atom $-$ the simplest yet the most experimentally relevant adsorbate $-$ to zigzag graphene nanoribbons (ZGNRs). We show that the $π$-magnetism governs the chemistry of ZGNRs, giving rise to a site-dependent reactivity of the carbon atoms and driving the hydrogenation process to the nanoribbon edges. Conversely, the chemisorbed hydrogen atom governs the $π$-magnetism of ZGNRs, acting as a spin-$\frac{1}{2}$ paramagnetic center in the otherwise antiferromagnetic ground state and spin-polarizing the charge carriers at the band extrema. Our findings establish a comprehensive picture of the peculiar interplay between chemistry and magnetism that emerges at the zigzag edges of graphene.

Merve Yılmaz, Monireh Bakhshpour, Ilgım Göktürk et al.

The heterogeneity and metastatic features of cancer cells lead to a great number of casualties in the world. Additionally, its diagnosis as well as its treatment is highly expensive. Therefore, development of simple but effective diagnostic systems which detect the molecular markers of cancer is of great importance. The molecular changes on cancer cell membranes serve as targets, such as HER2/neu receptor which is detected on the surface of highly metastatic breast cancer cells. We have aimed to develop a specific and simple quartz crystal microbalance (QCM)-based system to identify HER2/neu expressing breast cancer cells via a receptor-specific monoclonal antibody. First, the QCM chip was coated with polymeric nanoparticles composed of hydroxyethylmethacrylate (HEMA) and ethylene glycol dimethacrylate (EDMA). The nanoparticle coated QCM chip was then functionalized by binding of HER2/neu antibody. The breast cancer cells with/without HER2/neu receptor expression, namely, SKBR3, MDA-MB 231 and also mouse fibroblasts were passed over the chip at a rate of 10–500 cells/mL and the mass changes (Δm) on cell/cm² unit surface of sensor were detected in real-time. The detection limit of the system was 10 cells/mL. Thus, this QCM-based HER2/neu receptor antibody functionalized system might be used effectively in the detection of HER2/neu expressing SKBR3 breast cancer cells.

Shoyang Gadis Supratania, Saepudin Rahmatullah, Neneng Windayani

Secondary metabolites are part of the discussion of Natural Product Organic Chemistry which demands a practicum process in lectures. This research aims to determine process skills through the application of inquiry-based worksheets on secondary metabolite analysis of three types of Indonesian medicinal plants. In the worksheet, there were several expected goals, including developing students' abilities in designing experiments, conducting experiments, and communicating both orally and in writing. The method used in this research was a One-Shot Case Study with 18 students taking Natural Product Organic Chemistry courses. The instruments used were learning descriptions, inquiry-based worksheets, observation sheets, assessment sheets (psychomotor, presentations, and reports). The results of the worksheet application showed that the students' ability obtain an average value of 84.15 with a very good category. The ability to design experiments, conduct experiments, and communicate orally and in writing obtained results of 77.16 (good categories), 92.50 (very good), and 82.80 (very good), respectively. This inquiry-based worksheet can be used in the study of Natural Product Organic Chemistry, especially in secondary metabolites.

Michael Ryan, Sarah Shandera, James Gurian et al.

Dark matter that is dissipative may cool sufficiently to form compact objects, including black holes. Determining the abundance and mass spectrum of those objects requires an accurate model of the chemistry relevant for the cooling of the dark matter gas. Here we introduce a chemistry tool for dark matter, DarkKROME, an extension of the KROME software package. DarkKROME is designed to include all atomic and molecular processes relevant for dark matter with two unequal-mass fundamental fermions, interacting via a massless-photon mediated $U(1)$ force. We use DarkKROME to perform one-zone collapse simulations and study the evolution of temperature-density phase diagrams for various dark-sector parameters.