The spectral properties of isolated molecules can differ significantly from those of the same molecules dissolved in aqueous solution [1].
Multiscale Quantum Mechanics (QM)/Classical models are highly effective in simulating solvated molecules by dividing the system into two components: the solute, treated at the QM level, and the solvent, modeled classically [2-4].
Among these approaches,...
Clean water is among the most important resources and there is a continuously rising need for energy-efficient, simple upcycling methods. We use molecular modelling to tailor nanoparticle functionalization for cost-efficient recovery of polluted water. So far, this has been demonstrated for extracting crude oil [1], micro-/nanoplastics [2], glyphosate [3] and polychlorinated biphyenyls [4]....
Since their discovery in 2004, carbon nanodots (CNDs) have emerged as a promising class of carbon-based nanoparticles due to their properties: intense photoluminescence, low toxicity, excellent biocompatibility and easy surface functionalization.[1] Their synthesis employs straightforward bottom-up and top-down methods, which dictate the functional groups present on their surface, their size...
G-protein coupled estrogen receptors (GPERs) play a critical role in cellular signalling; yet the precise nature of their interaction with estrogen (EST) remains a subject of debate [1–4]. While recent studies have questioned whether EST binds directly to GPER [4], our molecular dynamics (MD) simulations provide compelling evidence in favor of such an interaction. Using MD simulations, we...
Opioids are one of the most commonly used group of drugs in pathological pain treatment due to their remarkable analgesic effect. The main target for opioids is the transmembrane receptor μ-opioid receptor 1 (MOR1), which belongs to the G protein-coupled receptor superfamily (GPCR). Several kinases, such as G protein-coupled receptor kinases, cyclic AMP-dependent protein kinase, protein kinase...
Title: A Million-fold Increase in C-H Bond Acidity Gives Palladium a Key Advantage in C(sp${}^3$)-H Activation Compared to Nickel
A Modular Software Approach to Intermolecular Interaction Analysis
Computational analysis of intermolecular interaction patterns, and prediction of optimal configurations, is a frequently encountered problem arising in a wide range of subjects, such as molecular docking, conformer analysis and crystal structure prediction. While different fields may employ their own preferred models...
The absorption of high-energy radiation and following photo-ionization leads to an enhanced reactivity
towards processes such as rearrangements and fragmentations. While experimental techniques such as
photo-electron photo-ion coincidence (PEPICO) spectroscopy can suggest the species formed at defined
binding energies, ab initio molecular dynamics simulations can explore, from a theoretical...
Molecular dynamics (MD) simulations are routinely used to study the atomistic behavior of molecular systems. Unfortunately, conventional MD simulations often struggle to adequately sample the full configurational space of the process of interest because the requisite timescales exceed practical computational limits. To overcome this, enhanced sampling techniques such as replica exchange...
Molecular Hamiltonian matrix reduction techniques based on hybrid quantum classical network community detection method.
davide.castaldo@phys.chem.ethz.ch
Quantum phase estimation (QPE) is a flagship algorithm for quantum simulation on fault-tolerant quantum computers. However, recent resource estimates[1] suggest that surpassing classical simulation techniques requires millions of gates and hundreds of logical qubits. Consequently, significant effort is being devoted to developing QPE-like algorithms that...
Surfaces play a fundamental role in all materials processes, in most chemical processes and in the growth or formation of all solid-state materials, especially semiconductors and new 2-D materials. Over the years our ability to rigorously calculate their properties has improved, starting from simple model systems to more complicated systems. Computational advances aimed at handling larger and...
RNA is emerging as a promising therapeutic target due to its central role in regulating diverse cellular functions. However, accurately predicting ligand binding affinities to RNA remains a major computational challenge, largely due to RNA’s intrinsic flexibility and structural heterogeneity. In this work, we benchmark two alchemical free energy methods—Thermodynamic Integration (TI)1 and the...
aims PAX: Automated, Parallel Active Learning for Machine Learning Force Fields
We present ab initio molecular simulation Parallel Active eXploration (aims PAX), an automated framework for constructing diverse and high-quality datasets for training machine learning force fields (MLFFs) [1] through active learning (AL). This software combines the electronic structure code FHI-aims [2] with the...
An improved guess for the variational calculation of charge-transfer excitations in large molecular systems
Nicola Bogoa, Zeyi Zhangb,c, Martin Head-Gordonb,c and Christopher J. Steina,d
a) Department of Chemistry and Catalysis Research Center, TUM School of Natural Sciences, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, christopher.stein@tum.de
b) Pitzer...
In the realm of nanotechnology and molecular engineering, photoswitches play a key role as structural elements converting light into mechanical work. In particular, switchable chromophores embedded in complex molecular environments – such as molecular machines and self-assembled monolayers on surfaces – offer unique opportunities for the precise control of material properties and molecular...
Sodium batteries have attracted increasing attention as cost-effective and sustainable alternatives to lithium-ion batteries. Sodium is naturally abundant, cheaper, and operates at a lower voltage than lithium [1]. Recently, metal anode batteries have gained prominence over metal-ion systems due to their higher theoretical capacities. However, sodium metal anode batteries using conventional...
Atropisomerism is a form of stereoisomerism caused by restricted rotation about hindered single bonds.1,2 Atropisomerism plays a critical role in pharmaceutical drug development, where the stereochemical properties of a molecule can significantly impact its function. Approximately 30% of recently approved FDA drugs possess potential atropisomeric axes,3 highlighting the significance of...
The conformational search of small molecules has become increasingly relevant in recent years after the significant speedups in computation chemistry, and the developments of new efficient algorithms for the task. In that regard, we recently published a new Global Optimization Algorithm (acronym GOAT)1, which has been shown to be among the best of its kind and can cover a wide range of...
Consideration of the conformation of chemical systems is a highly important initial step of a reaction modeling investigation in computational chemistry, since the error introduced due to a higher energy conformer can be on the order of, or greater than, the energy differences that explain reaction mechanisms and selectivities. Unfortunately, computationally cheap, low levels of theory that...
Title: Benchmarking the Performance of Density Functional Approaches in Describing Interactions Between Cation-exchanged Zeolites and Pharmaceuticals and Personal Care Products (PPCPs)
N.B.: See the attachment for the abstract.
Reaction optimisation plays a fundamental role in the drug discovery process; for many this is at the reaction design stage[1]. This optimisation process is often expensive and time consuming, and generally follows one of two approaches, the first being the use of a chemist’s intuition (this however relies on the chemist having knowledge of the reaction domain) with the alternative being a...
DNA is a fundamental molecule of life, and its folding is critical for gene regulation, medical applications, and disease prevention. While proteins like histones are known to drive highly ordered DNA packaging, both experimental and theoretical studies have shown that DNA duplexes can also associate selectively in the absence of proteins, mediated by small molecules such as polycations.1 In...
Enzymes are the key molecular machinery that enables chemical transformations on the timescale of life. Throughout evolution, enzymes have developed specific substrate scope, stereospecificity and catalytic proficiency. In recent years, routines to improve enzyme stability through amino acid substitutions have become commonplace. However, it is still more challenging to manipulate the...
CO2 Activation on Single-Atom Catalysts: Importance of the Supporting Matrix
Single-Atom Catalysts (SACs) are emerging as a new frontier in heterogeneous catalysis.1,2 They are made of metal atoms atomically dispersed on a supporting matrix. Computational chemistry offers the ability to study catalytic processes with atomic-level precision, enabling the rationalization and even prediction...
We present the development of a new ReaxFF reactive force field parametrization tailored for modelling CO₂ hydrogenation on ruthenium-functionalized zeolites. The force field is based on the CHOAlSi ReaxFF parameters and was reparametrized using extensive DFT data from a prior study, which characterized key elementary steps leading to CO, CH₄, CH₃OH, CH₂O and HCOOH gas products on a single Ru...
Cina Foroutan-Nejad
Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
cina.foroutan-nejad@icho.edu.pl
A century after G. N. Lewis introduced his foundational model of chemical bonding, its core principles remain central to our understanding of molecular structure. Traditionally, neighboring atoms in a Lewis structure are assumed to share stabilizing interactions....
HDAC8 is a histone deacetylase enzyme that plays a key role in the development of various diseases in humans, including cancers, neurodegenerative diseases, and alcohol use disorder1. Although HDAC8 is classified as a Zn-dependent metalloenzyme, the available information regarding the affinity of different divalent metal ions, such as Fe²⁺, Ni²⁺, Co²⁺, and Mg²⁺, toward the HDAC8 active site...
Difluoro-boron β-diketonate (DFB) amide derivatives, such as (S)-DFB-PhEt-amide and (S)-DFB-Hex-amide, have emerged as promising candidates for applications in optoelectronics and sensing due to their mechano-responsive chiroptical properties. Despite their potential, the molecular origins of these behaviours are still not fully understood. This work presents a detailed computational study...
Hemocyanins (Hc), proteins commonly known for its extracellular roles in oxygen (O2) sensing, transport, and storage in many invertebrates,[1] have an intriguing and poorly understood intracellular presence. Emerging evidence suggests a significant correlation between oxidative stress and increased intracellular Hcs levels, implicating an active role of Hcs in the antioxidant response.[2] In...
From the first ambimodal bispericyclic cycloaddition reaction reported by Caramella et al.[1] in 2002, the number of reactions observed to show a post-transition state bifurcation (PTSB) have steadily increased. [2,3] Many of these ambimodal transitions states (TSs) involve a single PTSB. That is, one TS leads to a reaction coordinate that bifurcates after crossing the TS region into two paths...
In today's world, the quest for green alternatives has become paramount across industrial sectors such as chemicals, textile, pharmaceutical and agriculture because they are facing a persistent challenge with increasing energy consumption during operation of their chemical reactions. In this regard, polyoxometalates (POMs), metal oxide clusters composed of early transition metals in high...
At the dawn of artificial intelligence and self-driving laboratories for materials design, automated generation of unbiased atomistic models that capture the complexity of molecular fluids in a computationally efficient way is a persistent challenge. This lack of atomistic models is especially relevant for biobased oils and bitumen to be used in more resilient and sustainable roads. Pavements...
Ligand-coated gold nanoparticles (AuNPs) can serve as advanced nanosensors capable of selectively detecting organic molecules in solution. [1] When combined with NMR-based protocols, analyte signals can be probed directly without the need for secondary reporters or analytical standards. [1] A key aspect of such approach is the formation of self-assembled monolayers surrounding the AuNP core,...
Abstract: C-terminal truncation of α-synuclein (α-Syn) has emerged as a critical modulator of its liquid-liquid phase separation and amyloid aggregation, processes that are closely linked to the pathology of neurodegenerative diseases such as Parkinson’s disease (PD) and Alzheimer’s disease (AD). While the functional implications of α-Syn truncation have been increasingly recognized, the...
Structured ternary fluid (STF) mixtures consist of a small amphiphilic molecule, called a hydrotrope, that enhances the miscibility of two other immiscible components, typically oil and water. STFs, also called surfactant-free microemulsions or ultra-flexible microemulsions, have been shown to provide unprecedented control in the crystallisation of glycine polymorphs under ambient...
We aim to present a novel methodology for diagnosing latent instabilities within data-driven molecular dynamics (MD) simulations. Referred to as cumulative latent instability (CLI) analysis, this approach is grounded in the theoretical premise that all regression techniques, regardless of their capacity for extrapolation, are inherently prone to producing unreliable or artefactual predictions...
The inverse design of molecules with target properties is a long-standing challenge in chemistry [1]. This fundamental paradigm shift in computational chemistry has the potential to accelerate the discovery of new functional compounds such as catalysts and drugs, moving beyond traditional rational design strategies [1]. Yet, de novo generation of molecules is challenged by the complexity of...
G protein-coupled receptors (GPCRs) represent membrane proteins of significant pharmacological importance, being the target of more than one-third of commercially available drugs. 1-5 These receptors are activated by orthosteric ligands, undergoing substantial conformational changes that facilitate the coupling with diverse effector proteins.6-7 To achieve precise control over the...
Understanding the origin of photoluminescence (PL) in carbon dots (CDs) remains a fundamental challenge due to the structural diversity and chemical complexity arising during their synthesis. While early hypotheses attributed PL primarily to carbogenic cores, mounting evidence points to molecular fluorophores (MFs) and their dynamic interactions within the CD matrix as key contributors to the...
All-solid state (ASSB) batteries are one of the most promising alternatives of Li-ion liquid technology. ASSB have several advantages1, such as greater stability, better safety, and higher energy density2, but also an intrinsic, and still unsolved, problem caused by their solid nature, the low ion mobility. Amorphous Lithium thiophosphates, LPS (xLi2S-(1-x)P2S5 ) are among the most promising3...
Rett syndrome is a genetic disorder affecting the development of both brain and nervous system, primarily impacting girls. It's a rare and orphan disease, meaning it has a prevalence of 1 in 10,000 to 15,000 girls, and furthermore, there's no enough development of therapeutic drugs to improve its symptoms [1]; it has recently been reported that the molecule fluoxetine has the capacity to...
Mark R. Wilson, Elliot K. Findlay
Department of Chemistry, Durham University, Science Laboratories, Stockton Road, Lower Mountjoy,
Durham, DH1 3LE, UK
email Mark.Wilson@durham.ac.uk
Soil-release polymers (SRPs) are important components of fabric care formulations. They play an important role in cleaning by modifying the surface of fabrics such as polyester. SRPs change the surface...
Anion sensing is a crucial area of research due to its applications in medical diagnostics, environmental analysis and industry. Lanthanide complexes have been actively studied for anion sensing in biological media as they have a positively charged central cation that can provide strong electrostatic interactions with the anions. In addition, their unique photophysical properties such as high...
This work develops a model for interpreting macroscopic kinetic constants in elementary reactions, particularly when mass transport and chemical reactions occur on comparable timescales, as in enzymatic catalysis. We focus on bimolecular exchange reactions, specifically SN2 nucleophilic substitutions in haloalkanes, using bromide and chloromethane as a case study.
Our approach employs a...
The A/B conformational equilibrium of DNA is essential for many biological processes, including protein-DNA recognition and the formation of DNA/RNA hybrid duplexes. However, existing AMBER force fields such as OL15, OL21, and bsc1 significantly underestimate the stability of A-DNA, which may lead to unrealistic conformational behaviour or even destabilization of protein–DNA complexes in...
Molecular modelling can give critical insight into the properties and behaviour of pharmaceutical crystals. Classical Molecular Dynamics enables modelling large systems accounting for solvent and thermodynamics effects. It also provides time resolved information otherwise inaccessible to stationary DFT calculations or Monte Carlo (simulations).
In the present work, we will discuss our...
DFT study on the synthesis of urea through electrocatalytic co-reduction of CO2 and NO3- on Cu and Ag surfaces
EuCompChem2025 – Ben Connaughton – Poster
Covalent Triazine Frameworks (CTFs) are a class of 2D organic materials that have attracted increasing attention over the past decade due to their high density of surface-active sites, efficient charge separation, fast carrier mobility, low recombination rates, chemical stability, and tuneable band gaps [1,2]. In this study, water splitting was investigated on both free-standing and...
Biomass-derived molecules represent a promising resource for the development of a sustainable chemical industry. However, their relatively large size and structural complexity pose significant challenges in elucidating their catalytic conversion mechanisms. In this context, computational chemistry offers powerful tools to complement experimental investigations. This work focuses on the...
The electrochemical nitrogen reduction reaction (NRR) presents a sustainable route for ammonia production under ambient conditions. MXenes, with their unique physicochemical properties, have shown promise as electrocatalysts for NRR. However, the competitive hydrogen evolution reaction (HER) limits their selectivity. Here, we propose a strategy leveraging the in-situ electrochemical formation...
The challenge of finding an earth-abundant non-toxic perovskite material suitable for solar cell applications brought about FASnX3, where the formamidium (FA) molecule replaces the (usually) large A cation and Sn bypasses the use of Pb, while keeping the electronic band gap in the range suitable for the visible spectrum light absorption.[1]
We investigate systematically the electronic...
The practical implementation of deep learning (DL) methods for chemistry applications relies on encoding chemical structures into machine-readable formats that can be efficiently processed by computational tools. One Hot Encoding (OHE) and Morgan fingerprints (MF) are established representations of alphanumeric categorical data in expanded numerical matrices or vectors. We have developed...
Here you find my abstract for the conference attached. Title: "Computational Analysis of Mechano-Sensitive Chiral Luminescence in Organic Materials: a TDDFT Approach"
Validating quantum chemical simulations of Oxygen Evolution on Single-atom catalysts
Elisabetta Inico, Giovanni Di Liberto, Gianfranco Pacchioni
Università degli Studi di Milano-Bicocca, Dipartimento di Scienza dei Materiali, Via Roberto Cozzi 55, 20125 Milan, Italy
elisabetta.inico@unimib.it
Single Atom Catalysts (SACs) consist of isolated metal atoms stabilized on a support,...
Combining Theory and Experiments for Modeling the Conformational and Environmental Effects on the Spectroscopical Features of Red-Adsorbing Dyes
The development of efficient and economically viable dye-sensitized solar cells (DSSCs) hinges on a molecular-level understanding of the photophysical behavior of dye sensitizers.[1,2,3]
Squaraine dyes, with their strong red-light absorption, are...
Description of Charge-Transfer states for large systems by Range Separated functionals within polTDDFT
Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, Trieste, Italia
PIERPAOLO.D’ANTONI@phd.units.it
Time-dependent density functional theory (TDDFT) has become the method of choice for simulating the optical properties of large molecular...
Zr-Doping of P2-NaxMn0.625Ni0.375O2-Layered Oxides for High-Energy Na-Ion Battery Cathodes: New Insights from First-Principles
Na-ion batteries (NIBs) are at the forefront of energy storage technology due to larger abundance of raw materials and enhanced cost-effectiveness compared to Li-ion counterparts [1]. Despite the great advances achieved in last decades, identification of...
Quantum chemical (QM) calculations for life science applications have traditionally been constrained to small model systems, or computationally inexpensive but lower-accuracy methods, due to computational limitations. Most biomolecular modeling approaches rely on empirical parametrization and thus, at least indirectly, on some sort of training, which introduces biases and restricts their...
Capturing Chemical Reactivity and Entropy with Machine Learning Potentials
Rolf David,1 Oscar Gayraud,1 Jensie Low,1 Guillaume Stirnemann,2 Damien Laage,2 Anne Milet1
1 DCM, Université Grenoble Alpes, CNRS, 38000 Grenoble, France
2 CPCV, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne University, CNRS, 75055 Paris, France
rolf.david@univ-grenoble-alpes.fr
Chemical...
Photobiocatalysis has recently emerged as a valuable strategy for conducting chemical reactions that are challenging with conventional organic chemistry tools. This approach involves the use of photenzymes, i.e. enzymes that absorb light to promote substrate conversion. The photexcitation of these catalysts enables access to electronic excited states with different properties compared to the...
The fate of the hesitating proton: Adsorption of Ethanol in H-ZSM-5
MCSCF/FQ Analytical Nuclear Gradients: A Novel Methodological Development for Multireference Multiscale Modeling
Multiscale approaches are valuable methods for accurately describing molecules embedded in complex environments, such as solutions. Among them, the Multiconfigurational Self-Consistent Field/Fluctuating Charges approach (MCSCF/FQ) [1] combines a multireference quantum...
The Ultrafast Fluorescence of a DNA-Protein Photo-Crosslinking Model, interpreted by Non-Adiabatic Molecular Dynamics
Isolation of transient nucleoprotein complexes in their biological conformation is a challenging task: a promising technique is to induce in vivo crosslinking between the nucleic acid and the protein,...
Confinement Potential for QM and QM/MM Optimization with Implicit Solvent under Non-Periodic Boundary Conditions
A current limitation in the geometric optimization of solute/solvent clusters containing a large number of solvent molecules, also including an implicit model for the solvent bulk, both at the QM and QM/MM level, concerns the stability of solvent molecules placed within the...
This talk discusses our work to develop a fast approach to organic molecular crystal structure prediction (CSP) by using previously predicted CSP landscapes of similar molecules to guide sampling within our structure searches. We discuss the method developed, initial results found, and the promise of the approach considering the ‘big data’ direction of the CSP field[1]. We will also touch upon...
Enhancing Catalyst Optimization with Robust Validation of MLR Models: A Systematic Workflow and Web Application
L. Falivene1, L. Cavallo2
1Università degli studi di Salerno, Via Papa Paolo Giovanni II, 84100 Fisiciano, SA, Italy
2King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia lafalivene@unisa.it
The development of efficient catalysts is a key...
Photoinduced Proton Coupled Electron Transfer (PCET1,2) reactions constitute an important class of reactions of biological3 and technologic4 relevance. They are increasingly recognized in areas such as synthetic chemistry and photocatalysis as well as in energy transformation reactions in natural and artificial systems.5 From a mechanistic point of view, these reactions can be distinguished by...
Heterocyclic Carbenes for Tunable Functionalization of Oxide Surface.
N-Heterocyclic carbenes (NHCs) [1] exhibit excellent ligand properties as surface modifiers, owing to their structural diversity, tunable electronic properties, and strong affinity for a broad range of elements. These features make them highly attractive for applications in materials science and catalysis. [2] To...
Machine learning potentials (MLPs) aim to bridge the gap between force fields and ab initio methods, allowing for accurate calculations with a reduced computational cost. This capability promises to benefit several research areas. For example, in crystal structure prediction, highly accurate methods are required to capture small energy differences between different crystal structures [1]. In...
The integration of graph theory into the analysis of molecular dynamics (MD) simulations offers a powerful and versatile framework for addressing complex structural identification problems[1,2]. By representing atomic or molecular interactions as nodes connected by edges within a graph, it is possible to use a vast array of well-established, highly-optimized algorithms originally developed for...
Li-ion solvation shell in PVDF-Based Quasi-Solid Electrolytes: A Molecular Perspective
Nicole Ceribelli1, Giovanni Di Liberto1 and Livia Giordano1
1Department of Materials Science, University of Milano – Bicocca, via R. Cozzi 55, 20125 Milano, Italy
n.ceribelli@campus.unimib.it
The development of high-performance Lithium-metal batteries has long been at the forefront of energy...
Light-driven molecular rotary motors represent an elegant way to convert photon energy into controlled unidirectional motion and are thus directly linked to the development of nanoscale devices [1]. Among these, overcrowded alkene-based rotary motors have garnered significant interest as prototypical systems for investigating photoinduced structural dynamics [2]. Extensive experimental and...
Taming the Reactivity of Nickelate/Cation(s) Ion Pairs in Catalysis: DFT Insights
Metal-ate complexes are highly reactive species that can facilitate elementary steps in catalysis, such as oxidative addition or highly hindered C-C bond creation. Controlling their formation and tuning their reactivity is appealing, but this requires a detailed picture of the parameters governing their...
Single-Atom Catalysts on Goldene
Silvia Picello, //(a) Elisabetta Inico, //(b) Clara Saetta , //(a) Giovanni Di Liberto (b), Gianfranco Pacchioni (b)
(a)Università degli Studi Milano-Bicocca, Dipartimento di Scienze Chimiche Geologiche e Ambientali
(b)Università degli Studi Milano-Bicocca, Dipartimento di Scienza dei Materiali
c.saetta@campus.unimib.it
In single-atom...
We introduce a new extension of the Mapping Approach to Surface Hopping (MASH) method, called Semifocused MASH (SMASH). To assess its accuracy, we compare SMASH with the Fewest Switches Surface Hopping (FSSH) method, both with and without decoherence corrections, on various molecular systems. Our results show that SMASH reproduces population dynamics with similar accuracy, while significantly...
Conformations of Model G-quadruplexes
Snezhana M. Bakalova, Jose Kaneti
Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences
Acad. G. Bonchev str., Block 9, 1113 Sofia, Bulgaria
snezhana.bakallova@orgchm.bas.bg
Our simplest model of a G-quadruplex consists of two guanine Hoogsteen-bonded quartets, stacked onto each other and neglects the connecting...
Title:
Validating DFT predictions of CO₂ adsorption on TiO₂ via FTIR spectroscopy: a path toward efficient catalyst design
Cytochrome P450-mediated mechanisms play a significant role in drug metabolism, with estimates indicating that 75% of commercially available drugs are metabolized by only 6 of the 57 human CYP enzymes [1]. These heme-containing cytochromes P450 display a broad spectrum of ligand specificity [2], a property enabled in part by the flexible protein region adjacent to the binding site....
Complex absorbing potentials for density functional theory
Charlotte Titecaa,b, Yifan Jianga, Frank De Proftb, Thomas-C. Jagaua
aDivision of Quantum Chemistry and Physical Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001 Leuven, Belgium
bResearch Group of General Chemistry (ALGC), Vrije Universiteit Brussel,...
Primases are pivotal for DNA replication. Cellular archaeoeukaryotic primases consist of small catalytic and large accessory domains. The catalytic domain cannot synthesize the primer in the absence of accessory domain, which regulate the function of the primases.Analogously, the catalytic domain (Prim_Pol) of the archaeal plasmid primase (pRN1) is activated by a helical bundle domain (HBD)...
Thermally activated delayed fluorescence (TADF) systems, including multi-resonance (MR) and inverted singlet-triplet gap (INVEST) emitters, show great potential for applications such as organic light-emitting diodes due to their high emission efficiency. However, accurately predicting their electronic properties remains computationally challenging due to the delicate balance of electronic...
Metal-organic frameworks (MOFs) have emerged as a revolutionary class of materials characterized by remarkable versatility and extensive applications across various scientific disciplines. MOFs, composed of metal nodes interconnected by organic linkers, exhibit exceptional tunability, high surface areas, and intriguing porosity. These distinctive attributes confer upon MOFs extraordinary...
Guanosine-rich tracts of nucleic acids self-assemble into stacks of stable square planar guanine quartets, having specific regulatory roles on their own function. The meaning is, possible stable aggregates of biomolecules control storage and transfer of information potentially involved in complete cell life cycles. [1] Smaller molecules are the human means to interfere with these cycles with...
Single Atom Catalysts (SACs) are an emerging frontier in the field.1 Computational chemistry offers a valid framework to access the atomistic details of catalytic processes, to rationalize or even predict novel systems. The state-of-the-art approach to model and to rationalize these objects takes insight from heterogeneous catalysis.2
In this presentation I will discuss the key ingredients...
Most computational methods for biomolecular modeling rely on empirical parametrization, limiting their predictive power and applicability. This challenge is particularly pronounced for complex biomolecular targets such as RNA, metalloproteins, and targets for covalent binding, which often fall outside the applicability domain of standard force fields and require extensive parametrization...
The importance of dispersion forces for structural stability, molecular recognition, reactivity, and catalytic properties in molecular systems, from materials to biology, is well recognized. For instance, the relaxation dynamics of the initial excited state involved in the photoisomerization process of chromophores are highly influenced by their surrounding environment. [1] Since computational...
SARS-CoV-2 is the etiological agent for the novel coronavirus disease 2019 (COVID- 19) global pandemic. Coronavirus replicates in host cell cytoplasm via a large membrane-associated RNA replication/transcription machinery comprising at least sixteen virus-encoded non-structural proteins (nsp1 to nsp16) [1]. Among non-structural proteins nsp10, nsp14 and nsp16 are the key components of RNA...
The ability of certain materials to generate electric charge in response to mechanical stress is derived from their non-centrosymmetric crystal structures, which produces a wide array of applications in sensing, actuation, and energy harvesting1. Organic molecular crystals, characterized by their structural tunability, sustainability, and biocompatibility, present a promising platform for the...
The development of stable and tunable polycyclic aromatic compounds (PACs) is crucial for the advancement of organic optoelectronics. Conventional PACs, such as acenes, often suffer from poor stability due to photooxidation and oligomerization, which are linked to their frontier molecular orbital energy levels. To address these limitations, we designed and synthesized a new class of π-expanded...
We demonstrate the application of our innovative ‘instantaneous pK’ approach to the molecular dynamics simulation of crystallite models exposed to an acidic solvent environment. For this, the bulk solution properties pH and pK are scrutinized into local aspects and effectively characterized for individual molecules of crystal faces, edges and steps, respectively. To illustrate this concept, we...
Molecular Dynamics (MD) simulation is a crucial computational tool for investigating nucleic acids (RNA, DNA), proteins, and other (bio)molecular systems, generating large volumes of data daily. However, the interoperability and reusability of these datasets remain significant challenges.[1] We present IDA (Integrated DAtabase of force fields and datasets from experiments and MD simulations),...
The design of polymer membranes with high CO₂ selectivity is essential for advancing gas separation technologies and carbon capture [1]. In this work, we develop highly interpretable machine learning models to predict the permeability of polymer membranes—particularly towards CO₂ and N₂—based on the chemical structure of their repeat units. A key challenge in this field is the scarcity and...
It was recently reported that Pt quinoxdt dithiolene complexes show a photochemical response, which markedly depends on the excitation wavelength revealing an anti-Kasha (AK) behavior. AK response originates from a competition between the functional process in upper photo-excited states and internal conversion towards the lowest excited state of a given multiplicity. Experimental evidence...
Since the 80s, when Ned Seeman [1] first envisioned the idea of building artificial structures using DNA, the field of DNA nanotechnology [2] has grown exponentially, especially due to the potential of combining light and DNA in applications beneficial to humans, such as phototherapy and optoelectronics. However, two main factors have limited its expansion: on one hand, canonical nucleobases...
Locally Concentrated Electrolytes for Al-S Batteries, a Molecular Simulation Investigation
Aluminum-sulfur (Al-S) batteries are emerging as a promising alternative to lithium-ion (Li-ion) batteries due to their lower cost, safety, and environmental advantages[1-2]. Aluminum, being abundant and less reactive than lithium, enhances battery stability and affordability, making Al-S batteries...
The topic of solid electrolytes for energy storage systems is both fascinating and crucial from an
environmental and sustainability perspective. Liquid electrolytes, commonly made from lithium
compounds, face low stability and high cost. Furthermore, lithium extraction is not sustainable for the
environment or local communities. Thus, researchers are eager to develop safer and more...
Mechanistic Insights into the Fe(II)-Catalyzed ROP of Challenging Aliphatic Lactones: A DFT Study
The growing concern over plastic pollution and microplastic contamination has intensified efforts to identify sustainable alternatives to fossil-derived polymers. In this context, aliphatic polyesters from cyclic esters (lactones) have emerged as promising candidates, particularly when designed...
Histone deacetylase inhibitors (HDACi) have demonstrated emerging therapeutic potential in cancer treatment by inhibiting the activity of histone deacetylase enzymes (HDACs)1. Currently, only a limited number of HDACi have been approved by drug regulators for use as anticancer drugs. SAHA, a hydroxamic acid, was the first drug approved in 2007 by the FDA as an anticancer agent2. Chidamide 3,...
Solvation effects on thermodynamic properties of chemical systems can be captured by integrating-out the solvent degrees of freedom for a given geometric solute configuration to yield an effective solvent-mediated free energy surface (“potential of mean force”, PMF). Based on this philosophy, a plethora of “implicit solvation models” has emerged over the years, from continuum electrostatics...
Modeling vertical excitation energies in solution using the Density matrix renormalization group/Fluctuating charges approach
M.Rinaldi1, C.Sepali1, A.M. Kirk1, C.Amovilli2, C.Cappelli1,3
1Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126, Pisa, Italy
2Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via...
Global warming and climate change are directly related to increased atmospheric CO2 levels, which are currently higher than ever and continue to growth. Current strategies for CO2 reduction are mainly emission mitigation strategies, so that the rate of increase of global CO2 emissions from fossil resource utilization has slowed recently. However, utilizing CO2 as a carbon source for production...
Soil release polymers (SRPs) are amphiphilic polymers found in modern detergent formulations, whose primary operations are to modify synthetic fabric surfaces to allow water transport and to prevent the redeposition of oil-based soil particles during the wash cycle.1 In this work, SRPs are modelled at fabric surface-water interfaces using dissipative particle dynamics (DPD) and Hamiltonian...
DNA can adopt a variety of secondary structures beyond the canonical double-stranded form (dsDNA). Among these, the guanine quadruplex (G4) has been widely studied for its role in gene expression and cancer, as G4s are found in many oncogenic promoters and at telomeres [1]. This has driven efforts to detect and track G4s in cells using near-infrared fluorescent probes [2]. A key example is the...
Two-antennary oligoglycines represent a novel class of biocompatible amphiphilic compounds, rationally designed through preliminary molecular modelling [1]. These molecules consist of a central hydrophobic alkyl core bound to two hydrophilic oligoglycine chains, forming a symmetric bola-amphiphilic structure. In aqueous media, they spontaneously assemble into stable supramolecular structures...
The production of energy from nuclear sources generates a variety of radioactive wastes, and in particular Radioactive Liquid Organic Waste (RLOW). RLOW contains a wide range of organic molecules and radioactive species along with halogens, heavy metals, nitrates, carbonates, sulfates and other components. To be compatible with existing waste management systems, RLOW must undergo...
Molecular Simulation of Graphene Oxide-Ionic Liquid Electrolyte Interface in Sodium-Ion Batteries Using DFTB-MD
Mirella Fonda Maahurya,b, Aditya Wibawa Saktib,c, Hiromi Nakaib
aChemistry Department, Faculty of Science and Technology, Pattimura University, Ambon, Indonesia
bChemistry and Biochemistry Department, School of Advance Science and Engineering, Waseda University, Tokyo,...
The methanol-to-olefins (MTO) process utilizes acidic zeolites to convert methanol into olefins and plays a
pivotal role in the production of Sustainable Aviation Fuels (SAFs)1. This process involves a complex network
of reactions, with multiple competing pathways and mechanisms2. The initial and critical step is the
dehydration of methanol to form dimethyl ether (DME)3. Experimental and...
The many-body expansion (MBE) of the lattice energy offers a route to an ab initio description of molecular solids based on systematic wave-function approximations. However, MBE can only be practical if one can deal with the daunting number of n-body contributions. To this end, we employ a multi-level approach (Figure 1). CCSD(T) is only required for the first and second coordination shells....
The project will introduce a rational design of ligands to finely tune nanoparticle shell thickness and density, complemented by functionalization strategies for supercrystals aimed at reinforcing interparticle interactions and reducing inter-nanoparticle spacing.
Ab initio simulations based on density functional theory (DFT) are employed to predict electronic, structural, and magnetic...
Unai Calvo, Fernando Ruipérez, Aizeti Burgoa, Jon Mattin Matxain
POLYMAT, Centro Joxe Mari Korte, Avda. Tolosa, 72, 20018, Donostia-San Sebastian, Spain
unai.calvo@polymat.eu
In this work, we investigate the interactions at the interfaces of metal (per)oxides with thermoplastic vulcanizates
(TPVs), specifically focusing on the XHNBR/PA6 system. XHNBR (carboxylated hydrogenated nitrile...
A recent algorithm to solve the TDDFT equations in the space of the density fitting auxiliary basis set has been developed and implemented in ADF/AMS [1]. The TDDFT equations are recast to a non-homogeneous linear system, whose size is much smaller than in Casida formulation, allowing to calculate a wide portion of the absorption spectrum for large systems. The method extracts the spectrum...
Chlorite dismutase (Cld) is one of the rare enzymes capable of forming oxygen-oxygen bonds. Cld has been identified in a very small number of anaerobic bacteria that can use perchlorate as the final electron acceptor in their electron transport/respiration chain. It has been proposed that the catalytic cycle of Cld involves the binding of chlorite to the enzyme's active site, followed by the...
Weak non-covalent interactions remain a challenging area for most Density Functional Approximations, and the inclusion of empirical potentials has proven to be an effective way to address their limitations. Recently, we have proposed an alternative approach based on the coupling of a non-empirical double hybrid functional, PBE-QIDH, with a specifically developed basis set named DH-SVPD. This...
Nanodiamonds (NDs) have emerged as potential candidates for versatile platforms in nanomedicine, offering unique properties that enhance their utility in drug delivery, imaging, and therapeutic applications. To improve their biocompatibility and nanomedical applicability, NDs are coated with organic polymer chains, such as polyethylene glycol (PEG), which are well known to prolong their blood...
Optimizing the mRNA Binding Affinity of Antisense Oligonucleotides with Simple Nucleobase Modifications
Antisense therapy has emerged as a powerful strategy for treating genetic disorders—particularly rare “orphan” diseases—as well as viral infections and, more recently, certain cancers.[1] Antisense oligonucleotide (ASO) therapeutics rely on high-affinity, sequence-specific...
Innovation:
Utilizes Fourier Neural Operators (FNOs) to model continuous 3D physical landscapes (hydrophilic/hydrophobic surfaces).
Embeds physical properties directly into the molecular generation process, enhancing physical realism and relevance.
Methodology:
Evolution from LSTM-based generators [2] to GPT-based transformers to current dual-FNO-enhanced PINO-GPT architectures.
FNO...
The accurate prediction of hydration free energies (HFEs) is an important task in different areas, as the thermodynamic cost of solvation is one of the key factors in processes from protein-ligand binding to chemical reactions. Hence, much effort has been spent in predicting the HFE from electronic structure calculations and molecular dynamics simulations as well as, in recent years, machine...
The objective of the conducted research was to develop a quantum chemical method that enables modeling of interactions between high-velocity, massive, charged particles and an arbitrarily chosen molecule. The proposed method finds broad application across various fields of science. In the context of radiotherapy, a tool capable of accurately describing excitations induced by protons is highly...
Hydrogen-based compounds demonstrate high-temperature superconductivity under pressure, offering promising avenues for exploring metal hydrides with elevated critical temperatures (𝑇c), while hydrides comprising H2 molecular units were previously deemed unfavorable.1 Searching for new forms of hydrogen within metal hydrides promised a route for developing novel high-temperature...
Non-covalent interactions (NCIs) are fundamental to the structure, stability, and function of molecular systems across chemistry and biology [1]. The Non-Covalent Interaction (NCI) method offers a visual and intuitive means to identify regions of weak interactions by analysing low-density and low-gradient features in electron density data. Since its introduction, NCI has become a widely...
Enantiomers of chiral molecules behave differently in chiral environments. This is typically due to interactions with a chiral host system, such as a chiral reagent or catalyst in a synthetic context, a target protein in the context of drug discovery or a chiral stationary phase in chiral chromatography. The most obvious route for studying these interactions in solution phase is through MD...
Johnson Matthey (JM) envisions a cleaner, healthier world for present and future generations. As global leader in sustainable technologies, the company leverages science to accelerate the net-zero transition for its clients. Through scientific innovation, the company improves the lives of millions worldwide. JM is focused on facilitating four critical transitions: reducing transport emissions,...
Accurate modeling of electronic effects in protein–protein interactions (PPIs) remains a significant challenge in computational biophysics. Classical force fields fail to describe polarization and charge transfer, while full quantum mechanical (QM) methods are often computationally prohibitive. To address this, we developed a multiscale protocol that integrates molecular dynamics, system...
The reverse Water-Gas Shift (rWGS) reaction enables the conversion of CO2 into CO, a key intermediate for e-fuel synthesis. Ni-based catalysts are active for rWGS but suffer from limited selectivity due to the competing methanation reaction. In contrast, Cu-based catalysts exhibit high selectivity but lower activity. Alloying these metals has been explored as a strategy to improve the catalyst...
Semiclassical methods are based on classical molecular dynamics and they recover quantum mechanical effects by summing the contribution over all the classical paths of the Feynman Path Integral propagator. In Miller’s semiclassical initial value representation (SCIVR)[1] formulation of the Herman-Kluk propagator, the sum over frozen guassian wavepackets reproduces quantum effects, including...
Sequential MD-QM approach to compute chemical properties of Brønsted amorphous aluminosilicate catalysts
Charles Rubirigi, Benoît Champagne
NISM (Namur Institute of Structured Matter), University of Namur (UNamur), B-5000 Namur, Belgium
charles.rubirigi@unamur.be
Amorphous silica-based materials are often used as support for catalysis experiments. The insertion of heteroelements (i.e.,...
The global growing demand for energy storage is pushing the research for new battery materials with improved performance, safeness, and environmentally friendly synthesis, usage, and disposal.
All-Solid-State Sodium Batteries (ASSSB) are attracting increasing attention from both academia and industry as strong candidates for grid-scale energy storage. However, their development requires...
Sodium-ion batteries (NIBs) are a sustainable alternative to lithium-ion batteries (LIBs) due to the abundance and low cost of sodium [1]. Although NIBs and LIBs operate based on similar principles, the differences in ionic radius and standard electrode potential between the two ions require the development of new cathode materials. NASICON-type materials (Natrium Super Ionic CONductors), such...
Carbon dots (CDs) are extensively studied nanomaterials with broad application potential due to their bright, tunable photoluminescence (PL), high (photo)stability, low toxicity, and excellent biocompatibility, as well as their emerging promise in photocatalysis. However, understanding the origins of their PL and photocatalytic (PC) behavior remains incomplete [1,2], largely due to the...
Carnitine O-acetyltransferase (CRAT) is a mitochondrial enzyme central to acetyl-CoA/carnitine homeostasis and metabolic flexibility. Mutations in the CRAT gene, such as the p.Tyr110Cys variant associated with early-onset Leigh syndrome, impair mitochondrial function and energy metabolism [1]. Here we present a structure-based virtual screening and docking workflow that enabled the...
The escalating threat of antibiotic resistance underscores the urgent need for innovative therapeutics, with antimicrobial peptides (AMPs) emerging as viable alternatives due to their diverse mechanisms of action (Fjell et al., 2011). This study introduces a systematic strategy to design two classes of AMPs with distinct bactericidal mechanisms: proline-rich peptides, which disrupt...
The HER conducted in alkaline electrolytes could pave the way to produce hydrogen as a green fuel, as it enables the use of cost-effective and abundant transition metal-based catalysts.1 However, the slow water dissociation kinetics in alkaline environments still hinders its development.2,3 Recent advances have highlighted the potential of transition metal dichalcogenides, such as MoS2, as...
Antibiotics resistance is rapidly becoming an important needing of nowadays society, due to the inefficiency of many widely adopted drugs, such as penicillins and carbapenems. This takes place because a number of bacteria involved in the onset of severe human’s diseases, like Escherichia coli, Klebsiella pneumoniae, Acinetobacter, Pseudomonas aeruginosa, and Enterobacter cloacae, have...
Hardness [1] is a key property that determines how solid materials respond mechanically to applied stress. Understanding the mechanisms underlying hardness at the atomic scale is crucial for designing materials with enhanced mechanical performance. In this work, we employ molecular dynamics (MD) simulations to perform nano-scale indentation tests, offering new insights into the fundamental...
The NPC1L1 sterol transporter: dynamics and interaction with natural compounds with inhibitory activity
Niemann-Pick C1-Like 1 (NPC1L1) is a transmembrane protein (Figure 1) essential for cholesterol uptake in cells, which starts with the binding to the extracellular N-terminal domain (NTD). The cholesterol molecule then passes through a tunnel connecting the luminal domains to the...
The reported experimental discovery of a ferroelectric nematic (NF) phase is an exciting new development in liquid crystal research. [1-3] The new phase has several potential applications in displays and novel technology due to its unprecedented polarization. However, the origins of the phase are poorly understood, leading to derivatives of the first two mesogens to be discovered, making up...
In this work, we employ time-dependent density functional theory (TDDFT) to investigate the optical properties of Au-based hybrid bimetallic nanoalloys, modeling their growth via classical molecular dynamics using the LoDiS package and metal–metal interactions based on the second-moment approximation of the tight-binding scheme (TBSMA). Transition metals (TMs) selected from Au, Ag, Pd, Pt, and...
Theoretical Insights into CO₂ Activation on α-Bi₂O₃ under Operating Conditions
The increasing use of fossil fuels over recent decades has triggered a global energy crisis, marked by the rapid depletion of these resources and the substantial release of carbon dioxide (CO₂) into the atmosphere [1]. CO₂ levels are projected to reach 570 ppm by 2100, a rise that contributes to critical...
VCD (vibrational circular dichroism) spectroscopy is established as a common and reliable method for investigating the absolute configuration of small molecules.1 However, in order to obtain a detailed understanding of the preferred conformation, suitable computer-assisted methods are necessary to enable a reliable conformational search and predict the experimental spectrum.1 Yet, the...
Rare-earth complexes are attracting attention as clean energy conversion materials utilizing chromophores for efficient photo-excited energy conversion that emit light having well defined narrow bands in different spectral ranges with long lifetimes and high quantum yields. The dithiocarbamate ligands (dtc, S2CR) are a special class of chromophores that have been poorly studied in relation...
Theoretical tautomer prediction as a testbed for theory-based experimental uncertainty analysis
Magnesium-based batteries represent a promising post-lithium battery technology due to magnesium's low cost and high natural abundance. Among the few materials exhibiting good Mg ion conductivity, the spinel phase MgSc₂Se₄ stands out as a particularly promising solid electrolyte candidate.[1] While the bulk properties of MgSc₂Se₄ are already well understood, advancing toward practical...
European project MIMIC-KeY (www.mimickey.eu) aims at creating synthetic extracellular vesicles (EVs) and demonstrating their use with the specific delivery of therapeutic cargo for treating lysosomal bone metabolic disease. Here we present a brief report on computational analyses that assisted the design of artificial nanoparticles consisting of a breakable organosilica core (allowing high...
Single-atom catalysts (SACs) have been developed as a promising alternative for the design of highly active and selective catalysts, with experimental evidence confirming their successful synthesis. In a SAC catalyst, typically a transition metal – most commonly a precious metal – is embedded onto a support, and the resulting active site catalyzes chemical transformations relevant to energy...
It is known that the synthesis of tubulin and microtubules is part of the processes of cell division which makes it a potential target in the development of new chemotherapeutic agents for cancer as well as parasitic infections treatment [1]. Several binding sites are known on the surface of tubulin, but the best studied for the purpose of designing polymerization inhibitors are the colchicine...
Nitrogenases are enzymes that reduce atmospheric nitrogen (N2) into bioavailable ammonia (NH3), thereby facilitaIng the nitrogen cycle and enabling life on Earth [1,2]. Nitrogenases can be divided into three main classes based on the idenIty of the heteroatom in the acIve site: molybdenum nitrogenase (Mo-nitrogenase), vanadium nitrogenase (V-nitrogenase), and iron- only nitrogenase...
The development of efficient and sustainable catalysts is a cornerstone in the global effort to address pressing environmental challenges, particularly the conversion of carbon dioxide (CO₂) into value-added products. Among the emerging strategies, single-atom catalysts (SACs) have garnered significant attention due to their exceptional atom utilization, tunable electronic properties, and...
The field of asymmetric catalysis has revolutionized organic synthesis over the past fifty years, not only by making new reactions possible or faster, but also by promoting the synthesis of a single stereoisomer as the main product.[1] However, the development of new chiral catalysts remains a real challenge that often results in a long and laborious process, requiring the synthesis and...
Interfacial polymerization (IP) between tetraethylenepentamine (TEPA) and 4,4’-methylenebis(cyclohexyl isocyanate) (HMDI) at the water/hexadecane interface proceeds too rapidly to effectively control reaction kinetics or tailor polymer morphology. To elucidate the underlying mechanism, we performed quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and experimental...
