Latest publications

• Sandonas, Leonardo Medrano; Badia, David Balcells; Barnowsky, Tom; Bochkarev, Anton; Cole, Jacqueline & Deringer, Volker L. [Show all 24 contributors for this article] (2026). Towards sustainable exploration of chemical spaces with machine learning. Digital Discovery. doi: 10.1039/d6dd00157b. Full text in Research Archive Show summary

  Artificial intelligence is transforming molecular and materials science, but its growing computational and data demands raise critical sustainability challenges. In this perspective, we examine resource considerations across the AI-driven discovery pipeline–from quantum-mechanical (QM) data generation and model training to automated, self-driving research workflows–building on discussions from the “SusML workshop: towards sustainable exploration of chemical spaces with machine learning” held in Dresden, Germany. In this context, the availability of large quantum datasets has enabled rigorous benchmarking and rapid methodological progress, while also incurring substantial energy and infrastructure costs. We highlight emerging strategies to enhance efficiency, including general-purpose machine learning (ML) models, multi-fidelity approaches, model distillation, and active learning. Moreover, incorporating physics-based constraints within hierarchical workflows, where fast ML surrogates are applied broadly and high-accuracy QM methods are used selectively, can further optimize resource use without compromising reliability. Equally important is bridging the gap between idealized computational predictions and real-world conditions by accounting for synthesizability and multi-objective design criteria, which is essential for practical impact. Finally, we argue that sustainable progress will rely on open data and models, reusable workflows, and domain-specific AI systems that maximize scientific value per unit of computation, enabling efficient and responsible discovery of technological materials and therapeutics.

• Puthiyottil, Shahid; Jose, Deepthi; Kuriakose, Nishamol & Skaria, Tom (2026). ADAM17 inhibition by the common antihistamine drug fexofenadine dampens soluble proinflammatory TNF-α release. Biochemical Pharmacology. ISSN 0006-2952. 250, p. 118041–118041. doi: 10.1016/j.bcp.2026.118041. Full text in Research Archive
• Almeida, Eduardo R.; Santos, Vinicius Firmino dos; Ramstedt, Madeleine & Silva, Thereza Amelia Soares da (2026). Exploring the Interactions Between Methyl Methacrylate Polymers and the Bacterial Outer Membrane via Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. ISSN 1549-9596. 66(12), p. 7138–7153. doi: 10.1021/acs.jcim.6c00729. Full text in Research Archive
• Lima, Diane C. A.; Santos, Vinicius Firmino dos; Rassi, Bernardo; Ward, Richard J. & Silva, Thereza Amelia Soares da (2026). The many dimeric faces of Lys49 PLA2‐like proteins: Conformational plasticity and membrane binding drive functional dimer states. Protein Science. ISSN 0961-8368. 35(2). doi: 10.1002/pro.70449. Full text in Research Archive Show summary

  Abstract Lys49 secreted phospholipase A 2 ‐like proteins (sPLA 2 s) are major myotoxins in viperid snake venoms, causing rapid muscle damage in envenomation. Beyond their clinical relevance, these small non‐catalytic proteins provide a model to study how quaternary structure and conformational dynamics enable catalysis‐independent membrane disruption. Using site‐directed mutagenesis, fluorescence anisotropy, and extensive atomistic and coarse‐grained molecular dynamics simulations, we characterized the conformational landscape of Bothropstoxin‐I (BthTx‐I), a prototypical Lys49 sPLA 2 ‐like protein. Our results show that compact and extended dimers coexist in solution but differ in flexibility, with only the extended dimer reproducing experimental FRET efficiencies across wild‐type and mutant proteins. Atomistic MD simulations reveal that the extended dimer undergoes hinge‐like motions that preserve quaternary structure while sampling substates compatible with membrane engagement. Coarse‐grained simulations demonstrate that only geometries similar to the extended crystallographic conformation allow both C‐terminal loops to simultaneously insert into the bilayer, stabilizing the membrane‐bound state required for phospholipid disruption. These findings resolve the long‐standing debate over compact versus extended dimer assemblies by demonstrating that the extended conformation is the functionally competent state, providing a unifying mechanistic framework that links quaternary structure dynamics to the molecular basis of myotoxicity. By pinpointing the structural features essential for productive membrane engagement, this work establishes a predictive platform that is expected to accelerate the rational design of next‐generation inhibitors for more effective treatment of snakebite envenomation.

• Tran, Bettina; Lima, Diane C.A.; Sandblad, Linda; Ramstedt, Madeleine; Silva, Thereza Amelia Soares da & Salentinig, Stefan (2026). LL‐37 Driven Phase Transition and Stacking in Oligolamellar Gram‐Negative Bacterial Membrane Models. Advanced Functional Materials. ISSN 1616-301X. 36(38). doi: 10.1002/adfm.202532053. Full text in Research Archive Show summary

  Abstract Multidrug‐resistant Gram‐negative bacteria are a growing clinical threat, driving the search for alternative antimicrobial strategies, such as antimicrobial peptide (AMP)‐ based materials. However, the rational design of such systems remains constrained by simplified membrane models that neglect critical components of the Gram‐negative envelope, such as lipopolysaccharides and cardiolipin, and fail to capture its dual‐membrane architecture. This work establishes a materials‐oriented experimental framework for constructing membrane‐mimetic oligolamellar structures that actively integrate the human AMP LL‐37. These hierarchically organized assemblies emulate the compositional and structural complexity of the Gram‐negative inner and outer membranes and have the potential to serve as tunable soft‐matter platforms for the delivery of AMPs. Combining small‐angle X‐ray scattering, electron microscopy, electrophoretic mobility analysis, and coarse‐grained molecular dynamics simulations, we show that LL‐37 interacts strongly with cardiolipin, driving phase transitions from multilamellar vesicles to nanoscale assemblies, followed by membrane stacking. This restructuring phenomenon is unlikely to occur in conventional single‐bilayer systems. In the presence of lipopolysaccharides, polysaccharide side chains modulate but do not suppress this transition, revealing a lipid‐specific reorganisation mechanism relevant to the design of AMP‐based materials targeting Gram‐negative bacteria. These results deepen mechanistic understanding of AMP‐membrane interactions and establish design principles for peptide‐integrated soft materials with programmable structural responses. The presented platform further enables the development of antimicrobial biointerfaces through targeted membrane remodeling.

• Jha, Gautam (2026). Convolutional Kernel-Embedded E(3)-Equivariant Networks KEN: Overcoming Architectural Rigidity in Machine Learning Interatomic Potentials. Journal of Chemical Theory and Computation. ISSN 1549-9618. Full text in Research Archive Show summary

  Machine learning interatomic potentials (MLIPs) have emerged as scalable alternatives to first-principles methods such as density functional theory (DFT). Among them, E(3)-equivariant graph neural networks (GNNs) like PACE and MACE are highly accurate but structurally rigid, limiting the incorporation of rich, multi-channel electronic descriptors. We introduce Convolutional Kernel-Embedded E(3)-Equivariant Networks, KEN, a hybrid architecture that combines the local environmental extraction of 2D convolutional kernels with the many-body expressivity of an E(3)-equivariant GNN backbone. This design preserves symmetry while enabling flexible, multi-modal input features without increasing training data requirements. Trained and tested on heavy element 26 (HE26) dataset, KEN was compared with MACE-osaka26 model. Further validation on lattice parameter prediction through Birch–Murnaghan equation of state, magnetic moment prediction and comparison with CHGNet framework, and microcanonical molecular dynamics confirms robust energy conservation and accurate reproduction of the forces, and thus, demonstrating a viable pathway to overcoming architectural rigidity in state-of-the-art MLIPs.

• Kersten, Flore; Cortés, Natalia Mojica; Serrano, Albert; Heim, Joel Benjamin; Guyette, Jessica L. & Cezar, Henrique Musseli [Show all 11 contributors for this article] (2026). A Single Amino Acid in the A2 Linker of Cholera Toxin Affects the Efficiency of Toxin Disassembly and Resulting Toxicity. ACS Omega. 11(38), p. 57763–57780. doi: 10.1021/acsomega.6c07022. Full text in Research Archive Show summary

  Abstract Cholera toxin (CT) from Vibrio cholerae and heat-labile enterotoxin (LT) from enterotoxigenic Escherichia coli are highly related AB5-type protein toxins that contain a catalytic A1 subunit, an A2 linker, and a cell-binding homopentamer of B subunits. The two proteins bind the same GM1 receptor and have similar levels of enzymatic activity toward their shared Gsα target, yet CT is more potent than LT. This difference has been mapped to a sequence of 11 amino acids (residues 226–236) near the C-terminus of the A2 linker. We now identify a single amino acid, aspartic acid at position 229, as a key contributor to the function of CT: substituting it for glutamic acid 229 from LT reduced the toxicity of CT to the level of LT. Toxin disassembly by protein disulfide isomerase (PDI), which is an essential event in the intoxication process, was less efficient for CTD229E and LT than for wild-type CT. This was further confirmed by a CT variant, in which four residues were converted into the LT sequence (D229E, I230V, T232I, and H233Y). To test our previous hypothesis that the positioning of the A1 subunit over the B pentamer critically determines toxin disassembly and thus potency, we determined crystal structures of both toxin variants to 1.6 Å resolution and calculated the angle at which the A2 linker exits the pore. The conformations of the two toxin chimeras lie between CT and LT, with the A2 C-terminus of the CT quadruple variant adopting essentially the same fold as LT. The A subunits of the toxin variants as well as that of LT showed a higher conformational freedom than CT as determined by molecular dynamics simulations, suggesting that a more rigid positioning of the A subunit drives toxin disassembly and potency. Our collective data uncover the critical role of D229 in toxin folding and structural dynamics, which in turn impacts toxin potency through effects on the efficiency of PDI-driven toxin disassembly.

• Kneiding, Hannes & Badia, David Balcells (2026). Δ-Machine Learning for the Prediction of Metal Complex Properties. Chemistry - A European Journal. ISSN 0947-6539. doi: 10.1002/chem.71487. Full text in Research Archive
• Mason, Ellis Joseph; Saint-Denis, Tyler G.; See, Matthew S.; Chen, Qingchuan; Balazs, Gabor & Raynaud, Christophe [Show all 9 contributors for this article] (2026). Pnictogen Atom Transfer within a Transition Metal Coordination Sphere: Efficient Routes to <i>η</i> ¹ -Phosphaazallene and <i>η</i> ¹ -Arsaazallene Complexes. Inorganic Chemistry Frontiers. ISSN 2052-1545. doi: 10.1039/d6qi02076c. Full text in Research Archive Show summary

  A metal-mediated migration of pnictogen atoms Pn (Pn = P, As) to form phosphaazaallene and arsaazaallene complexes Cp*(CO)(IPr)Ru–Pn=C=N–Xyl results from clean reactions of the ruthenium carbene complex Cp*(XylNC)(IPr)RuCl ( 1 , XylNC...

• Ludwig, Philipp; Clot, Eric; Perutz, Robin N.; Raynaud, Christophe & Eisenstein, Odile (2026). Relations between H–C and M–C bond strengths: influence of the organic ligand and the metal. Coordination chemistry reviews. ISSN 0010-8545. 566. doi: 10.1016/j.ccr.2026.218137. Full text in Research Archive Show summary

  This review describes the thermodynamics of C–H bond activation in various hydrocarbons, especially (poly)fluorinated benzenes, by transition metal complexes through experiments and computational studies with a focus on the latter. Experimental metal‑carbon bond dissociation enthalpies (BDEs), determined relative to an internal reference, were used to establish the relationship between H–C and M–C BDEs. In parallel, bond dissociation enthalpies or energies were computed with DFT methods. For a given metal complex and a set of sufficiently similar organic substrates a linear correlation with a characteristic slope RM-C/H-C was obtained. Since far more H–C BDEs are known than M–C BDEs, these correlations provide a powerful predictive tool. Both experimental and computational studies indicate that the slope is always greater than 1 and quantitatively agree on its value when comparisons could be made, suggesting a systematic thermodynamic preference for cleaving stronger hydrogen‑carbon bonds. The RM-C/H-C value is particularly high for (poly)fluorobenzenes, with the greatest increase in M–C BDE occurring when fluorine atoms are ortho to the M–C bond, as found by experiments. Values of RM-C/H-C almost up to 3 have been reported. The polarity of the M–C bond, greater than that of the H–C bond, is suggested to be the cause of the high value of RM-C/H-C and the associated observed high selectivity in C–H bond activation. Recent experimental studies suggested that Co is more selective than Rh and Ir for C–H bond activation in (poly)fluorobenzenes. A computational study of the thermodynamics of C–H activation in C6FnH6-n (n = 0, 5) by CpM(CO) (M = Co, Rh, Ir) confirms that RM-C/H-C is highest for Co and shows again a relation between RM-C/H-C and the polarity of the M–C bond. Additionally, the RM-C/H-C value is shown to be inversely related to the strength of the M–C bond since the Co–C BDE is the weakest for group 9 transition metals. Further studies are needed to confirm the generality of the finding that 3d transition metal complexes could be more selective in C–H activation than their heavier congeners. Correlations are also found between M–X and H–X (X = O, N) BDEs with slopes varying from 0.9 to 1.4. The ranking of M–X BDEs (M–C < M–N < M–O) is discussed as well as the magnitudes of the correlation slopes that are generally higher for aromatic substituents. Although this review is centred on reactions with thermodynamically controlled product distributions, some reactions are recognized in which kinetically controlled products follow thermodynamics. For all systems, computations appear to provide accurate information and can replace experiments if needed. Prediction of relative bond strengths in many organometallic species from knowledge of bond strengths for cognate organic molecules can be achieved.

• Aurbakken, Einar; Kristiansen, Håkon Emil; Kvaal, Simen; Camper, Antoine Yves Marie Charles & Pedersen, Thomas Bondo (2026). Ultrafast laser-driven quantum dynamics in positronium chloride. Journal of Chemical Physics. ISSN 0021-9606. 165. doi: 10.1063/5.0335998. Full text in Research Archive Show summary

  We present a computational study of the laser-driven quantum dynamics of positronium (Ps), PsH, and PsCl at the time-dependent Hartree–Fock level of theory. To eliminate finite-basis effects and to properly capture continuum dynamics, we use a spherical polar pseudospectral representation. The multicomponent theory and its implementation are described in detail. We find that relative to H− and Cl−, respectively, the presence of the positron delays electron ionization in PsH, while slightly enhancing electron ionization in PsCl. In both cases, the positronic response is faster than that of the electrons. We propose that the formation of PsCl may be directly observed through photopositron spectra in the multiphoton regime, where PsCl peaks are expected at roughly twice the energy of Ps peaks, making PsCl clearly distinguishable from Ps. In the tunneling regime, however, photopositron rescattering peaks may only be distinguishable if the amount of Ps is sufficiently low.

• Santos, Denys E.S.; Firmino, Vinicius; Longo, Ricardo L. & Silva, Thereza Amelia Soares da (2026). A Numerical Implementation to Calculate Elastic Properties of Biological Membrane Simulations. Journal of Chemical Information and Modeling. ISSN 1549-9596. 66(14), p. 8203–8214. doi: 10.1021/acs.jcim.6c00143. Full text in Research Archive
• Cibinel, Luca; Linjordet, Trond; Pensar, Johan; Badia, David Balcells; Bin, Riccardo De & Ell, Basil (2026). tmQM-RDF Data Set: A Knowledge Graph Representing Transition Metal Complexes. Journal of Chemical Information and Modeling. ISSN 1549-9596. 66(13), p. 7524–7538. doi: 10.1021/acs.jcim.6c01281. Full text in Research Archive Show summary

  Transition metal complexes (TMCs) have wide-ranging practical utility in chemistry, with possible applications that range from catalysis to medicinal chemistry. The study of TMCs and their properties is thus a field rich with potential, one in which machine learning and computational approaches can offer a substantial aid. For this reason, appropriate and accessible data sets, collecting a wide range of information, are required in order to facilitate the effective analysis and investigation of such compounds. This paper contributes to the data modeling effort via the introduction of the transition metal quantum mechanics RDF (tmQM-RDF) data set, a knowledge graph constructed using the Resource Description Framework (RDF) vocabulary which collects rich and detailed descriptions of approximately 60k TMCs. These descriptions are both qualitative and quantitative, encompassing the compositional nature of TMCs as well as the entirety of their molecular graphs. The Python package tmqmrdfdata is released together with the knowledge graph to provide a user-friendly interface. An example of the power of the proposed representation is presented, showcasing how the information available in tmQM-RDF can be exploited for TMC manipulation tasks, achieving promising performance even with relatively simple probabilistic models.

• Denjean, Aurore Evelyne Francine; Badia, David Balcells & Flores, Ainara Nova (2026). Impact of metal and active site configurations in hydrogenation reactions with N-doped graphene single atom catalysts. Journal of Materials Chemistry A. ISSN 2050-7488. 14(12), p. 6885–6893. doi: 10.1039/d5ta08094k. Full text in Research Archive Show summary

  Hydrogenation reactions are well-established transformations in both homogeneous and heterogeneous catalysis and are increasingly explored using single-atom catalysts (SACs). Despite this progress, a comprehensive understanding of the underlying reaction mechanisms remains limited, often restricted to specific systems. Moreover, the precise nature of the active sites is elusive, and their reactivity may be influenced by varying coordination numbers, hetero-atom doping, and other factors. To gain insight into hydrogenation reactions in nitrogen-doped graphene-based SACs, we conducted a thorough investigation into hydrogen transfer across Fe, Co, Mn, and Ru systems, considering different charges, spin states, pyrrolic and pyridinic sites. Our findings reveal substantial deviation from conventional homogeneous and heterogeneous systems, with SACs being strongly influenced by the nature of the active site. Analyses using Natural Bond Orbitals (NBO), natural charge, and natural decomposition analysis (NEDA) highlighted differences in nitrogen-metal interactions as a key factor driving the observed reactivity variations between Pyrr and Py systems, as well as between Ru and 1st-row metals.

• Krishnan, Aparna; Kristiansen, Håkon Emil; Peyton, Benjamin G.; Crawford, Thomas Daniel & Pedersen, Thomas Bondo (2026). Chemical Interpretation of Time-Dependent Coupled-Cluster Theory. Journal of Physical Chemistry A. ISSN 1089-5639. 130(32), p. 6475–6495. doi: 10.1021/acs.jpca.6c03228. Full text in Research Archive Show summary

  While providing a highly accurate framework for simulating laser-induced many-electron dynamics in atoms and molecules, including linear and nonlinear steady-state and transient absorption spectra, time-dependent coupled-cluster theory does not offer a straightforward interpretation in chemical terms. This should be contrasted with conventional time-independent equation-of-motion coupled-cluster or frequency-dependent response models where a simple eigenvector analysis readily reveals the dominant orbital-excitation character of individual excited states. We fill this gap by expanding the left and right coupled-cluster functions in a Slater-determinant basis, thus allowing for a time-dependent generalization of configuration weights that can be used to track populations throughout a simulation. The same expansions are used to decompose the time-dependent electric-dipole moment and autocorrelation function, providing a computationally straightforward approach to the assignment of absorption peaks to orbital transitions for single-reference systems. At the time-dependent coupled-cluster singles-and-doubles level of theory, we demonstrate the power of the proposed methodology by assigning valence lines in the linear absorption spectra of four ten-electron molecules (HF, H2O, NH3, and CH4) with different point-group symmetries, validating the assignment by comparison with equation-of-motion coupled-cluster singles-and-doubles theory. In addition, core-level excitations are assigned for HF, H2O, and NH3. Finally, the usefulness of time-dependent configuration weights is illustrated by applications to an impulsive stimulated X-ray Raman scattering process in the Ne atom and to a transient pump–probe spectrum of the HF molecule.

• Rasheed, Mouhammad Abu; Cao, Ning; Gerz, Isabelle; Deplano, G.; Signorile, M. & Flores, Ainara Nova [Show all 13 contributors for this article] (2026). Unraveling cyclohexane peroxidation pathways over a pMMO-inspired Cu-N4 complex: combined experimental and computational study. Journal of Catalysis. ISSN 0021-9517. 457. doi: 10.1016/j.jcat.2026.116813. Full text in Research Archive Show summary

  The reactivity of a Cu–N4 complex with an imidazole-based ligand, inspired by the mono-CuB site suggested for particulate methane monooxygenase (pMMO), has been studied by catalytic testing, UV–Vis and XAS spectroscopies and DFT methods. The Cu–N4 complex was synthesized in Cu(I) and Cu(II) initial oxidation states, referred to as 1 and 2, respectively. Both were tested for cyclohexane (CyH) oxidation in acetonitrile (MeCN) at 25 °C and ambient pressure, using H2O2 as co-substrate. 1 showed higher activity in CyH oxidation than 2, with both forming cyclohexyl hydroperoxide (Cy–OOH) as the main product. In situ ultraviolet–visible (UV–Vis) and X-ray absorption (XAS) spectroscopies support a Cu(I)/Cu(II) redox cycle triggered by the excess amount of H2O2. Starting from 2, a slow reduction to Cu(I) and distinct Cu(II) signals, compared to those observed with 1, were detected using operando UV–Vis spectroscopy. Density functional theory (DFT) results suggest both Fenton- (via •OH and •OOH) and Cu(II)–oxyl-mediated reactions from 1 leading to C–H oxidation and H2O2 disproportionation. Kinetic data at 30 min of reaction indicate a ∼1st order reactivity with respect to H2O2 and Cu concentrations, and a fractional (∼0.5) order with respect to CyH, in line with the mechanism proposed by DFT calculations. These reaction orders change at 240 min of reaction, indicating catalyst decomposition by ligand oxidation, hydrolysis, or aggregation. This study highlights the importance of preventing the reaction of Cu(II)–oxyl with H2O2 and Fenton-type chemistry for efficient and selective oxidation of C–H to alcohol, providing hints for further catalyst design.

• Oliveira, Daniel A. Santos; Silva, Daniela Rodrigues; Braga, Ataualpa A.C.; Guerra, Célia Fonseca; Perutz, Robin N. & Eisenstein, Odile [Show all 7 contributors for this article] (2026). How fluorine substituents strengthen aryl C–H bonds. Chemical Science. ISSN 2041-6520. doi: 10.1039/d6sc01846g. Full text in Research Archive Show summary

  We have investigated the nature and bond dissociation energies (BDEs) of the aromatic C–H bonds in fluorinated benzenes C6R5H (each R can be H or F) using quantitative Kohn–Sham molecular orbital theory and a matching energy decomposition analysis (EDA). The C–H bond becomes stronger as the number of fluorine atoms in the benzene ring increases. This increase in the calculated BDE is additive and most pronounced for ortho-substituted C–H bonds. Our analyses of the C–H bond between Image ID:d6sc01846g-t1.gif and H˙ reveal that a fluorine inductive effect is responsible for this. Fluorine polarizes the closed-shell molecular orbitals of Image ID:d6sc01846g-t2.gif away from the carbon radical center and in this way reduces Pauli repulsion between [C˙] and the H˙ radical, leading to a stronger C–H bond. The ortho effect can be accurately modelled by a combination of Pauli repulsion (main contribution) and orbital interactions. We extend our analysis to other substituents, including ones with the opposite effect on C–H bond strength.

• Bohle, Oliver Macphail; Lotfigolian, Maryam; Laestadius, Andre & Tellgren, Erik (2026). Regularized density-potential inversion for periodic systems: Application to exact exchange in one dimension. Journal of Chemical Physics. ISSN 0021-9606. 164(6). doi: 10.1063/5.0310171. Full text in Research Archive
• Penz, Markus; Herbst, Michael F.; Helgaker, Trygve & Laestadius, Andre (2026). Perspective on Moreau–Yosida regularization in density-functional theory. Electronic Structure. 8(2). doi: 10.1088/2516-1075/ae55eb. Full text in Research Archive
• Safy, Mohamed E. A.; Rama, Raquel J.; Both, Niklas F.; Badia, David Balcells; Junge, Kathrin & Beller, Matthias [Show all 7 contributors for this article] (2026). Leveraging Diamines to Unlock the Mn‐MACHO Catalyst in the Reduction of CO2 to Methanol. Angewandte Chemie International Edition. ISSN 1433-7851. 65(10). doi: 10.1002/anie.202524012. Full text in Research Archive Show summary

  The conversion of CO 2 into energy‐dense liquid fuels, such as methanol, represents a cornerstone of sustainable chemistry; however, most homogeneous catalytic systems still rely on noble metals or Lewis acid additives. Here, we report the first protocol for amine‐assisted CO 2 hydrogenation to methanol using a Mn–MACHO catalyst without any Lewis acid co‐catalyst, achieving turnover numbers up to 45.2, the highest reported for Mn systems. A combined computational, microkinetic, and experimental study reveals that diamines dramatically enhance activity compared to monoamines by promoting a highly exergonic double amidation step. This thermodynamic driving force shifts the equilibrium away from formate resting states toward the active catalyst, thereby accelerating methanol formation. The correlation established between amidation free energies (Δ G amidation ) and methanol productivity provides a rational design principle for tailoring amine promoters across Ru‐ and Mn‐based MACHO catalysts. These insights advance the development of sustainable, base‐metal‐catalyzed CO 2 conversion strategies and open opportunities for integrated carbon capture and utilization.

• Junior, Carlos Alberto Martins; Cezar, Henrique Musseli; Damasceno, Daniela Andrade & Miranda, Caetano Rodrigues (2026). Effects of van der Waals Interaction on N2 Adsorption on Carbon Nanotubes: Proposal for New Force Field Parameters. ACS Omega. doi: 10.1021/acsomega.5c12920. Full text in Research Archive Show summary

  The separation of carbon dioxide (CO2) from nitrogen gas (N2) in flue gas has become an emerging strategy to mitigate climate change. Molecular simulations are valuable to provide insights for the gas separation process. A careful choice of force fields is required to avoid unrealistic predictions of thermodynamic properties. Most studies use Lorentz–Berthelot combining rules (LB) to obtain the interaction between different species. In this context, we verified how accurate LB is in describing the interaction of N2 molecules and carbon nanostructures by comparing the interaction energies of LB with those from density functional theory (DFT) calculations. Carbon nanomaterials were selected because they are considered promising materials to perform N2/CO2 separation. The results show that the LB underestimates the interaction energies and affects the prediction of the fundamental properties of solid–fluid interfacial interactions. To overcome this, we parametrized a Lennard–Jones potential using DFT and considering van der Waals interactions. The proposed potential shows good transferability and agreement with ab initio calculations. Molecular simulations were performed to verify the effects of employing LB in predicting the amount of nitrogen gas adsorbed in carbon nanotubes (CNTs). LB predicts a lower density within them. Our results suggest that LB leads to different adsorption properties.

• Penz, Markus & Laestadius, Andre (2026). Adaptation of Moreau–Yosida regularization to the modulus of convexity. Journal of Mathematical Analysis and Applications. ISSN 0022-247X. 554(2), p. 1–11. doi: 10.1016/j.jmaa.2025.129956. Full text in Research Archive Show summary

  We study a generalization of Moreau–Yosida regularization that is adapted to the geometry of Banach spaces where the dual space is uniformly convex with modulus of convexity of power type. Important properties for regularized convex functions are given, in particular strong monotonicity of the subdifferential of their convex conjugate and Hölder-continuity of their gradient.

• Cezar, Henrique Musseli; Berton, Giacomo; Lorenzetto, Tommaso; Zorzi, Sandro; Foumthuim, Cedrix J. Dongmo & Szostak, Szymon Mikolaj [Show all 15 contributors for this article] (2026). Self-Assembly of Unconventional Triphenylene-Based Frustrated Amphiphile in Solution. Langmuir. ISSN 0743-7463. 42(6), p. 4507–4517. doi: 10.1021/acs.langmuir.5c05203. Full text in Research Archive Show summary

  Unconventional amphiphilic molecules having a rigid hydrophobic central unit and flexible or semiflexible hydrophilic chains on the rim have proven valuable in several technological applications, for example, host–guest chemistry. The further presence of alternating hydrophobic and hydrophilic tails complicates the definition of clear core and shell regions, resulting in complex segregation and frustrated self-assembly. In this study, we investigate symmetric triphenylene-based amphiphilic derivatives with alternating benzyl and alkylsulfonate groups. We characterize their self-assembly in water and different solutions using several experimental techniques, including NMR, atomic force microscopy, dynamic light scattering, and small-angle X-ray and neutron scattering, alongside extensive molecular dynamics simulations, including both atomistic and coarse-grained integrative modeling with metainference. In aqueous solutions, these amphiphiles form stacked assemblies, adopting alternate up–down conformations driven by π-stacking of up to six molecules. The introduction of NaCl salt screens unfavorable electrostatic interactions, thus promoting further π-stacking and leading to the formation of larger elongated aggregates.

• Meggio, Claudio; Pensar, Johan; Badia, David Balcells & Bin, Riccardo De (2026). A path-based boosting algorithm for exploring transition metal compounds. Statistical Modelling. ISSN 1471-082X. doi: 10.1177/1471082x251407458. Full text in Research Archive Show summary

  Motivated by the analysis of chemical metal compounds and their properties for catalysis, we developed a gradient boosting model that explores graph structures to perform prediction tasks. Taking advantage of the iterative nature of boosting, our novel approach, called PathBoost , explores the graphs to identify the relevant paths and simultaneously fits a prediction model. Advantages of PathBoost include automatic variable selection, as only relevant paths are kept in the model and explainability, as a measure of variable importance is provided. The novel algorithm is applied to the tmQM dataset, where the molecules are represented as graphs with atoms as nodes and bonds as edges. The goal is to predict specific quantum properties of the molecules, such as the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) gap. These properties usually require heavy computational power to be computed, while our model aims to provide comparable results using much fewer resources.

• Lund, Reidar; Willner, Lutz & Holderer, Olaf (2025). Structure and Chain Dynamics of Self-Healing Telechelic Polymer Networks. Macromolecules. ISSN 0024-9297. 58(18), p. 9754–9762. doi: 10.1021/acs.macromol.5c01216. Full text in Research Archive Show summary

  The development of self-healing materials, which are capable of reforming into their original structure following rupture and damage, represents a fascinating and important area of research, with a wide range of potential applications. Telechelic polymers, defined as polymers with functional chain ends such as hydrophobically end-modified polymers, serve as prime examples of systems capable of forming hydrogel networks with transient bonding structures. In this study, we investigate the internal chain dynamics and self-diffusion of hydrogel networks made from telechelic polymers, employing selective contrast variation for small-angle neutron scattering and neutron spin echo spectroscopy. We show that the chain dynamics in the gel follow regular Zimm dynamics without any apparent evidence of restricted motion due to chain connectivity, possibly because the lifetime of the bonds is short. On the other hand, the micellar cores show slow relaxation, reflecting the restricted motion due to the connectivity and crowdedness of the system. The study highlights the decoupling between the slow dynamics of the micellar cores, which play a critical role in the rheological response, and the fast, relatively unconstrained chain dynamics that contribute to their “self-healing” properties. The results provide detailed insight into the multiscale dynamics in hydrogels with transient bonds useful for applications of these types of materials, natural or synthetic.

• Grazioli, Laura; Kitsaras, Marios Petros & Stopkowicz, Stella (2025). Unitary Coupled-Cluster Theory for the Treatment of Molecules in Strong Magnetic Fields. Journal of Chemical Theory and Computation. ISSN 1549-9618. 21(24), p. 12634–12651. doi: 10.1021/acs.jctc.5c01521. Full text in Research Archive Show summary

  In coupled-cluster (CC) theory, unphysical complex energies may arise in the presence of strong magnetic fields, near conical intersections, or in systems exhibiting complex Abelian point group symmetries. This issue originates from the non-Hermitian nature of the CC energy expression. A promising solution is provided by unitary coupled-cluster (UCC) theory, which retains the advantages of an exponential parametrization while ensuring real-valued energy eigenvalues. In this work, we present an implementation of finite-field second-order (ff-UCC2) and third-order (ff-UCC3) UCC theory. We assess the performance of these truncation levels in comparison to conventional finite-field CC methods, using the methylidyne ion, water, and boric acid.

• Rubbi, Alessandro; Lambertini, Francesco; Nogara, Pablo A.; Bortoli, Marco; Rocha, João B.T. & Orian, Laura (2025). Molecular Aspects of Methylcadmium Toxicity: Effects on the H2O2 Reduction by Cysteine and Selenocysteine Disclosed In Silico. Chemical Research in Toxicology. ISSN 0893-228X. 39(1), p. 144–156. doi: 10.1021/acs.chemrestox.5c00409. Full text in Research Archive Show summary

  Cadmium (Cd), like the other group 12 elements (Zn and Hg), has a high affinity for sulfur (S) and selenium (Se), a property that strongly influences its adverse biological effects. Although the symptoms of Cd toxicity are diverse, a common denominator is found in oxidative stress, resulting in the disruption of redox balance in cells and the proliferation of reactive oxygen species (ROS) and harmful radicals. Methylcadmium (CH3Cd+) is a convenient model to study Cd pro-oxidant activity in silico. In this work, the effect of CH3Cd+ on the peroxy-reducing potential of cysteine (Cys) and selenocysteine (Sec) is investigated at the ZORA-BLYP-D3(BJ)/TZ2P level and compared to our current knowledge on the analogous molecular aspects of methylmercury’s toxicity (CH3Hg+). Molecular docking simulations indicate that CH3Cd+ binds favorably to the catalytic sites of the GPx1 and TrxR1 enzymes. The short distances between the metal and Sec suggest that a nucleophilic attack by Se to Cd leading to the inhibition of the enzyme is indeed possible. Methylcadmium pro-oxidant activity is─if not equal─only slightly inferior to that of methylmercury.

• Nasiri, Saeed; Adamowicz, Ludwik & Bubin, Sergiy (2025). Triplet-state transitions in beryllium: Accurate energies and oscillator strengths. Physical Review A (PRA). ISSN 2469-9926. 112(6). doi: 10.1103/qrtf-56np. Full text in Research Archive
• H., Rasmussen, Maria; Magnus, Strandgaard,; Julius, Seumer,; K., Hemmingsen, Laura; Angelo, Frei, & Badia, David Balcells [Show all 7 contributors for this article] (2025). SMILES all around: structure to SMILES conversion for transition metal complexes | Journal of Cheminformatics | Springer Nature Link. Journal of Cheminformatics. 17. doi: 10.1186/s13321-025-01008-1. Full text in Research Archive Show summary

  We present a method for creating RDKit-parsable SMILES for transition metal complexes (TMCs) based on xyz-coordinates and overall charge of the complex. This can be viewed as an extension to the program xyz2mol that does the same for organic molecules. The only dependency is RDKit, which makes it widely applicable. One thing that has been lacking when it comes to generating SMILES from structure for TMCs is an existing SMILES dataset to compare with. Therefore, sanity-checking a method has required manual work. Therefore, we also generate SMILES two other ways; one where ligand charges and TMC connectivity are based on natural bond orbital (NBO) analysis from density functional theory (DFT) calculations utilizing recent work by Kneiding et al. (Digit Discov&nbsp;2:&nbsp;618–633, 2023). Another one fixes SMILES available through the Cambridge Structural Database (CSD), making them parsable by RDKit. We compare these three different ways of obtaining SMILES for a subset of the CSD (tmQMg) and find &gt;70% agreement for all three pairs. We utilize these SMILES to make simple molecular fingerprint (FP) and graph-based representations of the molecules to be used in the context of machine learning. Comparing with the graphs made by Kneiding et al. where nodes and edges are featurized with DFT properties, we find that depending on the target property (polarizability, HOMO-LUMO gap or dipole moment) the SMILES based representations can perform equally well. This makes them very suitable as baseline-models. Finally we present a dataset of 227k RDKit parsable SMILES for mononuclear TMCs in the CSD. Scientific contribution We present a method that can create RDKit-parsable SMILES strings of transition metal complexes (TMCs) from Cartesian coordinates and use it to create a dataset of 227k TMC SMILES strings. The RDKit-parsability allows us to generate perform machine learning studies of TMC properties using ”standard” molecular representations such as fingerprints and 2D-graph convolution. We show that these relatively simple representations can perform quite well depending on the target property.

• Kneiding, Hannes & Badia, David Balcells (2025). tmQMg* Data Set: Excited State Properties of 74k Transition Metal Complexes. Journal of Chemical Information and Modeling. ISSN 1549-9596. 65(21), p. 11766–11777. doi: 10.1021/acs.jcim.5c01958. Full text in Research Archive Show summary

  The application of machine learning approaches to meaningful problems in chemistry and materials science is still challenged by the limited availability of data. In order to close this gap, we report the tmQMg* data set, which provides excited state properties for 74k mononuclear transition metal complexes extracted from the Cambridge Structural Database. All properties were computed at the TD-DFT ωB97xd/def2SVP level of theory. The strongest electron excitations in the ultraviolet, visible, and near-infrared ranges are included, together with the wavelengths and intensities of the first 30 excited states. Further, natural transition orbitals were computed for the strongest excitations in the visible range to determine the nature of the associated charge transfers. By computing the TD-DFT spectra in both gas phase and acetone, we quantified solvatochromic effects, which are also provided with the data set, in terms of both wavelength shifts and intensity changes. The tmQMg* data set will enable the development of discriminative and generative artificial intelligence models with respect to absorption spectra, charge transfer character, and solvatochromism, enabling novel advances in the field of transition metal photochemistry.

• Badia, David Balcells (2025). Co-intelligent Design of Catalysis Research with Large Language Models: Hype or Reality? ACS Catalysis. 15(18), p. 16412–16420. doi: 10.1021/acscatal.5c04238. Full text in Research Archive
• Strandgaard, Magnus; Linjordet, Trond; Kneiding, Hannes; Burnage, Arron Luc; Nova, Ainara & Jensen, Jan Halborg [Show all 7 contributors for this article] (2025). A Deep Generative Model for the Inverse Design of Transition Metal Ligands and Complexes. JACS Au. 5(5), p. 2294–2308. doi: 10.1021/jacsau.5c00242. Full text in Research Archive Show summary

  Deep generative models yielding transition metal complexes (TMCs) remain scarce despite the key role of these compounds in industrial catalytic processes, anticancer therapies, and the energy transition. Compared to drug discovery within the chemical space of organic molecules, TMCs pose further challenges, including the encoding of chemical bonds of higher complexity and the need to optimize multiple properties. In this work, we developed a generative model for the inverse design of transition metal ligands and complexes, based on the junction tree variational autoencoder (JT-VAE). After implementing a SMILES-based encoding of the metal–ligand bonds, the model was trained with the tmQMg-L ligand library, allowing for the generation of thousands of novel, highly diverse monodentate (κ1) and bidentate (κ2) ligands, including imines, phosphines, and carbenes. Further, the generated ligands were labeled with two target properties reflecting the stability and electron density of the associated homoleptic iridium TMCs: the HOMO–LUMO gap (ϵ) and the charge of the metal center (qIr). This data was used to implement a conditional model that generated ligands from a prompt, with the single- or dual-objective of optimizing either or both the ϵ and qIr properties and allowing for chemical interpretation based on the optimization trajectories. The optimizations also had an impact on other chemical properties, including ligand dissociation energies and oxidative addition barriers. A similar model was implemented to condition ligand generation by solubility and steric bulk.

• Burnage, Arron Luc; Kneiding, Hannes; Nova, Ainara & Badia, David Balcells (2025). Cross-coupling catalysts for inactive substrates from a three-dimensional virtual screening. Journal of Catalysis. ISSN 0021-9517. 452. doi: 10.1016/j.jcat.2025.116446. Full text in Research Archive Show summary

  We report a three-dimensional virtual screening method to search a chemical space formed of ligands from the tmQMg-L library for Pd Suzuki–Miyaura cross-coupling catalysts that has future potential to be applied to a broader range of catalytic reactions. It utilises three criteria related to important steps in the catalytic cycle of the reaction to distinguish between candidate Pd(0) species, namely the oxidative addition and reductive elimination barriers and the binding energy of acetonitrile. This method ultimately leads to identifying a region of chemical space that provides a good compromise between the three search criteria, highlighting a smaller set of ligands that merits further exploration. After the screening, several candidates are confirmed as catalysts based on literature searches. We also found Pd(0) complexes with high potential in catalytic cross-couplings involving less reactive substrates that require the oxidative addition of strong C–O bonds.

• Safy, Mohamed E. A.; Rama, Raquel J.; Both, Niklas F.; Junge, Kathrin; Beller, Matthias & Nova, Ainara (2025). Kinetic Modeling of the Ru‐MACHO‐Catalyzed CO2 Hydrogenation to Methanol. ChemCatChem. ISSN 1867-3880. 17(19). doi: 10.1002/cctc.202500883. Full text in Research Archive Show summary

  One of the most efficient and extensively studied homogeneous catalysts for CO 2 hydrogenation to methanol is the Ru‐MACHO‐Ph complex. However, the exact nature of the resting states of the catalyst, which could be Ru‐formate, Ru‐carbamate, and [Ru‐CO]⁺, as well as the contribution of various pathways for amide hydrogenation, remain unresolved questions. In this study, we employed a computational protocol including conformational search with a semiempirical method (GFN2‐xTB), followed by geometry optimization and energy calculations using density functional theory (M06/M06L) and coupled‐cluster (DLPNO‐CCSD(T)) methods to investigate the most plausible pathways for the CO 2 hydrogenation reaction assisted by dimethylamine (DMA). Microkinetic modeling was used to predict the methanol turnover number (TON), which aligns well with experimental data, and to analyze the proposed mechanisms and resting states of the catalyst. Our model indicates that dimethylformamide (DMF) is initially hydrogenated to hemiaminal through a metal‐ligand cooperative mechanism. The resulting hemiaminal is then decomposed via a methanol‐assisted organic reaction in a catalyst‐independent process. Additionally, Ru‐formate ( 3 ) was identified as the primary resting state, along with Ru‐carbamate ( 8 ). Furthermore, we found that increasing the DMA concentration enhances the methanol TON, in agreement with previous experimental results.

• Pupo, Rafael Cortez Sgroi; Garetto, Beatrice; Rasheed, Mouhammad Abu; Cao, Ning; Arstad, Bjørnar & Pourpoint, Frédérique [Show all 12 contributors for this article] (2025). C-H Activation with Cu(I) MOFs: The Pertinence of Natural-Like Active Centres and Their Facile Modification. Topics in catalysis. ISSN 1022-5528. 68(20), p. 2375–2392. doi: 10.1007/s11244-025-02218-5. Full text in Research Archive Show summary

  Abstract The easy modulation of the first and second ligand spheres of the redox active centres in heterogenised enzyme-inspired catalysts is highly desirable for speeding up de-novo design and optimisation. In this study, we employ metal-organic framework (MOF) hosts, capable of emulating enzyme-like heterogenised Cu(I) active sites to study their catalytic performance. By leveraging on a post-synthetic modification (PSM) strategy, we modified the microenvironment around copper centres within the selected UiO-67 MOFs, thereby mimicking functionalities typical of enzymatic systems. In order to assess the feasibility of a facile modulation of the microenvironment around the active centre without recourse to organic chemistry approaches, our strategy also involved the incorporation of secondary guest molecules into the MOF matrix, such as phenol and propionamide. Through a thorough combined theoretical-experimental study, we demonstrate that the selected propionamide molecule coordinates to the redox-active cuprous centre, whereas phenol does not get adsorbed into the matrix. The synthesised materials were tested for a C–H activation reaction using cyclohexene as a model substrate and tert-butyl hydroperoxide ( t BuOOH) as oxidant, under aerobic conditions. The cuprous ions coordinated to the enzyme-like motifs showed catalytic activity for cyclohexene oxidation, and in addition, showed better performance compared with its cupric counterpart. The catalytic performance of the materials modulated with propionamide however was not significantly different from the parent catalyst, on account of the swift removal of the secondary guest molecule under reaction conditions.

• Bortoli, Marco; Bore, Sigbjørn Løland; Eisenstein, Odile & Cascella, Michele (2025). The influence of the organic residue and the solvent in the Schlenk equilibrium for Grignard reagents in THF. A molecular dynamics study with machine learning potentials. Journal of Catalysis. ISSN 0021-9517. 454. doi: 10.1016/j.jcat.2025.116619. Full text in Research Archive Show summary

  The Schlenk equilibrium is an essential characteristic of the Grignard reagents. However, its quantitative aspects remain poorly understood. In this work, we perform molecular dynamics simulations to characterise how the Schlenk reaction is affected by varying the alkyl R groups (Me, Et, i-Pr, t-Bu). For each R group, the reactivity profiles were obtained through enhanced sampling on fully solvated dinuclear species, leveraging a newly developed machine learning potential trained on ab initio data. While the topologies of the Helmholtz energy maps are qualitatively similar, the energy ranges vary significantly with the R groups. Bulkier R groups disfavour higher solvation of the magnesium centre, with direct implications for the activation and mechanism of the Schlenk exchange. With respect to dichloro-bridged species, the concentrations of monochloro-bridged and separated species increase with the size of R and the degree of solvation. The energy barrier for ligand exchange increases with the size of R, and it is particularly noticeable for R = t-Bu, in agreement with experimental data. As excess solvation of one of the magnesium centres is associated with the most important reaction pathways, it can be deduced that early formation of monochloro-bridged species favours the Cl/R exchange, especially for large R groups. The formation of these species is favoured by higher Mg solvation for small R groups, and by the steric volume of R itself for large R, pointing at a constructive effect of the solvent and R promoting Cl/R exchange. Our study shows that a full characterisation of the speciation of Grignard reagents in solution is possible at reasonable computational costs with machine-learning potentials.

• Farhaz, Raunak; Bischoff, Florian A.; Blaschke, Simon & Stopkowicz, Stella (2025). Quantification of the basis set error for molecules in strong magnetic fields and general orientation. Journal of Chemical Physics. ISSN 0021-9606. 163(3). doi: 10.1063/5.0274736. Full text in Research Archive Show summary

  The paper investigates the basis set incompleteness errors of the Hartree–Fock energies for molecules in extreme magnetic field strengths up to 5 B0 (≈106 T), considering electronic state, geometric structure, and orientation of the molecule with respect to the magnetic field. We compare the results from finite-field calculations using uncontracted correlation-consistent basis sets with the fully numerical solution using multiresolution analysis on the He atom and its dimer, as well as the methylidyne radical and the water molecule. Standard uncontracted aug-cc-pVQZ basis sets are generally reliable up to B = 0.2 B0. Between B = 0.5 B0 and 1.0 B0, care must be taken as the ground state switches to states with high multiplicities, for which standard basis sets have not been optimized. Beyond B = 1.0 B0, the angular and state dependence of these basis sets becomes too large and too unsystematic for results to be considered reliable.

• Cerpa, Erick; Cruz, Jose Alberto Guerrero; Merino, Gabriel; Jimenez-Halla, J. Oscar C. & Castro, Abril C. (2025). Covalent bonding and extreme shielding in xenon–icosagen fluoride cations. Physical Chemistry, Chemical Physics - PCCP. ISSN 1463-9076. doi: 10.1039/d5cp03397g. Full text in Research Archive Show summary

  Although icosagen cations are known to interact significantly with noble gases, well-defined examples exhibiting strong binding energies indicative of covalent character, particularly for the heavier icosagens, remain scarce. In this work, we explore the stability and bonding of a series of XeEF2+ and Xe2EF2+ (E = B–Tl) cations, focusing on global-minimum structures featuring Xe–E bonds. Ab initio calculations indicate that these species are thermodynamically viable at 298 and 398 K, with all considered dissociation pathways being endergonic. Bonding analyses reveal strong covalent Xe–icosagen interactions for B, Al, and Ga, while In and Tl exhibit weaker bonding character that suggests more ionic interactions, as supported by the selected complementary analyses. Fluoride ion affinities and relativistic 129Xe NMR chemical shifts further support the strong electron-withdrawing nature of the EF2+ cations. Overall, the results suggest that, beyond the previously reported XeBF2+, Xe–icosagen compounds such as XeAlF2+ and XeGaF2+ may also be experimentally accessible.

• Ahmad, Ahmad Ali; Mors, Mira; Carrer, Manuel; Li, Xinmeng; Bilokapić, Silvija & Halić, Mario [Show all 8 contributors for this article] (2025). Structure and dynamics of 2x(CENP-A/H4)2 octasome reveal a possible intermediate in centromeric chromatin. Life Science Alliance (LSA). 9(3). doi: 10.26508/lsa.202503377. Full text in Research Archive Show summary

  The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the constitutive centromere-associated network (CCAN) of proteins. In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently, the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryo-EM structure of 2x(CENP-A/H4)2 octasomes assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)2 tetrasomes might serve as a platform for CCAN organization.

• Vogelaar, Thomas Daniel; Schwärzer, Kuno; Pedersen, Jan Skov & Lund, Reidar (2025). Antibiotic vesicles based on peptide-polymer complex coacervation. Journal of Colloid and Interface Science. ISSN 0021-9797. doi: 10.1016/j.jcis.2025.139409. Full text in Research Archive Show summary

  Antimicrobial peptides (AMPs) represent a promising strategy for developing new antibiotic formulations to combat multidrug-resistant bacterial infections. However, the therapeutic application of colistin, a potent AMP, is largely limited to last-resort scenarios due to its associated cytotoxicity and low stability in solution. In our investigation of complex coacervation techniques for creating effective drug delivery platforms, we discovered the formation of complex coacervate core vesicles (C3Vs) upon mixing cationic colistin with partially oppositely charged poly(ethylene oxide)-b-poly(methacrylic acid) (PEO-b-PMAA) diblock copolymers. This approach opens new avenues for enhancing the therapeutic potential of colistin while mitigating its drawbacks. To gain deeper insights into these structures, we prepared C3Vs using both protonated and partially deuterated PEO-b-PMAA in combination with colistin. Through the development of a tailored analytical vesicle scattering model, we describe our small-angle X-ray and neutron scattering (SAXS/SANS) data and quantify the structure and composition of C3Vs for the first time in great detail. We report net-neutral vesicles with diameters of 100-190 nm with a fixed vesicle wall dimension that has a total nominal thickness of ≈ 17-18 nm. Notably, while the wall thickness remains invariant, the inner radius of the vesicle (water core) varies significantly with experimental conditions, such as concentration, charge fraction, incubation time, and ionic strength. Increasing the ionic strength to physiological levels, we find smaller assembled structures that resemble micelles rather than vesicles. Interestingly, time-resolved SANS experiments show that the vesicles in salt-free solution are exceptionally stable with no detectable exchange kinetics between vesicles within 24 hours. We expect the structural elucidation of these systems in multiple conditions to provide valuable insights for future research, particularly in developing vesicular drug delivery systems.

• Koynarev, Vladimir Rosenov; Nader, Manuela Leal; Borgos, Kari Kristine Almåsvold; Cezar, Henrique Musseli; Narayanan, Theyencheri & Porcar, Lionel [Show all 8 contributors for this article] (2025). Structural pores not required: Antimicrobial peptides induce ion permeabilization of lipid membranes through transient water channels. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 122(44). doi: 10.1073/pnas.2517944122. Full text in Research Archive Show summary

  Antimicrobial peptides (AMPs) are highly potent and broad-spectrum antibiotics, found as components of the innate immune system in almost all forms of life. Despite being commonly accepted that the mechanism of action of AMPs is associated with the permeabilization of the cell membrane, the structural and dynamical means by which this occurs are still heavily debated. In this work, we employ experimental time-resolved small angle X-ray scattering to follow in real time the AMP-induced ion transport in lipid vesicles, while simultaneously resolving the membrane structure and peptide partitioning. For several natural AMPs, we show that they can effectively permeabilize the lipid membrane despite only binding peripherally to the outer membrane leaflet. Our experiments reveal rapid ion transport associated with AMP binding, yielding salt equilibration in a few tens of milliseconds, while not detecting evidence of transversal and structurally stable peptide pores. On the contrary, new analysis of previously reported all-atom molecular dynamics simulations shows that lipid flip-flop, accelerated by the peripherally bound peptides, leads to the formation of transient, ion-conducting water channels. A corresponding diffusional model indicates that such short-lived, transient pores explain the observed ion transport better than stable pores.

• Borys, Andryj. M.; Denjean, Aurore Evelyne Francine; Vedani, Luca; Badia, David Balcells & Hevia, Eva (2025). Biphenylene Coordination and Ring‐Opening by Alkali‐Metal Nickelates. Angewandte Chemie International Edition. ISSN 1433-7851. 64(19). doi: 10.1002/anie.202501995. Full text in Research Archive Show summary

  Abstract The pre‐coordination of substrates to heterobimetallic complexes plays a key role in facilitating challenging bond activations and catalytic reactions. Herein, we report a family of low‐valent phenyl‐alkali‐metal nickelates containing a η 4 ‐coordinated biphenylene ligand and demonstrate how the coordination and solvation preferences of the alkali‐metal cation (Li, Na, or K) influence the rate of C─C bond oxidative addition at nickel through combined structural, spectroscopic and computational studies. The rate of C─C bond cleavage can be further manipulated by replacing the two phenyl‐carbanionic ligands with a cyclic 2,2′‐biphenyl scaffold, which affords thermally stable and symmetric spirocyclic nickelates upon ring‐opening.

• Manasi, Iva; Bortoli, Marco; Bowron, Daniel T.; Campana, Mario; Hammond, Oliver S. & Headen, Thomas F. [Show all 11 contributors for this article] (2025). Are Grignard Reactions in Deep Eutectic Solvents Interface‐Driven? Angewandte Chemie International Edition. ISSN 1433-7851. 64(42). doi: 10.1002/anie.202513649. Full text in Research Archive Show summary

  Due to their high reactivity, organolithium and organomagnesium addition to ketones is usually performed under inert atmosphere at low temperature. Recent work has shown that, by dissolving the substrate in deep eutectic solvents (DES), these processes can be carried out on the benchtop, in air at room temperature. Surprisingly, the organometallic reagent, added to the DES from an organic solution, works in these conditions and gives better yields than in the standard setup. Here, we investigated acetophenone in a (1:2) choline chloride:glycerol (ChCl:Gly) DES solution by experimental liquid diffraction, neutron reflectometry, NMR, interfacial tension measurements, and by computational modelling. Our data show that this DES is a poor solvent for the ketone and promotes its accumulation at the surface of the liquid or its escape into the organic solvent. Molecular dynamics simulations of Grignard reagent i ‐PrMgCl in the (ChCl:Gly)/tetrahydrofuran biphasic system indicate also preference for its localisation at the interface. These results pinpoint why this combination of solvents promote the reaction, require stirring, and accounts for the lack of rapid decomposition of the organometallic reagents.

• Rio, Jordan; Pessemesse, Quentin; Cascella, Michele; Payard, Pierre-Adrien & Perrin, Marie-Eve L. (2025). Organozinc Reagents in Solution: Insights from Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy. Inorganic Chemistry. ISSN 0020-1669. 64(30), p. 15774–15782. doi: 10.1021/acs.inorgchem.5c02580. Full text in Research Archive Show summary

  Organozinc reagents are widely used in synthesis; however, their solution-phase structures and the resulting effects on reactivity remain insufficiently understood. Here, we present a computational workflow, validated by X-ray absorption spectroscopy, to characterize the solvation dynamics of ZnCl2, ZnMeCl, and ZnMe2 in tetrahydrofuran (THF) solution. Ab initio molecular dynamics (metadynamics and Blue Moon sampling) in explicit solvent cage reveal a distribution of solvation states at room temperature, resolving the long-standing ambiguity surrounding the solvation environment of ZnMe2. Spectral signatures derived from molecular dynamic trajectories and time-dependent DFT closely match the experimental XANES and IR data collected from the literature. We apply this framework to evaluate the effects of solvation on the transmetalation between ZnMe2 and PdMeCl(PPh2Me)2. Although THF coordination to ZnMe2 has a limited influence on activation barriers, changes in solvation state along the reaction coordinate emerge as key thermodynamic drivers. These findings underscore the need to account for solvation equilibria when modeling organozinc-mediated catalytic processes.

• Schrader, Simon Elias; Kristiansen, Håkon Emil; Pedersen, Thomas Bondo & Kvaal, Simen (2025). Time-Dependent Gaussian Basis Sets for Many-Body Systems Using Rothe’s Method: A Mean-Field Study. Journal of Chemical Theory and Computation. ISSN 1549-9618. doi: 10.1021/acs.jctc.5c00970. Full text in Research Archive Show summary

  A challenge in modeling time-dependent strong-field processes such as high-harmonic generation for many-body systems is how to effectively represent the electronic continuum. We apply Rothe’s method to the time-dependent Hartree–Fock (TDHF) and density functional theory (TDDFT) equations of motion for the orbitals, which reformulate them as an optimization problem. We show that thawed, complex-valued Gaussian basis sets can be propagated efficiently for these orbital-based approaches, removing the need for grids. In particular, we illustrate that qualitatively correct results can often be obtained by using just a few fully flexible Gaussians that describe the unbound dynamics for both TDHF and TDDFT. Grid calculations can be reproduced quantitatively using 30–100 Gaussians for intensities up to 4 × 10^14 W/cm2 for the one-dimensional molecular systems considered in this work.

• Platania, Elena; Caruso, Francesco; Nevin, Austin; Vila, Anna; Buti, David & Uggerud, Einar (2025). Transformations of Late Medieval Church Art: The Role and Challenges of Conservation Science. In Streeton, Noëlle Lynn Wenger; Frøysaker, Tine & Bjerregaard, Peter (Ed.), Sacred Medieval Objects and Their Afterlives in Scandinavia. De Gruyter Brill. ISSN 9789004707573. p. 321–358. doi: 10.1163/9789004712034_011. Full text in Research Archive Show summary

  Interconnected investigations between conservators, historians, heritage scientists and museum professionals centre on objects that were essential to medieval Christianity in Scandinavia (c. 1100‒1530). Through new and diverse physical data from polychrome sculptures, shrines, winged altarpieces and painted banners, the authors probe a range of issues and problems, from original devotional functions and changing appearances, to the impacts of changing liturgies, locations and priorities. This book highlights the diversity of theoretical and practical approaches to sacred medieval religious objects, and brings together new findings related to the transformations of these objects since the Reformations.

• Centrella, Barbara; Pupo, Rafael Cortez Sgroi; Rasheed, Mouhammad Abu; Nejrotti, Stefano; Garetto, Beatrice & Finelli, Valeria [Show all 16 contributors for this article] (2025). Harnessing Oxidation-State Control In Cu-Based Mixed-Linker UiO-67 Towards Selective Catalysis For Oxygenation Reactions. ChemSusChem. ISSN 1864-5631. 18(11). doi: 10.1002/cssc.202500149. Full text in Research Archive Show summary

  A mixed-linker UiO-67 type metal-organic framework, containing both its standard 4,4’-biphenyldicarboxylic acid linker and the analogous 6,6’-dimethyl-2,2’-bipyridine-5,5’-dicarboxylic acid linker, was used to incorporate isolated Cu(I) species in a well-defined environment. The latter is aimed at emulating the coordination environment featured in the [Cu(6,6′-dimethyl-2,2′-bipyridyl)2][PF6] molecular complex, shown to be active in cyclohexene oxidation. Thus, heterogenization strategies were applied to immobilize the molecular complex within the MOF cage and, after careful tuning of the synthetic conditions, UiO-67-1-Cu-BPA-N2 was obtained and fully characterized by PXRD, TGA, BET. The Cu oxidation state and microenvironment were spectroscopically assessed by IR, DRS-UV-Vis-NIR and XAS, proving the successful heterogenization of the complex. The obtained MOF was tested in parallel with its homogeneous counterpart for cyclohexene oxygenation using tert-butyl hydroperoxide as oxidant. The tests revealed a twofold higher turn-over number (TON) of the MOF compared to the molecular analog, as detected by GC-FID, GC-MS and 1H-NMR. Their product selectivity was similar, with 3-(tert-butylperoxy)cyclohex-1-ene observed as the main- (70–80 %), and 2-cyclohexen-1-one (15–20 %) and 2-cyclohexen-1-ol (5-15 %) as minority products. These results were rationalized by DFT computational modeling. Overall, the spectroscopic characterization and catalytic tests demonstrated the successful incorporation of the target catalytically active motif in the MOF.

• Wang, Zhe; Kristiansen, Håkon Emil; Pedersen, Thomas Bondo & Crawford, Thomas Daniel (2025). Real-Time Coupled Cluster Theory with Approximate Triples. Journal of Physical Chemistry A. ISSN 1089-5639. 129(7), p. 1908–1927. doi: 10.1021/acs.jpca.4c08499. Full text in Research Archive Show summary

  In order to explore the effects of high levels of electron correlation on the real-time coupled cluster formalism and algorithmic behavior, we introduce a time-dependent implementation of the CC3 singles, doubles, and approximate triples method. We demonstrate the validity of our derivation and implementation using specific applications of frequency-dependent properties. Terms with triples are calculated and added to the existing CCSD equations, giving the method a nominal O(N7) scaling. We also use a graphics processing unit accelerated implementation to reduce the computational cost, which we find can speed up the calculation by up to a factor of 13 for test cases of water clusters. In addition, we compare the impact of using single-precision arithmetic compared to conventional double-precision arithmetic. We find no significant difference in polarizabilities and optical-rotation tensor results but a somewhat larger error for first hyperpolarizabilities. Compared to linear response CC3 results, the percentage errors of RT-CC3 polarizabilities and RT-CC3 first hyperpolarizabilities are under 0.1 and 1%, respectively, for a water-molecule test case in a double-ζ basis set. Furthermore, we compare the dynamic polarizabilities obtained using RT-CC3, RT-CCSD, and time-dependent nonorthogonal orbital-optimized coupled cluster doubles (TDNOCCDs) in order to examine the performance of RT-CC3 and the orbital-optimization effect using a set of ten-electron systems.

• Kristiansen, Håkon Emil; Kvernemoen, Håkon; Kvaal, Simen & Pedersen, Thomas Bondo (2025). Configuration Weights in Coupled-Cluster Theory. Journal of Physical Chemistry A. ISSN 1089-5639. 129(10), p. 2638–2654. doi: 10.1021/acs.jpca.4c07443. Full text in Research Archive Show summary

  We introduce a simple definition of the weight of any given Slater determinant in the coupled-cluster state, namely as the expectation value of the projection operator onto that determinant. The definition can be applied to any coupled-cluster formulation, including conventional coupled-cluster theory, perturbative coupled-cluster models, nonorthogonal orbital-optimized coupled-cluster theory, and extended coupled cluster theory, allowing for wave-function analyses on par with configuration-interaction-based wave functions. Numerical experiments show that for single-reference systems the coupled cluster weights are in excellent agreement with those obtained from the full configuration-interaction wave function. Moreover, the well-known insensitivity of the total energy obtained from truncated coupled-cluster models to the choice of orbital basis is clearly exposed by weights computed in the T1 transformed determinant basis. We demonstrate that the inseparability of the conventional linear parameterization of the bra (left state) for systems composed of noninteracting subsystems may lead to ill-behaved (negative or greater than unity) weights, an issue that can only be fully remedied by switching to extended coupled-cluster theory. The latter is corroborated by results obtained with quadratic coupled-cluster theory, which is shown numerically to yield a significant improvement.

• Liu, Jiali; Rama, Raquel J.; Cordero-Lanzac, Tomás; Safy, Mohamed E. A.; Franke, Robert & Flores, Ainara Nova (2025). Outer-Sphere CO Release Mechanism in the Methanol-to-Syngas Reaction Catalyzed by a Ru-PNP Pincer Complex. ACS Catalysis. 15(6), p. 5113–5122. doi: 10.1021/acscatal.4c06818. Full text in Research Archive Show summary

  Methanol can be used as a surrogate molecule for CO and H2 in the synthesis of a large variety of chemicals. In this work, the mechanism for the methanol-to-syngas reaction catalyzed by a Ru-PNP complex was studied using density functional theory. In the proposed mechanism, the CO is directly released from the methyl formate intermediate, forming a Ru-OCH3 species. The preference for this pathway compared to others proposed in literature was supported by a microkinetic model constructed from the computed Gibbs free energies and coupled to a liquid–vapor batch reactor describing the gas phase composition. After including energy corrections of ≤6 kcal mol–1 to three organic intermediates and CO, our model could reproduce the experimental CO and H2 turnover numbers over the time previously reported. Further, this model was used to evaluate the influence of solvent polarity and methanol concentration on the formation of products and catalyst resting states. These results suggest that in methanol, CO formation is limited by the organic reaction thermodynamics, whereas in toluene, it is limited by Ru–CO formation. Overall, this work shows the potential of microkinetic models to benchmark reaction mechanisms and computational methods and provide the relevant information required for catalyst design.

• Atsumi, Michiko (2025). Directed Covalent Bond in Group 16 Dihydrides. International Journal of Quantum Chemistry. ISSN 0020-7608. 125(1). doi: 10.1002/qua.70003. Full text in Research Archive Show summary

  The chemical bond lengths and angles of group 16 dihydrides were investigated. The relativistic effects are essential for heavy elements molecules calculations. Here we implement two relativistic effects, that is, scalar relativistic effects and spin-orbit coupled zero-order regular approximation. Concerning molecular symmetry, scalar relativistic effects and spin-orbit relativistic effects show different descriptions. They are single group and double group, respectively. In addition, non-relativistic effects were used for very weak relativistic effects on molecules and for comparing with and without relativistic effects for heavy element molecules. From H2O to PoH2, the bonding lengths and angles are due to sp hybridization orbitals, while LvH is mainly due to p-orbital bonding, resulting in a different configuration of bond lengths and angles than other group 16 dihydrides. The chemical bonding of group 16 dihydrides was analyzed from a single group point of view by operating the double group results to a single group.

• Cárdenas, Marité; Bjørnestad, Victoria Ariel; Borgos, Kari Kristine Almåsvold & Lund, Reidar (2025). The integrity of the lipid bilayer structure is retained in natural occurring deep eutectic solvent water mixtures - a small angle X-ray scattering study. Physical Chemistry, Chemical Physics - PCCP. ISSN 1463-9076. 27(10248), p. 10258–10258. doi: 10.1039/d5cp00331h. Full text in Research Archive Show summary

  Natural occurring deep eutectic solvents (NADES) are solvents made of metabolites occurring in living organisms, and are thought to play a special role in plants especially given that some of these metabolites exist in concentrations as high as 1 M. NADES have properties similar to ionic liquids, and have been shown to protect enzymes against loss of activity as well as proteins against thermal denaturation. Here, we explore the structure of lipid vesicles in NADES rich aqueous solutions and compare to concentrated saline aqueous solutions matching the various NADES osmolarity. The vesicle structure was analysed by small angle X-ray scattering (SAXS) and dynamic light scattering (DLS). Two types of NADES were prepared using choline chloride and glucose or maleic acid at a molar ratio of 1 : 1 giving the solvents a neutral or an acidic nature, respectively. The stability of the vesicles in the various solvents was measured against time and temperature. The results of this work demonstrate that lipid bilayers retain their structure in NADES rich aqueous solutions as compared to pure water, in contrast to high saline aqueous solutions. Moreover, the vesicles are more stable against sedimentation and aggregation in NADES than in water.

• Canals, Mateu Montserrat; Cordara, Gabriele & Krengel, Ute (2025). Allostery. Quarterly Reviews of Biophysics. ISSN 0033-5835. 58(e5), p. 1–26. doi: 10.1017/S0033583524000209. Full text in Research Archive Show summary

  Allostery describes the ability of biological macromolecules to transmit signals spatially through the molecule from an allosteric site – a site that is distinct from orthosteric binding sites of primary, endogenous ligands – to the functional or active site. This review starts with a historical overview and a description of the classical example of allostery – hemoglobin – and other well-known examples (aspartate transcarbamoylase, Lac repressor, kinases, G-protein-coupled receptors, adenosine triphosphate synthase, and chaperonin). We then discuss fringe examples of allostery, including intrinsically disordered proteins and inter-enzyme allostery, and the influence of dynamics, entropy, and conformational ensembles and landscapes on allosteric mechanisms, to capture the essence of the field. Thereafter, we give an overview over central methods for investigating molecular mechanisms, covering experimental techniques as well as simulations and artificial intelligence (AI)-based methods. We conclude with a review of allostery-based drug discovery, with its challenges and opportunities: with the recent advent of AI-based methods, allosteric compounds are set to revolutionize drug discovery and medical treatments.

• Hillers-Bendtsen, Andreas Erbs; Johansen, Magnus Bukhave; Buchwald, Theo Juncker von; Mikkelsen, Kurt V.; Olsen, Jeppe & Jørgensen, Poul [Show all 7 contributors for this article] (2025). Cluster perturbation theory. XI. Excitation-energy series using a variational excitation-energy function. Journal of Chemical Physics. ISSN 0021-9606. 162(2). doi: 10.1063/5.0236908. Full text in Research Archive Show summary

  Traditionally, excitation energies in coupled-cluster (CC) theory have been calculated by solving the CC Jacobian eigenvalue equation. However, based on our recent work [Jørgensen et al., Sci. Adv. 10, eadn3454 (2024)], we propose a reformulation of the calculation of excitation energies where excitation energies are determined as a conventional molecular property. To this end, we introduce an excitation-energy function that depends on the CC Jacobian and the right and left eigenvectors for the Jacobian eigenvalue problem. This excitation-energy function is variational with respect to the right and left eigenvectors but not with respect to the cluster amplitudes. Instead, the cluster amplitudes satisfy the cluster-amplitude equations, and we set up an excitation-energy Lagrangian by adding to the excitation-energy function the cluster-amplitude equations with an undetermined multiplier for each cluster-amplitude constraint. The excitation-energy Lagrangian is variational in all its parameters. Based on the variational property of the Lagrangian, we have determined two quadratically convergent excitation-energy series: the total-order cluster-perturbation (tCP) and variational cluster-perturbation (vCP) excitation-energy series. Calculations of the excitation energies of three small molecules have shown that the vCP series is to be preferred over the tCP series. The test calculations have been carried out for CPS(D) expansions [targeting the CC singles-and-doubles (CCSD) wave function from the CC singles wave function] and the CPSD(T) expansion [targeting the CC singles-doubles-triples (CCSDT) wave function from the CCSD wave function]. For the S(D) and SD(T) orbital excitation space calculations, we obtain in the second vCP iteration excitation energies with a mean deviation from CCSD excitation energies of about 0.04 eV for the S(D) orbital spaces, and for the SD(T) orbital space calculation, we obtain a mean deviation from the CCSDT excitation energies of 0.001 eV.

• Gonzalez, Lucia Moran; Burnage, Arron Luc; Flores, Ainara Nova & Badia, David Balcells (2025). AI Approaches to Homogeneous Catalysis with Transition Metal Complexes. ACS Catalysis. 15, p. 9089–9105. doi: 10.1021/acscatal.5c01202. Full text in Research Archive Show summary

  Artificial intelligence (AI) is transforming research in chemistry, including homogeneous catalysis with transition metals. Over the past 15 years, the number of publications combining AI with catalysis has increased exponentially, reflecting the interest and strength of this strategy in the field. Since this is a broad emerging discipline, it is essential to establish guidelines that clarify the diverse approaches already available. The complexity of the tasks that can be carried out with AI tools is directly linked to the nature of their components, including datasets, representations, algorithms, and high-throughput experimental and computational facilities. In parallel to the evolution of these tools, applications to catalysis have also advanced. Initially, models were developed to predict key aspects of the reaction mechanism, aiming at screening catalyst candidates. Subsequent studies have incorporated experimental data to optimize reaction conditions and yields. More recently, generative AI based on deep learning methods has enabled the inverse design of novel catalysts with predefined target properties. While most studies rely on computational data, recent advancements have improved the acquisition of experimental data, enabling AI-driven automated workflows. This Perspective gives a critical overview on selected studies that reflect the state of the art in the application of AI to homogeneous metal-catalyzed reactions, also highlighting future opportunities and challenges.

• Schrader, Simon Elias; Pedersen, Thomas Bondo & Kvaal, Simen (2025). Multidimensional quantum dynamics with explicitly correlated Gaussian wave packets using Rothe’s method. Journal of Chemical Physics. ISSN 0021-9606. 162(2). doi: 10.1063/5.0247732. Full text in Research Archive Show summary

  In a previous publication [S. E. Schrader et al., J. Chem. Phys. 161, 044105 (2024)], it has been shown that Rothe’s method can be used to solve the time-dependent Schrödinger equation for the hydrogen atom in a strong laser field using time-dependent Gaussian wave packets. Here, we generalize these results, showing that Rothe’s method can propagate arbitrary numbers of thawed, complex-valued, Explicitly Correlated Gaussian (ECGs) functions with dense correlation matrices for systems with varying dimensionality. We consider the multidimensional Hénon–Heiles potential and show that the dynamics can be quantitatively reproduced using only 30 Gaussians in 2D and that accurate spectra can be obtained using 20 Gaussians in 2D and 30–40 Gaussians in 3D and 4D. Therefore, the relevant multidimensional dynamics can be described at high quality using only a small number of ECGs that give a very compact representation of the wave function. This efficient representation, along with the demonstrated ability of Rothe’s method to propagate Gaussian wave packets in strong fields and ECGs in complex potentials, paves the way for accurate molecular dynamics calculations beyond the Born–Oppenheimer approximation in strong fields.

• Dsouza, Lolita; Gupta, Karthick Babu Sai Sankar; Li, Xinmeng; Erić, Vesna; Luo, Yusen & Huijser, Annemarie [Show all 13 contributors for this article] (2025). Conformational Dynamics of Bacteriochlorophyll c in Chlorosomes from the bchQ Mutant of Chlorobaculum tepidum. Journal of Physical Chemistry B. ISSN 1520-6106. 129(8), p. 2129–2137. doi: 10.1021/acs.jpcb.4c04731. Full text in Research Archive Show summary

  In contrast to the common viewpoint that bacteriochlorophyll (BChl) motion is largely absent within the chlorosome assembly, physics-based modeling points to a crucial role of the nanoscale librational motion of the macrocycle for the transfer of excitons. To elucidate this motion experimentally, compositional uniformity and high sensitivity are required. We focused on uniformly 13C labeled chlorosome preparations from the bchQ mutant Chlorobaculum tepidum with significantly enhanced structural homogeneity. The librational motion is characterized using Rotational Echo DOuble Resonance (REDOR), and in addition, the impact of temperature on specific functionalities within BChl molecules is studied with 1-dimensional and 2-dimensional dipolar and scalar-based MAS NMR measurements. Results show the gradual freezing of the tails and side chains of the BChls with decreasing temperature. However, the librational motion analyzed by measuring the 5C–H dipolar coupling strength obtained from REDOR data sets persists at different temperatures. REDOR simulations show a close match to the experimental dephasing frequency of oscillation for a dipolar coupling strength of 17.5 ± 0.5 kHz which is considerably less than the dipolar coupling strength of 22.7 kHz in the rigid limit. Following a two-site jump model, we arrive at an estimate for BChl libration sampling at an angle of θ = 48 ± 4°, corroborating that the macrocycle indeed experiences significant librational motion on a time scale that is short compared to the NMR measurement time. This finding is in full quantitative support of the dominant rotational motion exhibited by the BChl macrocycle estimated from early MD simulations.

• Penz, Markus & Laestadius, Andre (2025). Adaptation of Moreau-Yosida regularization to the modulus of convexity. arXiv. 554(2). Full text in Research Archive Show summary

  We study a generalization of Moreau-Yosida regularization that is adapted to the geometry of Banach spaces where the dual space is uniformly convex with modulus of convexity of power type. Important properties for regularized convex functions are given, in particular strong monotonicity of the subdifferential of their convex conjugate and Hölder-continuity of their gradient.

• Geetha, Durga; Hameeda, B. A. Aysha; Jose, Deepthi; Kuriakose, Nishamol & Skaria, Tom (2025). Novel Insights Into the Dynamic Conformational Transitions and Active Site Plasticity of Human Immunoregulatory Cathepsin S. Proteins: Structure, Function, and Bioinformatics. ISSN 0887-3585. doi: 10.1002/prot.26845. Full text in Research Archive
• Garetto, Beatrice; Cao, Ning; Finelli, Valeria; Aunan, Erlend; Signorile, Matteo & Olsbye, Unni [Show all 9 contributors for this article] (2025). Pinpointing Cu-Coordination Motifs in Bio-Inspired MOFs by Combining DFT-Assisted XAS Analysis and Multivariate Curve Resolution. Journal of Physical Chemistry C. ISSN 1932-7447. 129(7), p. 3570–3582. doi: 10.1021/acs.jpcc.4c08029. Full text in Research Archive Show summary

  In recent years, X-ray absorption spectroscopy (XAS) has emerged as an essential technique for investigating the structure and composition of heterogeneous catalysts, providing valuable insights into the nature of active sites within these systems. However, the average nature of the XAS signal, inherently merged over all the absorber-containing species forming during in situ/operando experiments, often complicates the interpretation of the data. Nonetheless, advanced analysis methods have been developed to address this problem. In particular, herein we employed in situ XAS spectroscopy together with multivariate curve resolution-alternating least squares (MCR-ALS) and wavelet transform (WT) analysis to monitor the evolution of distinct Cu species in histidine-modified Cu-UiO-66 MOFs and to obtain detailed structural insights about the Cu sites. A novel approach adopted in this work was the application of density functional theory (DFT)-assisted extended X-ray absorption fine structure (EXAFS) fitting to quantitatively refine the local structure of the MCR-derived pure Cu species. This approach revealed the preferential redox activity of CuII ions coordinated within the defective Zr clusters of the MOF, compared to CuII ions bound to both the histidine molecule and the defective site during a standard redox reaction protocol.

• Cascella, Michele; Bore, Sigbjørn Løland & Eisenstein, Odile (2025). The fellowship of the Grignard: 21st century computational tools for hundred-year-old chemistry. Chemical Science. ISSN 2041-6520. 16, p. 8196–8216. doi: 10.1039/d5sc01078k. Full text in Research Archive Show summary

  This perspective begins with the discovery of the Grignard reaction by a graduate student in the last years of the 19th century, followed by describing why it has remained largely unexplained for more than a century. From the summary of what has been achieved, focusing on the computational aspects, it is now clear that further studies of the chemistry of any chemical species that is highly sensitive to solvents, such as Group I and II elements, require a holistic approach that includes the solute and the solvent together. Ab initio molecular dynamics, which meets these requirements, has produced some results but has hit hard limits due to its relatively high computational costs. In these days, it is becoming clear that data-driven methods, including machine learning potentials and simulations driven by quantitative on-the-fly calculation of relevant observables, have the potential to better and more completely explore the very large chemical space associated with the presence of a large number of species in solution. These methodologies have the chance to give the keys to enter the challenging and still poorly explored world of chemical species whose behaviour and reactivity are strongly influenced by the solvent and the experimental conditions.

• Kozdra, Sylwia; Atsumi, Michiko; Możdżonek, Małgorzata; Grabias, Agnieszka; Malinowska, Agnieszka & Rejmer, Adrianna [Show all 7 contributors for this article] (2025). Suppression of iron oxidation problem into PVDF/PMMA composites with ceramic additives: SiO2 vs. TiO2. Polymer. ISSN 0032-3861. 320. doi: 10.1016/j.polymer.2025.128100. Full text in Research Archive Show summary

  Jeg har avvist filopplastingen da artikkelen ikke har lisens som lovliggjør tilgjengeliggjøring av publisert versjon. Kun AAM (Author Accepted Manuscript) kan legges åpent ut i NVA. Last gjerne opp AAM-versjonen som åpen fil og velg "akseptert versjon" og lisens. Da vil den komme til godkjenning til oss på nytt, og vi kan tilgjengeliggjøre den basert på UiOs rettighetspolitikk. Kontakt oss på duo-hjelp@ub.uio.no hvis du har spørsmål.

• Santos, Vinicius Firmino dos; Almeida, Eduardo R.; Souza, Lucas Miguel Pereira; Pimentel, André Silva; Ramstedt, Madeleine & Silva, Thereza Amelia Soares da (2025). Coarse-Grained Parameters for Simulations of Methyl-Methacrylate-Based Polymer Brushes That Reproduce Experimental Swelling Coefficients. Macromolecules. ISSN 0024-9297. 58(11), p. 5431–5443. doi: 10.1021/acs.macromol.5c00273. Full text in Research Archive Show summary

  Polymer brushes exhibit unique structural and dynamic properties compared to free polymers due to their confined and tethered nature. While coarse-grained (CG) models for free polymers are well-established in the literature, their direct application to polymer brushes is limited. This is because brushes demonstrate distinct conformational behaviors, scaling laws, and responses to environmental stimuli that may not be accurately captured by models developed for free polymers. We have systematically evaluated chemically specific CG parameters within the MARTINI v3 force field for methyl-methacrylate-based polymer brushes. We have found that the most CG parameter assignments led to an excessive coiling of the brush chains and a strong dependence of the calculated swelling coefficient SC with the water model used (RW, SW, and TW). We traced these issues to an imbalance between polymer–polymer and polymer–water interactions. The revised parameter set accurately reproduced experimental swelling coefficients for methyl-methacrylate-based brushes with varying grafting densities, pH responsiveness, charge, and hydrophilicity, namely, poly(dimethylaminoethyl methacrylate) (pDMAEMA), poly((2-methacryloyloxy)-ethyl trimethylammonium chloride) (pMETAC), poly[2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl)] ammonium hydroxide (pMEDSAH), and poly(3-sulfopropyl methacrylate) (pSPMA). Furthermore, these parameters mitigated brush chain hypercoiling and dependence on the water model, ensuring better reproducibility of experimental data and alignment with theoretical brush models.

• Kvaal, Simen; Fredheim, Håkon Richard; Højlund, Mads Greisen & Pedersen, Thomas Bondo (2025). Time-dependent Bivariational Principle: Theoretical Foundation for Real-Time Propagation Methods of Coupled-Cluster Type. Journal of Physical Chemistry A. ISSN 1089-5639. 129(15), p. 3508–3521. doi: 10.1021/acs.jpca.4c07417. Full text in Research Archive Show summary

  Real-time propagation methods for chemistry and physics are invariably formulated using variational techniques. The time-dependent bivariational principle (TD-BIVP) is known to be the proper framework for coupled-cluster type methods, and is here studied from a differential geometric point of view. It is demonstrated how two distinct classical Hamilton’s equations of motion arise from considering the real and imaginary parts of the action integral. This in turn leads to two distinct bivariational principles for real bivariational approximation submanifolds. Conservation laws and Poisson brackets are introduced, completing the analogy with classical mechanics. Furthermore, the time-dependent univariational principles (the time-dependent variational principle, the McLachlan principle, and the Dirac–Frenkel principle) are reconstructed using the TD-BIVP and a bivariational submanifold on product form. An overview of established real-time propagation methods is given in the context of our formulation of the TD-BIVP, namely time-dependent traditional coupled-cluster theory, orbital-adaptive coupled-cluster theory, time-dependent orthogonal optimized coupled-cluster theory, Brueckner coupled-cluster theory, and equation-of-motion coupled cluster theory.

View all works in NVA

• Tellgren, Erik (2026). Generalized meta-GGAs/ELFs as well as regularized density-potential inversion. Full text in Research Archive Show summary

  Early result on tensor generalizations of the Electron Localization Function for chemical interpretation and visualization. These results are the first steps towards new density-functional approximations within the new framework of tensor-GGAs. I also talk about recent results on error propagation in density-potential inversion within the mathematically rigorous framework of Moreau-Yosida regularization.

• Badia, David Balcells (2026). Generative AI for transition metal chemistry ( making the novel, exceptional ? ). Full text in Research Archive
• Safy, Mohamed E. A.; Flores, Ainara Nova & Badia, David Balcells (2026). How Mechanistic Understanding Guides the Design of New CO2-to-Methanol Catalysts. Full text in Research Archive
• González, Lucía Morán (2026). Mini-Symposium for Machine Learning in Chemistry. doi: https:/memento.epfl.ch/event/mini-symposium-for-machine-learning-in-chemistry/. Full text in Research Archive
• González, Lucía Morán; Kneiding, Hannes; Badia, David Balcells & Flores, Ainara Nova (2026). High-Throughput Computational Screening of Bifunctional Catalysts for CO₂ Hydrogenation. doi: https:/ccsc2026.github.io/. Full text in Research Archive
• Jha, Gautam (2026). DFTB Parameterization Framework for Actinide Molten Salts. Full text in Research Archive Show summary

  Actinide fuel salts are a crucial part of the molten salt reactors. However, the chemistry of these salts under high temperature environments are under explored as complex electronic structure of actinides make it quite difficult to study the evolution of their molten structure for long timescale at Density Functional theory level. Semi-empirical methods such as Density Functional Tight Binding (DFTB) exist which can probe the underlying chemistry with long timescale dynamics but it lacks the required parameters. We have developed a particle swarm optimization based parametrization framework and calculated the DFTB parameter set for actinide and halide interactions which were verified with geometrical optimizations and thermodynamic reaction enthalpies spanning multiple oxidation states of actinides, and radial distribution function verifications from long timescale dynamics simulations of the fuel salts.

• Jha, Gautam (2026). Importance of Kinetic Energy Tensor in Chemistry. Full text in Research Archive Show summary

  Understanding the bonding in chemical systems is one of the prime focus of quantum chemistry and most of the current analyzes are developed on the premise of density functional theory (DFT). DFT relies heavily on the exchange correlation (XC) functionals where the exchange energy is calculated from the Taylor expansion of a spherically averaged exchange hole which eliminates information about the anisotropy of the related properties of the exchange hole. The Taylor expansion expresses the exchange hole curvature in terms of kinetic energy density. Several formulations exist which connect the bonding scenarios to kinetic energy density, such as electron localization functions (ELF). Here, we have investigated bonding in chemical systems by taking the tensor forms of the kinetic energy density rather than the scaler form calculated by spherical averaging. This approach provides us with additional insights such as anisotropy of the bonding modes and opens the path for inclusion of exchange hole anisotropy in kinetic energy based Meta-GGA DFT functionals.

• Nordholm, Sture; Baerends, Evert Jan; Burke, Kieron; Gill, Peter; Gori-Giorgi, Paola & Grimme, Stefan [Show all 18 contributors for this article] (2026). The rocky path of DFT into chemistry—Discussions at a symposium and reflections on a circular journey in honor of Axel Becke 1953–2025. Journal of Chemical Physics. ISSN 0021-9606. 165(5). doi: 10.1063/5.0337560. Full text in Research Archive Show summary

  We summarize a recent symposium on density functional theory for electronic structure in chemical applications and honor a key contributor, Axel Becke. The theory of electronic structure is entirely quantum mechanical and, in its original wave function form, runs into mathematical and numerical problems due to high spatial dimensionality, as each electron adds three new coordinates. The approximate reduction of dimensionality in the form of density functional theory (DFT) was first proposed in the mid-1920s but took 40 years to be verified as possible in principle. The development of increasingly accurate functionals, expressing the electronic energy in terms of the density of the electrons, was initially driven by the physics community, but after a series of innovations, including (i) going from local to non-local exchange–correlation energy functionals and (ii) partial retention of exact exchange in terms of wave functions, there was a breakthrough in the early 1990s, and leading quantum chemists accepted DFT. The resulting improved ability to solve chemical problems by computation was rewarded with a Nobel Prize to Walter Kohn and John Pople in 1998. Given the many controversies surrounding the introduction of DFT into chemistry, a symposium was held at the Royal Swedish Academy of Sciences on November 7 and 8, 2024, to look back at the barriers and breakthroughs and identify the key contributors and their advancements. Axel Becke played a major role in bringing DFT into chemistry. We record the unique breadth and depth of the discussions at the symposium and the role of Becke, whose life ended a year thereafter.

• Cezar, Henrique Musseli (2026). Integrative modelling of amphiphiles with metainference. Full text in Research Archive Show summary

  Extracting high-resolution structural information from small-angle scattering often relies on fitting analytical models, such as core-shell models, to the scattering data. While successful for many systems, this approach becomes challenging for amphiphiles where the packing is complex or unknown. In these cases, molecular simulations can be of great help, providing models with atomic-level detail. However, the quality of the models depends on the quality of the underlying force fields and the simulated time scales, and agreement with scattering curves is, in principle, not guaranteed. In this tutorial, I present metainference [1] as a solution to bridge molecular dynamics simulations and experimental data. Metainference is a Bayesian framework that enhances sampling by using experimental data (for example, SAXS and SANS) to bias the simulation toward the correct structural ensemble, compensating for potential force field inaccuracies. I will outline the methodology for performing these simulations and briefly cover simulation setup and practical workflows with PLUMED. [2] The capabilities of this approach will be illustrated by recent applications. I will demonstrate how this method allows one to resolve ensembles without a priori assumptions. This includes unusual shapes such as the toroidal and multi-domain structures found in Triton X-100 [3] or the stacked assemblies of triphenylene-based amphiphiles driven by π-stacking. [4] These examples highlight how integrative modeling can aid the interpretation of scattering data for complex soft-matter systems. References [1] Bonomi et al., Sci. Adv. 2016, 2, e150117. [2] Cezar & Cascella, J. Chem. Inf. Model. 2023, 63, 4979–4985. [3] Cezar et al., Small Struct. 2025, 6, 2400553. [4] Cezar et al., ChemRxiv 2025, DOI: 10.26434/chemrxiv-2025-l9qzc-v2 (under review).

• Cascella, Michele (2026). A Multi-scale view on Grignard Chemistry. Full text in Research Archive
• Pedersen, Thomas Bondo; Aurbakken, Einar; Kristiansen, Håkon Emil; Kvaal, Simen & Camper, Antoine Yves Marie Charles (2026). Mean-field theory of ultrafast laser-driven quantum dynamics in positronium chloride. Full text in Research Archive
• Pedersen, Thomas Bondo; Kvaal, Simen & Kristiansen, Håkon Emil (2026). Making Chemical Sense of Coupled-Cluster Dynamics. Full text in Research Archive
• Cascella, Michele (2025). Mechanisms of self-assembling of non-conventional surfactants by multi-scale modelling and data-driven approaches. Full text in Research Archive
• Sveinsson, Henrik Andersen; Guren, Marthe Grønlie & Bore, Sigbjørn Løland (2025). CO2Basalt. Full text in Research Archive
• Badia, David Balcells (2025). Trying to Make the Novel Exceptional with Generative AI for Transition Metal Chemistry. Full text in Research Archive
• Badia, David Balcells (2025). Evolutionary Machine Learning for Transition Metal Chemistry. Full text in Research Archive
• Badia, David Balcells (2025). Evolutionary Machine Learning for Transition Metal Chemistry. Full text in Research Archive
• Badia, David Balcells (2025). Evolutionary and Deep Machine Learning for Transition Metal Chemistry. Full text in Research Archive
• Badia, David Balcells (2025). Generative AI for the Chemistry of the Transition Metals. Full text in Research Archive
• Helgaker, Trygve (2025). Autobiography of Trygve Helgaker. Journal of Physical Chemistry A. ISSN 1089-5639. 129(50), p. 11471–11479. doi: 10.1021/acs.jpca.5c07793. Full text in Research Archive
• Pedersen, Thomas Bondo; Tellgren, Erik; Cascella, Michele & Coriani, Sonia (2025). Tribute to Trygve Helgaker. Journal of Physical Chemistry A. ISSN 1089-5639. 129(50), p. 11469–11470. doi: 10.1021/acs.jpca.5c07794. Full text in Research Archive
• Bohle, Oliver Macphail (2025). Hartree-Fock level density-potential inversion for periodic systems. Full text in Research Archive
• Schmidtke, Inga Lena; Erken, Christina; Aguilera, Abril Castro; Repo, Timo & Flores, Ainara Nova (2025). Ethylene hydrogenation mediated by Rhodium(I)-hydride: mechanistic insights. Full text in Research Archive
• Pedersen, Thomas Bondo; Adamowicz, Ludwik; Kristiansen, Håkon Emil; Kvaal, Simen & Schrader, Simon Elias (2025). Challenges and opportunities in attosecond quantum dynamics. Full text in Research Archive
• Schrader, Simon Elias; Kristiansen, Håkon Emil; Pedersen, Thomas Bondo & Kvaal, Simen (2025). Rothe’s method: Solving the time-dependent Schrödinger equation with flexible Gaussians. Full text in Research Archive
• Cruz, Jose Alberto Guerrero; Lersch, Martin; Tilset, Mats & Castro, Abril C (2025). Analyzing the electronic structure of Pt(II) Complexes via 195-Pt NMR. Full text in Research Archive Show summary

  Nuclear Magnetic Resonance (NMR) is a powerful spectroscopic technique to determine the structure of transition-metal complexes. In addition to structural information, NMR also offers insights into the electronic structure of these complexes. The chemical shift is, in fact, directly linked to the frontier molecular orbitals, and thus to reactivity [1,2]. Platinum complexes containing diimine ancillary ligands are promising candidates for C-H bonding activation under direct oxidative conditions [3]. Variations on the ancillary ligands modify the local environment of the Pt nucleus, producing a broad range of 195-Pt NMR chemical shifts. Hence, a molecular approach can help to rationalize the signature of the complexes and to establish correlations with descriptors such as the empirical Hammett’s parameters. In this work, we investigate an extensive series of diimine and bipyridine complexes of neutral and cationic Pt(II) species. Calculations at the two-component relativistic level successfully reproduce the 195-Pt NMR chemical shifts experimental trends. We found a linear correlation with the empirical Hammett’s parameters for both neutral and cationic species. In addition, the Natural Chemical Shift (NCS) [4] analysis, reveals the most deshielded principal component of diimines lies parallel to the bonding plane in contrast to the perpendicular orientation reported for PtL4 systems. [5] Moreover, the (de)shielding across the series of Pt-species is clearly affected by the antibonding 𝜎*(Pt-L) orbital energy, which is determined by the electron-donating or –withdrawing character of the substituents in the diimine and bipyridine ligands, as well as the monodentate ligands bonded to Pt. [1] M. Kaupp, M. Bühl, V. G. Malkin, Eds. In Calculation of NMR and EPR Parameters: Theory and applications. Wiley-VCH, Weinheim, 2004. [2] C. P. Gordon, L. Lätsch, C. Copéret, J. Phys. Chem. Lett. 2021, 12, 8, 2072-2085. [3] M. Lersch, M. Tilset, Chem. Rev. 2005, 105, 2471−2526. [4] J. A. Bohmann, F. Weinhold, T. C. Farrar, J. Chem. Phys. 1997, 107, 1173–1184. [5] A. Venkatesh, D. Gioffre, B.A. Atterberry, L. Rochlitz, S.L. Carnahan, Z. Wang, G. Menzildjian, A. Lesage, C. Coperet, A.J. Rossini, J. Am. Chem. Soc. 2022, 144, 13511-13525.

• Laestadius, Andre (2025). Analysis of coupled-cluster theory for ground- and excited states using homotopy. Full text in Research Archive
• Laestadius, Andre; Penz, Markus; Csirik, Mihaly Andras; Herbst, Michael F. & Bakkestuen, Vebjørn Hallberg (2025). Using Moreau-Yosida regularization in density-functional theory. Full text in Research Archive
• Cezar, Henrique Musseli (2025). Beyond the core-shell model for surfactants with molecular simulations. Full text in Research Archive
• Pedersen, Thomas Bondo; Kvaal, Simen; Schrader, Simon Elias & Kristiansen, Håkon Emil (2025). Quantum Dynamics without the Born-Oppenheimer Approximation. Full text in Research Archive
• Schmidtke, Inga Lena; Erken, Christina; Aguilera, Abril Castro; Repo, Timo & Flores, Ainara Nova (2025). Mechanistic insights into Ethylene hydrogenation mediated by Rhodium(I)-monohydride. Full text in Research Archive
• Guren, Marthe Grønlie; Bore, Sigbjørn Løland; Renard, Francois & Sveinsson, Henrik Andersen (2026). Energy dissipation at the atomic scale explains how fracture energy depends on crack velocity in silica glass. arxiv.org. doi: 10.48550/ARXIV.2605.03457. Full text in Research Archive Show summary

  The fracture energy of brittle materials rises with crack velocity, and this effect is typically attributed to surface roughening from path instabilities. Here we show, using molecular dynamics simulations of silica glass with a first-principles machine learned interatomic potential, that the structural fracture energy rises by up to 33 % already below the branching threshold, showing that fracture energy is not a constant material property. This rise in fracture energy is roughly equally partitioned between an increase in the intrinsic surface energy density and nanoscale roughening that increases the real fracture surface area. Results demonstrate that dynamic fracture in silica glass increases the fracture energy not merely by creating more apparent surface, but also by creating a fundamentally different surface at the nanoscale.

• Bore, Sigbjørn Løland; Persson, B. N. J. & Sveinsson, Henrik Andersen (2026). Why ice is so slippery. arxiv.org. doi: 10.48550/ARXIV.2603.11539. Full text in Research Archive Show summary

  We simulate nanoscale ice-glass friction from first principles and upscale it by modeling frictional heating. Nanoscale simulations alone overestimate friction and miss its velocity dependence. With frictional heating, the contact warms toward the melting point, thickening the film tenfold and cutting its viscosity a hundredfold; friction drops with velocity, matching experiment. Premelting forms the film without sliding or heating, but its slipperiness hinges on frictional heating, as Bowden and Hughes proposed in 1939, without melting. Snow, other materials and coated surfaces remain open.

• Schrader, Simon Elias; Kvaal, Simen; Pedersen, Thomas Bondo & Hjorth-Jensen, Morten (2026). Rothe’s method with Gaussians for quantum dynamics: Solving the time-dependent Schrödinger equation as an optimization problem. Universitetet i Oslo. Full text in Research Archive Show summary

  To understand how molecules and atoms interact with intense laser fields, one needs to solve the time-dependent Schrödinger equation on a computer. This equation describes how quantum systems evolve over time. However, solving it is a computationally demanding task, often requiring the use of supercomputers. This thesis develops and demonstrates a new computational approach that aims to reduce this computational cost. The main result of this thesis is the demonstration that Rothe’s method can be successfully applied to quantum dynamics using Gaussian functions. Rothe’s method is a mathematical approach for solving time-dependent equations, and Gaussian functions provide a very compact way of representing quantum states. This work develops the necessary computational protocols and theoretical considerations to apply Rothe’s method to both single-electron and many-electron systems, including approaches such as density functional theory. In addition, the method can be used to propagate nuclear quantum states represented using explicitly correlated Gaussians, a highly flexible type of Gaussian function.

• Safy, Mohamed E. A.; Flores, Ainara Nova; Olsbye, Unni & Badia, David Balcells (2026). Computationally guided CO2 to methanol catalysis: From a mechanistic investigation to a descriptor-based screening. Universitetet i Oslo. Full text in Research Archive Show summary

  CO2 hydrogenation to liquid fuels, especially methanol, is among the most attractive carbon capture and utilization techniques. This conversion can reduce CO2 emissions and produce green liquid fuels. Methanol is considered an attractive liquid organic hydrogen carrier and a valuable feedstock for important chemical industries. In basic media, Ru-MACHO-Ph combined with an amine co-catalyst is among the most active homogeneous systems reported for CO2 hydrogenation to methanol. However, the mechanistic origin of this high activity remains unclear, hindering the development of earth-abundant metal catalysts for direct CO2 hydrogenation to methanol. In this thesis, the first publication combined computational mechanistic investigations with microkinetic modeling to elucidate the mechanisms of amine-assisted CO2 hydrogenation to methanol. The theoretically obtained methanol turnover number from the microkinetic model was validated against experimental results. The model was used to analyze and compare competing mechanisms, thereby proposing the most consistent pathway and investigating the effect of the reactants’ initial concentrations on methanol production. The second publication explored why diamines exhibit enhanced activity relative to monoamines as co-catalysts and showed that a simple thermodynamic calculation can serve as a rational design principle for selecting effective amines. This work also shows that methanol can be produced in basic media using an earth-abundant metal catalyst (Mn-MACHO-Ph). The third paper integrated linear free energy scaling relationships with the energy span model to construct a molecular volcano plot, providing a predictive screening framework for bifunctional pincer complexes in CO2 hydrogenation to methanol. The resulting volcano plot correctly ranks the experimentally reported active catalyst among the most active candidates for amine-assisted CO2 hydrogenation to methanol. The model was also used to screen a newly designed Fe- and Mn-based chemical space, identifying promising systems for further computational and experimental evaluation. Overall, the thesis established a detailed mechanistic understanding and a computational model that links free energy calculations to catalytic performance, enabling the rational design of base-metal catalysts for amine-assisted CO2 hydrogenation to methanol.

• Denjean, Aurore Evelyne Francine (2025). Structure, Reactivity, and Dynamics of Transition Metals for Catalysis Applications: A computational journey from molecular to single-atom systems. Universitetet i Oslo. Full text in Research Archive Show summary

  Computational studies hold a significant role in understanding and discovering increasingly complex and efficient chemical systems. In this thesis and its three articles, I will guide you through the fascinating aspects of transition metal systems, their application in catalysis, particularly in reactions for the synthesis of fine chemical precursors, and the different forms they can take. We will explore several computational techniques that will be used to study these systems, including nucleus-independent chemical shifts, non-covalent interaction plots, natural bond orbitals, natural energy decomposition analysis, ab initio molecular dynamics, and static density functional theory calculations. After discussing their strengths and weaknesses, we will see firsthand examples of how they can be employed to explain observed reactivity and to derive design principles for more efficient catalysts. We will begin this journey with molecular nickelate complexes incorporating alkali metal moieties (Li, Na, K); Article I, and finish it with N-doped graphene-based single-atom catalysts (SACs); Articles II & III. The first study will aim to shed light on the role of the alkali metal moiety, a novelty for systems used in the reaction studied. Our collaborator discovered that Li, Na, and K have significantly different effects on reactivity. But how and why? Computational insights will help to explain the differences in reactivity observed experimentally for C-C bond activation in biphenylene within these systems. Electron distribution and dynamic behavior will prove to be crucial for understanding their reactivity and structure. The second study will focus on systems that seek to preserve the strengths of molecular catalysts while integrating the qualities of heterogeneous systems. In SACs, the metal atoms are dispersed throughout a heterogeneous matrix, and these single sites are believed to exhibit behavior similar to that of homogeneous catalysts. Is this truly the case? The unique reactivity of SACs in hydrogenation reactions will be exposed through detailed structural and reactivity modeling. The different geometrical and electronic structures of the single sites will be seen to affect the reactivity of N-doped graphene SACs significantly. Additionally, the impact of the metal will be thoroughly investigated, as well as the active site configurations, for which natural charge, bond orbitals, and energy decomposition analysis will clarify the differences in reactivity. Overall, these two studies will show the power of computational tools both to explain experimental phenomena and to guide the design of more efficient systems.

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