jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Rishabh K. Singh | Yu‐Hsuan Joni Shao | Het Patel | Mason Hooten | Meenakshi Dutt
Source: ChemRxiv (preprint, 2025-04-21)
Field: Chemistry — Spectroscopy

COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS OF SOFT MATTER RELEVANT TO THE PHARMACEUTICAL INDUSTRY Soft materials are critical to the pharmaceutical industry for their role in formulations, delivery of active compounds or understanding relevant physiological processes. This chapter will focus on coarse-grained (CG) approaches and models that have been used in conjunction with the Molecular Dynamics (MD) simulation method to investigate soft materials of interest to various applications in pharmaceutical sciences. This chapter also discusses several examples of CG MD simulations used to scientifically probe molecules with different chemistries. Soft matter ; Molecular dynamics ; Pharmaceutical industry ; Dynamics (music) ; Computer science ; Chemistry ; Statistical physics ; Biochemical engineering ; Physics ; Computational chemistry ; Engineering ; Biotechnology ; Biology ; Physical chemistry Adsorption, diffusion, and thermodynamic properties of materials
Authors: Shubham Sewariya | Nistha Mishra | Sagar Panchal | Shrikant Kukreti | Ramesh Chandra
Source: Scientific Reports (article, 2025-09-30)
Field: Materials Science — Materials Chemistry

Probing into 9’-substituted Suzuki-coupled noscapine ionic liquids as potent microtubule targeting anticancer agents with hemoglobin affinity On a global scale, lung cancer accounts for 18% of all cancer deaths making it the most lethal cancer. To restrain this, there has been continual research in the domain of microtubule-targeting anticancer agents but issues like toxicity, immunosuppression, effective delivery to tumor site, etc. persist to impede their clinical success. Unlike the other existing drugs in this regime; noscapine (a non-opioid alkaloid) is testified to be an intrinsically safer drug with minimal side effects. In this work, we have synthesized and evaluated novel 9'-substituted suzuki-coupled noscapine ionic liquid(s) as effectual anticancer drug(s) against non-small cell (H1299) lung cancer. We have devised a synthetic route (employed suzuki coupling for subsuming the biaryl pharmacophore and combined it with the idea of active pharmaceutical ingredient-based ionic liquids (API-ILs)) to yield the desired API-ILs followed by their characterization using associated analytical techniques like NMR, HRMS, etc. Following this, we have performed SAR analysis of the API-ILs using molecular docking with the target tubulin protein and preliminary in vitro screening against H1299 (non-small cancer) cells to opt for the most promising analogue i.e., [p-NO<sub>2</sub>-Nos]I. Upon finding the most potent ionic liquid, we carried out MD simulations and MM-PBSA/GBSA calculations to get an insight into its interaction with tubulin and human hemoglobin using computational and spectroscopic studies respectively. From computational studies, we inferred that [p-NO<sub>2</sub>-Nos]I forms a stable complex with tubulin mainly driven by non-polar interactions. From spectroscopic studies, we disclosed that [p-NO<sub>2</sub>-Nos]I binds to human hemoglobin (Hb) in a 1:1 stoichiometric ratio with a binding constant (K<sub>b</sub>) of ~ 1.38 × 10<sup>5</sup> M<sup>-1</sup> at 298 K. Finally, we have examined the cytotoxicity of [p-NO<sub>2</sub>-Nos]I against H1299 cancer cell line and compared it to [9-Br-Nos]IBr<sub>2</sub>, noscapine and Paclitaxel. The IC<sub>50</sub> values for [p-NO<sub>2</sub>-Nos]I came out to be 67.84 ± 4.84 µM at 48 h and 19.67 ± 3.1µM at 72 h, both of which were significantly lower than [9-Br-Nos]IBr<sub>2</sub> and Noscapine. The potent [p-NO<sub>2</sub>-Nos]I was further screened using A549 cell line and similar results were observed relative to H1299 cell line. Overall, these findings envelop the potential of such enhanced spindle poisons against lung cancer. Pharmacophore ; Noscapine ; Tubulin ; Docking (animal) ; Yield (engineering) ; In vitro ; Drug ; Drug discovery ; Virtual screening ; Hemoglobin Mesoporous Materials and Catalysis ; Ionic liquids properties and applications ; Synthesis and Biological Evaluation
Authors: Arpita Srivastava | Debabrata Ganguly | Anubhav Kumar | Sharad Goyal | Sambhu Bhadra | Sujith Nair | Renji Issac
Source: Research Square (preprint, 2025-06-24)
Field: Materials Science — Polymers and Plastics

Determination of Compatibility in Polymer-Polymer and Polymer-Resin Systems through Molecular Dynamics Simulations Polymer ; Natural rubber ; Compatibility (geochemistry) ; Materials science ; Composite material ; Elastomer ; Hildebrand solubility parameter ; Styrene-butadiene ; Molecular dynamics ; Polyurethane ; Polymer science ; Chemical engineering ; Polymer chemistry ; Chemistry ; Styrene ; Copolymer ; Computational chemistry Polymer Nanocomposites and Properties ; Polymer crystallization and properties ; Advanced Polymer Synthesis and Characterization
Authors: Paulo Siani | Edoardo Donadoni | Giulia Frigerio | M.C. D’Alessio | Cristiana Di Valentin
Source: Journal of Composites Science (article, 2025-06-07)
Field: Materials Science — Surfaces, Coatings and Films

Computational Study of Ultra-Small Gold Nanoparticles with Amphiphilic Polymer Coating Nanomedicine is rapidly evolving, with tailored nanoparticles enabling precise cellular-level interventions. Despite significant advances, challenges, such as rapid clearance and off-target effects, hinder the clinical translation of many nanosystems. Among the available nanoplatforms, gold nanoparticles (AuNPs) stand out due to their unique surface chemistry, low toxicity, and excellent biocompatibility. In this work, we present a multi-level computational investigation of ultra-small AuNPs coated with non-conventional amphiphilic polymer chains via atomistic and coarse-grained molecular dynamics. Through high-level-resolution atomistic simulations, we investigate how variations in grafting density impact the collective behaviors of these amphiphilic polymer chains within the coating by quantifying relevant conformational, structural, and energetic descriptors, such as the radius of gyration, terminal group presentation, polymer coating thickness, brush height, and solvation energy. Our results reveal a conformational shift of polymer chains from coiled to stretched as grafting density increases, with a direct effect on the polymer conformational regime, terminal group presentation, and coating thickness. In parallel, we further benchmark low-level coarse-grained models using the atomistic data as a reference, demonstrating their ability to correctly reproduce the atomistic trends. This computational investigation reveals how key descriptors vary with grafting density and provides the tools for conducting similar studies on broader time and length scales, thereby advancing the rational design of nanosystems for nanomedicine. Nanomedicine ; Materials science ; Polymer ; Nanotechnology ; Coating ; Amphiphile ; Molecular dynamics ; Nanoparticle ; Radius of gyration ; Dissipative particle dynamics ; Chemical physics ; Copolymer ; Chemistry ; Computational chemistry ; Composite material Polymer Surface Interaction Studies ; Pickering emulsions and particle stabilization ; Advanced Polymer Synthesis and Characterization
Authors: Andreas A. Buchheit | Jan-Erik Busse
Source: elib (German Aerospace Center) (preprint, 2025-04-16)
Field: Materials Science — Materials Chemistry

Epstein zeta method for many-body lattice sums Many-body interactions arise naturally in the perturbative treatment of classical and quantum many-body systems and play a crucial role in the description of condensed matter systems. In the case of three-body interactions, the Axilrod-Teller-Muto (ATM) potential is highly relevant for the quantitative prediction of material properties. The computation of the resulting energies in d-dimensional lattice systems is challenging, as a high-dimensional lattice sum needs to be evaluated to high precision. This work solves this long-standing issue. We present an efficiently computable representation of many-body lattice sums in terms of singular integrals over products of Epstein zeta functions. For three-body interactions in 3D, this approach reduces the runtime for computing the ATM lattice sum from weeks to minutes. Our approach further extends to a broad class of n-body lattice sums. We demonstrate that the computational cost of our method only increases linearly with n, evading the exponential increase in complexity of direct summation. The evaluation of 51-body interactions on a two-dimensional lattice, corresponding to a 100-dimensional sum, can be performed within seconds on a laptop. We discuss techniques for computing the arising singular integrals and compare the accuracy of our results against computable benchmarks, achieving full precision for exponents greater than the system dimension. Finally, we apply our method to study the stability of a three-dimensional lattice system with Lennard-Jones two-body interactions under the inclusion of an ATM three-body term at finite pressure, finding a transition from the face-centered-cubic to the body-centered-cubic lattice structure with increasing ATM coupling strength. This work establishes the mathematical foundation for an ongoing investigation into the influence of many-body interactions on the stability of matter. Lattice (music) ; Computation ; Exponential function ; Quantum ; Lattice model (finance) ; Quantum computer ; Exponent ; Lattice field theory Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Quantum many-body systems
Authors: P. Sivaprakash | A. Viji | S. Krishnaveni | Kumar Kavya | Deokwoo Lee | Ikhyun Kim
Source: International Journal of Molecular Sciences (article, 2025-10-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Comprehensive Computational Study of a Novel Chromene-Trione Derivative Bioagent: Integrated Molecular Docking, Dynamics, Topology, and Quantum Chemical Analysis This work thoroughly investigated the compound 4-(2,5-Dimethoxyphenyl)-3,4-dihydrobenzo[g]chromene-2,5,10-trione (DMDCT) using molecular docking, quantum chemical analysis, and vibrational spectroscopy methodology. The medicinal chemistry group has been particularly interested in chromene and benzochromene derivatives due to their wide range of pharmacological actions, including anticancer, antibacterial, anti-inflammatory, antioxidant, antiviral, and neuroprotective capabilities. In this connection, DMDCT has been explored to evaluate its biological, electrical, and structural properties. DFT using the B3LYP functional and 6-31G basis was established to conduct theoretical computations with the Gaussian 09 program. The findings from these computations provide insight into the following topics: NBO interactions, optimal molecular geometry, Mulliken charge distribution, frontier molecular orbitals, and MEP. Second-order perturbation theory has been used to assess stabilization energies arising from donor-acceptor interactions. Furthermore, general features such as chemical hardness, softness, and electronegativity were studied. The results suggest that DMDCT has stable electronic configurations and biologically relevant active sites. This integrated experimental and theoretical study supports the potential of DMDCT as a practical scaffold for future therapeutic applications and contributes valuable information regarding its vibrational and electronic behavior. Electronegativity ; Natural bond orbital ; Quantum chemical ; Density functional theory ; Mulliken population analysis ; Quantum chemistry ; Electronic structure ; Gaussian ; Perturbation theory (quantum mechanics) ; Computation Nonlinear Optical Materials Research ; Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Ritika Yadav | Kirti Sharma | Harbinder Singh | Mohit Sanduja
Source: ChemistrySelect (article, 2025-12-01)
Field: Chemistry — Organic Chemistry

In Silico Evaluation of Antimicrobial Activity, Target Binding, and Drug‐Likeness Properties of Pyridine–Pyrrole Conjugates ABSTRACT In this study, novel pyridine–pyrrole conjugates were computationally designed to explore their synergistic antimicrobial potential against bacterial and fungal targets. Molecular docking and molecular dynamics simulations were performed using gyrase B and OleP to evaluate binding affinity and structural stability. Compounds RY1 and RY2 demonstrated significant binding energies, as confirmed by Molecular Mechanics (MM) Generalized Born Surface Area (GBSA) calculations, and stable protein–ligand interactions during 100 ns simulations. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses revealed favorable pharmacokinetic parameters and toxicity profiles compared to ciprofloxacin, with RY2 showing enhanced antifungal activity and safety. These findings highlight the promising role of pyridine–pyrrole conjugates, especially RY2, as lead candidates for the development of new antimicrobial agents to counteract drug resistance. In silico ; Antimicrobial ; Docking (animal) ; DNA gyrase ; Antifungal ; Molecular dynamics ; Conjugate ; Molecular model ; Drug ; Toxicity Synthesis and Reactivity of Heterocycles ; Synthesis and Characterization of Pyrroles ; Synthesis and biological activity
Authors: Zhongquan Chen | Pim van der Hoorn | Björn Baumeier
Source: Physical review. B./Physical review. B (article, 2025-06-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Uncertainty quantification in multiscale models of charge transport in organic semiconductors: Influence of the exchange-correlation functional This study investigates the impact of exchange-correlation functional choices on the predictive accuracy of multiscale models for charge transport in organic semiconductors (OSCs). A hybrid functional approach is applied to analyze uncertainties in key parameters influencing charge mobility, focusing on the Hartree–Fock exchange fraction. Using 2-methyl-9,10-bis(naphthalen-2-yl)anthracene as a test system, molecular dynamics and density functional theory are combined to compute reorganization energies, site energies, and electronic coupling elements. Monte Carlo sampling quantifies the uncertainty propagation, revealing that site-energy variations dominate transport property uncertainties, while coupling elements contribute minimally. The findings underscore the need for accurate parameter determination and functional selection, with implications for enhancing the reliability of first-principles-based multiscale modeling frameworks in OSC design. Organic semiconductor ; Charge (physics) ; Semiconductor ; Statistical physics ; Correlation ; Charge exchange ; Materials science ; Chemical physics ; Biological system ; Physics ; Mathematics ; Optoelectronics ; Quantum mechanics ; Biology Organic and Molecular Conductors Research ; Organic Electronics and Photovoltaics ; Semiconductor materials and interfaces
Authors: Chaohang Xu | Ran Bi | Sijing Wang | Xiaojun Tang | Xiaolong Zhu | Guochun Li
Source: Polymers (article, 2025-08-30)
Field: Chemistry — Organic Chemistry

Effects of Poly(ethylene oxide) on the Foam Properties of Anionic Surfactants: Experiment and Molecular Dynamics Simulation Water-soluble polymers are often used as additives to adjust the foam properties of surfactant. In this study, the effects of water-soluble polymer poly(ethylene oxide) (PEO) on foam properties of two anionic surfactants, i.e., ammonium lauryl ether sulfate (ALES) and sodium dodecyl sulfate (SDS), were investigated by experimental and molecular dynamics simulation methods. Experimental results show that the addition of PEO can reduce the foaming ability of the two surfactants, but the inhibitory effect of PEO on the foaming ability is weakened at high surfactant concentration. Compared with ALES, PEO has a more significant inhibitory effect on the foaming ability of SDS. With the increase in PEO concentration, the half-life time of foam drainage in surfactant/water-soluble polymer composite systems gradually increases. The synergistic effect between PEO and ALES is stronger than that between PEO and SDS, resulting in a longer half-life time of foam drainage in ALES/PEO composite system. Molecular dynamics simulation results indicate that the addition of PEO can decline the air-water interface thickness of bubble films and the tail tilt angle of surfactant molecules at the air-water interface. The reduction in tail tilt angle means that the surfactant molecules are more vertical to the air-water interface and the hydrophobic interaction between adjacent tail chains of surfactants is weakened, which is unfavorable to the formation of bubble films, thus decreasing the foaming ability of surfactants. Because the ALES/PEO system has larger air-water interface thickness and surfactant tail tilt angle than the SDS/PEO system, the inhibitory effect of PEO on the foaming ability of ALES is weaker than that of SDS. Adding PEO can lower the peak position of the first hydration layer of surfactant head groups, increase the number of hydrogen bonds, and reduce the diffusion coefficient of water molecules, so that the surfactant/water-soluble polymer system has longer half-life time of foam drainage than the pure surfactant system. Due to the synergistic effect between ALES and PEO, the ALES/PEO system has a higher peak value of the first hydration layer of surfactant head groups, more hydrogen bonds, and lower diffusion coefficient of water molecules than the SDS/PEO system. Therefore, the half-life time of foam drainage in the ALES/PEO system is longer than that in the SDS/PEO system. Ethylene oxide ; Molecular dynamics ; Materials science ; Chemical engineering ; Oxide ; Poly ethylene ; Dynamics (music) ; Ethylene ; Composite material ; Copolymer ; Polymer ; Chemistry ; Organic chemistry ; Computational chemistry ; Catalysis Surfactants and Colloidal Systems ; Pickering emulsions and particle stabilization ; Advanced Polymer Synthesis and Characterization
Authors: Vishal Boddu | Denis Davydov | Paul Steinmann
Source: Multiscale Science and Engineering (article, 2025-06-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A Fully Nonlocal Quasicontinuum Method for Ionic Crystals Abstract The quasicontinuum (QC) method has been established as an important tool to bridge atomistic and continuum descriptions. Though numerous variants of the QC method have been developed, till date the QC method has not been applied to ionic crystals to the same extent as it has been applied to simple crystals, such as metals. However, most multi-functional crystalline materials that are indispensable in various scientific and technological applications, have a multilattice structure and consist of ions interacting via the long-range Coulomb potential. Developing and extending the QC method for such ionic crystals is a significant leap in broadening the applicability of the method as this will allow simulating material behavior that is not possible or practical with molecular mechanics due to the enormous computational costs involved.To achieve this, we propose an extension to the QC method to model and simulate ionic crystals on multiple length scales with seamless transition from atomistics to the continuum. In doing so, a new approach for imposing kinematic constraints (on all the basis atoms of a unit cell) is realized in a fully nonlocal QC setting. In addition, a cutoff-based method is used for coarse-graining Coulomb interactions in ionic crystals owing to their charge-ordering property. The proposed method is employed to simulate surface effects of a ferroelectric nanocube such that the region near surfaces are modeled with an atomistic resolution and the interior with a coarse-grained resolution. As a result, the electric polarization profile of the nanocube is numerically determined for the first time in a QC setting. Ionic bonding ; Materials science ; Classical mechanics ; Physics ; Ion ; Quantum mechanics Multiferroics and related materials ; Ferroelectric and Piezoelectric Materials ; Numerical methods in engineering
Authors: Carl Öster | Reinier de Vries | Juan Li | Denis Qoraj | Sascha Lange | Chaowei Shi | Wojciech Kopeć | Bert L. de Groot | Adam Lange
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-08-18)
Field: Chemistry — Organic Chemistry

Atomistic Mechanism of Calcium-Mediated Inward Rectification of the MthK Potassium Channel by Solid-State NMR and MD Simulations Abstract Inward rectification is a fundamental but poorly understood phenomenon in potassium channel physiology. Despite its physiological importance, the exact mechanism has remained elusive. In this work, we uncover a previously unrecognized calcium-mediated gating mechanism in the MthK potassium channel that sheds new light on this essential process. By combining state-of-the-art proton-detected solid-state NMR spectroscopy with atomistic molecular dynamics simulations, we reveal that divalent calcium ions bind to a novel site just below the selectivity filter, physically obstructing the outward flow of potassium ions whereas inward flow is still possible - analogous to a molecular ball check valve. Secondly, the binding of Ca 2+ to the newly identified site leads to stabilization of the selectivity filter and allows us to directly observe ion–ion interactions in the filter. These results offer direct experimental support for the long-debated “direct knock-on” mechanism, in which potassium ions move through the filter, without water co-transport. Rectification ; Solid-state nuclear magnetic resonance ; Potassium ; Solid-state ; Chemistry ; Calcium ; Potassium channel ; Chemical physics ; Mechanism (biology) ; Materials science ; Biophysics ; Thermodynamics ; Physical chemistry ; Nuclear magnetic resonance ; Physics ; Biology ; Organic chemistry Coordination Chemistry and Organometallics ; Advanced NMR Techniques and Applications ; Solid-state spectroscopy and crystallography